2.1-2.

6 Biology Review
2.1

Molecular biology: explains living processes in terms of the chemical substances

involved (investigating biological activity at a molecular level - study of compounds
and molecules that make up life).

Why is carbon able to form a wide diversity of stable compounds: Can form four
chemical bonds to other arms because of its valence electrons (covalent bonds =
single and double bonds)

Describe carbohydrates: most organic compound found in nature composed of C,

H, O (CH20) + energy source (short-term energy storage) + sugar molecules +
body breaks down carbs into glucose + composed of monomers called
monosaccharides (building blocks of disaccharides and poly)

Describe lipids: non-polar hydrophobic molecules + cell membrane (phospholipid,

cholesterol) + long term energy storage + signaling molecules (steroids) + glycerol
backbone, 2 fatty acid tails, phosphate group

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 Describe proteins: large, complex molecules + enzymes + structural material +
peptide + amino acids

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 Describe nucleic acids: large biomolecules + genetic material of all cells and
determines the inherited features of an organism + DNA functions as a master code
for protein assembly, while RNA is involved in the manufacturing of proteins +
nucleotides

Glucose and ribose:

Saturated fatty acid:

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 Generalized amino acid:

How does the artificial synthesis of urea helped to falsify vitalism: Vitalism is the
theory that the origin and phenomena of life are due to a vital principle, which is
different from purely chemical or physical forces. In 1828, Friedrich Wöhler
synthesized urea accidentally while trying to prepare ammonium cyanate. This was
the first piece of evidence against the vitalism theory.Vitalism was a doctrine that
dictated that organic molecules could only be synthesised by living systems. Urea is
a waste product of nitrogen metabolism and is eliminated by the kidneys in
mammals. The artificial synthesis of urea demonstrates that organic molecules are
not fundamentally different to inorganic molecules.

Role of enzymes in metabolism: Help catalyze metabolic reactions. When an

enzyme binds to a substrate, it stresses and destabilizes the bond in the substrate.
This reduces the overall energy of the level of substrate transition state. The

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 reaction rate is the amount of reaction over time. Lipases: This group of enzymes
help digest fats in the gut. Amylase: In the saliva, amylase helps change starches
into sugars. Maltase: This also occurs in the saliva, and breaks the sugar maltose
into glucose. Rubisco: photosynthesis.

Anabolic (requires energy) vs. catabolic (releases energy): Catabolism (water is

consumed) is the breakdown of complex molecules into simpler molecules including
the hydrolysis of macromolecules into monomers. Anabolism (water is released as
a product) constructs molecules from smaller units (endergonic).

Condensation (ana): synthesis of complex molecule from small reactant

molecules (water is a byproduct)

Hydrolysis (cata): breakdown of large reactant molecule into small units in the
presence of water (consumes water)

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 Molecular bio describes living processes via the interactions of the chemical
substances involved

living organisms are created from carbon compounds mentioned above

Carbon atoms form 4 covalent bonds with others

metabolism refers to the enzyme-catalyzed reactions in a cell or organism

anabolism is the synthesis of complex molecules from simpler molecules

catabolism is the breakdown of complex molecules into simpler molecules

2.2

Structure of water:

Water vs. methane: methane is non polar so it has a lower specific heat and latent
heat of vaporization + methane is gas composed of 4 H atoms and 1 C, it is held by
covalent bonds unlike water. This is due to polarity and hydrogen bonding (water
has stronger intermolecular bonds than methane while methane can only form weak
dispersion forces (water has a high electronegativity of oxygen, methane's carbon
has a lower electronegativity). It takes more energy to break these bonds than
methane, therefore, we would expect water to have a higher specific heat due to
these strong forces.

Cohesive: water molecules have high affinity for one another (stick together). Helps
water take up water at their roots.

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 Adhesion: clinging of water molecules to other substances. Water molecules stick to
the cell walls of plant’s thin veins which helps prevent the water falling backwards
due to gravity.

Thermal properties: high specific heat, high melting point, high boiling point, high
heat of vaporization (H bonds between water molecules require a lot of energy to
break. Its high specific heat capacity helps stabilize temperatures on Earth by
storing a lot of heat and transferring it to other regions through the hydrologic cycle.
High specific heat makes it resistant to temperature change, allowing life forms to
maintain relatively constant internal temperatures.

Solvent properties: UNIVERSAL SOLVENT, can dissolve many substances

because of its polarity (polar attraction of large quantities of water molecules can
weaken intramolecular forces like ionic bonds which results in the dissociation of the
atoms). HYDROPHILIC (polar and ions) VS HYDROPHOBIC (fats and oils) +
Sodium Chloride (blood), oxygen, glucose, amino acids + On a biological level,
water's role as a solvent helps cells transport and use substances like oxygen or
nutrients.

Sweat cools: That's because cooling your body via sweating relies on a principle of
physics called "heat of vaporization."
 It takes energy to evaporate sweat off of your skin, and that energy is heat. As your
excess body heat is used to convert beads of sweat into vapor, you start to cool
down.

Explain how the solubility of substances in water affects the way they are
transported in blood: BLOOD IS MAJ. OF H20, CAN EITHER MIX WITH BLOOD
OR NOT —> NaCI can separate into Na+ and CI- to be transported in the blood +
oxygen is soluble in low amounts, may of oxygen is transported by hemoglobin +
glucose can travel freely in the blood because of its hydroxyl groups + lipids (fats
and cholesterol) are non polar and hydrophobic so they can't dissolve in blood, so
they form complexes with lipoproteins to be transported through the bloodstream
(sugars can be partially broken down depending on how complex they are)

water molecules are polar, they have a positive and negative end

waters cohesive, adhesive, thermal, and solvent properties can be explained by

hydrogen bonding and dipolarity

hydrophilic substances are attached to water and hydrophobic are repelled by water

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 2.3

Explain how monosaccharide monomers are linked together in condensation

reactions to form disaccharides and polysaccharides: Monosaccharide monomers
are linked together through a condensation reaction, which involves the removal of
a water molecule to form a glycosidic bond. The hydroxyl (-OH) group on the
anomeric carbon of one monosaccharide reacts with the hydroxyl group on the non-
anomeric carbon of another monosaccharide, resulting in the formation of a
glycosidic bond between the two monosaccharides. The condensation reaction
between two monosaccharides forms a disaccharide, such as sucrose (glucose +
fructose) or lactose (glucose + galactose). When multiple monosaccharides are
linked together through glycosidic bonds, a polysaccharide is formed. Examples of
polysaccharides include cellulose, starch, and glycogen.

Describe the structure and function of storage polysaccharides (cellulose and starch
in plants and glycogen in humans and other mammals):

Cellulose is a structural polysaccharide found in cell walls of plants. Linear

molecule composed of B glucose subunits bound in 1-4 linkages. Because it
has B glucose it is indigestible for most animals (no enzyme to break down)

Starch: energy storage polysaccharide in plants. Composed of a glucose

subunits with 1-4 linkages. Exists in 2 forms - amylose (linear and helical
molecule, less soluble) amylopectin (branched and has additional 1-6 linkages)

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 Explain role of lipids in energy storage: long-term energy storage. When the body
requires energy, lipids are hydrolyzes (or broken down) into fatty acids and glycerol,
which can then be metabolized into ATP. hydrophobic so they can be stored for a
long time. compact.

Explain how triglycerides are formed by condensation from fatty acids and glycerol:
Triglycerides are formed by the condensation of one molecule of glycerol and three
molecules of fatty acid. A condensation reaction between glycerol and a fatty acid
(RCOOH) forms an ester bond. The R-group of a fatty acid may be saturated or
unsaturated. The process of esterification involves the removal of a water molecule
between the hydroxyl (-OH) group of the glycerol molecule and the carboxyl (-
COOH) group of a fatty acid molecule, resulting in the formation of an ester bond.
This process is repeated three times, with each fatty acid molecule being esterified
to a different hydroxyl group on the glycerol molecule, resulting in the formation of a
triglyceride molecule.

Describe the structure of fatty acids, distinguishing saturated, unsaturated,

monounsaturated, and polyunsaturated fatty acids: Fatty acids are long
hydrocarbon chains with a carboxyl group (-COOH) at one end. They are the
building blocks of lipids, including triglycerides, phospholipids, and cholesterol

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 esters. They can be saturated or unsaturated, depending on the presence of double
bonds between carbon atoms. Saturated fatty acids are those that do not contain
any double bonds between carbon atoms in their hydrocarbon chain so they are
linear. They are typically solid at room temperature and are found in animal fats,
such as butter, lard, and cheese. Unsaturated fatty acids are those that contain one
or more double bonds between carbon atoms in their hydrocarbon chain. They are
bet and are typically liquid at room temperature and are found in vegetable oils,
such as olive oil, canola oil, and soybean oil. Unsaturated fatty acids can be further
classified as monounsaturated or polyunsaturated, depending on the number of
double bonds in their chain. Monounsaturated fatty acids (MUFAs) are those that
contain one double bond between carbon atoms in their hydrocarbon chain.
Examples of MUFAs include oleic acid (18 carbons) found in olive oil and avocados.
Polyunsaturated fatty acids (PUFAs) are those that contain two or more double
bonds between carbon atoms in their hydrocarbon chain.

Distinguish between cis- and trans-: Cis: The hydrogen atoms attached to the
carbon double bond are on the same side. (bent) Trans: The hydrogen atoms
attached to the carbon double bond are on different sides. (linear). Trans fatty acids
do not commonly occur in nature and are typically produced by an industrial
process called hydrogenation. Trans fatty acids are generally linear in structure
(despite being unsaturated) and are usually solid at room temperature.

Outline the evidence for the health risks of trans fats and saturated fatty acids: Fats
and cholesterol cannot dissolve in blood and are consequently packaged with
proteins (to form lipoproteins) for transport. Low density lipoproteins (LDL) carry
cholesterol from the liver to the rest of the body. High density lipoproteins (HDL)
scavenge excess cholesterol and carry it back to the liver for disposal. Hence LDLs
raise blood cholesterol levels (‘bad’) while HDLs lower blood cholesterol levels
(‘good’)High intakes of certain types of fats will differentially affect cholesterol levels
in the blood. Saturated fats increase LDL levels within the body, raising blood
cholesterol levels. Trans fats increase LDL levels and decrease HDL levels within
the body, significantly raising blood cholesterol levels. Unsaturated (cis) fats
increase HDL levels within the body, lowering blood cholesterol levels. CHD,
CLOGGING OF ARTERIES (LDL)

Evaluate the evidence for health claims about lipids: These health claims are made
based on evidence collected in a number of ways- epidemiological studies

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 comparing different population groups, intervention studies that monitor cohorts
following dietary modifications, experimental designs utilising animal models or data
based on autopsies. Evidence Supporting Health Claims-

A positive correlation has been found between the intake of saturated fats and
the incidence of CHD in human populations. Counter: Certain populations do
not fit this trend (e.g. the Maasai tribe in Africa have a fat-rich diet but very low
rates of CHD).

Intervention studies have shown that lowering dietary intakes of saturated fats
reduces factors associated with the development of CHD (e.g. blood cholesterol
levels, blood pressure, etc.) Counter: Validity of intervention studies is
dependent on size and composition of cohort, as well as the duration of the
study

In patients who died from CHD, fatty deposits in diseased arteries were found to
contain high concentrations of transfats. Counter: Genetic factors may play a
role (e.g. blood cholesterol levels only show a weak association to dietary
levels)

Monosaccharide monomers are joined by condensation reactions to form

disaccharides and poly

different types of fatty acids

unsaturated can be cis or tans

triglycerides come from condensation from 3 fatty acids and 1 glycerol

BMI= weight (kg) / height m2

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 2.4

Polypeptides are formed from amino acids linked together by condensation

Polypeptides are synthesized in ribosomes from 20 different amino acids

A huge range of polypeptides is possible because the amino acids can be linked
together in any sequence

Genes code for the amino acid sequence of polypeptides (amino acids are coded
by the genome sequence within the cell)

A protein may consist of one polypeptide or of multiple polypeptides linked together

The 3D conformation of a protein is determined by the amino acid sequence

Proteins have a very wide range of functions in living organisms

A proteome is the full set of proteins in an individual; it is unique to each individual

Amino acids can be covalently joined together in a condensation reaction to form a

dipeptide and water (peptide bond —> long chains of amino acids are polypeptides
, can be broken down through hydrolysis which requires water to reverse the
process)

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 Primary structure: order of amino acid sequence (how chain will fold —> different
amino acid sequences will fold into different configurations due to the chemical
properties of the R groups)

Secondary: regular arrangement of the polypeptide chains stabilized by hydrogen

bonds (alpha helices, beta pleated)

Tertiary: 3D structure of the polypeptide:

The tertiary structure of a polypeptide chain will be determined by the

interactions between the variable side chains. These interactions may include
hydrogen bonds, disulphide bridges, ionic interactions, polar associations, etc.
The affinity or repulsion of side chains will affect the overall shape of the
polypeptide chain and are determined by the position of specific amino acids
within a sequence. Hence, the order of the amino acid sequence (primary
structure) determines all subsequent levels of protein folding.

Quaternary: more than one polypeptide chain linked together.

Denaturation:

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 Denaturation is a structural change in a protein that results in the loss (usually
permanent) of its biological properties

Because the way a protein folds determines its function, any change or
abrogation of the tertiary structure will alter its activity

Temperature

High levels of thermal energy may disrupt the hydrogen bonds that hold the
protein together

As these bonds are broken, the protein will begin to unfold and lose its capacity
to function as intended

Temperatures at which proteins denature may vary, but most human proteins
function optimally at body temperature (~37ºC)

pH

Amino acids are zwitterions, neutral molecules possessing both negatively

(COO) and positively (NH) charged regions

Changing the pH will alter the charge of the protein, which in turn will alter
protein solubility and overall shape

All proteins have an optimal pH which is dependent on the environment in

which it functions (e.g. stomach proteins require an acidic environment to
operate, whereas blood proteins function best at a neutral pH)

Protein functions:
Structure

Collagen: A component of the connective tissue of animals (most abundant

protein in mammals)

Spider silk: A fiber spun by spiders and used to make webs (by weight, is
stronger than kevlar and steel)

Hormones

Insulin: Protein produced by the pancreas and triggers a reduction in blood

glucose levels

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 Glucagon: Protein produced by the pancreas that triggers an increase in blood
glucose levels

Immunity

Immunoglobulins: Antibodies produced by plasma cells that are capable of

targeting specific antigens

Transport

Haemoglobin: A protein found in red blood cells that is responsible for the
transport of oxygen

Cytochrome: A group of proteins located in the mitochondria and involved in the

electron transport chain

Sensation

Rhodopsin: A pigment in the photoreceptor cells of the retina that is responsible

for the detection of light

Movement

Actin: Thin filaments involved in the contraction of muscle fibres

Myosin: Thick filaments involved in the contraction of muscle fibres

Enzymes

Rubisco: An enzyme involved in the light independent stage of photosynthesis

2.5

Enzymes have an active site to which specific substrates bind

molecules movement and collision of the enzyme’s active site with the substrate are
required for catalysis

the rate of activity of enzymes depends on temperature, pH, and substrate

concentration

enzymes can be denatured

enzymes can be immobilized to be used in industry

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 The active site is the region on the surface of the enzyme which binds to the
substrate molecule

The active site and the substrate complement each other in terms of both shape
and chemical properties

Hence only a  substrate is capable of binding to a particular enzyme’s active site

specific

All enzymes possess an indentation or cavity to which the substrate can bind with
high specificity – this is the active site

The shape and chemical properties of the active site are highly dependent on the  of
the enzyme tertiary structure

Like all proteins, enzyme structure can be modified by external factors such as high
temperatures and extreme pH

These factors disrupt the chemical bonds which are necessary to maintain the
tertiary structure of the enzyme

Any change to the structure of the active site (denaturation) will negatively affect the
enzyme’s capacity to bind the substrate

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 Methods to produce lactose free milk:

Lactose-free milk can be produced by treating the milk with the enzyme lactase.
The lactase is purified from yeast or bacteria and then bound to an inert
substance (such as alginate beads). Milk is then repeatedly passed over this
immobilized enzyme, becoming lactose-free. ADVANTAGES: as a source of
dairy for lactose-intolerant individuals, as a means of increasing sweetness in
the absence of artificial sweeteners (monosaccharides are sweeter tasting), as
a way of reducing the crystallization of ice-creams (monosaccharides are more
soluble, less likely to crystallize), as a means of reducing production time for
cheeses and yogurts (bacteria ferment monosaccharides more readily)

2.6

The nucleic acids DNA and RNA are polymers of nucleotides

DNA differs from RNA in the number of strands present (single vs. double), base
composition (ATCG vs. AUCG), and type of pentose (deoxyribose vs. ribose)

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 DNA is a double helix composed of two antiparallel strands of nucleotides linked by
hydrogen bonding between complimentary base pairs (the strands of a DNA double
helix are said to be "antiparallel" because the have the same chemical structure, but
are opposite in direction… this means that the 3' hydroxyl end of one strand is
opposite the 5' phosphate group of the other strand.)

Explain how Crick and Watson elucidates the structure of DNA using model making:
Using trial and error, Watson and Crick were able to assemble a DNA model that
demonstrated the following: DNA strands are antiparallel and form a double helix.
DNA strands pair via complementary base pairing (A = T ; C Ξ G) Outer edges of
bases remain exposed (allows access to replicative and transcriptional proteins)

Nucleotides of RNA and DNA:

Describe the structure of nucleic acids (DNA and RNA) identifying the differences
between them:

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 Double-helix model of NDA

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