Biology Chapter 2: Molecular Biology

● Nucleic acids are one of the major carbon-based groups. There are three major examples of
nucleic acids in nature: adenosine triphosphate (ATP), deoxyribonucleic acid (DNA), and
ribonucleic acid (RNA)
● Both DNA and RNA are polymers of nucleotides. Individual nucleotides are referred to as
monomers and always consist of three major parts: one phosphate group, one 5-carbon
monosaccharide, and a single nitrogenous base.
● The sugar differs in the nucleotides of DNA and RNA. DNA nucleotides contain the pentose
known as deoxyribose and RNA nucleotides contain ribose.
● The replication of DNA is semi-conservative and depends on complementary base pairing.
● Helicase unwinds the double helix and separates the two strands by breaking hydrogen bonds.
● DNA polymerase links nucleotides together to form a new strand, using the pre-existing strand as
a template.
● Transcription is the synthesis of mRNA copied from the DNA base sequences by RNA
polymerase.
● Translation is the synthesis of polypeptides on ribosomes.
● The amino acid sequence of polypeptides is determined by mRNA according to the genetic code.
● Codons of three bases on mRNA correspond to one amino acid in a polypeptide.
● Translation depends on complementary base pairing between codons on mRNA and anticodons
on tRNA.
● Molecules needed for DNA replication:
○ enzymes needed for replication, which include helicase and a group of enzymes
collectively called DNA polymerase
○ free nucleotides, which are nucleotides that are not yet bonded and are found floating
freely in the nucleoplasm, some contain adenine, some thymine, some cytosine, and some
guanine.
● DNA replication:no DNA molecule is ever completely “new”
○ Helicase: begins at a point in or at the end of a DNA molecule, and moves one
complementary base pair at a time, breaking the hydrogen bonds so the double-stranded
DNA molecule becomes two separate strands.
○ A free nucleotide locates on one opened strand at one end, and then a second nucleotide
can join the rst. This requires these two nucleotides to become covalently bonded
together, because they are the beginning of a new strand. The formation of a covalent
bond between two adjoining nucleotides is catalysed by one of the DNA polymerase
enzymes that are important in this process.
○ A third nucleotide then joins the rst two, and the process continues in a repetitive way for
many nucleotides. The other unzipped strand also acts as a template for the formation of
another new strand.
○ Ensures that two identical copies of DNA are produced from one original.
● Protein Synthesis: control that DNA has over a cell (transcription/translation)
○ DNA indirectly controls the biochemistry of carbohydrates, lipids, and nucleic acids with
the production of enzymes.
 ○ Transcription: produces RNA
■ Genes - sections of DNA that code for polypeptides (any one gene is a specific
sequence of nitrogenous bases found in a speci c location in a DNA)
■ mRNA - an intermediary molecule that carries the message of the DNA (the
code) to the cytoplasm where the enzymes, ribosome, and amino acids are found.
■ Nucleoplasm - contains free nucleotides for DNA replication and free RNA
nucleotides.
■ Each of these is different from the DNA counterpart, because RNA nucleotides
contain the sugar ribose not deoxyribose. Another major difference is that no
RNA nucleotides contain thymine; instead there is a nitrogenous base unique to
RNA, called uracil.
● Transcription Process:
○ Begins when an area of DNA of one gene becomes unzipped
○ Only one of the two strands of DNA will be used as a template to create the mRNA
molecule. An enzyme called RNA polymerase is used as the catalyst for this process.
○ mRNA is always shorter than the DNA that it is copied from, as it is a complementary
copy of only one gene
○ The sequence of mRNA nucleotides is the transcribed version of the original DNA
sequence. This sequence of nucleotides making up the length of the mRNA is typically
enough information to make one polypeptide (composed of amino acids covalently
bonded together in a specific sequence)
○ Triplet - any set of three bases that determines the identity of one amino acid; when a
triplet is found in an mRNA molecule, it is called a codon or codon triplet.
● Translation: production of a polypeptide
○ Each RNA type:
■ mRNA, messenger RNA, as described above, each mRNA is a complementary
copy
■ of a DNA gene and has enough genetic information to code for a single
polypeptide
■ rRNA, ribosomal RNA, each ribosome is composed of rRNA and ribosomal
protein
■ tRNA, transfer RNA, each type of tRNA transfers one of the 20 amino acids to
the ribosome for polypeptide formation.
○ Once an mRNA molecule has been transcribed, the mRNA detaches from the single-
strand DNA template and oats free in the nucleoplasm. At some point, the mRNA will
float through one of the many holes in the nuclear membrane (nuclear pores) and will
then be in the cytoplasm.
● Translation Process:
○ mRNA will locate a ribosome and align with it, so that the rst two codon triplets are
within the boundaries of the ribosome.
○ a specific tRNA molecule now floats in: its tRNA anticodon must be complementary to
the first codon triplet of the mRNA molecule.
 ○ amino acid: its identity was originally determined by the strand of DNA that transcribed
the mRNA being translated.
○ translated. While
○ The first tRNA ‘sits’ in the ribosome holding the rst amino acid, a second tRNA floats in
and brings a second (again specific) amino acid. The second tRNA matches its three
anticodon bases with the second codon triplet of the mRNA. Ttwo specific amino acids
are now being held side by side. An enzyme then catalyses a condensation reaction
between the two amino acids, and the resulting covalent bond between them is called a
peptide bond.
○ The bond is then broken between the first tRNA molecule and the amino acid that it
transferred in. This bond is no longer needed, as the second tRNA is currently bonded to
its own amino acid, and that amino acid is covalently bonded to the first amino acid. The
first tRNA floats away into the cytoplasm and invariably reloads with another amino
acid of the same type. The ribosome that has only one tRNA in it now moves one codon
triplet down the mRNA molecule. This, in effect, puts the second tRNA in the ribosome
position that the first originally occupied, and creates room for a third tRNA to float in,
bringing with it a third specific amino acid.
○ The process repeats, as another peptide bond forms, the ribosome moves on by another
triplet, and so on. The process continues until the ribosome gets to the last codon triplet.
The final codon triplet will be a triplet that does not act as a code for an amino acid,
instead it signals ‘stop’ to the process of translation. The entire polypeptide breaks away
from the final tRNA molecule, and becomes a free-floating polypeptide in the cytoplasm
of the cell.
● Polymerase Chain Reaction:
○ Means by which DNA replication can be carried out artificially in a laboratory setting.
However, it can only replicate rather short segments of DNA. By replicating DNA
segments, scientists can produce huge numbers of these segments to study and analyse. It
is often used in forensic situations when only a limited amount of the original DNA has
been recovered at a crime scene.
○ DNA Polymerase: Taq polymerase (Enzyme used in PCR)
■ stable at high temps
■ from a bacterium called Thermus aquaticus (Taq)
■ bacterium occurs naturally in hot springs, and its enzymes are not denatured at
high temperatures, including the specific DNA polymerase that it possesses
■ Greatly increased the number of discoveries in the eld of gene technology.
● Cellular Respiration: controlled release of energy from organic compounds to produce ATP
○ respiration’ refers to a variety of biochemical pathways that can be used to metabolize
glucose.
○ ATP from cellular respiration is immediately available as a source of energy in the cell.
○ Anaerobic cell respiration gives a small yield of ATP from glucose.
○ Aerobic cell respiration requires oxygen and gives a large yield of ATP from glucose.
○ Cells break down (or metabolize) their organic nutrients by slow oxidation. A molecule,
such as glucose, is acted on by a series of enzymes. The function of these enzymes is to
catalyse a sequential series of reactions in which the covalent bonds are broken (oxidized)
 one at a time. Each time a covalent bond is broken, a small amount of energy is released.
The ultimate goal of releasing energy in a controlled way is to trap the released energy in
the form of ATP molecules. If a cell does not have glucose available, other organic
molecules may be substituted, such as fatty acids or amino acids.
● Process of Cellular Respiration:
○ Glycolysis:
■ Glucose enters a cell through the plasma membrane and floats in the cytoplasm.
An enzyme modifies the glucose slightly, then a second enzyme modifies this
molecule every more. This is followed by an entire series of reactions that
ultimately cleaves the 6-carbon glucose into two 3-carbon molecules. Each of
these 3-carbon molecules is called pyruvate. Some, but certainly not all, of the
covalent bonds in the glucose are broken during this series of reactions. Some of
the energy that is released from the breaking of these bonds is used to form a
small number of ATP molecules. Notice in Figure 2.43 that two ATP molecules
are needed to begin the process of glycolysis and a total of four ATP molecules
are formed. This is referred to as a net gain of two ATP (a gain of four ATP
minus the two ATP needed at the start).
■ Takes place in cytoplasm, results in the net gain of two ATP molecules per
glucose molecule and results in the production of two pyruvate molecules.
○ 2 Main Anaerobic Pathways: breakdown of organic molecules for ATP production in an
anaerobic way is also called fermentation.
■ Alcoholic Fermentation: yeast example
● Thus yeast cells take in glucose from their environment and generate a
net gain of two ATP by glycolysis. The organic products of glycolysis are
always two pyruvate molecules. Yeast then converts both of the 3-carbon
pyruvate molecules to molecules of ethanol. Ethanol is a 2-carbon
molecule, so a carbon atom is ‘lost’ in this conversion. The ‘lost’ carbon
atom is given off in a carbon dioxide molecule. Both the ethanol and
carbon dioxide that are produced are waste products from the yeast and
are simply released into the environment. Bakers’ yeast is added to bread
products for baking because the generation of carbon dioxide helps the
dough to rise.
■ Lactic Acid Fermentation: a person exercising without enough oxygen example
● In this situation, the person’s pulmonary and cardiovascular systems
(lungs and heart) supply as much oxygen to the body’s cells as is
physically possible. If the person’s exercise rate then exceeds his or her
body’s capacity to supply oxygen, at least some of the glucose entering
into cell respiration will follow the anaerobic pathway called lactic acid
fermentation.
● Cells that are aerobic normally take the two pyruvate molecules and
metabolize them further in an aerobic series of reactions. But if a cell is
not getting a sufficient amount of oxygen for the aerobic pathway, i.e. is
in a low-oxygen situation, excess pyruvate molecules are converted into
lactic acid molecules. Like pyruvate, lactic acid molecules are 3-carbon
 molecules, so there is no production of carbon dioxide. What benefit
does this serve? Lactic acid fermentation allows glycolysis to continue
with a small gain of ATP in addition to the ATP that is generated through
the aerobic pathway.
○ Aerobic Cell Respiration:
■ Cells that have mitochondria usually use an aerobic pathway for cell respiration.
Begins with glycolysis; net gain of 2 ATP and 2 pyruvate molecules. The two
pyruvate molecules then enter a mitochondrion and are metabolized further.
■ Each pyruvate first loses a carbon dioxide molecule and becomes a molecule
known as acetyl-CoA. Each acetyl-CoA molecule enters into a series of reactions
called the Krebs cycle. During this series of reactions, two more carbon dioxide
molecules are produced from each original pyruvate molecule that entered it. The
Krebs cycle is said to be a cycle because it is a series of chemical reactions that
begin and end with the same molecule. This reacquisition of the beginning
molecule allows this series of chemical reactions to be repeated over and over
again (see Figure 2.46). Some ATP is generated directly during the Krebs cycle
and some is generated indirectly through a later series of reactions directly
involving oxygen. Aerobic cell respiration breaks down (or completely oxidizes)
a glucose molecule and the end-products are carbon dioxide and water plus a
much higher number of ATP molecules than anaerobic respiration yields.
● Photosynthesis: production of carbon compounds in cells using light energy
○ Visible light has a range of wavelengths, with violet the shortest wavelength and red the
longest.
○ Chlorophyll absorbs red and blue light most effectively, and refl ects green light more
than other colours.
○ Oxygen is produced in photosynthesis from the photolysis of water.
○ Energy is needed to produce carbohydrates and other carbon compounds from carbon
dioxide.
○ Temperature, light intensity, and carbon dioxide concentration are possible limiting
factors on the rate of photosynthesis.
○ Glucose - the most common chemical energy produced from photosynthesis and the most
common molecule that organisms use for fuel in the process of cell respiration; covalent
bonds
○ Substances can do one of only two things when they are struck by a particular wavelength
(colour) of light. They can:
■ absorb that wavelength (if so, energy is being absorbed and may be used)
■ reflect that wavelength (if so, the energy is not being absorbed and you will see
that colour).
○ Stages of Photosynthesis:
■ First Stage: a set of reactions that ‘trap’ light energy and convert it to the
chemical energy of ATP.
■ Second Stage: a set of reactions in which ATP is used to help bond carbon
dioxide and water molecules together to create a sugar, such as glucose.
○ First Stage of Photosynthesis:
 ■ In this set of reactions, chlorophyll (and other photosynthetic pigments) absorb
light energy and convert that energy to a form of chemical energy, speci cally
ATP. In addition, light energy is used to accomplish a reaction that is called
photolysis of water. In this reaction, a water molecule is split into its component
elements: hydrogen and oxygen.
■ The oxygen that is split away due to the photolysis of water is typically released
from the plant leaf as a waste product. From the plant’s perspective, the useful
products formed during this stage of photosynthesis are ATP and hydrogen.
○ Second Stage of Photosynthesis: 6CO2 + 6H2O → C6H12O6 + 6O2
■ The second stage of photosynthesis is a series of reactions collectively referred to
as the light-independent reactions. ATP and hydrogen are used as forms of
chemical energy to convert carbon dioxide and water into useful organic
molecules for the plant. Glucose, a typical product of photosynthesis, is an
organic molecule. It requires six inorganic carbon dioxide molecules to form one
glucose molecule.
■ This conversion of an inorganic form of an element to an organic form is known
as fixation. Therefore, photosynthesis can be described as a series of reactions in
which carbon dioxide and water are xed into glucose, and oxygen is produced as
a by-product.
○ Measuring the rate of Photosynthesis:
■ The photosynthetic rate is highly dependent on many environmental factors,
including the intensity of light and air temperature.
■ Measuring the rate of oxygen production or carbon dioxide intake is considered
to be a direct measurement of photosynthetic rate as long as a correction is made
for cell respiration. Another common method for measuring photosynthesis is to
keep track of the change in biomass of experimental plants. However, the mass of
plants is considered to be an indirect reaction of photosynthetic rate, as an
increase or decrease in biomass may be caused by a whole variety of factors as
well as the photosynthetic rate.