4 DNA and polypeptide synthesis

Students:
•• construct appropriate representations to model and compare the forms in which DNA exists in eukaryotes and
INQUIRY QUESTION prokaryotes (ACSBL076) ICT
Why is polypeptide •• model the process of polypeptide synthesis, including: (ACSBL079)
synthesis important? – transcription and translation
– assessing the importance of mRNA and tRNA in transcription and translation (ACSBL079)
– analysing the function and importance of polypeptide synthesis (ACSBL080)
– assessing how genes and environment affect phenotypic expression (ACSBL081) CCT L
•• investigate the structure and function of proteins in living things L
Biology Stage 6 Syllabus © NSW Education Standards Authority for and on behalf of the Crown in right of the State of New South Wales, 2017
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 Have you ever wondered how our genes give us

Science Photo Library/Gunilla Elam

visible features? How they play a part in determining
characteristics such as height and build, eye colour and
skin colour – and what influence, if any, the environment
has? To understand the continuity of life at the organism
level, we need to explore how genes translate into physical
and behavioural features in our bodies and chemical
structures such as proteins in our cells.
As you learned in the previous chapter, the continuity
of life describes how new organisms arise from living
organisms of the same type. The continuity of life is
maintained at the cellular level by cell division (mitosis
and meiosis) and at the molecular level by DNA. At the
whole-organism level, continuity of life depends on
physical and chemical features in organisms that result
when the instructions in DNA are translated into proteins.
FIGURE 4.1 DNA base sequences are expressed
Questions in science drive research. After the structure as proteins.
and mode of replication of DNA were discovered, the next
questions asked were:
◗◗ Is the genetic code universal?
◗◗ Are the structure and function of DNA in prokaryotes the same as in eukaryotes?
◗◗ How does the coded sequence of nucleotides in DNA produce proteins?
Research into gene functioning continued after the development of the Watson and Crick model
and the more scientists learned, the more they wanted to find out. Scientists began investigating gene
regulation – how and why some genes ‘switch on’ to produce a product in some cells and not in others.
For example, why is it that skin cells make the pigment melanin, but bone cells do not? And why is it that
bone cells make bone, but skin cells do not?
In this chapter you will study DNA in prokaryotes and eukaryotes, and how DNA codes for proteins.

4.1 DNA in prokaryotes and eukaryotes

The basic principles of molecular biology and genetics apply to both prokaryotes and eukaryotes, and
genetic evidence points towards all present-day cells having evolved from a common ancestor. The
genetic code is universal – the same nucleotide base-pairing code is used in all living organisms, both
prokaryotes and eukaryotes, to instruct protein synthesis. Both types of cells use a similar mechanism to
translate information from DNA into polypeptides and proteins within the cell.
The basic principles learned from experiments performed with one type of cell have been found to
apply to other cell types. This has led to a common model system used in the study of molecular biology,
whereby the study of the functioning of genes in simple cells is also applied to more complex organisms.
The bacterium E. coli is commonly used to study genetics at the molecular level. These bacteria grow
easily, divide every 20 minutes when kept at 37°C and model the same type of translation (how mRNA
is decoded for the production of proteins) as eukaryotic cells. The metabolism of E. coli is very precisely
regulated and so it is an ideal example for molecular biologists to use in experiments to research
how genes are regulated and expressed. The main differences between bacterial genetics and that of
eukaryotes is at the level of gene expression (how instructions in DNA are converted into a product such
as a protein).

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 Prokaryotic DNA
The DNA of prokaryotes and eukaryotes is chemically the same, but it differs in how it is structurally
arranged into chromosomes and packaged inside the cells. Its location inside these cells is also different,
and there are slight differences in the processes of DNA replication and transcription (how instructions
in DNA are used to make mRNA and initiate protein synthesis).

Cell wall Ribosomes Location and structure

Pili
As you learned in Year 11, prokaryotic cells are ‘primitive’
cells with a much simpler structure than eukaryotic
cells. They contain a single chromosome in the form of
a circular strand of DNA (Fig. 4.2). This chromosome has
no membrane around it and floats in the cytoplasm, in
a dense region known as the nucleoid. The DNA codes
for proteins that will be made on ribosomes in the
surrounding cytoplasm.
The circular, double-stranded prokaryotic DNA
is not a helix, but two circles of single-stranded DNA
twisted around each other like two pieces of string,
each joining at its own ends. The direction and number
Bacterial of twists contributes to the coiling and supercoiling of
flagellum
circular DNA.
Cytoplasm
Non-chromosomal DNA
Capsule Chromosome: Plasma Plasmid:
DNA membrane DNA Prokaryotic cells may have one or more small rings
of non-chromosomal DNA, called plasmids, floating
FIGURE 4.2 A prokaryotic cell, with DNA in a chromosome and in
plasmids separately in the cytoplasm (Fig. 4.2). The genes on these
plasmids code for features that are not essential to the
survival of the cell, but often provide bacteria with a
Science Photo Library/Dr. Gopal Murti

selective advantage, such as resistance to antibiotics.

Plasmids replicate independently of the chromosome.

Packaging of prokaryotic DNA

The circular chromosomal DNA of prokaryotes is about
1300 µm in length. It needs to fit into a cell such as
E. coli, which is only about 3 µm in length. When E. coli
DNA is isolated intact, the circular DNA is found to be
supercoiled and forms loops around a central protein
to form a nucleoid. The dense protein differs from the
histone proteins that package DNA in eukaryotic cells.
The dense protein is sometimes referred to as the
scaffold (Fig. 4.3).
Prokaryotes have evolved over millions of years, having
been exposed to many and varied selective pressures.
Scientists believe that, as a result, they have evolved a more
refined mechanism for regulating gene expression (an
operon system) than complex eukaryotic organisms such
FIGURE 4.3 Electron micrograph of a ruptured E. coli showing a
nucleoid – looping strands of DNA around a central protein (scaffold) as humans.

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 Eukaryotic DNA
Eukaryotic DNA is located in a membrane-bound nucleus within the cell. Individual DNA molecules are
arranged into a number of separate chromosomes, and each chromosome is larger and more complex
than the chromosome in a prokaryotic cell. The DNA of a single chromosome in the fruit fly Drosophila
is 1.2 cm in length. Each human cell contains approximately 2 metres of DNA arranged as a total of
46 chromosomes.
Although eukaryotes have many more chromosomes than prokaryotes, the number of chromosomes
is not a measure of how complex the organism is. For example, the Chinese giant salamander has
60 chromosomes, but is less complex than a human (Table 4.1).

TABLE 4.1 Chromosome number in eukaryotes

ORGANISM NUMBER OF CHROMOSOMES (2n)

Fruit fly (Drosophila melanogaster)   8

Eastern grey kangaroo 16

Earthworm 36

Cat 38

Peanut 40

Human 46

Orangutan 48

Platypus 52

Sheep 54

Chinese giant salamander 60

Horse 64

Black mulberry 308

In most eukaryotic cells there is a large proportion of non-coding DNA (DNA that is not used directly
to make products such as proteins or RNA) in sequences called introns. In humans, only 3% of DNA is
coding DNA (DNA that contains sequences that code for products such as proteins or RNA). These coding
sequences in DNA are called exons. The exact function of non-coding DNA is still being researched; it
is thought to play a role in the spatial organisation of genes as well as in the control of gene expression.
Introns are almost never found in prokaryotes. There are two schools of thought on this – introns may
have accumulated during the evolution of eukaryotes, or they may have been lost from prokaryotes as
they evolved, simplifying their genome to allow them to divide rapidly.

Packaging of eukaryotic DNA

The DNA of eukaryotes is linear rather than circular and it also winds around proteins (called histones)
tightly, but it does not supercoil. It coils in a way that forms nucleosomes – bead-like structures made
up of long sequences of DNA wrapped around eight histone protein cores, similar to the way cotton is The effect
wrapped around a cotton reel (Fig. 4.4). Unlike nucleiods, which have only one type of protein, there are of histone
binding on gene
five main types of histones in eukaryotic cells, and all play a role in packaging DNA. DNA has a series expression is
of folding patterns, around different histones. Histones contain a large number of positively charged dealt with on
page 131
amino acids, which allow them to bind to the negatively charged phosphates of DNA. As a cell progresses (Fig. 4.21).
through the cell cycle, the nature of chromatin changes (page 84 and Fig. 5.3, page 152) and these changes
are thought to be linked to histone binding.

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 a b Chromosome

Histones
Science Photo Library/Gunilla Elam

1400 nm

Linker DNA

DNA wound around Centromere

a cluster of histone
molecules
2 nm

Nucleosome Chromatin Nucleosome

(10 nm diameter)
30 nm
700 nm

DNA
10 nm

FIGURE 4.4 Eukaryotic DNA: a DNA coiled into nucleosomes; b top: a chromosome, showing chromatin; bottom: nucleosomes condensed into chromatin

Non-nuclear DNA in eukaryotes

Mitochondria and chloroplasts are organelles in eukaryotic cells that contain their own DNA. This DNA,
referred to as non-nuclear DNA, is inherited independently of nuclear (chromosomal) DNA. Non-nuclear
mitochondrial DNA (mtDNA) is found in the respiratory organelles of cells. The discovery of mtDNA has
proved extremely useful in studies of evolutionary relatedness.
mtDNA can be used to trace maternal inheritance. During sexual reproduction, the egg and sperm
each contribute half the zygote’s total DNA. However, sperm cells have very little cytoplasm and the larger
egg cell therefore contributes all the cytoplasm (and the organelles within it, including mitochondria).
Because mitochondria have their own mtDNA and replicate independently of the nucleus, all
mitochondria in a female lineage possess identical mtDNA (unless there is a mutation).
Mitochondrial DNA (mtDNA) is a very small (70 nm in diameter), circular molecule with only 37 genes
(Fig. 4.5). Thirteen of these genes make proteins that function in the electron transport chain during
chemical respiration in mitochondria. The other 24 genes make RNA molecules (22 make tRNA and
2 make rRNA, which you will learn about later in this chapter).
Each mitochondrion contains
rRNA Cytochrome b about 5–10 circular DNA molecules
and each cell has between 100 and
Human ancestry 1000 mitochondria. As a result,
testing Non-coding
Read about mtDNA region
small samples of tissue yield a
used to determine large amount of mtDNA. This
human ancestral lines.
DNA is easy to sequence because
NADH it is so short (16 500 base pairs in
Cytochrome c dehydrogenase
oxidase humans), compared with nuclear
tRNA DNA (around 3 billion base pairs in
Forensics and
humans).
mtDNA ATPase The rate of mutation of mtDNA
Read about mtDNA
used in human
is about ten times that of nuclear
identification. DNA.
Sequencing of mtDNA is used
FIGURE 4.5 A model of a mitochondrial DNA molecule, showing
some genes (70 nm diameter) more often than sequencing of
nuclear DNA, because the increased
variability of mtDNA makes it very useful for evolutionary studies (such as relatedness testing) as well as
for forensic biology (identity testing) and human ancestry studies.

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 The use of mtDNA is of advantage, because mitochondria:
Mixing of paternal
◗◗ are inherited only from the mother, which allows tracing of a direct genetic line and maternal
genes during
◗◗ do not combine paternal and maternal genes, as nuclear DNA does (mixing genes during gamete crossing over in
formation and fertilisation) meiosis is dealt
with in Chapter 5.
◗◗ occur in large numbers in every cell, so they are easy to access and sample
◗◗ evolve very quickly because mtDNA does not have repair enzymes, and so mutations arise often
during replication.
You may wonder how, if mtDNA can undergo so many mutations, the mitochondria are still able to
function. Most changes in mtDNA are in sequences that do not code for proteins and so those mutations Mitochondrial
disease
are usually not harmful. In some instances, if mutations occur in DNA that does code for respiratory
Read about
proteins, mitochondrial disease may result. (See the weblinks for more information.) mitochondrial
disorders, genetic
testing and diagnosis.
KEY CONCEPTS

●● Nuclear DNA is present inside the nucleus of each of our cells, and has about 3 billion base
pairs and around 20 000 protein-coding genes.
●● The mitochondrial genome exists outside the cell nucleus, and has 13 protein-coding genes,
24 genes coding for RNA and about 16 500 base pairs.
●● mtDNA has a higher rate of mutation than nuclear DNA, making it easier to identify differences
between closely related individuals.
●● mtDNA is used to study evolutionary relatedness, construct evolutionary trees, investigate
family relatedness and identify people in forensic science.

INVESTIGATION 4.1

Modelling DNA in prokaryotes and eukaryotes

INTRODUCTION
Scientists have used several kinds of cells and organisms as models, to try to investigate and explain aspects Information and
of molecular biology such as DNA structure and replication, and its role in gene expression. In simple cells or communication
technology
organelles that have their own short, single molecule of DNA, the features of DNA are much easier to study. capability
Initially molecular biologists used these simple cells as experimental models to work out how DNA functioned.
As technology improved and biologists gained a greater understanding of DNA structure and functioning, they
moved on to studying similar processes in more complex cells to find out whether they followed the same pattern.
Table 4.2 outlines the features of some simpler cells and organelles that make them particularly
advantageous as experimental models.

TABLE 4.2 Genomes used as models for studies of molecular genetic mechanisms, compared with the human genome
mtDNA (HUMAN) PROKARYOTE (E.coli ) YEAST (S. cerevisiae) EUKARYOTE (HUMAN)

Genome size (base pairs) ± 16 500 4.6 million 12 million ± 3 billion

Number of genes 37 ± 4 300 ± 6 000 ± 20 000

Types of proteins encoded 13(and 24 RNAs) 4 000 5 000 100 000

Number of chromosomes 1 1 16 46

Significance of genome for Maternal inheritance allows study Small size makes Three times larger Complex and large
study of direct lineages. High rate of analysis easy. than E.coli, but amounts of non-
substitution mutations makes much simpler than coding DNA makes
it easier to distinguish between humans. it more difficult to
individuals. study.

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 Alamy Stock Photo/Science Photo Library/Molekuul

Science Photo Library/Alfred Pasieka

a b

FIGURE 4.6 a Linear DNA of eukaryotes and b circular DNA of prokaryotes

TASK

1 Y
 ou are required to use a model to describe, simplify, clarify and/or provide an explanation of the
structure of DNA in eukaryotes and prokaryotes. Make sure you consider which features of DNA you
Cells as intend demonstrating in your model (benefits of the model) and which features you will not be showing
experimental (limitations of the model).
models for
molecular biology 2 
Write up your investigation as a scientific report, under the headings: Aim, Materials, Risk assessment
Prokaryotes such and safety, Method, Results (the model itself ), Discussion (benefits and limitations of the model) and
as E. coli, through
invertebrate Conclusion.
eukaryotes such as
yeast, fruit flies and 3 
Peer review the models produced by at least two other groups of students. Using what you have learned
many others from these models, the information you have researched and information in this textbook, draw up a table
to compare the forms in which DNA exists in eukaryotes and prokaryotes.
Compare DNA under the following headings:
•• Chromosomal structure
Comparison of •• Packaging
prokaryote and
eukaryote DNA •• Genetic information stored.

RESOURCES
Use the weblinks as a starting point for your research.

The complexity EX TENSION

of eukaryotic
genomes In your model, include one aspect of the functioning of DNA (such as replication and/or the start of
polypeptide synthesis).
KEY CONCEPTS

●● Prokaryotic DNA is a circular, double-stranded DNA molecule, supercoiled to form a nucleoid

and found in the cytoplasm.
●● Eukaryotic DNA is a linear double-stranded helix wound around histones to form
nucleosomes.
●● Eukaryotic cells also have non-nuclear DNA, such as mtDNA in mitochondria in the cytoplasm.
Prokaryotic cells have non-chromosomal DNA in the form of plasmids.

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 CHECK YOUR
1 Explain the meaning of the following terms:
UNDERSTANDING
a gene expression
b genome 4.1
c nucleosome
d nuceloid.
2 Explain what is meant by the statement: ‘The genetic code is universal’.
3 Give one similarity and two differences between prokaryotic and eukaryotic chromosome structure.
4 Compare the structure and functioning of non-chromosomal DNA in eukaryotes and prokaryotes.
5 Calculate the length of one human chromosome in comparison with the chromosome of a fruit fly.

4.2 Polypeptide synthesis

In the 1950s, Francis Crick proposed that DNA led to the formation of RNA, which in turn led to the
synthesis of proteins. Experimental evidence supported his proposal. The ‘flow of genetic information’
became known as the ‘central dogma of molecular biology’ (Fig. 4.7). In 1961, Francis Crick and Sydney
Brenner provided the missing link to decoding DNA, with their discovery that genes use three-letter
‘words’ or triplets of bases called codons to code instructions for each amino acid in a protein chain.

FIGURE 4.7 The

central dogma of
DNA RNA Protein molecular biology –
a summary of the
Replication Transcription Translation flow of genetic
information resulting
in gene expression

Scientists already knew that polypeptides were chains of amino acids and that these polypeptides
Assumed
joined to form proteins. It took about five more years to reveal specifically which triplet coded for which knowledge: refer
particular amino acid. In 1968, Marshall Nirenburg received a Nobel Prize for his work in cracking the to Biology in
Focus Year 11,
genetic code for protein synthesis, listing the 60 triplets that code for each of the 20 amino acids in Chapter 3,
proteins (Fig. 4.15, page 125). Section 3.2, Cell
requirements:
A polypeptide is a molecule made up of a chain of many amino acids, joined by peptide bonds proteins and
(Fig. 4.8). There are about 20 different amino acids that can be linked together in a linear sequence, to nucleic acids.

form chains of up to 300 amino acids in length.

Amino acid Peptide bond FIGURE 4.8 Amino

acids joined together
by peptide bonds
form the polypeptide
chains that make up
proteins.

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 One or more polypeptides twist and join together into a particular three-dimensional shape, forming
proteins in cells. The sequence and arrangement of amino acids determines the configuration of the
protein (Fig. 4.9). Any change in the amino acid sequence may result in a change in the shape of the
protein molecule and this could affect the ability of the protein to carry out its function in the cell.

a b
Shutterstock.com/chromatos

Science Photo Library/Laguna Design

Chain A Chain A

FIGURE 4.9 A protein, the hormone insulin: a a simple model showing that insulin is made up of two polypeptide chains
joined at the points indicated (see red arrows); b a 3D molecular model of the structure of insulin

The ‘gene concept’ in molecular biology is that genes in a cell contain all the information for the
synthesis and functioning of cellular components. When the end product of a gene has been made by
the cell, we say the gene has been ‘expressed’. In specialised cells in multicellular organisms, only certain
genes are expressed in each cell type. Coded instructions for the production of a particular protein
(or group of proteins) are said to be ‘switched on’ in the DNA of that cell. This ensures that each cell
develops the necessary structures, in keeping with the type of tissue to which it belongs. For example, in
skin tissue, genes for the pigment protein melanin and the protein keratin are switched on in each cell,
ensuring that the cells become skin cells. Different genes are expressed in nerve cells, muscle cells and
bone cells (Fig. 4.10).
Attribution 4.0 License (https://creativecommons.org/licenses/by/4.0/)
OMICS International All Rights Reserved © 2018. Creative Commons

Mesenchymal stem cells The process of polypeptide synthesis

DNA never leaves the nucleus – the molecules are too large
to pass through the pores in the nuclear membrane. This is
just as well, as DNA molecules hold the original copy of all
Adipocytes
Neurons instructions for future generations of cells. In order for a cell to
make the particular group of proteins it needs, not all the DNA
Muscle cells
is needed; only the relevant instructions for proteins required in
that cell are accessed in the DNA nucleotide sequence. Because
Chondrocytes the DNA remains in the nucleus, an intermediate molecule
called messenger RNA (mRNA) is created and this carries a
Osteoblasts
transcribed copy of the relevant instructions from the nucleus
FIGURE 4.10 Cells differentiate and specialise as a result of to the ribosomes in the cytoplasm. The ribosomes are the cell
gene expression. ‘machinery’ that subsequently translates the message carried by
the mRNA into a cell product such as protein (Fig. 4.11).

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 Shutterstock.com/Designua
DNA
tRNA
1 1. DNA is transcribed
into RNA.
4. More amino
acids are added.
mRNA 3. Amino acid

Gr
Nucleus 3

ow
5 attaches to tRNA.

in
g
Transcription

pr
5. tRNA breaks

o
4

te
off and picks up

in
Amino acid
another amino acid.
2

2. mRNA attaches to
a ribosome.

Ribosome
NA
mR Translation

FIGURE 4.11 Gene expression involves the information in DNA being decoded during transcription into RNA (1) and
subsequently translated into a product such as a protein (2–4).

Nucleic acids involved in polypeptide synthesis: DNA, mRNA and tRNA

Two types of nucleic acids are essential in the process of polypeptide synthesis: DNA and RNA. There are
three types of RNA, each with a specific role to play.

DNA
DNA consists of long chains of nucleotides wound into a double helix. The sequence of nucleotide bases
determines the meaning of the message – this is because it codes for the sequence of RNA nucleotides
and, ultimately, the sequence of amino acids that form the polypeptide chain.

RNA
Like DNA, RNA is a nucleic acid made up of a chain of nucleotides, but it differs from DNA in the following
ways:
◗◗ Most RNA is single-stranded.
◗◗ The sugar in RNA is ribose sugar (not deoxyribose sugar as in DNA).
◗◗ RNA has the nitrogenous base uracil (U) instead of thymine (T).
There are three types of RNA: messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA).
◗◗ messenger RNA (mRNA) is single-stranded and is not twisted into a helix (Fig. 4.12a). mRNA molecules
are a few thousand bases long, much shorter than DNA. They are found in both the nucleus and the
cytoplasm. mRNA functions as an intermediate molecule, carrying information from DNA in the
nucleus to the ribosomes in the cytoplasm.
◗◗ transfer RNA (tRNA) molecules occur in the cytoplasm. Each molecule is 75 nucleotides long and
twisted into the shape of a clover leaf (Fig. 4.12b). At one end of the tRNA are three unpaired bases,
called an anticodon, which attach the tRNA to its complementary bases (codon) on the mRNA strand.
The other end of the tRNA is able to bind with an amino acid temporarily. Each tRNA molecule will
only attach to one particular amino acid. The specific sequence of three bases at the anticodon end
determines which amino acid will be carried by that tRNA.
◗◗ ribosomal RNA (rRNA) forms a structural part of ribosomes (Fig. 4.12c) and is made in the nucleolus
of the cell.

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 Using a computer analogy, you could say that DNA is the operating system, mRNA is the software,
tRNA is the machinery (such as a 3D printer) and protein is the product created.

a b c
Amino acid Ribosome

Uracil

Anticodon

Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA)

FIGURE 4.12 Three types of RNA: a mRNA, b tRNA and c rRNA (combined with protein to make a ribosome)

Transcription
Transcription occurs when an enzyme, RNA polymerase, binds to a section of DNA and begins building
Transcription
animation a chain of RNA nucleotides to form a complementary strand of RNA. Figure 4.13 shows the details of this
Work through the process. (The number of each step in the description below matches the sequence of numbered steps in
interactive animation
and make notes as Figure 4.13.)
you go, to create a
summary of the steps 1 RNA polymerase binds to a part of the DNA called the promoter and the DNA ‘unzips’ – that is, the
involved.
DNA unspirals, hydrogen bonds between the two strands break, and the strands separate over a short
length. This happens only in that part of the DNA that contains the gene to be used. Only one strand
of DNA contains the genetic information to make a protein; rather confusingly, it is called the non-
coding strand or sense strand; the other strand is called the coding strand (it has the same code as the

Translation (basic)
mRNA being made) or antisense strand.
Work though the 2 Transcription of the gene is controlled by the enzyme RNA polymerase. The sense strand of the DNA
interactive animation
and draw a flow chart acts as a template and RNA nucleotides are assembled, forming a complementary single-stranded
of the steps involved. mRNA molecule (that is, DNA is transcribed into mRNA). The sequence of nucleotide bases on
the mRNA molecule is the same as the DNA coding strand, except that it has U instead of T. (In
eukaryotes, ‘editing’ or splicing of pre-mRNA may take place at this point. This is dealt with in more
detail on page 124.)
3 The mRNA moves out of the nucleus and into the cytoplasm, where it encounters some of the millions
Translation
(advanced) of ribosomes in the cell. Usually one mRNA molecule is read by a large number of ribosomes, so
Play the interactive multiple chains of the same polypeptide product are produced from one mRNA template molecule.
animation and make a
summary of the steps
involved.
Translation
4 Translation occurs when the ribosomes move along the mRNA molecule and, as they do so, they
attach tRNA molecules to mRNA by temporarily pairing the bases of the tRNA anticodons with their
complementary triplets of bases (codons) on the mRNA.
Translation 5 The amino acids from the tail end of each tRNA are linked to one another by an enzyme to form a
Watch the video of
translation in real polypeptide chain. Each amino acid is then spliced off its tRNA carrier.
time.
6 The tRNAs move away from the mRNA, leaving the growing chain of amino acids, and move back into
the cytoplasm where they can pick up another amino acid and be reused.

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 7 The polypeptide chain is then processed in the cell. It may be joined to one or more other polypeptides
and be further processed and folded into the correct shape for its functioning, forming the final
protein end product.
8 The mRNA is broken down into its individual nucleotides, which can be reused.

Cell nucleus
C C
G
G A
T

2 Transcription

Antisense strand
G C A

(coding strand)
C

G
T of DNA
A
T

‘Sense’ strand
T A

mRNA being
—U

or ‘non-coding’
— C

transcribed from DNA

C

strand of DNA
A

(the nucleotide U is
— U

T
T

used in mRNA in the

— A

A
G

place of T)
— C

C
A

1 RNA
— A

A
T

polymerase
— U

T
G

— G

G
T

— A

Nuclear membrane
A

G
A

A
— U
C

C
— C

U
T

RNA
nucleotide
pool 4 Translation

mRNA leaves through

3 nuclear pore
—
———————————
U C
U A C U A C A U G A 5

U A G

7 mRNA
6 U A C enters the
Peptide
bond A U G C ribosome
U A C U A C A U G A U
Amino acid
tRNA

tRNA moves into Ribosome

cytoplasm to ‘Start’ triplet 8
pick up a new A UG or codon
A A G
C

amino acid
Anticodon
A

Pool of amino acids

U

C
U
G

RNA nucleotides

Key DNA RNA amino acids tRNA

FIGURE 4.13 The biochemical process of protein synthesis in a cell

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 TABLE 4.3 Types of nucleic acids in cells and their role in polypeptide synthesis
DEOXYRIBONUCLEIC ACID (DNA) Macromolecule made of a double strand of nucleotides held together by weak hydrogen bonds between
base pairs; the ladder-like structure is twisted into a double helix and may be circular (prokaryotes) or linear
(eukaryotes); contains the sugar deoxyribose and the bases adenine, thymine, cytosine and guanine
NUCLEAR DNA (nDNA) DNA arranged as chromosomes in the nucleus of a eukaryotic cell

MITOCHONDRIAL DNA (mtDNA) Small molecules of DNA found in mitochondria; also known as extra-chromosomal DNA or non-nuclear DNA

RIBONUCLEIC ACID (RNA) Single-stranded molecule of nucleotides containing the sugar ribose and the bases adenine, uracil,
cytosine and guanine
MESSENGER RNA (mRNA) A single-stranded long RNA molecule containing the sugar ribose and the bases adenine, uracil,
cytosine and guanine; it is transcribed from a DNA template (non-coding strand); carries codons
(base triplets) that instruct amino acid assembly by ribosomes
TRANSFER RNA (tRNA) A small RNA molecule folded into a clover shape; carries an anticodon of three bases at one end and
a specific amino acid at the other end; works with the ribosome to transfer the correct amino acid for
inclusion in sequence to form a polypeptide
RIBOSOMAL RNA (rRNA) The RNA component of a ribosome which, together with protein, forms the ribosome subunits
needed to translate mRNA into a polypeptide chain
KEY
CONCEPTS

●● Transcription occurs when the double helix DNA unzips and a single strand of mRNA is made,
using part of the non-coding strand of a DNA molecule as a template.
●● Translation occurs when mRNA is ‘read’ by ribosomes and translated into a polypeptide, with
the help of tRNA.

RNA processing
In eukaryotic cells, mRNA that is transcribed from DNA is termed pre-mRNA, as further editing of this
RNA takes place in the nucleus before it acts as a template for translation into a polypeptide. Pre-mRNA
contains coding sequences of nucleotides, called exons, which will be translated into amino acid chains
(remember, exons are expressed as proteins). What scientists did not realise at first was that in between
these exons are sequences of nucleotides called introns, which do not code for amino acid assembly.
Directly after transcription, mRNA is edited (or spliced) and introns are removed (Fig. 4.14) by a
complex molecule called a spliceosome. The result of this splicing is the formation of a mature mRNA
RNA splicing of
molecule, which then moves from the nucleus to the cytosol for translation by ribosomes. The instructions
introns for splicing the mRNA are found within the introns – they code for their own removal.

FIGURE 4.14 mRNA Exon Exon Exon Exon

splicing and gene DNA Intron 1 Intron 2 Intron 3 Intron 4
regulation: following
gene transcription,
Transcription and removal of introns
mRNA alternative
splicing takes place, 1 2 3 4
whereby non- Pre-mRNA
coding intervening Alternative splicing
intron sequences
are removed by a
'spliceosome' to form
mature mRNA. Mature mRNA 1 2 3 1 2 4
Protein X Protein Y

Splicing is the second step in gene regulation and serves an important purpose in complex
organisms. A strand of mRNA produced from one gene is not always spliced in the same way. Alternative
ways of splicing mRNA give rise to different versions of the same protein. For example, in humans,
Alternative immunoglobulins (antibodies) are produced in response to a particular pathogen, such as a bacteria
splicing
or a virus (pages 398 and 402–403). Within a short space of time, the body produces different forms of
Read about how
alterative splicing antibodies or immunoglobulins specific to the invader. This is done by alternative splicing of mRNA,
introduces protein
diversity.
producing proteins that have a similar structure and/or function but are not identical. These are termed
isoproteins. Many complex organisms such as vertebrates have up to five times as many proteins in their

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 bodies as invertebrates (such as worms and beetles), but only twice as many genes. Alternative splicing
provides a mechanism to explain this.
Eukaryotes have a large amount of non-coding DNA, originally termed ‘junk DNA’ (by Japanese
American biologist Susumo Ohno in 1972), as scientists did not know its purpose. For many years,
biologists ignored this DNA, but recent studies of non-coding DNA using advanced technology show that
its removal disrupts development of individuals in the embryonic state. Further research is showing that
non-coding DNA affects the shape of chromatin and how tightly DNA is wound around histones. When
some parts of this non-coding DNA are expressed, chromatin is less tightly packed, leading to the likelihood Non-coding
and ‘junk’ DNA
that non-coding DNA determines whether or not certain genes are read. Large portions of non-coding are dealt with
DNA may therefore be involved in regulating which genes are expressed in particular cells, resulting in the in more detail
in Chapter 7 on
differentiation of cells into particular tissue types. The term ‘junk’ DNA today is reserved only for that part pages 243–4.
of non-coding DNA that is not involved in gene regulation, DNA for which no known function has been
found. With the completion of the Human Genome Project, a large team of researchers has now joined a
project called ENCODE to work through the huge amounts of non-coding DNA to find out its function.
As mentioned previously, the universal genetic code of nucleotides in DNA and its transcribed
sequence in mRNA determines the amino acid sequence in proteins that are synthesised. Figure Is ‘junk DNA’
our genome’s
4.15 outlines the nucleotide codons in mRNA that correspond with the 20 amino acids made during equivalent of
translation on the ribosomes. The codon AUG is the start codon, signifying where translation should be a high-level
operating system?
initiated. There are three stop codons: UAA, UAG and UGA. The mRNA codon table (Fig. 4.15) can be Does ‘junk DNA’ play
used to work out the sequence of amino acids that will be created in a polypeptide, based on a DNA and a role in embryo
development? Read
mRNA sequence. Note that there is more than one codon that codes for each amino acid, creating some about the ongoing
debate.
flexibility for errors in the genetic code.

Amino acid key Second base

Ala = alanine U C A G
Arg = arginine
UUU UCU UAU UGU U
Asn = asparagine Phe Tyr Cys
UUC UCC UAC UGC C
Asp = aspartic acid U Ser
UUA UCA UAA Stop UGA Stop A
Cys = cysteine Leu
UUG UCG UAG Stop UGG Trp G
Gln = glutamine
Glu = glutamic acid CUU CCU CAU CGU U
His
Gly = glycine CUC CCC CAC CGC C
C Leu Pro Arg
His = histidine CUA CCA CAA CGA A

Third base
First base

Gln
Ile = isoleucine CUG CCG CAG CGG G
Leu = leucine
Lys = lysine AUU ACU AAU AGU U
Asn Ser
Met = methionine A AUC Ile ACC AAC AGC C
Thr
Phe = phenylalanine AUA ACA AAA A
AGA
AUG Met/ ACG Lys Arg G
Pro = proline AAG AGG
Start
Ser = serine
Thr = threonine GUU GCU GAU GGU U
Asp
Trp = tryptophan GUC GCC GAC GGC C
G Val Ala Gly
Tyr = tyrosine GUA GCA GAA GGA A
GCG Glu
GUG GAG GGG G
Val = valine

Use the bases along the sides and top of the table to find the base sequence you are looking for.
The cell where the three converge gives the abbreviation of the amino acid that is coded.
Note: Each amino acid may be coded by more than one codon.
FIGURE 4.15 mRNA codon table

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 INVESTIGATION 4.2

A practical and secondary-source investigation to model

polypeptide synthesis
In this investigation, you will gather and process information from several sources to gain an understanding
of the process of protein synthesis, and develop your own simple model to explain the sequence of steps
involved in the process.
A model of protein synthesis can be developed in a number of ways:
1 class activity: video and group model creation
2 role play: students role play the processes of transcription and translation (also find YouTube video clips on
protein synthesis and other relevant websites)
3 assessment task: model and oral presentation
4 computer-generated model.

PART A: SECONDARY-SOURCE INFORMATION/STIMULUS MATERIAL

Watch the video Protein synthesis or another suitable video showing an animated version of protein synthesis.
Protein synthesis (See the weblink.)

PART B: PRODUCING A MODEL

Working in groups of up to four, use the materials provided to build a working model to demonstrate
polypeptide synthesis.
1 Decide as a group:
a what materials you will use to depict the structures involved in the process
b how you will make the necessary structures out of the materials provided
Literacy
c how the parts will be assembled on the butcher’s paper to create your working model
d who will make which structures
e any colour-coding that may make the model easier to understand
f the minimum number of nucleotide sequences you need to use so the resulting polypeptide chain
that your model makes contains at least four amino acids.
2 Remember to include in your model a representation of:
a both the nucleus (or part of a nucleus) where transcription
occurs, and the cytoplasm where translation occurs
b the four different nucleotide bases present in your DNA
and RNA strands
c ribsosomes, tRNA and amino acids.
3 Labels, arrows and/or numbers are useful to indicate the
sequence of events (Fig. 4.16).

PART C: PRESENTING THE MODEL FIGURE 4.16 Creating a model of protein

synthesis
Use the model to give a short oral explanation (as a group) of the
process of protein synthesis to your classmates. Be aware of the
limitations of your model – these will be assessed by the class at the end of each presentation.
You may be asked to explain any of the following concepts, using your model.
1 Outline how a change in DNA sequence can result in changes in proteins produced and therefore changes
in cellular activity.
2 Explain how mutations in DNA may lead to the production of a non-functional protein.
3 Explain why the ‘one gene – one protein’ hypothesis was altered to the ‘one gene – one polypeptide’
hypothesis.

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 PART D: REPORT
WS
Write a report on the model that you and your group presented.
The process
1 Outline the purpose of developing this model. Homework
of protein
2 List the materials. synthesis

3 Justify the validity of your model.

4 Discuss any limitations of your model.
5 Acknowledge all secondary sources, using an accepted referencing style. WS

PART E: DO IT YOURSELF Protein

Homework
synthesis
View the presentation and complete the worksheet, The process of protein synthesis, using the mRNA codon presentation
table in Figure 4.15 to translate a protein from a given DNA sequence. (See the link provided.)

Function and importance of polypeptide synthesis: genes

to proteins
A gene is considered the smallest unit of heredity. Chemically, each gene is a portion of DNA with a
specific sequence of bases that encodes for a particular trait that can be passed from parent to offspring.
A locus is the position of a gene on a chromosome. The coded information within genes determines how How much
DNA codes for
living things look, behave and function – that is, it influences particular characteristics (phenotypes). protein?
A chromosome can therefore be described as a linear sequence of genes. The total amount of genetic List the following
structures in
material that an organism has in each of its cells is called its genome. order of size, from
Specific staining techniques are used to show banding patterns on chromosomes (Fig. 4.17) and smallest to largest:
chromosome, gene,
these bands correspond on homologous pairs of chromosomes. The banding patterns can also be used DNA, nucleotide,
base, genome.
to identify the positions of particular genes on chromosomes (Fig. 4.18). With modern technology,
particular genes can be marked with fluorescent tags that show up on the chromosome, assisting gene
mapping. Specific genes can therefore be associated with a particular physical feature or trait. Alleles are
different forms of the same gene (Fig. 4.18).
Maternal Paternal
chromosome chromosome
Science Photo Library/L. Willat, East Anglian Regional Genetics Service

Locus 1 a A
This locus contains
genes A and B b B

Locus 2
This locus contains C c
gene C

Centromere

d D Gene D : alleles D or d

E e Gene E : alleles E or e

f F Gene F : alleles F or f

FIGURE 4.17 Human karyotype with 46 chromosomes,

showing the banded patterns of gene loci FIGURE 4.18 Genes located on homologous chromosomes

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 Changing definition of a gene
The definition of a gene has changed as biologists come to understand more about how genes
function. At first, a gene was defined as a sequence of nucleotides that codes for one protein. Advances in
understanding of the biochemical functioning of cells have led to the definition changing to a sequence
of nucleotides that codes for one polypeptide chain. More recent research has shown that some genes
code for rRNA and tRNA, which are not proteins at all, and that in other instances one gene may
code for more than one polypeptide sequence (due to the splicing and rearrangement of blocks of
mRNA before translation). Therefore the definition of a gene may need to change to a more functional
concept: a sequence of nucleotides that codes for any molecular cell product.
KEY CONCEPTS

●● A gene is made up of linear sequences of nucleotides that code for a cell product, such as a
polypeptide chain.
●● In eukaryotes, mRNA may be processed after transcription (introns are spliced out) before it
passes into the cytoplasm and binds with ribosomes to direct the formation of a polypeptide.
●● mRNA is translated, with the help of tRNA on ribosomes, into polypeptide chains. A table of
mRNA codons has been created from researched evidence, showing which triplets of bases code
for which amino acid.
●● The process of polypeptide synthesis may be modelled, but all models have limitations.
●● Homologous chromosomes carry genes for the same traits in the same position (locus), but
these genes may have alternative forms (alleles).
●● Specific genes are associated with specific traits and are expressed in specialised cells.

CHECK YOUR
UNDERSTANDING 1 Compare DNA and mRNA in terms of structure and function.
2 Distinguish between the three types of RNA, state where each is found and outline the role of each in
4.2 polypeptide synthesis.
3 The genetic code is sometimes described as a triplet code. Explain what this means.
4 Draw a diagram to show the meaning of the following terms: chromosome, gene, allele, locus.
5 Distinguish between the terms gene, genome and trait.
6 Draw a flow chart to model the process of polypeptide synthesis. Identify two benefits and one limitation
of your flow chart model.

How genes and the environment

4.3 affect phenotypic expression
Is the ability to play sport inherited? Why does tightrope walking tend to run in families? Is shyness
The genotype is
the set of genes in genetically determined or does the environment in which we grow up influence this? What about
an organism’s DNA intelligence? Why do identical twins who are separated at birth and later reunited often show unexpected
that is responsible
for a particular similarities, such as having the same hobbies, liking the same foods and even choosing the same career?
trait. Genotype can If they are genetically identical, why do these twins have differences, such as different susceptibility to
be determined by
biological testing. certain diseases?
The phenotype is the The phenotype of an organism is often defined as its physical appearance, but today we know that
physical expression,
or characteristics, phenotype includes the sum of all gene products. The term phenotype in this context includes the
of that trait and can structure, behaviour and physiology of an organism.
be determined by
observation. We also know that the genotype (genetic blueprint) of every cell is the same, yet each cell becomes a
specific type of cell in a particular tissue. This specialisation of cells is brought about by controlling the
expression of genes within the cells. Gene expression is the translation of genes into their protein end

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 products. These products determine the physical and chemical features typical of each cell type and the
overall phenotype of an organism.
Some variations in organisms are genetically determined (‘nature’), whereas others are influenced
by the environment (‘nurture’). Many variations arise as a result of an interaction between the two – the
environment can influence how genes are expressed. The term ‘nurture’ here refers to a wider influence
of the environment than just the nurturing one of the home; it includes all environmental influences.
Gene expression has been studied for
over half a century, with biologists intent on

Getty Images/hartcreations
finding out how the gene sequence shows up
as the phenotype. For example, how does DNA
determine what blood group a human belongs
to, what colour fur an animal has and how tall a
plant grows?
Studies of both plants and animals show
that, although genes may be direct determinants
of phenotype, gene expression can be enhanced
or masked by factors in the environment. In twin
studies, the phenotypes of identical twins (with FIGURE 4.19 Identical twins: any differences are due to
identical genotypes) have been analysed. The effects of the environment.
Identical twins
reasoning behind this is that any phenotypic have identical
genes, but may
differences between identical twins must reflect the influence of the environment. Studies of twins not have identical
separated at birth have formed a major part of these studies, because the effect of ‘nature’ (genotype) and gene expression,
a difference
‘nurture’ (environment) can then be explored independently. that may be
More recent research involves biologists investigating how the environment influences gene influenced by
epigenetics.
expression at a molecular level, leading to a field of study called epigenetics. Some results suggest that
the environment may chemically modify DNA in individuals and in this way affect gene expression. This
chemical modification is not a change in the sequence of bases in the genome (as in mutations), but WS
instead seems to involve chemical markers or tags being added to DNA.
Extension: Investigating
Homework
alcoholism, IQ and
height
Gene expression and phenotype
Genes that are expressed dictate the types of proteins in cells and, as a result, the overall phenotype of
organisms. A great deal of current research involves using stem cells to try to find out how cells ‘know’
what kind of cell to become. Stem cells are unspecialised cells that are capable of dividing and becoming
specialised tissue. Embryonic stem cells are capable of dividing and giving rise to any type of tissue within
an organism, and so they are termed pluripotent (pluri = many; potent = potential). Stem cells also occur in The epigenetics
some adult tissue (adult stem cells) but these are not pluripotent, as they are only able to give rise to cells of identical
twins
of one tissue type. Stem cells undergo asymmetric division – they give rise to two daughter cells, one of Describe the
model that was
which will continue to divide and another that will follow the path of differentiation. Studies have shown used to represent
that when stem cells differentiate, special proteins called transcription factors appear to control which epigenetic
modification of
genes in the cells are transcribed. These transcription factors therefore determine the developmental chromosomes.
pathway of a cell and the type of tissue it will become.
It is interesting to note that, because each step in the process of gene expression is regulated by
WS
proteins, genes must produce the proteins that regulate their own expression. The accurate synthesis of
proteins according to DNA instructions is therefore of ultimate importance in assembling amino acids Epigenetics: chemical
Homework
modification of gene
in the correct order in each polypeptide, as this gives rise to the three-dimensional structure of each expression that may be
protein – essential for the correct functioning of cells and to produce an overall phenotype in organisms inherited

that is free of disorders.

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 Environmental effects on gene expression and phenotype
The coat colour of Siamese cats is determined by a colour mutation (Fig. 4.20a, b). Cats that have the
allele C have uniform pigmentation of their fur over all parts of their bodies. However, cats that are
homozygous recessive for the mutant allele c have dark pigmentation at the extremities of their bodies –
the tips of their ears, tail, legs and face. These are also the areas of poorer circulation – the last to obtain
heat from the blood (think of which parts of your body get cold first in really low temperatures). Pigment
can be produced by the allele c only at low temperatures. Other parts of the cat’s body are subjected to
higher body temperatures and so no dark pigment is produced. As the cat gets older, these areas may
darken more as circulation becomes poorer and a greater proportion of each extremity is colder. The
phenotypic expression of colour is therefore influenced by the temperature of the environment.
An example of the effect of the environment on plant phenotype is seen in flower colour in hydrangeas.
The acidity or alkalinity of the soil influences the colour of the flowers. Hydrangeas growing in acidic soil
develop blue flowers, whereas those grown in alkaline soil develop pink flowers (Fig. 4.20c, d).
Another example of how the environment affects phenotype is when a change in temperature or pH
causes a change in the shape of the active site of an enzyme, increasing or decreasing its binding with the
substrate and therefore affecting its functioning (refer to Year 11 work on enzymes).
A simple example of how the environment affects gene expression can be seen in the growth of
humans. Human height and infant birth weight have a genetic basis, but lack of nutrients or the presence
of toxins (such as those in cigarette smoke) can restrict growth. Another well-researched example is
that of the disease phenylketonuria (PKU). This is a rare genetic disease whereby the amino acid
phenylalanine builds up in the body and results in symptoms that become increasingly severe as time
passes. These symptoms range from behavioural and emotional problems through to developmental
delays such as stunted growth, seizures and brain damage. Early intervention with a diet low in proteins
that contain phenylalanine can affect gene expression, slowing down the onset of the disease and keeping
the symptoms at bay.

Getty Images/iStock/catman73
Getty Images/iStock/pixalot

a b

Getty Images/iStock/dkapp12

c d
Getty Images/lillisphotography

FIGURE 4.20 The effect of environment on phenotype: a young Siamese cat; b dark-tipped older Siamese cat; c blue
hydrangea in acidic soil; d pink hydrangea in alkaline soil

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 Regulation of genes for phenotypic expression
Gene expression can be understood in terms of the switching on and off of genes, as needed. Investigations
into gene expression have shown that gene expression may be regulated at various stages of DNA
transcription into RNA and its subsequent translation into proteins, as discussed below. An interesting
part of this research is that gene expression may also be affected by changes in the cellular environment.

Gene regulation by modifying DNA for transcription

Initiation of transcription seems to be determined by how densely DNA is bound to histones and this in
turn affects gene expression. Epigenetics explores how chemical modifications to either the histones or the
chemical structure of DNA (without changing the base sequence) may affect the density of DNA binding
and, in turn, affect the switching on or off of genes. Regions of DNA that are tightly bound are inaccessible
to RNA polymerase, the enzyme that starts transcription. Chemical changes such as methylation (adding
a methyl group) and acetylation (adding an acetyl group) to non-base parts of DNA or to histones has been
found to affect transcription. Generally, DNA methylation represses transcription, and loss of methylation
activates genes. This is because methylation appears to increase the density of binding between DNA
and histones, acting as a ‘muffler’ in silencing gene expression, whereas adding an acetyl group seems to
have the reverse effect, making DNA accessible to RNA polymerase and thereby promoting transcription
(Fig. 4.21). Methylation and/or acetylation of histones may have similar effects on DNA binding and
gene expression. This raises the question of whether these epigenetic changes can be inherited from
one generation to the next. Research shows that most epigenetic markers are wiped clear at the start of
embryonic development, but some are not, leading to interesting current research into whether changes
in the environment that cause ‘tagging’ of DNA with epigenetic markers can cause heritable variations.

Shutterstock.com/ellepigrafica
DNA inaccessible, gene inactive
Methylation
Me Me

Methyl group Me Me

b
Acetylation 10 nm
Histone tail
Ac Ac

Ac Ac
Acetyl group DNA accessible,
gene active

Histone

Ac
Ac
Ac Ac

FIGURE 4.21 Chemical changes affect transcription and gene expression: a methylation of DNA makes it tightly packed,
which ‘silences’ the genes because they cannot be accessed by transcription factors and be expressed; b acetylation of DNA
promotes transcription.

Cancer was the first human disease to be linked to epigenetics. In 1983, researchers investigated the
chemical structure of DNA in diseased tissue from patients with colorectal cancer and compared it with
DNA in normal tissue from the same patients. The DNA in the cancerous cells of these patients had less
methylation than DNA in normal tissue from the same patients. DNA that is not being transcribed in a
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 cell is normally methylated (it has a methyl group added to its cysteine base) and this turns off the genes.
A decrease in DNA methylation can cause abnormally high gene activity – this is typical of cancer cells,
which divide uncontrollably. Too much methylation can also be harmful, by not allowing the action of
protective tumour suppressor genes. This has led to a flourish in research to investigate links between
epigenetics and disease.

Gene regulation during the transcription process

Elongation of RNA and the termination of transcription are other steps in the process of transcribing
DNA to mRNA where regulation of gene expression may occur. Protein factors influence whether mRNA
elongation continues or terminates, and production of these factors relies on other genes. If the production
or binding of transcription factors is affected, gene expression will be affected. These proteins that regulate
transcription are also produced by genes, so this means that some genes encode their own functioning.

Post-transcription gene regulation – modifying and processing RNA

Processing of mRNA before it leaves the nucleus is thought to be one of the most common forms of gene
regulation in eukaryotes. RNA processing and modification may involve:
◗◗ alternative splicing (removing introns) – as described on page 124 (Fig. 4.14)
◗◗ regulating the length of time for which mRNA remains stable. The longer an mRNA molecule lasts,
the more protein will be translated. If the mRNA degrades more quickly, less protein will be made.
Small non-coding RNA molecules called microRNA (miRNA) can silence mRNA after transcription.
The miRNA molecules may pair with and silence mRNA by:
◗◗ cutting RNA into two pieces
◗◗ making RNA unstable by shortening its poly(A) tail
◗◗ interfering with the translation of RNA on ribosomes.

Post-translation gene regulation – modifying proteins

After translation, the protein product made from mRNA may be inactive until a chemical is added, or it
may be active until a chemical group is removed, regulating phenotypic expression.

A summary of stages at which gene expression in eukaryotes may be regulated is shown in Figure 4.22.

Nucleus
Degraded mRNA
Pre-mRNA
Mature
Open DNA mRNA mRNA
Polypeptide Active protein
Chromatin

6 Post-translational
modification (folding,
An operon is a set glycosylation,
of genes that is transport, activation,
transcribed under 1 Chromatin 2 3 RNA 4 mRNA 5 degradation of protein)
the control of an remodelling Transcription processing stability Translation
operator gene.
It includes the Cytoplasm
structural genes, an
operator gene and a
regulatory gene. FIGURE 4.22 Regulation of gene expression in eukaryotes

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 The regulation of gene expression in prokaryotes differs from that of eukaryotes, because prokaryotes
do not have introns. Bacterial gene regulation has been studied in detail by looking at the LAC operon.
The LAC operon relies on the fact that some bacteria use lactose for sustenance, but most bacteria use
glucose. If no glucose is present, bacteria turn on a gene that allows them to turn lactose into glucose.

INVESTIGATION 4.3

A secondary-source and practical investigation into the effects

of environment on gene expression and resulting phenotype
You may do either investigation A or B, or both. Or you might wish to conduct investigation A and design (but
not conduct) investigation B. Conducting investigation B is an advanced option and your choice will depend
on the resources available in your school, your areas of interest and investigative skills, and the time and
resources available to your teacher. Conducting investigation B may be part of a depth study.

INVESTIGATION A
You are to plan and conduct an investigation to demonstrate the effect of environment on the phenotype of
‘genetic barley’.

BACKGROUND INFORMATION
Both genotype and environment may influence the phenotype of an organism. For an investigation to be
valid, there can be only one variable – in this case, either genotype or environment. Because this investigation
explores the effect of environment on phenotype, the genotypes of the organisms used in this investigation
must be kept the same (genotype is a controlled variable). This will ensure that any change evident in
phenotype has been influenced by the change made to the environment. Genetic barley is an F1 hybrid where
all seedlings are genetically similar. This is an example of a plant that may be used to allow you to determine
the effects of environment on the phenotype of a plant. There are others that may be used, depending on your
preferences and those of your teacher, and on the availability of equipment.

METHOD

1 Identify and clearly express the problem.

2 Form a clear hypothesis.
Refer to
3 Choose appropriate equipment and conduct a risk and safety assessment. Chapter 1 to
revise how to
4 Use a logical scientific method – select a suitable strategy to investigate the question, one that allows valid formulate a
and reliable results to be collected. hypothesis, plan a
valid investigation
5 Identify controls and variables and use an adequate sample size. and communicate
6 Measure, observe and record results in accessible and recognisable forms; carry out repeat trials as your findings.
appropriate.
7 Use appropriate data collection techniques.
8 Assess the accuracy of your measurements and calculations, and the relative importance of the data
gathered.
9 Draw valid conclusions from the data – identify trends and patterns, justify inferences and conclusions, and
generate plausible explanations related to your observations and to contradictions in data and information.

RESULTS
Use appropriate methods to analyse, process and present your results.
Present your investigation in the form of a scientific report.

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 DISCUSSION

1 Conduct a secondary-source investigation to find results of other similar investigations. Assess whether
they support or refute the findings of your own practical investigation, and how they may add to your
findings.
Evaluate the methodology that you used and describe how you could improve your investigation plan.
Revise experimental
error in Chapter 1, 2 Explain what may have given rise to the patterns, trends and/or relationships in your discussion. Use
pages 19-21. secondary resources to help you explain the science behind your findings.
3 Justify why you could/could not make a valid deduction as to whether the changes in phenotype that
you observed and measured were due to the effect of the environment and were not due to genetic
differences.
4 Assess the reliability and accuracy of your investigation, discussing any errors that may have arisen due to
experimental error.
5 Evaluate the methodology that you used in your investigation and use secondary sources to help you
suggest improvements to this method. Explain how you would modify your investigation plan to improve
it for a future investigation of this type.
6 As a whole class, discuss the advantages and disadvantages of conducting this investigation.

CONCLUSION
Draw a valid conclusion based on your results. (There should be no inferences or explanations in your
conclusion.)

INVESTIGATION B (ADVANCED)
This part is a secondary-source and practical investigation into the effects of environment on gene expression
and resulting phenotype in prokaryotes.
1 Secondary source investigation – research theoretical background information.
Go to the weblink and read the Jacob-Monod hypothesis for gene regulation.
Jacob-Monod 2 Practical investigation – research practical background information on experimental design for an
hypothesis for
gene regulation investigation of this kind.
In the weblink Gene induction, read the experimental design to investigate the expression of a gene in the
bacterium E. coli that is switched on in the presence of lactose, noting how both qualitative and quantitative
data can be collected for the investigation.
3 Design a practical investigation (optional for advanced study).
Gene induction Using your understanding of the practical methodology, as well as your knowledge of how the β-galactose
structural, regulator and operator genes work together, design an investigation to find out what would happen
to the production of β-galactosidase if one of the genes was mutated or a different sugar was introduced. To
help you decide on your investigation question and design, follow these steps:
a Create a chart:
What do we know?
LAC operon
Explain how a What do we think we know?
repressor protein
prevents the What do we want to find out?
transcription of RNA
and how the presence
Think of a specific question, such as:
of lactose in the – What would happen if the regulator gene was deleted by a mutation?
environment affects
this. – Does glucose have a similar effect on the enzyme to that of lactose?
b State the hypothesis of the original experiment described in step 2. Create your own (revised)
hypothesis for what you wish to find out.
c Design an investigation to test your hypothesis.
Using your understanding of the procedure above and the functioning of the structural, regulator and
operator genes for β-galactose manufacture, design a practical investigation that could be conducted using

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 the equipment available in a school. Research methods that may be applied using simpler equipment, if
necessary.
d Conduct the experiment (if your school has the resources).
e Use secondary sources to find results of other similar investigations and assess whether they support or
refute the findings of your primary investigation, or to add to your findings. Use your secondary-source
investigation to research answers to the questions that have arisen as a result of your investigation, to
find out whether or not your experimental results are as expected in the literature, and to explain the
science behind your findings. Evaluate the methodology that you used and describe how you could
improve on your investigation plan.
f As a class, formulate new, revised hypotheses that could be researched further. (You do not need to
conduct this further research.)

INVESTIGATION 4.4

Secondary source investigation to assess how genes

and environment affect gene expression
You are to research, analyse and evaluate the available literature to assess how genes and the environment Literacy
affect phenotypic expression. You will need to identify and research the effect of both genes and the
environment on at least one phenotypic trait.
Critical and
Your research may lead you to studies that explore epigenetics as well. If so, take care to evaluate the validity, creative
reliability and accuracy of your sources and use your critical thinking skills to draw an evidence-based conclusion. thinking
Once you have read widely, formulate a research question or hypothesis. When gathering information, Personal
bring together the results of different studies, pointing out where researchers agree or disagree, and where and social
capability
significant questions remain. Draw your own conclusions, presenting your perspective as an evidence-based
argument, and identify any gaps in the research to indicate directions for future research.
The difference between a research question and a research hypothesis depends on how much is known in
the field. If a large amount of literature is already available and you are able to make a prediction about results, Review
formulate a hypothesis. If little is known and you need to explore to find information, use a research question. proposing
Remember to group the literature according to common themes and then explain the link between the a research
question and
research question/hypothesis and the literature reviewed. formulating a
Follow the three rules of effective research: hypothesis in
Chapter 1,
•• variety (use a range of key words and multiple sources) pages 11–12.
•• reliability (use information from trusted sources)
•• consistency (ensure information is relevant to the topic).
At the end, pair up so that you can peer assess a literature review written by another member of your class.
As a class, determine criteria for peer assessment before you begin writing your literature reviews.

PART A: CRITIQUE A LITERATURE REVIEW Literature

review: Is the
Read how to write a literature review (Chapter 1, page 9) and then read the example of a simple literature ability to dance
determined by
review at the weblink provided here. Critique the example on the weblink, outlining three strong points and genes?
two areas where it could be improved.

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 PART B: CONDUCT YOUR LITERATURE REVIEW

1 Do wide reading to define the topic and make some notes on opposing points of view.
2 Formulate (write) a research question or hypothesis to narrow down your secondary-source investigation.
(See page 8 on proposing a hypothesis or research question.) Write a list of key words that you could use to
find answers to your research question.
3 Find relevant articles using databases, Internet search engines and library catalogues. Outline opposing
points of view in the research and critically analyse the validity of views expressed in your sources. (See
page 10 on evaluating sources.) Draw a conclusion to your research question through an evidence-based
argument. Acknowledge your sources using an accepted referencing style.
4 Communicate your information clearly and accurately. Use the correct structure for writing a literature
review: introduction, body and conclusion. See page 9 for more details on how to structure a literature
review and what type of information to include in each part.
Remember to use correct scientific terms and keep the language at a level that is suitable for Year 12
students to peer review your work.
5 Draw your own conclusions about the research, based on your findings. Express your perspective on the
strengths and weaknesses of the research you are reviewing and use your findings to support your judgement.
Your literature review should be 400–800 words. This may vary, depending on your research question and
the depth of your research. Seek permission from your teacher before making your literature review longer
than this. Remember: it is quality, not quantity, that counts.
6 Peer review at least one literature review written by someone else in your class, using criteria drawn up by
the class. See page 4 in Chapter 1 for a reminder of what to look for when conducting a peer review.
KEY CONCEPTS

●● Gene expression is the switching on and off of genes to make the required proteins and other
end products in particular cell types.
●● Phenotypic expression is the result of gene expression – the structure, physiology and
behaviour of an individual as a result of genes that have been expressed.
●● Some variations within a population are due to the influence of the environment, rather than
having a genetic (DNA sequence) basis.
●● Identical twins have identical genotypes, and therefore any phenotypic differences can be
attributed to environmental influences.
●● An example of variation brought about by the environment is the difference in colour of flowers
in hydrangeas (dependent on pH of the soil).
●● Chemical modifications of DNA that do not involve a change in the sequence of nucleotides are
termed ‘epigenetic’ modifications. They may be the mechanism by which some environmental
factors bring about variation. The result is a change in phenotype without a change in genotype.
●● Epigenetic changes show links to disease, including cancers and metabolic diseases.

CHECK YOUR
UNDERSTANDING 1 Using examples, explain how:
a genes affect phenotype
4.3 b the environment may affect phenotype in a manner that is not heritable
c the environment may affect phenotype in a manner that is heritable.
2 Identify reasons why cells do not express all the genes in their genomes.
3 Outline how the packaging of DNA affects gene expression.
4 Compare the effects of methylation and acetylation of DNA on gene expression.
5 Explain, using an example, how epigenetics may account for a phenotypic change.
6 How do scientists account for the fact that humans have fewer genes than the number of types of proteins
in cells?

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 The structure and function
4.4 of proteins in living things
Proteins are the most abundant organic molecules in cells. They are responsible for forming the basic
Revise your
structure of cells and for carrying out all the work in cells, by controlling all chemical reactions. Year 11 work on
protein structure.

Structure of proteins
Proteins are made up of one or more long chains of nitrogen-containing amino acids. Each chain is called WS

a polypeptide. Each protein within an organism is folded into a particular shape that is crucial to its Protein revision
Homework

functioning. Proteins bind with other molecules to carry out their functions, and so their shape and
chemical properties (such as electrical charge and attraction to water) allow the proteins to function in
a particular way. If a single chain
of amino acids is
longer than 40-
Chemical structure of proteins 50 amino acids
and folded in a
Proteins contain the chemical elements carbon, hydrogen, oxygen and nitrogen, and sometimes sulfur. specific manner,
These elements combine to form amino acids, which are the building blocks of proteins. There are about it is termed a
protein. If the
20 amino acids; they can be put together in chains of up to 300 amino acids. The amino acids in each chain is shorter
linear sequence or polypeptide chain are held together by chemical bonds (forces of attraction) known than 40-50
amino acids and
as peptide bonds. One or more polypeptides can be twisted together into a particular shape, resulting in combines with
the overall structure of a protein. The sequence and arrangement of the amino acids determines the type other chains
to fold into a
of protein, in the same way that sequences of the letters of the alphabet can be used to make words and functional protein,
then sentences. it is termed a
polypeptide.

Models of the
a protein insulin
can be seen on
H ‘Acid’ page 120
group (Fig. 4.9).
‘Amino’
group HN C COOH H CH COOH

Nitrogen C CH2
present
CH2 Represented NH2
as

Proline Glycine

b Polypeptide
S S
Protein
S S

Specific sequences of amino acids

FIGURE 4.23 Protein structures: a structural formula of two amino acids, proline and glycine. The hydrocarbon chains
of amino acids differ in length and are known as the ‘R’ group; b two polypeptide chains of amino acids held together by
peptide bonds (chain), with chains held together by sulfide bonds, making up a protein (e.g. insulin)

Physical structure of proteins

The structure of proteins can be described at four levels: primary, secondary, tertiary and quaternary
(Fig. 4.24).

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 a Primary structure b Secondary structure
The amino acid sequence With folding as a result of hydrogen bonding

HO O
H
C C C
N
H O C
C C H
H N C O N C
N C C
C O H N O
Peptide C C
C
HO
bond N H O C
C
N C
H
C N
O C N H O
C
C C H HO
H N C O or N C O
N C
O
Amino C O H N O
HO
C C
acids C
N C
H
N H O C C N
O
O C N H O
C C
H N C O
Alpha helix
C O H N
C C
H Pleated sheet
N
H

d Quaternary structure c Tertiary structure

The relationships between With secondary folding caused by interactions between
individual subunits the polypeptide and its immediate environment

FIGURE 4.24 The four levels of protein structure: a primary, b secondary, c tertiary and d quaternary

The basic structure of a protein is a polymer of amino acids, arranged in linear chains or polypeptides,
and is termed its primary structure. However, it is the shape of the protein, not merely the amino acid
sequence, that determines its function. Proteins have a hierarchy of folding that gives them their specific
Proteins made up shapes.
of a single
polypeptide chain The secondary structure is the three-dimensional arrangement of the polypeptide chain. The
have primary, secondary structure forms as a result of the amino acid chain becoming linked by hydrogen bonds, either
secondary and
tertiary structure. twisting the polypeptide into a spiral (alpha helix) typical of a fibrous protein, or folding it into a pleated
Proteins made up sheet rather than a spiral, also held together by hydrogen bonds.
of more than one
polypeptide chain Further folding leads to the tertiary structure that is seen in more complex proteins such as globular
have quaternary proteins. Certain forces of attraction between alpha helices and pleated sheets (such as disulfide bonds)
structure.
cause the polypeptide to fold into a more complex three-dimensional shape.
Quaternary protein structure occurs in proteins that are made up of two or more polypeptide chains
that link to create a more complex three-dimensional structure.
A single protein molecule may contain more than one type of protein structure. For example, the silk
of a spider contains pleated sheets joined by less ordered alpha helices.
Some proteins, called conjugated proteins, are linked to a non-protein part called a cofactor. If the
cofactor is tightly bound, it is termed a prosthetic group and may be organic or an inorganic metallic ion.

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 The blood pigment haemoglobin contains inorganic iron as its prosthetic group. If a cofactor is loosely
bound to an enzyme, it is known as a coenzyme (often an organic molecule such as a vitamin).
The primary structure of a protein (the linear amino acid sequence) determines the secondary and
tertiary structure of the protein, particularly those amino acids that are involved in forming bonds to
create the spiral or pleated sheets. If the incorrect amino acid is inserted in a polypeptide chain, this may
lead to a change in the bonding properties of an essential part of the protein and therefore change its
secondary, tertiary and quaternary structures, which could change the functioning of the protein. The
resulting protein often functions less effectively and the change may even be lethal. For example, in the
inherited red blood cell disease known as sickle cell anaemia, a single amino acid change in the protein
haemoglobin is the cause. The amino acid glutamate is replaced by a valine. This distorts the shape of Sickle cell
anaemia is dealt
the haemoglobin protein (changes it to long fibres) and affects its ability to transport oxygen. This is with in more
not a lethal mutation, unless inherited in both maternal and paternal copies of the gene. Occasionally, a detail in chapters
5 and 7.
change in an amino acid may lead to improved functioning of a protein. Changes such as these are the
cause of random variation in a population that is subject to natural selection. For example, if a change in
an enzyme has no effect on the organism at the natural ambient temperature, but allows it to function
more efficiently in high temperatures, then an environmental change such as global warming may result
in that individual surviving and passing on its gene to the next generation.

Types of proteins in cells

As you have learned, the structure and shape of proteins determine their functions, which range from
structural support to cell communication, movement, defence against diseases and cell biochemistry.
Different types of tissues contain different proteins, coded by DNA that is switched on during cell
differentiation.
Fibrous proteins form structural components of cells and tissues; together with water, they form
the basic structure of protoplasm (the cytoskeleton). Fibrous proteins are long and insoluble in water.
Collagen is an example of a long, stringy protein that is coiled and very strong (Fig. 4.25a). It is commonly
found in skin, along with another fibrous protein, elastin. These proteins are also present in ligaments
and tendons. Keratin is a fibrous protein in hair and nails.
Globular proteins are usually spherical in shape and are compact and soluble in water. They are
often transport proteins, such as haemoglobin in the blood (Fig 4.25b). Immunoglobulins (antibodies),
hormones and enzymes are other examples of globular proteins.
Getty Images Plus/iStock.com/ HYPERLINK "https://www.gettyimages.com.au/search/
photographer?family=creative&photographer=Molekuul" Molekuul

a b
Shutterstock.com/Blamb

Polypeptide
chain
b chain

Iron

Heme
a chain

Collagen Haemoglobin

FIGURE 4.25 Fibrous and globular proteins: a collagen, a fibrous protein; b haemoglobin, a
globular protein

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 KEY CONCEPTS
●● Proteins are macromolecules (polymers) made up of one or more polypeptide chains that are
formed by sequences of amino acids linked by peptide bonds.
●● Proteins contain the chemical elements nitrogen, carbon, hydrogen, oxygen and sometimes
sulfur.
●● Proteins have a primary structure (sequence of amino acids in polypeptide chains), secondary
structure (polypeptide chain arranged in a helix or pleats), tertiary structure (3D shape formed
by folding the secondary structure) and quaternary structure (two or more polypeptide chains
combined).
●● The sequence of amino acids in a protein is responsible for the overall bonding, folding and
3D shape of a protein, which determines its ability to function. A change in one or more amino
acids in the sequence has the potential to alter the entire structure of a protein.
●● There are three main types of protein: fibrous, globular and conjugated.

CHECK YOUR
UNDERSTANDING 1 Name four structural proteins in cells and state the function of each.
2 Identify three types of functional proteins in cells and, using an example of each, explain how they
4.4a function.
3 Name the types of bonds that form between amino acids in a polypeptide and explain how they form.
4 Outline the primary, secondary and tertiary structure of a protein.
5 Using examples, explain how an amino acid substitution in a polypeptide may affect its functioning.

Functions of proteins
The biological properties of proteins depend on the interactions of the proteins with each other and with
other molecules. For example, enzymes bind with substrates to catalyse reactions, regulatory proteins
control DNA replication and turn on genes, antibodies bind with pathogens, and hormones bind with
receptors on target cells.
The tertiary structure and three-dimensional shape of a protein determines its ability to bind tightly
and specifically with these molecules, and therefore determines its ability to function effectively.
Proteins are reusable, and reactions between them and their binding molecules (called ligands) are
reversible.
Proteins can be classified into categories according to their functions. In the section that follows,
Types of proteins proteins are grouped into five categories according to function. Note that each category may be
Explore the different
types of proteins and
subdivided into further groups – see the weblink for proteins grouped into nine categories, according to
their function. function.

Structural proteins – support and movement

Structural proteins are often fibrous and stringy (such as collagen and elastin), and found in connective
tissues such as skin, cartilage, bone, tendons and ligaments. Structural proteins also make up shells in
invertebrates, and are in hair, nails and hooves in vertebrates.
Structural proteins such as tubulin (in microtubules) are responsible for forming the cytoskeleton,
which maintains the shape of cells. Microtubules also allow movement in cells. For example, cilia and
flagella in cells move as microtubules slide along each other, and a similar action causes spindle fibres to
contract.
Contractile proteins also occur in cells, allowing movement to occur. For example, in muscle, the
protein actin slides along another protein, myosin, to allow the muscle to contract (Fig. 4.26). Actin is
also found in microfilaments in cells and these are responsible for contraction of the cytoplasm, allowing
the cell membrane to pinch off during cytokinesis in animal cells, and the crawling movement of protists
such as amoeba.

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 Enzymes – control of biochemical reactions
Enzymes are protein molecules involved in all biochemical aspects of cellular metabolism. (See Year 11
Review Biology
course work.) They catalyse reactions such as those in the chemical respiration pathway and in digestion. in Focus Year 11,
The shape of an enzyme’s active site determines its binding specificity and therefore its ability to function. Section 3.3 on
enzymes.
Enzymes are particularly important in gene functioning, replicating, repairing and transcribing DNA to
make new proteins.

Shutterstock.com/Blamb
Sarcomere

Myofibril or fibril (complex organelle

composed of bundles of myofilaments) Sarcomere
(contractile
unit of a myofibril)
Sarcomere
(relaxed muscle)

Thin (actin) filament Thick (myosin) filament

FIGURE 4.26 Thick myosin filaments in muscle slide along thin actin
filaments, allowing the muscle to contract.

Proteins for cell communication, cell signalling and

biological recognition
Cells communicate by means of chemical signals. Some proteins embedded in membranes form channels
See Biology in
to carry substances that are essential for cell functioning between cells and the environment (Fig. 4.27). Focus Year 11,
(Revise your Year 11 work on the structure and functions of cell membranes.) For example, nerve cells Chapter 3, on the
structure of the
and cells in kidney tubules rely on proteins embedded in the cell membrane to act as a sodium pump, cell membrane.
regulating the intake and output of sodium ions so that the cell can function.

Extracellular environment
Protein Exterior surface of
Carbohydrate cellular membrane
Cholesterol

Transport Receptor Recognition Adhesion Phospholipid

protein protein protein protein bilayer
Intracellular environment
FIGURE 4.27 A view of the fluid mosaic model of part of the cell membrane, showing embedded and surface proteins.

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 Cell signalling and biological recognition
Some proteins, such as hormones and neurotransmitters, act as chemical messengers between cells.
They communicate messages to a cell about the environment around it and trigger responses in the
target cell’s functioning. Receptor proteins in the membranes of cells are responsible for receiving these
signals. Biological recognition between chemical messengers and their target cells is essential. Receptor
proteins must therefore have a shape that is exactly reciprocal to the shape of the molecule with which
it binds.
Some receptors on the surfaces of cells are genetically determined. Some of these receptors act as
markers that allow a body to recognise its own cells and the cells of foreign invaders (pathogens) that
need to be destroyed. This helps the body to fight disease. Antibodies are defence proteins that may be
attached to cell membranes or floating freely in body fluids. Antibodies (also called immunoglobulins)
Antibodies are dealt
with in more detail recognise foreign invaders by the different proteins on the surfaces of their cells (called antigens); the
in Chapter 11. antibodies bind with these antigens to signal to other defence cells in the body that the invading antigens
need to be destroyed (See Chapter 12 for more details.)

Transport and storage proteins

Some proteins bind to and carry or store chemicals in the body. These are termed ligand-binding proteins
and must be able to bind easily with the chemical (ligand) and also release it when and where it is needed.
How a firefly’s tail
An example is haemoglobin, which has an affinity for (attraction to) oxygen, particularly when oxygen
makes light is present in high concentrations. Haemoglobin loses its affinity for oxygen in areas where there is a low
Identify the series of oxygen concentration (and high carbon dioxide concentration), such as in active tissues. The protein
proteins involved in
generating light, and changes shape when the oxygen level changes, and this adaptive ability of the protein is essential to its
classify each into a
group according to its functioning.
function.
Some proteins store chemicals for use by the organism – for example, ferritin stores iron, while
albumin (in egg whites) and casein (in milk) store amino acids.

Sensory proteins – responding to stimuli

Refer to Chapter 18, Some proteins change their shape or biochemical activity in response to stimuli (changes in the
page 612 to learn environment). For example, opsins are proteins in the retina (innermost layer) of the eye that detect light.
more about the
functioning of the When light is absorbed by cells in the retina, these proteins undergo a change in molecular arrangement
protein opsin in and start a series of reactions in which light energy is transformed into electrical and chemical signals
vision.
that can be interpreted by the brain.
KEY CONCEPTS

●● Proteins are grouped according to their structure or functioning to make it easier to remember
and compare them.
●● Structural proteins form the structural and functional part of cell membranes. Some proteins in
the cell membrane also function in communication and regulate the movement of substances
across the cell membrane.
●● Some proteins, such as myosin and actin in muscle cells, are responsible for cell motility,
joining together to form filaments that allow movement.
●● Storage and transport proteins bind and store or carry other molecules in cells. For example,
histones package DNA in a compact form, the protein ferritin stores iron and haemoglobin
carries oxygen.
●● Some proteins regulate metabolic functioning – these include enzymes (chemical catalysts) and
chemical messengers such as hormones and neurotransmitters.
●● Proteins involved in cell recognition include antibodies, which defend against disease.

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 Technology, big data and the investigation of protein structure
and function
Today, we can predict expected amino sequences in proteins, as we have increased our understanding
of how the millions of nucleotides in a sequence of DNA are decoded. Sequencing the nucleotides of
complete sets of genes in organisms is a field known as genomics. Proteomics is the large-scale study of
sets of proteins produced in an organism or biological system to find out how the proteins in a variety
of cell types work together. Studies of both genomics and proteomics have made major leaps in recent
years as a result of advances in computer technology. (See the weblink.)
The genome of an organism remains more or less the same in different cells over time, but the
proteome is more complex. Various cell types produce different sets of proteins and these are often
modified after translation. Different genes are expressed in different cell types, so there are an enormous
number of proteins to be identified and studied.
Analysis of proteins has also made rapid advances over the past 30 years or so, as has analysis of DNA
and gene functioning.
X-ray crystallography was first used over a century ago. Over the past 60 years or so, it has been used
to study biological macromolecules (large molecules). Advances in the study of proteins were slow at first,
as X-ray diffraction technology needed to evolve to produce sufficiently strong X-ray beams to provide
diffraction images that could be measured. The images and methods of gathering data were sufficient
Timeline of
for small molecules, but collecting data for large molecules such as proteins took many days or weeks. genomics and
The study of the first protein (myoglobin) whose entire structure was recorded was published in proteomics
Record in order ten
1958. By 1971, a worldwide database, the Protein Data Bank (PDB), had been created and seven protein major discoveries
structures had been deposited in the PDB, all determined using single-crystal X-ray diffraction. The relating to our
understanding of
numbers increased slowly – by 1973, two more proteins had been deposited. DNA and protein
synthesis.
Because one protein may have between five and 50 different modified forms, each allowing the
protein to perform a different function, the process of determining protein structure was slow and the
goal enormous. What was needed were high-brilliance sources of X-ray radiation to speed up the crucial
diffraction measurements, and a way to analyse the data quickly.
These requirements were met over the next ten to twenty years. The development of the synchrotron
(a particle accelerator) brought about this change. A synchrotron emits electromagnetic radiation where Human
charged particles can be accelerated to move at speeds close to the speed of light. The particles can Genome
Project
be forced to change direction by a magnetic field. Synchrotron technology improved and by the 1990s,
the construction of a third-generation synchrotron with a ring size of over a kilometre gave the high-
resolution images required. This, together with the advent of high-performance computing and the use
of recombinant methods for protein production, advanced the study of proteins. Molecular biologists
were able to record and create models of the structures of thousands of proteins and bank this data in
a relatively short space of time. The graph in Figure 4.28 compares the numbers of protein structures
determined using synchrotron radiation (orange) and conventional sources of radiation (blue) between
1985 and 2009.
The field of combined computer science and genetics is known as bioinformatics. People who work
in this field develop methods and software for analysing and interpreting biological data. It is an area
of science that combines the disciplines of biology, computer science, mathematics, statistics and
engineering.
Advances in computer technology have led to the rapid storage and manipulation of big data
(extremely large volumes of data), greatly accelerating the study of proteomics. Today, the detailed
analysis of protein structure to identify functions and interactions is assisted by 3D visualisation
computer technology. For example, some programs allow protein structure to be ‘sorted’ according to
the arrangement of particular chemical elements within the molecule, bonding patterns, the line-up of
atoms in sequence or the overall structure and shape of the protein. This is extremely useful for exploring
how changes in amino acid sequences affect protein structure. A number of proteins targeted by medical
research for cancers are currently being studied in this way, using big data.

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 Source: US National Library of Medicine
6000
Conventional radiation source
Synchrotron
5000

4000

Number of deposits
3000

2000

1000

0
1985 1990 1995 2000 2005 2010
Year of deposit

FIGURE 4.28 The number of protein structures deposited

annually in the Protein Data Bank

INVESTIGATION 4.5

Information and Secondary-source investigation into protein structure

communication
technology and function
capability

You are required to investigate a specific protein and create a multimedia presentation of your information
(Investigation part 1), after which you will research one of two specific named proteins (Investigation part 2).

PART 1: INVESTIGATING A PROTEIN OF YOUR CHOICE

Rotatable and Investigate the structure of a particular protein of your choice (list of suggestions in point 3 below) and how a
zoomable 3D
structure of change in its structure could affect its functioning.
proteins
1 Create a multimedia presentation of 8–10 slides, outlining information about the structure of a protein of
your choice, its functions and its potential applications.
2 Find a video clip of the protein functioning, as well as a weblink to a computer simulation program that
allows visualisation of the protein in three dimensions. Insert the sites as hyperlinks in your multimedia
Cn3D presentation.
A visualisation tool
for biomolecular
3 Outline the impact that a change in the structure of this protein may have on its functioning. Some
structures, sequences examples of proteins that you may wish to select for your research are: motor protein kinesin; proteins
and sequence
alignments.
involved in DNA replication such as bacterial DNA gyrase; reverse transcriptase; tumour suppressor
proteins such as p53; metabolic protein such as haemoglobin; proteins implicated in diseases such as
cardiovascular disease, Alzheimer’s disease, Parkinson’s disease; proteins involved in defence against
disease, such as immunoglobulins; major histocompatibility complexes (MHCs) or any protein of your
choosing.

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 Some weblinks are provided for you to begin your research. You need to find similar sites to complete the
research on your selected protein.

PART 2: HAEMOGLOBIN OR CY TOCHROME C 3D visualisation

of the structure
Research the importance of the amino acid sequence in a haemoglobin molecule or in cytochrome C and how of the p53
protein
these molecules may be used for relatedness studies in evolution. Use one of these molecules to explain the
importance of DNA transcription and translation being accurate when creating the amino acid sequence of
the polypeptides that make up the selected protein.

PART 3: BIOINFORMATICS (OPTIONAL – ADVANCED)

p53 and how
it functions
1 Do research to answer the following questions. in tumour
a What is bioinformatics? suppression

b What kind of work does a molecular diagnostics researcher do?

2 Explain how bioinformatics may be used in the work of a molecular diagnostics researcher.
OR
Write a job advertisement for a molecular diagnostician, outlining the knowledge and skills the person TED talk using
data to create
would need to have, to apply for this position. computer-
generated 3D
images

Personal and social

capability

Work and enterprise

KEY CONCEPTS

●● The study of a set of proteins in an organism is called proteomics.

●● Bioinformatics is a field of study that involves developing computer technology including
software tools for understanding and visualising enormous amounts of biological data. It is a
combination of biology, computer science, mathematics and engineering.

CHECK YOUR
1 Construct a table like the one below to compare the main functional categories of proteins in cells. UNDERSTANDING
CATEGORY OF
PROTEIN FUNCTION DESCRIPTION EXAMPLE 4.4b
Structural Support
Movement
Regulating Enzymes
metabolic
Hormones
functioning
Cell communication Signalling
Biological
recognition
Sensory proteins Response to
stimuli
Storage and Storage
transport
Transport

2 Distinguish between proteomics, genomics, big data and bioinformatics.

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 Cell wall Ribosomes

4 CHAPTER SUMMARY Pili

DNA and polypeptide synthesis: Why is polypeptide synthesis so important?

DNA IN PROKARYOTES

Bacterial
flagellum

Cytoplasm
Capsule Chromosome: Plasma Plasmid:
DNA membrane DNA

Chromosomal DNA: circular, double-stranded and supercoiled Non-chromosomal DNA: small rings of non-
into a nucleoid chromosomal DNA

DNA IN EUKARYOTES
Chromosome rRNA Cytochrome b

1400 nm
Non-coding
region

Centromere
NADH
Cytochrome c dehydrogenase
oxidase
2 nm
tRNA
Chromatin Nucleosome
ATPase
30 nm
700 nm

DNA
10 nm

Nuclear DNA: chromosome Non-nuclear DNA: mitochondrial DNA

Nuclear DNA is linear DNA packaged around histones (to mtDNA occurs in mitochondria in the cytoplasm, is
form nucleosomes), which play a role in regulating gene inherited down the maternal line and mutates at a
expression. higher rate than nuclear DNA.

POLYPEPTIDE SYNTHESIS
Step 1 DNA codes protein synthesis Step 2
DNA RNA pre-mRNA mRNA
Exon Exon Exon Exon
DNA Intron 1 Intron 2 Intron 3 Intron 4
Cell nucleus

Transcription and removal of introns

C C
G
G A
T

2 Transcription
Pre-mRNA 1 2 3 4
Antisense strand
G C A

Alternative splicing
(coding strand)
C

G
T of DNA
A
T

‘Sense’ strand
T A

mRNA being
—U

or ‘non-coding’
—A C

transcribed from DNA

C

strand of DNA
(the nucleotide U is
— U

T
T

used in mRNA in the

— A

A
G

place of T)
— C

C
A

1 RNA
Mature mRNA 1 2 3 1 2 4
— A

A
T

polymerase
— U

T
G

— G

G
T

Protein X Protein Y
— A

Nuclear membrane
A

G
A

A
— U
C

C
— C

U
T

Introns are spliced out (regulate gene expression).

—

RNA
nucleotide
pool 4 Translation

3
———————————
mRNA leaves through
nuclear pore
—
C U
Types
a of RNA: b c
U A C U A C A U G A 5
Amino acid Ribosome
U A G

mRNA

Transcription
7 U A C
Peptide 6 enters the
bond A U G C ribosome
U A C U A C A U G A U
Uracil
Amino acid

Instructions copied in a coded form from DNA,

tRNA

tRNA moves into Ribosome

cytoplasm to ‘Start’ triplet 8

carried by mRNA into the cytoplasm pick up a new A UG or codon

A A G Anticodon
C

amino acid
Anticodon
A

Pool of amino acids

U

Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA)

C
U
G

RNA nucleotides mRNA tRNA rRNA

Key DNA RNA amino acids tRNA

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 POLYPEPTIDE SYNTHESIS

Step 3 Translation into polypeptide chains

RNA protein

DNA
tRNA
1 1. DNA is transcribed
into RNA.
4. More amino
acids are added.
mRNA 3. Amino acid

Gr
Nucleus 3

ow
5 attaches to tRNA.

in
g
Transcription

pr
5. tRNA breaks

ot
4

ein
off and picks up Amino acid
another amino acid.
2

2. mRNA attaches to
a ribosome.

Ribosome
NA
mR Translation

Translation
mRNA is ‘read’ by ribosomes and translated into polypeptides, with the help of tRNA.

THE ENVIRONMENT CAN AFFECT PHENOTYPIC EXPRESSION

Gene expression is the switching on and off of

genes to make the required protein end products
in cells. Environment and epigenetics play a role.

Identical twins have the

same genotype. Any Hydrangea colour is affected by pH in the
differences are due to environment.
environmental influence.

Proteins produced Protein function

a Primary structure b Secondary structure

The amino acid sequence With folding as a result of hydrogen bonding

HO O
H
C C C
N
HO C
C C H
H N C O N C
N C C
C O H N O
Peptide C C
C
HO
bond N H O C
C
N C
H
C N
O C N H O
C
C C H HO
H N C O or N C O
N C
O
Amino C O H N O
HO
C C
acids C
N C
H
N H O C C N
O
O C N H O
C C
H N C O
Alpha helix
C O H N
C C
H Pleated sheet
N
H

d Quaternary structure
The relationships between
c Tertiary structure
With secondary folding caused by interactions between (DNA polymerase enzyme)
individual subunits the polypeptide and its immediate environment
depends on shape.

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 4 CHAPTER REVIEW QUESTIONS Qz

Review quiz

1 Draw a diagram and annotate it to explain the structure of 17 Draw a diagram to represent a thymine nucleotide of
a eukaryotic chromosome. DNA, labelling the three distinct chemical components.
Describe any changes you would need to make to your
2 Compare the chromosome of a eukaryote with that of a
diagram if this was a nucleotide of RNA.
prokaryote.
18 Compare the structure of fibrous and globular proteins.
3 Distinguish between the following structures:
a nucleoid and plasmid 19 Distinguish between a proteome and a genome, using
examples.
b scaffold and histone
c nuclear DNA and non-nuclear DNA in eukaryotes. 20 Construct a flow chart with words, arrows and diagrams,
to represent:
4 Identify one similarity and two differences between a
a the process of transcription of pre-RNA from DNA
plasmid and mtDNA.
b the subsequent editing of RNA to become mature RNA
5 Explain why mtDNA is useful for evolutionary studies.
c the process of translation.
6 List the following in order of genome size, from largest to
21 Create a flow chart with words and arrows to outline
smallest: prokaryote circular DNA, eukaryote nuclear DNA,
the sequence of events that occurs during transcription
yeast DNA, mtDNA.
and translation. Indicate on your flow chart which steps
7 What are histones? Describe their role in the nucleus of occur inside the nucleus and which steps occur in the
eukaryotic cells and in regulating gene expression. cytoplasm.
8 Using diagrams, explain how DNA is packaged in a 22 Compare transcription and translation in the DNA of
prokaryotic cell. prokaryotes and eukaryotes.
9 Define ‘gene’. Explain why the definition has changed over 23 Explain the difference between coding and non-coding
time. DNA.
10 Give three examples of how the environment affects gene 24 Identify the sequence of amino acids that would
expression and two examples of how the environment result from an mRNA molecule with the sequence
affects phenotype in a way that is not hereditary. AUUCGUGUAGCCGGUCGA.
11 Draw a Venn diagram to compare DNA and RNA. 25 Draw the non-coding strand of DNA that would have
given rise to the mRNA molecule in Question 24.
12 Use words and arrows to represent the central dogma of
molecular biology. 26 Discuss the importance of using models in biology,
referring to the discovery of the structure of DNA by
13 Give the full name of each of the following types of
Watson and Crick as an example.
nucleic acids in cells and outline the function of each:
a DNA 27 Construct a simplified diagram of a strand of DNA to show
a sequence of nucleotides 24 bases in length, following
b mRNA
the instructions below.
c rRNA
a Use a single line to represent the sugar-phosphate
d tRNA backbone and letters to represent the bases.
e mtDNA b Use the mRNA codon table in Figure 4.15 to make sure
f miRNA that the first triplet of bases on the DNA strand you
construct codes for a start codon in mRNA and that the
14 Do more complex organisms have a larger number of
last triplet of bases codes for a stop codon.
chromosomes? Use data to justify your answer.
28 Draw a diagram to show how the strand of DNA that you
15 List the following in order of size, from smallest to largest:
created in Question 27 would be:
a polypeptide, protein, amino acid, dipeptide
a transcribed into mRNA
b nucleic acid, nucleotide, chromosome, gene.
b translated into a polypeptide chain (use the mRNA
16 Draw a diagram to represent: codon table in Figure 4.15).
a a protein molecule, and label all parts listed in 29 Write two changes in bases that could occur in the DNA
Question 15a strand that you created in Question 27 that would not
b part of a chromosome, and label all parts listed in result in a change in the sequence of amino acids. Explain
Question 15b. why this is so.

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 30 Explain the importance of twin studies in genetics. 35 Explain what is meant by ‘gene expression’ and its
significance in living organisms. What, then, is the purpose
31 Describe three ways in which gene expression can
of polypeptide synthesis?
be regulated. You may use diagrams to assist your
explanation. 36 Design an investigation that a scientist could conduct to
show that exons are the only coding sequences expressed
32 Explain the importance of literature reviews in research.
in a protein.
33 Discuss the importance of bioinformatics in
understanding both DNA and protein functioning. Use the
information in Figure 4.28 to support your answer.
34 Write an extended response to discuss whether genes or
the environment have a greater influence on phenotype.
Support your arguments with current biological
knowledge.

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