Name CC

DNA structure and replication

1. DNA, and in some cases RNA, is the primary source of heritable information. Genetic
information is stored in and passed to subsequent generations through DNA molecules
and, in some cases, RNA molecules.

A. Identify the building blocks of DNA and label the parts in the
diagram
Monomers = building blocks
● Nitrogenous base - A, T, C, or G
● Phosphate group (what causes DNA to be negative)
● Sugar - deoxyribose
● Phosphodiester bond between the phosphate group and the sugar.
● Phosphate group = 5’ end

B. Identify the number of DNA strands found in a DNA molecule and Explain the orientation
of the DNA strands
There are two strands, making a double helix. The strands wrap around each other.
The strands are antiparallel, so they run opposite of each other
● 5’ —> 3‘
● 3’ —> 5’
C. Identify and label the following parts in a DNA molecule: nitrogenous bases, hydrogen
bonds, sugar phosphate, nucleotide

D. Explain the
importance of the
hydrogen bonds in
the DNA molecule
Hydrogen bonds in
the DNA molecule help to
bond together the
nitrogenous bases.

They help to hold the two

strands of the DNA molecule together by connecting complementary base pairs together (T—>
A,G—> C)

E. Explain what is meant by the 5’ and 3’ ends of the nucleotide

The 5’ end is the phosphate group at the end of one strand and the 3’ end is the sugar portion of
the strand.
They refer to the orientation of the carbon atoms

F. Identify and label the 5’ and 3’ ends in the following DNA molecule

G. Explain the importance of the 5’ and 3’

end in a DNA molecule
The 5’ and 3’ ends in a DNA molecule
determine its directionality/orientation
and help to determine the outcome of
certain processes such as DNA
replication and transcription. DNA
polymerase builds off the 3’ end, from a
5’ —> 3’ direction. RNA polymerase
does the same. Additionally, GTP caps and
poly-a tails are attached to the 5’ and 3’
ends to help prevent degradation.

2. DNA, and sometimes RNA, exhibits specific nucleotide base pairing that is conserved
through evolution
A. DESCRIBE a purine and IDENTIFY the purines in DNA

A purine is a classification of a nitrogenous base. Purines contain 2 rings. They are one of two
types of nitrogenous bases used to build DNA. The two purines in DNA are adenine and guanine.

B. DESCRIBE a pyrimidine and IDENTIFY the pyrimidines in DNA/RNA

A pyrimidine is another classification of a nitrogenous base. Pyrimidines contain 3 rings. The

three pyrimidines (in RNA and DNA) are uracil, cytosine, and thymine.
C. Label the purines and pyrimidines in the following DNA molecule
 D. Identify the base pairing rule AND EXPLAIN the base pairing rule
G must pair with C
A must pair with T
A purine must pair with a pyridine to ensure a consistent width since Purines (A + G) have two
rings while pyrimidines (C + T) have only one ring.
A must pair with T because of correct width and correct number of hydrogen bonds holding
them together (both require 2 hydrogen bonds)
G and C must pair together for the correct width and the correct number of bonds (both need 3)
E. PREDICT the percentage of A if the DNA has 30% C AND JUSTIFY
C = 30%
C=G
100 - 2(30) = 40
A=T
40/2 = 20
A = 20%
Since C and G pair the percentage each must be equal to each other. Since A and T pair the
percentage of each must be equal to each other. The total percentage for all must add to 100%
3. Prokaryotic and Eukaryotes contain chromosomes
A. Identify the number of chromosomes (as single or multiple) that exist in prokaryotes and
eukaryotes and Describe their shape (circular or linear)
Prokaryotes: single circular chromosome

Eukaryotes: multiple linear chromosomes

B. IDENTIFY the components of a eukaryote chromosome and DESCRIBE the arrangement

of the components in the chromosome
- Contains multiple histones (group of 8 proteins) with DNA wrapped around each histone.
The combination of histone and DNA is called nucleosome
- histones are tightly packed together is heterochromatin
- Histones that are separated (loosely packed) is euchromatin
C. DESCRIBE heterochromatin and euchromatin and EXPLAIN the importance of each type
of folding
Heterochromatin: tightly packed histones. RNA polymerase unable to enter and
transcription + translation is unable to occur (gene expression does not occur)
Euchromatin: loosely packed histones. RNA polymerase can enter and transcription can
occur. + translation (gene expression can occur)
D. Label the heterochromatin and euchromatin regions in the following diagram
4. DNA replication ensures continuity of hereditary information

A. Identify the phase in which DNA replication takes place and EXPLAIN the importance of
DNA replication

DNA replication takes place during the S phase of interphase

This ensures that there is the correct amount of DNA in the daughter cells after cell division.
B. Identify the direction DNA polymerase reads the template strand AND EXPLAIN why the
template strand is read in that direction
DNA polymerase reads the template strand in a 3’--> 5’ direction (building in a 5’ → 3’ direction).
The strand is read in that direction because DNA polymerase can only build off the 3’ prime.
C. Identify the direction in which DNA is synthesized
5’ → 3’

D. Draw in what the leading strand and

lagging strand would look like as they are
being made

E. Identify and Label which template strand

would form the continuous leading strand
and which strand would be the
discontinuous lagging strand

F. Explain why the leading strand is referred to as the continuous strand

It is made towards the replication fork as the helicase separates the DNA strands. The leading
strand does not have any breaks in the strand.
G. Explain why the lagging strand is referred to as the discontinuous strand
Made away from the replication fork. Must be made in fragments as the replication fork unwinds
DNA polymerase new nucleotides away from the fork. The fragments then need to be covalently
bonded to make it a continuous complete strand.
H. Describe what a replication bubble is and label the replication bubbles in the diagram
below

A replication bubble is where the helicase has separated the DNA strands from each other.
The replication bubble contains 2 replication forks.
I. For each of the circles below, DETERMINE if the end is 5” or 3’ and label them in the
diagram. (each circle needs to be labeled as either 3’ or 5’)

J. Identify and label the leading and lagging stands in the DNA replication diagram above
 K. EXPLAIN why a newly synthesized DNA strand is made from both continuous and
discontinuous DNA synthesis

DNA replication is semi conservative. Since there are two template strands from the original
DNA, the one template strand is read towards the replication fork and is made continuously
while the other template strand is made away from the replication fork and made discontinuous.

5. Describe the mechanisms by which genetic information is copied for transmission

between generations.

A. Identify and label the following structures in the diagram below: topoisomerase, single
stranded binding proteins, DNA polymerase (both of them), okazaki fragments, DNA
ligase, helicase, 3’, 5’, continuous strand, discontinuous strand, primase

B. Explain the purpose for each of the enzymes involved in DNA replication

● helicase

● topoisomerase
 ● Primase

● DNA polymerase

● Ligase

C. Describe the process of DNA replication

D. Explain what is meant by the phrase “ DNA replication is a semiconservative process”

E. Predict what would happen if a Ligase inhibitor was present AND JUSTIFY your
prediction

The okazaki fragments wouldn’t be able to connect

Would remain as fragments

F. Predict what would happen if a topoisomerase inhibitor was present AND JUSTIFY your
prediction
Name______________________________________________________ Unit 6 Transcription and
Translation

1. The sequence of the RNA bases, together with the structure of the RNA molecule, determines
RNA function
A. Describe the overall structure of RNA

B. Describe the differences between DNA and RNA

C. Explain the role for each of the following types of RNA

● mRNA

● tRNA
 ● rRNA

2. Genetic information flows from a sequence of nucleotides in DNA to a sequence of bases in

an mRNA molecule to a sequence of amino acids in a
protein.

A. Explain what is meant by the phrase “ Central

Dogma”

B. Describe how the phenotype of an organism is determined by its genotype.

the combination of genes in an organism determines the physical appearance (phenotype) of

the organism.

C. Identify the location where transcription takes place and Identify what is produced as a
result of Transcription
D. Identify the enzyme used in transcription and EXPLAIN its role in transcription

E. Describe the process of transcription

 F. Identify the direction in which RNA polymerase synthesizes mRNA molecules and
EXPLAIN why the RNA polymerase must synthesize mRNA in this direction

G. Draw a circle around the noncoding

strand and EXPLAIN why it is the
noncoding strand

The noncoding strand is the template/antisense strand bc it is complementary to the RNA. It

does not contain the code for the protein.

H. Draw a circle around the coding strand

and EXPLAIN why it is the coding
strand

The coding strand is the sense strand bc it is the code for the amino acid sequence which will
determine the protein produced
I. Explain how the selection of which DNA strand will serve as the template
Selection of which DNA strand serves as the template strand depends on the gene being
transcribed. THe transcription factors will attach to the DNA strand that will be transcribed and
translated

J. Identify the mRNA strand that would be produced from the following DNA strand
ATACCGTGACTA

3.In eukaryotic cells the mRNA transcript undergoes a series of enzyme-regulated modifications
A. Identify the location where RNA processing occurs

B. Describe what occurs to the pre- mRNA to process it into a mature mRNA
 C. Explain the importance for RNA processing

The introns are noncoding segments so they must be removed. If not removed the wrong amino
acids would be in the protein and produce the wrong shape protein. The poly A tail is added so
enzymes do not degrade it while moving through the cytosol. The GTP cap helps attach to
ribosome (also helps prevent degradation)

D. EXPLAIN how the same pre m-RNA strand can result in different mature mRNA strands

Excision (removal) of introns and splicing and of exons can generate different version of the
resulting mRNA molecule; this is known as alternative splicing.

4. Translation involves energy and many sequential steps, including initiation, elongation, and
termination.

A. IDENTIFY the location where translation takes place and IDENTIFY the molecule
produced at the end of translation
B. Explain the role of mRNA in protein synthesis, DETERMINE the number of nucleotides
that make up a codon AND DRAW a circle around each codon

C. EXPLAIN the role of tRNA in protein synthesis and IDENTIFY and label both the
anticodon and amino acid on the tRNA

D. Describe the overall structure of ribosomes AND EXPLAIN what ribosomes are made up of

E. DESCRIBE what is occurring at each

step in translation to produce a
polypeptide
 ● Initiation
Assembling all the RNA’s involved in protein synthesis at the codon start sequence
● small ribosomal subunit attaches to mRNA at start codon sequence
● tRNA carries the correct amino acid over based on the codon
● Large ribosomal subunit attaches

● Elongation
growth of polypeptide chain
● tRNA continues to bring the
corresponding amino acid over to
the growing polypeptide chain
● amino acids peptide bonded
together
● process continues along the mRNA until a stop codon is reached

● Termination
Termination - polypeptide is done being
assembled
● Separation of the types of RNA from teh
polypeptide chain
● Result is a polypeptide in its primary
structure which will then go on to fold
into secondary, tertiary, quaternary
structure based on the amino acids
present.
 F. Determine the polypeptide that would be produced based on the following mRNA strand

G. Explain why the analysis of DNA to compare individuals results in a greater estimate of
genetic variability than does analysis of amino acid sequences

different DNA sequences can code for the same amino acod

5. Nearly all living organisms use the same genetic code, which is evidence for the common
ancestry of all living organisms.
A. Describe the similarities of protein synthesis in Prokaryotes and Eukaryotes
- Transcription occurs using DNA as the template, and RNA polymerase as the enzyme
- Translation occurs at the ribosomes using the 3 types of RNA’s resulting in a polypeptide

B. EXPLAIN how transcription and translation varies between prokaryotes and Eukaryotes

- eukayotes have RNA processing after transcription

while prokaryotes do not have RNA processing
 C. Explain why transcription and translation can
happen at the same time in Prokaryotes but not
Eukaryotes
transcription occurs in eukaryotes inside the nucleus and
must do RNA processing before moving out of the nucleus
to the ribosomes. Prokaryotes do not have to do RNA
processing and transcription occurs in the cytosol where the ribosomes are located.

6. Genetic information in retroviruses is a special case and has an alternate flow of information
A. Identify the genetic contents of a retrovirus
- retroviruses have RNA as their genetic material
B. Viruses, just like prokaryotes and Eukaryotes, use their genetic content to produce
proteins. Describe the processes retroviruses must go through to produce a protein
REtroviruses must first make a DNA strand before protein synthesis can occur
RNA → DNA → RNA → protein
C. Explain why the central dogma does not apply to retroviruses
retroviruses start with RNA not DNA for their genetic content
D. EXPLAIN why During the infection cycle for a typical retrovirus, such as HIV, which uses
RNA as genetic material, the genetic variation in the resulting population of new virus
particles is very high

- Because retroviruses produce DNA from RNA during reverse transcription, there is no
proofreading so errors are introduced into the DNA strand and not corrected.

Name__________________________________________________ Unit 6 regulation of gene

expression & cell specialization

1. In prokaryotes, groups of genes called operons are transcribed in a single mRNA molecule.
The lac operon is an example of an inducible system

A. Explain the importance of the regulatory gene in the prokaryote and IDENTIFY the
molecule that is produced from the regulatory gene

- produces a protein called the repressor protein that controls protein synthesis
B. Describe how this regulatory gene is involved in the operons
the regulatory gene will be transcribed and translated into the regulatory repressor protein,
which can bind to the operator and stop protein synthesis
 C. Identify the structures that make up a lac operon

promoter region, operator region, structural genes (which will

be transcribed and translated into proteins)

D. Explain the purpose of the operator region

The operator region controls protein synthesis. This is where the repressor protein can bind to
stopping protein synthesis which conserves energy

E. Explain the importance of the promoter region

the promoter region is a location for RNA polymerase to bind to.

F. Describe how the repressor protein regulates gene expression in prokaryotes

If protein synthesis is not needed for the genes, the repressor protein, if it has the correct shape,
can bind to the operator region preventing RNA polymerase from functioning so transcription
cannot occur, preventing protein synthesis from occurring.

G. The Lac operon is an inducible operon. Explain what is means to be an inducible operon.
if the operon is inducible, that means it can be turned on. It is typically always off.
H. Explain how gene expression can occur in an inducible operon and EXPLAIN how lactose
is involved in the inducible operon

- in an inducible operon, since it is normally

turned off, the repressor is bound to the
operator region, preventing RNA polymerase from diong transcription
- When lactose is present, allolactose (isomer of lactose) binds to the repressor,
changing the shape of the repressor. The shape change causes the repressor to stop
binding to the operator region. RNA polymerase is then able to do transcription

1. Epigenetic changes can affect gene expression through reversible modifications of DNA or
histones.

A. Explain epigenetics

- epigenetics is the change to gene expression without

changing the genetic code (it can allow gene expression to
occur or not)
B. Describe how the methyl group causes changes in the
chromosome

- when the methyl tag is present, it causes the chromatin to tightly pack into
heterochromatin, preventing gene expression from happening
- When the methyl tag is removed, chromatin is loosely packed into euchromatin so gene
expression can occur.
 C. Explain the impact these epigenetic changes have on gene expression

It controls whether gene expression can occur. In some cases, methyl tags are removed from
genes that should not be expressed which can negatively impact the organism like producing
cancerous cells.

2. The phenotype of a cell or organism is determined by the combination of genes that are
expressed and the levels at which they are expressed

A. Since each cell contains all the genes of the organism, EXPLAIN how cells can express
different phenotypes

B. Promoter regions on DNA are involved with gene expression. Identify the location of
promoters and EXPLAIN their involvement with gene expression

C. Describe the involvement of transcription factors in

the expression of genes

transcription factors bind to the promoter region, activating or inactivating transcription. If

transcription factors are activating transcription, it
signals RNA polymerase to attach and begin
transcription of that gene.

D. Explain how signal transduction is involved in

phenotypic expression
4. In eukaryotes, groups of genes may be influenced by the same transcription factors to
coordinately regulate expression.
A. DESCRIBE how the same transcription factor can regulate/active gene expression of
multiple genes

The same transcription factor can bind to

multiple different promoter regions activating
different genes. This coordinates their
production at the same time coordinating
activity in the body (the transcription factor
can also at the same time bind to different
promoters causing gene expression to stop…
this is not pictured in the diagram to the
right)

B. Predict what would happen to gene expression if a chemical was bound to the
transcription factors. JUSTIFY your prediction
Transcription would not happen since the transcription factors would be unable to bind to the promoter region. RNA
polymerase would not attach so transcription would not happen and no protein would be made.

Name_________________________________________________ Unit 6 Mutations and

Biotechnology review

1. Disruptions in genes and gene products cause new phenotypes.

A. Identify environmental factors that increase the mutation rate in an organism,
and discuss their effect on the genome of the organism.

B. Identify the process that would produce errors in the DNA sequence and EXPLAIN why
the errors in the DNA could have an impact on the phenotype

Errors can occur in DNA replication or DNA proofreading which could result in the wrong
amino acid in the polypeptide sequence. Changing in the polypeptide would change the
secondary/tertiary/quaternary folding

C. Identify the type of mutation in each the

following DNA sequences and EXPLAIN the
impact the mutation would have on the
phenotype

Original DNA strand

TAG TTC AAA CCG CG T AAC A
TT
1- T A G T T T A A A CCG CG T AAC ATT

2- T A G A T C A A A CCG CG T AAC ATT

3- T A G TC AAA CCG CG T AAC ATT

D. PREDICT the impact a mutation to the gene coding for the repair enzyme would have on
the cell AND JUSTIFY your prediction

E. HIV infects cells that contain a CCR5 protein on surface of the plasma membrane. Some
individuals have a mutation in the CCR5 gene resulting in a smaller protein that remains
on the inside. If a person with the gene mutation was exposed to HIV, PREDICT the impact
the exposure would have on these individuals. JUSTIFY your prediction

F. Sickle cell anemia is caused by a point mutation that results in the red blood having an
altered shape. PREDICT the impact this mutation would have on an individual AND
JUSTIFY your prediction.

G. Explain why some DNA mutations are harmful while other DNA mutations are beneficial
2. Errors in mitosis or meiosis can result in changes in phenotype
A. Explain what non disjunction is

B. Describe the impact non disjunction has on individuals

C. DESCRIBE how nondisjunction happens in MEIOSIS I and EXPLAIN how it impacts the
chromosome number in the gametes

D. DESCRIBE how nondisjunction happens in MEIOSIS II and EXPLAIN how it impacts the
chromosome number in the gametes

3. Changes in genotype may affect phenotypes that are subject to natural selection. Genetic
changes that enhance survival and reproduction can be selected for by environmental
conditions
A. DRAW a plasmid and DESCRIBE its structure.
 B. DESCRIBE how transformation occurs in prokaryotes (bacteria) and EXPLAIN the
positive impact it has on prokaryotes

C. DESCRIBE the process of conjugation in prokaryotes and EXPLAIN the benefits to the
prokaryotes

D. Describe how the process of transduction brings about genetic variation in

prokaryotes

4. Genetic engineering techniques can be used to analyze

and manipulate DNA and RNA
A. Explain the uses of gel electrophoresis

B. Explain the purpose of restriction enzymes

C. Explain why the DNA fragments move through the gel

 D. Explain why DNA bands appear at different locations in the gel

E. Identify which fragments are able to move the furthest in the gel and EXPLAIN why they
are able to move the furthest

F. Identify which type of fragments stay closest to the well

G. Explain why the banding pattern for each individual is different even though the same
restriction enzyme is used

H. Explain the benefit of using PCR

5. In a transformation experiment, a sample of E.

coli bacteria was mixed with a plasmid containing the
gene for resistance to the antibiotic ampicillin (ampr).
The following results were obtained

A. DESCRIBE how transformation occurred in some

of the bacteria AND EXPLAIN how you would
know if transformation occurred
B. Describe the difference between wild type E. coli and E. coli and ampr plasmid.

C. Explain why plates I and III have full growth of bacteria

D. Identify the negative control in the experiment and EXPLAIN why it is the negative
control

E. Describe the results on plate II and EXPLAIN the results

F. Describe the results on plate IV and EXPLAIN the results