Protein Synthesis and Selection

Question 1

DNA Structure:

1. A double helix consisting of two polynucleotide strands
2. Each nucleotide is formed from deoxyribose, a phosphate group and a nitrogenous base
3. Both polynucleotides are made by joining adjacent DNA nucleotides by phosphodiester bonds (through condensation reactions, catalysed by DNA polymerase)
4. The two polynucleotide strands are held together by hydrogen bonds between complementary basis (Adenine to Thymine and Guanine to Cytosine)

Question 2

Eukaryotic DNA:
-Linear
-Associated with histones
-Contains introns

Prokaryotic DNA:
-Circular
-Not associated with histones
-Does not contain introns

Question 3

Introns are non-coding base sequences of DNA found within a gene

Question 4

mRNA

· This is a single stranded polynucleotide chain.

· It is a complementary copy of a single gene, from the TEMPLATE strand of DNA.

· mRNA’s length will vary depending upon the number of bases that make up the gene, so it is much shorter than DNA.

· The sequence of bases on the mRNA are complementary to the sequence of bases of the gene it is copying.

· Complementary bases pair rules: Guanine with Cytosine and Adenine with Uracil

Question 5

Contrasting DNA and mRNA:

-DNA is double stranded whereas RNA is single stranded

-DNA is longer whereas RNA is shorter

-Thymine in DNA whereas Replaced with uracil in RNA

-Deoxyribose in DNA whereas Ribose in RNA

-DNA has hydrogen bonds whereas mRNA doesn’t have hydrogen bonds

-DNA has introns whereas mRNA doesn’t have introns

Question 6

tRNA

-single stranded

-cloverleaf structure held by hydrogen bonds

-It has an amino acid attachment site where only a specific amino acid binds

-it also has a region of 3 bases known as an anticodon.

-anticodon is specific to the amino acid carried by the tRNA and is complementary to the codon on the mRNA.

-The role of the tRNA molecules is to carry a specific amino acid to the RIBOSOME [site of protein synthesis]

Question 7

Genome – complete set of genes in a cell

Question 8

Proteome – full range of proteins that a cell is able to produce

Question 9

Loci – position of a gene within chromosome

Question 10

Allele – a different version / form of a gene

Question 11

Gene- a DNA base sequence that codes for a sequence of amino acids in a polypeptide

Question 12

Exon:
Base sequence coding for a
polypeptide

Question 13

Transcription:
1. (DNA Helicase) Hydrogen bonds are broken so strands separate
2. Only one DNA strand acts as template
3. RNA nucleotides attracted to exposed bases
4. (Attraction) according to base pairing rule Adenine-Uracil, Cytosine-Guanine
5. RNA polymerase joins (RNA) nucleotides together forming phosphodiester bonds through condensation reactions
6. Pre-mRNA spliced to remove introns (in Eukaryotes)

Question 14

Translation:
1. mRNA binds to ribosome
2. Ribosome finds the START codon
3. Idea of two codons/binding sites
4. (Allows) tRNA with complementary anticodons to bind/associate with codon
5. (Catalyses) formation of peptide bond between amino acids (held by tRNA molecules) using energy from ATP
6. tRNA released as Ribosome moves along (mRNA to the next codon)/translocation described
7. Ribosome releases polypeptide into RER when the STOP codon is reached

Question 15

Describe the role of ATP in
the process of translation in
protein synthesis

Answer 15

1. Releases energy;
2. (So) peptide bonds form between amino acids OR (So) amino acid joins to tRNA;

Question 16

The Genetic Code is:

Universal – the same 3 bases on mRNA (codon) / DNA (triplets) code for the same amino acids in all organisms.

Question 17

The Genetic Code is:

Non-overlapping - A base from one triplet cannot be used in an adjacent triplet

Question 18

The Genetic Code is:

Degenerate - more than one codon codes for an amino acid.

There are 20 amino acids and 64 combinations of triplets / codons

Question 19

A mutation is any change to the DNA base sequence

Question 20

A gene mutation (single-point mutation) is a change to a single base in the DNA base sequence of a gene. These mutations occur randomly and happen spontaneously

Question 21

A mutation in DNA may result in a change in the PRIMARY STRUCTURE OF POLYPEPTIDES, sequence of amino acids in the polypeptide chain.

CONSEQUENCE:

· May alter the SECONDARY STRUCTURE (change the position of the weak Hydrogen bonds affecting the alpha helices and beta-pleated sheets)

· May alter the TERTIARY STRUCTURE (change the position of the weak Hydrogen, Ionic bonds between the R groups of amino acids and the Disulphide bonds) and may alter the BINDING site or ACTIVE site of enzymes and make the protein non-functional.

Question 22

A mutation in a gene coding
for an enzyme could lead to the production of a non-functional enzyme
Explain how

Answer 22

1. Change in base sequence (of DNA/gene);
2. Change in amino acid sequence / primary structure (of enzyme);
3. Change in hydrogen/ionic/ disulphide bonds;
4. Change in the tertiary structure/active site (of enzyme);
5. Substrate not complementary/cannot bind (to enzyme / active site) / no enzyme-substrate complexes form;

Question 23

Substitution mutation:
When one nucleotide in the DNA sequence is replaced by another
A substitution may not always be harmful as the substituted nucleotide may code in that triplet for the same amino acid.
This is known as a silent mutation, where the mutation does not change the amino acid coded for, so will have no effect on the polypeptide chain

Question 24

If a mutation causes a triplet to code for a STOP codon, this will cause the growing polypeptide chain to terminate prematurely and may not be able to perform it’s intended function (depending upon how early the termination occurred)

Question 25

Addition/Deletion mutations:
1 full DNA nucleotide base is Gained or Lost (within the GENE)

This results in an alteration of the base triplets from the mutation onwards. The reading frame has been shifted to the right / left by one base, and so is known as a frame shift.

The earlier this type of mutation occurs within a gene then more of the triplets coding for a polypeptide could be affected, so more of the amino acids would be altered. An addition / deletion that occurred towards the end of a sequence of bases, would have a lesser effect, but would still alter some amino acids at the end of a gene

Question 26

Mutagenic agents increase the rate of spontaneous mutation.

Mutagenic agents include:

1. High energy ionising radiation (X rays and gamma rays and alpha and beta particles) which damage the DNA molecule (bases) and chemicals that alter the DNA structure or interfere with DNA replication.
2. DNA reactive chemicals such as benzene, bromine and hydrogen peroxide. Nitrous acid can remove an NH2 group from cytosine in DNA, converting the base to Uracil.
3. Biological agents such as some viruses and bacteria.

Question 27

Chromosomal mutations:
A pair of homologous chromosomes may fail to separate during metaphase 1 or sister chromatids fail to separate in metaphase 2.
This is called chromosome non-disjunction
Down’s syndrome is the result of non-disjunction where
individuals have an extra chromosome 21

Question 28

Inversion mutations (chromosomal)

• when a segment of bases is reversed end to end

Question 29

Duplication mutations

A doubling of a part of a chromosome, of an entire chromosome, or even the whole genome

Question 30

Translocation mutations

When groups of base pairs relocate from one area of the genome to another, usually between non-homologous chromosomes

Question 31

An organism’s characteristics (Phenotype) is determined by the genotype (all the alleles an organism has) and its interaction with the environment.

Question 32

Genetic diversity (Gene pool) – the number of different alleles of genes in a population

Question 33

Mutations introduce new alleles to populations. Any mutation could provide a:

· Selective advantage

· Neutral (does nothing)

· Selective disadvantage

Question 34

Define ‘gene mutation’ and explain how a gene mutation can have:
* no effect on an individual
* a positive effect on an individual.

Answer 34

(Definition of gene mutation)
1. Change in the base/nucleotide (sequence of chromosomes/DNA);
2. Results in the formation of new allele; (Has no effect because)
3. Genetic code is degenerate (so amino acid sequence may not change); OR Mutation is in an intron (so amino acid sequence may not change); Accept description of ‘degenerate’, eg some amino acids have more than one triplet/codon.
4. Does change amino acid but no effect on tertiary structure; 5. (New allele) is recessive so does not influence phenotype; (Has positive effect because)
6. Results in change in polypeptide that positively changes the properties (of the protein) OR Results in change in polypeptide that positively changes a named protein; For ‘polypeptide’ accept ‘amino acid sequence’ or ‘protein’.
7. May result in increased reproductive success OR May result in increased survival (chances);

Question 35

Natural Selection:

Process by which organisms that are better adapted to their environment survive and reproduce in greater numbers, resulting in the increase of the frequency of the advantageous allele within the population.

Question 36

Predation, disease and competition for the means of survival result in differential survival and reproductive success,

Question 37

Natural selection:

· Variation exists within a population (caused by Mutation)

· Better adapted individuals more likely to survive and reproduce (differential reproductive success.

· These organisms are more likely to pass on their alleles.

· Those which are less well adapted fail to survive and reproduce.

· These organisms are less likely to pass on their alleles.

· Organisms are therefore subject to selection pressure due to the environment they live in.

· Selection pressure determines the spread of an allele within the gene pool.

· Selection pressures can be either BIOTIC or ABIOTIC.

Question 38

Stabilising Selection:
1) Selection against both extremes
2) Only mean phenotype will have reproductive success
3) Alleles for mean phenotype are passed on to future generations in greater numbers
4) Over time, frequency of mean alleles coding for mean phenotype increases
5) Alleles coding for both extreme phenotypes decrease

Question 39

Directional Selection:
1) Selection for only one extreme
2) Individuals with advantageous allele have increased reproductive success
3) Alleles for one extreme are passed on to future generations in greater numbers
4) Over time, frequency of this extreme allele coding for extreme phenotype increases
5) Alleles coding for other extreme phenotype decreases within the population

Question 40

Evolution by natural selection is a change in the allelic frequencies within a population

Question 41

Explain how selection
occurs in living organisms

1. Variation due to mutation;
2. Different environmental/abiotic/biotic conditions / selection pressures;
3. Selection for different/advantageous, features/characteristics/mutation/ /allele;
4. Differential reproductive success / (selected) organisms survive and reproduce;
5. Leads to change in allele frequency;
6. Occurs over a long period of time;

Question 42

Counting bacteria:
2^n

n - number of divisions

Question 43

Scientists perform a serial dilution to be able to count the bacteria colonies.

They can then multiply the number of colonies by the dilution factor to gain the number of colonies in the original culture medium.

Question 44

Serial Dilution:
-1 part culture medium and mixing 9 parts sterile water,
completes a 1/10 dilution
This divides the number of bacteria in the culture medium by 10
-By taking 1ml of the previous dilution and adding it to 9ml of sterile water you can create a 1/100, This divides the number of bacteria in the original culture medium by 100
-Repeating this process four more times will create a 1/1000, 1/10000, 1/100000 and 1/1000000 dilution of the original culture medium

Question 45

To work out the number of bacteria in the original culture medium:
Number of colonies x dilution factor

Question 46

Using a dilution which is too low to count the number of bacteria can lead to:
1. The count being unlikely to be reproducible and accurate. 2. as there are too many cells so they will be overlapping.

Question 47

Using a dilution which is too high to count the number of bacteria will lead to the original dilution being so diluted that there will be no remaining bacteria present to see.