Topic 1: DNA and Proteins

Question 1

What are the basic units of nucleic acids.

Answer 1

A nucleotide is the basic unit of a nucleic acid. It has three components:
A phosphate group
A sugar (two types are possible)
A base (four types are possible)

Question 2

What are the nucleotide bases

Answer 2

There are five bases found in nucleic acid:
Adenine 
Thymine 
Cytosine 
Guanine.

In RNA, thymine nucleotide base is replaced with uracil. The other three nucleotides remain unchanged.

Question 3

What are the types of RNA

Answer 3

Ribonucleic acid (RNA) consist of a single strand of polynucleotides. It is found in:
Transfer RNA (tRNA)
Messenger RNA (mRNA)
Ribosomal RNA (rRNA)
Micro RNA (miRNA)

Question 4

Whats the deal with chromosomes

Answer 4

Chromosomes in eukaryotic cells are made of chromatin, a mixture of DNA and proteins. DNA is coiled around proteins called histones.

Question 5

Describe the process of DNA replication

Answer 5

DNA replication is semiconservative as each new strain contains one original and one new polynucleotide strand. Enzymes involved:
DNA Helicase -breaks the weak bonds joining the strains
DNA polymerase enzyme- joins the free bases to the sugar phosphate backbone. Works in the 5’ to 3’ direction.
RNA primer- provides the starting point for DNA synthesis
Ligase- connects Okazaki fragments

Question 6

What are the three types of models

Answer 6

Conservative model is when the original double-stranded DNA molecule serves as the complete template for a DNA molecule made from two new strands.

Semi-conservative model is when the two strands of the original DNA molecule separate, and each strand serves as a template for a new DNA strand.

Dispersive model is when the original DNA molecule breaks into fragments that serve as templates for new DNA fragments

Question 7

How does DNA bond together?

Answer 7

Purines join with pyrimidines in the DNA molecule by way of breaking relatively weak hydrogen bonds with the bases forming cross-linkages. This leads to the formation of a double stranded molecule of two opposing chains of nucleotides:

Question 8

What is the DNA structure?

Answer 8

DNA Structure is that of phosphates linking neighbouring nucleotides together to form one half of a double-stranded DNA molecule.

Question 9

What are genes?

Answer 9

Genes are segments of DNA that code for proteins or RNA. Genes consist of exons, which are segments that code for the synthesis of proteins, and introns, which are segments that do not code for proteins. 249 bases per chromosome.

Question 10

Describe the process of transcription & Translation

Answer 10

Transcription is the genetic code copied from the DNA to mRNA (Messenger RNA). It occurs in the nucleus, uracil replaces thymine. Introns and exons are transcribe into a molecule called pre-mRNA.

1. Weak hydrogen bonds are broken by helicase or RNA polymerase
2. Free RNA nucleotides attached to exposed complementary bases.
3. RNA polymerase joins sugar phosphate backbone. mRNA strand detaches.

RNA splicing happens before translation the pre-RNA has introns removed by spliceosome, resulting in mature mRNA.

Codons
Every 3 nucleotides make a codon, they code for an amino acid.

There are 64 possible codons (43 ) as there are 4 bases and 3 positions on a codon. Resulting in 2o possible amino acids.

Codons are degenerate, some amino acids have multiple codons.

Codons are non-overlapping and don’t share codons.

Translation rRNA

Mature mRNA passes through nuclear pores into the cytoplasm

mRNA meets ribosomes in cytoplasm and the rough endoplasmic reticulum

Ribosomes (40% protein, 60% rRNA) made of small ribosomal subunit, which reads the mRNA, and a large ribosomal subunit.

rRNA catalyses proteins from amino acids

Translation tRNA

Transfer RNA (tRNA) transfer the amino acids to ribosome.

tRNA’s have a specific attachment site for the corresponding mRNA binding region called an anticodon.

Anticodon is a complementary sequence to the codon, which codes for an amino acid.

Translation

1. Mature mRNA attaches to small ribosomal unit.
2. tRNA transfer RNA to ribosome, hydrogen bonds form between tRNA anticodon and mRNA codon.
3. mRNA moves through, second tRNA transfers corresponding amino acids.
4. Large ribosomal subunit catalyses chemical reaction, forming peptide bonds between amino acids
5. Stage 3 and 4 are repeated until a stop codon is reached, Synthesised proteins moves to rough endoplasmic reticulum for modification.

Question 11

Whats the deal with amino acids

Answer 11

There are approximately 20 different amino acids found in proteins.

All amino acids have a common structure:
.The ‘R’ group is variable, which means that it is different in each amino acid.

Ten must be obtained from our diet. These are called essential amino acids.

Question 12

What is a polypeptide chain and how are they formed

Answer 12

A polypeptide chain is formed when amino acids are linked together via peptides bonds to form long chains.
The process of joining amino acids of called condensation.

A polypeptide chain may contain several hundred amino acids.

A polypeptide chain may be functional by itself but may also need to be joined to other polypeptide chains to be functional.

Question 13

What are proteins

Answer 13

Proteins are macromolecules, consisting of many amino acids joined together as polypeptide chains. Each cell contains several hundred to several thousand proteins.

Question 14

Elaborate on protein structures

Answer 14

Protein structure:

The conformation (or shape) a protein takes in dependent on the protein’s amino acid sequence. The ‘R’ groups of each amino acids each and interact with each other. These interactions determine the final confirmation of the protein.

A proteins conformation is central to its function, if the shape is altered then the protein may not be able to perform its biological function.

Proteins: Primary Structure

The primary (1) protein structure is the amino acid sequence.

Hundreds of amino acids link together to form polypeptide chains.

The chemical interaction (attraction and repulsion) of the individual amino acids helps define the final protein shape.

Proteins: Secondary Structure

The secondary (2) structure is the chain shape of the polypeptides chain.

There are two common types of secondary structure:
alpha-helix coil
beta-pleated sheets
Most proteins, e.g. lysozyme, contain a mixture of the two secondary structures, but the levels of each vary.

Secondary structure is result of hydrogen bond interaction between neighbouring CO and NH groups of the polypeptide backbone.

Proteins: Tertiary Structure

The tertiary (3) structure of a protein is the way in which it is folded (called its fold).

The protein folds because of interactions between the ‘R’ groups, or side chains on the amino acids. Several interactions may be involved:
. Disulfide bonding (reactions between two cysteine amino acids). These form the strongest links
. Weak bonding (ionic and hydrogen)
. Hydrophobic interactions.

Proteins: Quaternary Structure
Some proteins contain more than one polypeptide chain. The polypeptide chains, or subunits, aggregate together to become a functional unit. The aggregation of subunits is called the quaternary (4) structure of protein.

IN ESSENCE: There are four levels of protein structure.
Primary structure (1): The sequence of amino acids in a polypeptide chain

Secondary structure (2): The shape of the polypeptide chain (e.g. alpha-helix).
Tertiary structure (3): The overall conformation (shape) of the polypeptide caused by folding.

Quaternary Structure (4): The association of multiple subunits of polypeptides chains.

Question 15

What is the deal with protein denaturation

Answer 15

Protein Denaturation refers to the loss of a protein’s three-dimensional structure.
It occurs because the bonds responsible for maintaining protein structure are altered

It usually results in loss of function

It is often irreversible.
Examples of protein are seen in many everyday circumstances:

Cooking food denatures protein and makes it easier to digest.

Alcohols disinfect by denaturing bacterial and viral proteins.
Examples of agents that cause protein denaturation are:
Strong acids and alkalis
Heat and radiation
Heavy Metals
Detergents and solvents

Question 16

Whats the deal with globular proteins

Answer 16

Globular Proteins are very diverse in their structure.
They can exist as single chains or comprise several chains, as occurs in haemoglobin and insulin.
Properties of globular proteins:
Easily soluble in water
Tertiary structure is critical to function
Polypeptide chains are folded into spherical shape.

Functions of globular proteins:
Catalytic e.g. enzymes
Regulatory, e.g. hormones
Transport, e.g. haemoglobin 
Protective, e.g. antibodies

Question 17

Whats the deal with fibrous proteins

Answer 17

Fibrous Proteins form long shapes and are only found in animals.
Properties of fibrous proteins:
Water insoluble
Very tough physically; they may be supple or stretchy
Parallel polypeptide chains in long fibres or sheets
Functions of fibrous proteins:
Structural role in cells and organisms, e.g. collagen in connective tissue, bones, tendons
Contractile, e.g. myosin, actin

Question 18

Whats the deal with enzymes

Answer 18

The complexity of the active site is what makes each enzyme so specific. Enzymes have a specific region where the substrate binds and where catalysis occurs. This is called the active site. The active site is usually a cleft or pocket at the surface of the enzymes. Substrate modification occurs at the active site.

Enzymes are substrate specific, although specificity varies from enzyme to enzyme due to its structure:
High specificity: The enzyme will only bind with a single type of substrate

Low specificity: The enzyme will bind a range of related substrates, e.g. lipase hydrolyse any free fatty acid chain.
When a substrate binds to an enzyme’s active site, an enzyme-substrate complex is formed.

Question 19

Outline what substrate molecules are

Answer 19

Substrate molecules are the chemicals that an enzyme acts on. They are drawn into the cleft of the enzyme.

Question 20

Explain how active sites function

Answer 20

The active site contains both binding and catalytic regions. The substrate is drawn to the enzyme’s surface and the substrate molecule(s) are positioned in a way to promote a reaction: either joining two molecules together or splitting up a large one. The complexity of the active site is what makes each enzyme so specific

Question 21

Describe the lock and key model mechanism for enzymes.

Answer 21

The lock and key model of enzyme action, proposed earlier this century, proposed that that substrate was simply drawn into a closely matching cleft on the enzyme molecule.

Question 22

Induced Fit Model

Answer 22

More recent studies have revealed that the process is much more likely to involve an induced fit.

• A substrate approaches the active site of the enzyme.
• The substrate induces a complementary change in the active site of the enzyme. The shape of the active site is complementary to the shape of the substrate. The enzyme binds with the substrate forming an enzyme substrate complex.

The enzyme catalyses the reaction of its substrate forming one or more products. The products form a different shape to its substrate and diffuse away. The active site then reverts to its original shape.

Question 23

Explain the significance of biological catalysts

Answer 23

Catalysts speed up reactions by influencing the stability of bonds in the reactants. They may also provide an alternative reaction pathway, thus lowering the activation energy needed for a reaction to take place

Question 24

Outline the difference between catabolic and catabolic reactions

Answer 24

Catabolic Reactions involve the breakdown of a larger molecules into smaller components, with the release energy (they are exergonic).
Enzymes involved in catabolic reactions can cause a single substrate molecule to be drawn into active site.

Chemical bonds are broken, causing the substrate molecule to break apart to become two separate molecules.
Catabolic reactions include:
- Digestion: breakdown of large food molecules.
- Cellular respiration: Oxidative breakdown of fuel molecules such as glucose.

Anabolic reactions, smaller molecules are joined to form larger ones. These reactions are endergonic; they require the input of energy.
Enzymes involved in anabolic reactions can cause two substrate molecules to be drawn into the active site.
New chemical bonds are formed resulting in the formation of a single molecules.
Examples include: Protein synthesis: build-up of polypeptides from peptide units. Cellular respiration: Oxidation of fuel molecules such as glucose.

Question 25

Describe the effect temperature has on enzymes

Answer 25

Effect of Temperature
Enzymes often have a narrow range of conditions under which they operate properly. For most plant and animal enzymes, there is little activity at low temperature.
Enzyme activity increases with temperature, until the temperature is too high for the enzyme to function.
At this point enzyme denaturation occurs and the enzyme can no longer function.

Question 26

Describe the effect pH has on enzymes

Answer 26

Effect of pH
Enzymes can be affected by pH.
- Extremes of pH (very acid or alkaline) away from the enzyme optimum can result in enzyme denaturation
Enzymes are found in very diverse pH conditions, so they must be suited to perform in these specialist environments.
- Pepsin is a stomach enzyme and has an optimal working pH of 1.5, which is suited for the very acidic conditions of the stomach.
- Urease breaks down urea and has an optimal pH of near neutral.

Question 27

Factors Affecting Enzyme Reactions Rates

Answer 27

• Rate of reaction continues to increase with an increase in enzyme concentration.
• This relationship assumes non-limiting amounts of substrate and cofactors
• Rate of reaction increases and then plateaus with increasing substrate concentration.
• This relationship assumes a fixed amount of enzyme.

Question 28

Whats the deal with enzyme cofactors?

Answer 28

Enzyme Cofactors
Some enzyme requires cofactors to be active.
Cofactors are nonprotein component of an enzyme.
Cofactors can be:
- Organic molecules (coenzymes)
- Inorganic ions

Cofactors may be:
Permanently attached, in which case they are called prosthetic groups.
Temporally attached coenzymes, which detach after a reaction, and may participate with another enzyme in other reactions.

Question 29

Elaborate on the two types of enzyme inhibitors.

Answer 29

Enzymes can be deactivated by enzyme inhibitors
There are two types of enzyme inhibitors:
- Reversible inhibitors are used to control enzyme activity. There is often an interaction between the substrate or end product and the enzymes controlling the reaction.
- Irreversible inhibitors bind tightly and permanently to the enzymes destroying their catalytic activity. Irreversible inhibitors usually covalently modify an enzyme.
Many drug molecules are enzyme inhibitors.

Question 30

What are irreversible enzyme inhibitors

Answer 30

Irreversible Enzyme Inhibitors
Some heavy metals, such as cadmium, arsenic, and lead acts as irreversible enzyme inhibitors

They bind strongly to the sulfhydryl groups of the protein, destroying its catalytic activity.

Most heavy metals, e.g. arsenic, act as non-competitive inhibitors.
- Mercury (Hg) is an exception. It acts as a competitive inhibitor, binding directly to a sulfhydryl group in the active site of the papain enzyme.

Heavy metals are retained in the body, and lost slowly

Question 31

Whats are reversible enzyme inhibitors

Answer 31

Reversible Inhibitors

Reversible Inhibitors are used to control enzyme activity. There is often an interaction between the substrate or end product and the enzyme controlling the reaction.

Build-up of the end product or a lack of substrate may deactivate the enzyme. Competitive inhibition involves competition for the active site.

Non-competitive inhibitors work either to slow down the rate of reaction, or block the active site altogether and prevent its functioning (allosteric inhibition)

Question 32

What is the significance of gene expression and cell differentiaition

Answer 32

Nearly every cell contains the full set of genes (genome).

Only certain genes are expressed in each cell, providing cell differentiation.

Genes can be switched on or off (silenced), therefore regulating gene expression and protein synthesis.

The phenotype observed characteristics and behaviour, of an organism is determined by gene expression.
Phenotypes are influenced by:
- Concentration of structural proteins (Observable Features)
- Concentration of enzymes and hormones, which influence biochemical processes (Behaviour)

Question 33

Whats the deal with DNA Methylation?

Answer 33

Methyl groups (-CH3 ) can be added (methylation) or removed (demethylation) from the cytosine nucleotides only in the DNA molecule.

Methyl groups are added/removed by enzymes called DNA methyltransderases (DNMTs).

Adding a Methyl group silences gene expression by inhibiting RNA polymerase

Removing Methyl allows transcription to occur.

Question 34

What does chromatin remodelling consist of?

Answer 34

Chromatin is mixture of histone protein and DNA.
DNA is negatively charged, due to phosphate groups. Histones are positively charged, due to R group. The attraction of histone and DNA causes tightly packed heterochromatin. Heterochromatin is inaccessible to RNA polymerase, preventing transcription (gene switched off).

Acetyltransferases add negatively charged acetyl groups to the heterochromatin which neutralises the positively charged histones. This weakens the bonds between DNA and histones, forming loosely packed euchromatin. Euchromatin is accessible to RNA polymerase allowing transcription to occur (gene switched on).

Question 35

What are Non-Coding RNA (ncRNA)

Answer 35

ncRNA are transcribed but do not translate into proteins.

ncRNA are involved with epigenetics and control gene expression.

Question 36

Whats the deal with epigenetics

Answer 36

Epigenetic factors such as DNA methylation, chromatin remodelling regulate gene expression. The gene expression caused by epigenetics is heritable. It affects phenotype without changing the DNA sequence.

Epigenetic factors from a parent cell are passed onto daughter cells i.e. genes remain switched on/off. They are also passed onto offspring, generally controlled by ncRNA.

Environmental factors such as diet and drugs can cause epigenetic changes e.g. Type 1 diabetes.

Question 37

Describe the link between epigenetic and cancer

Answer 37

Two genes are important preventing cells from becoming cancerous:
- Proto-oncogene: promotes cell division.
- Tumour suppressing gene: Inhibits cell division and tumour development.
Decreased DNA methylation can activate Proto-oncogenes and trigger unregulated cell division.

Increased DNA methylation can switch off tumour suppressing genes.

Chromatin remodelling can influence the development of cancer.

Decreased histone acetylation converts euchromatin to heterochromatin, which can silence tumour supressing genes.

Increased histone acetylation converts heterochromatin to euchromatin, activating protooncogenes and unregulated cell division.

Question 38

What are the deal with mutations?

Answer 38

Mutations are changes that occur at the DNA level that may add, delete or rearrange genetic material.

Mutations can also be called Point Mutation: A mutation where one base pair is substituted for another. As a change at one base is enough to change the structure of a protein.

Question 39

What are the types of mutations

Answer 39

Silent has no effect on the protein sequence.

Missense results in an amino acid substitution.

Nonsense substitutes a stop codon for an amino acid

Frameshift mutation insertion or deletion of one or more bases.

Question 40

Explain how chromosomal mutation occurs and its effects.

Answer 40

Chromosomal mutation
A change in the number or structure of chromosomes
Caused by errors in cell division
Affect hundreds to thousands of genes

Deletion: loss of genetic material

Translocation: Genes exchanged between non-homologous chromosomes.

Duplication: gene copied more than once, creating many copies on a chromosome.

Inversion: Section broken off, reversed and inserted back in the chromosome.