1
Q
1a. Define the terms genome, chromosome, and gene.
A
- genome: collective term for all different DNA molecules within a cell or organism.
- chromosome: a large DNA-protein complex that helps organise the genome
- gene: DNA segment within a chromosome that carries genetic information to make protein or functional RNA
2
Q
1b. Describe the structure of a nucleotide (4 points)
A
- a simple repeating unit, consisting of a sugar, a nitrogenous base, and a phosphate
- deoxyribose sugars (DNA) have a H branch, and ribose sugars (RNA) has an OH branch
- carbon numbers counted clockwise from the O atom of the sugar
- nucleotides joined by an adjacent phosphate, forming a sugar-phosphate backbone
3
Q
1c. Describe the differences between DNA leading and lagging strands (3 points)
A
- leading strand: 5’ to 3’
- lagging strand: 3’ to 5’
- replication must be 5’ to 3’; the leading strand is synthesised continuously, while the lagging strand is synthesised in fragments (Okazaki fragments)
4
Q
1d. Describe the structure of DNA and its base pairing (2 points)
A
- cellular DNA exists in a double stranded, duplex form, e.g., a double helix
- each base is linked to another by hydrogen bonds. G-C bonds have 3 while A-T have 2, meaning G-C bonds are stronger
5
Q
1e. Name and describe the main enzymes involved in DNA replication (5 points)
A
- helicase: unwinds DNA
- primase: creates primers (short stretches of DNA, 18-25 nucleotides long, that bind polymerase)
- DNA polymerases: alpha (binds to primers and initiates transcription), delta and epsilon (major player in replication)
- ligase: glues together Okazaki fragments
- topoisomerase: winds the strands together
6
Q
1f. Describe what is meant by semi-conservative replication
A
- DNA replication uses one double helix to make two double helices, each of which contains one parental strand and one nascent strand
7
Q
- Describe the central dogma of molecular biology (4 points)
A
- DNA –> RNA –> protein
– one strand of DNA is used to synthesise an RNA copy; this is transcription. the initial RNA copy is known as the primary transcript
– the primary transcript undergoes processing, giving a mature RNA
– mRNA then synthesises a protein by translation - a major exception to the central dogma exists in the form of reverse transcription, which converts RNA –> DNA
8
Q
3a. Describe the structure and function of chromatin (2 points)
A
- during interphase, most chromatin exists in an extended state and is active (euchromatin)
- some chromatin is highly condensed and is inactive (heterochromatin)
9
Q
3b. What are histones? (2 points)
A
- positively charged proteins that wind around negatively charged DNA
- they help form structure of chromosomes and help control the functions of DNA
10
Q
3c. Describe the structure of centromeres (3 points)
A
- a region in the centre of a chromosome to which kinetochores will bind just prior to cell division
- heterochromatic region dominated by highly repetitive DNA
- microtubules attached to each kinetochore position the cell at metaphase
11
Q
3d. Describe the structure and function of telomeres
A
- structures at the end of chromosomes that maintain chromosomal integrity
- consists of many tandem copies of TTAGGG, which has an overhang with CCCTAA repeats
- if lost after breakage, the end of the chromosome is unstable, leading to fusion, recombination, or degradation
12
Q
- Describe ploidy within cells (5 points)
A
- ploidy: the number of copies of the basic chromosome set (n); in humans, n = 23
- DNA content of a single chromosome set (C); human cells are typically diploid (2C)
- sperm and egg cells are haploid (1C)
- some cells are polyploid (>2C), such as megakaryocytes in blood (16-64C)
- others are nulliploid (no nucleus), such as RBCs, platelets, and terminally differentiated keratinocytes
13
Q
5a. Describe the differences in meiosis in men and women (3 points)
A
- meiosis has two stages of division but only one stage of DNA replication, meaning cells are haploid (1C)
- in males, divisions are symmetric, producing 4 spermatozoa per meiosis
- in females, divisons are asymmetric; in meiosis I, an oocyte (secondary) and polar body (discarded) are produced; in meiosis II, the secondary oocyte produces a mature egg cell and second polar body.
14
Q
5b. Describe how meiosis gives rise to genetic diversity (2 points)
A
- independent assortment of paternal and maternal homologues, allowing 2^23 different combinations
- recombination: swapping of maternal and paternal DNA
15
Q
6a. Describe the process of transcription (4 points)
A
- TFIID (containing TBP [TATA binding protein] and TFs [transcription factors]) binds a TATA sequence -30 bases of the transcription site, creating a replication bubble
- RNA polymerase II continues in a similar way to DNA replication
- a C-G rich region creates a hairpin, followed by a poly-U site, which terminates transcription
- the poly-U site is replaced with a poly-A tail, and a G cap is added to the other end of the RNA strand, preventing 5’ exonucleases degrading the RNA
16
Q
6b. Describe the process of RNA splicing (and why some transcripts do not undergo splicing) (4 points)
A
- introns (noncoding) are removed to leave an exon (coding) sequence, which are covalently bonded
- most introns begin with a GT dinucleotide and end with an AG, marking the splice donor site (GU) and splice acceptor site (AG)
- splicing is performed by spliceosomes, protein factors, and snRNAs; all occurs within the nucleus
- 10% of genes do not undergo splicing at all, but instead alternative splicing patterns. notable examples include histone genes
17
Q
6c. Describe the five methods of alternative splicing (5 points)
A
- alternative 5’ splice site
- alternative 3’ splice site
- mutually exclusive exons: only one of a pair of exons is transcribed
- exon skipping
- intron inclusion
18
Q
7a. Describe the process of translation (5 points)
A
- mRNA is exported to the cytoplasm (from the nucleus)
- ribosomes bind to the 5’ end of an mRNA and moves along to find the translation start site (the AUG start codon).
- the ribosome has three sites: attachment (A), the P site (peptidyl), and E site (exit)
- tRNAs carry a specific amino acid (according to the mRNA codon) to the A site. this amino acid then forms a peptide bond with the amino acid in the P site and forms an amino acid chain
- the chain terminates after a stop codon is encountered, and the ribosome is released from the mRNA by binding a release factor
19
Q
7b. Describe the structure and function of codons (3 points)
A
- mRNA is translated three nucleotides at a time; the three nucleotides are known as a codon
- there are 64 possible codons (4 bases at each of the 3 codon positions = 4x4x4). 61 code for an amino acid (including the AUG start codon - methionine) and 3 are stop codons
- this process is degenerate (many amino acids have more than one codon) and unambiguous (each codon only codes for one amino acid or stop)
20
Q
7c. Describe the structure and function of tRNA (3 points)
A
- tRNA has a cloverleaf structure resulting from intramolecular hydrogen bonds
- they bind with mRNA codons by a 3 nucleotide sequence within the tRNA known as an anticodon
- according to their anticodon, tRNAs carry different amino acids covalently linked to their 3’ end
21
Q
8a. Describe the molecular types of post-translational modification (6 points)
A
- hydroxylation (forms an C-OH group from a C-H group); targets pro, lys, and asp
- carboxylation (adds a COO- group to glutamate); important in blood clotting factors
- acetylation (adds an acetyl group [CH3-CO] to lysine) and methylation (adds a methyl group [CH3] to lysine); causes switch between ‘on’ and ‘off’ states
- phosphorylation (adds a phosphate group to tyrosine, serine, and threonine); as for acetylation/methylation
- N/S-lipidation: adds lipid to glycine/cysteine; helps anchor membrane/proteins
- N/O-glycosylation: adds carbohydrate in Golgi; important functions in folding
22
Q
8b. Describe the higher level structures formed by post-translational modification (4 points)
A
- primary structure: simply the chain of amino acids
- secondary structure: carbon and branch reactions. can form alpha helix and beta sheets (hydrogen bonds)
- tertiary structure: interaction between R groups (forming globular and fibrous structures)
- quaternary structure: subunits joint to create a larger unit showing cooperativity
23
Q
- Name and describe the functions of noncoding RNA (ncRNA) (4 points)
A
- antisense RNA: negatively regulates gene expression (e.g., downregulation)
- miRNA (micro RNA) smaller than antisense, and also negatively regulates gene expression. thought to be important in early development
- snRNA (small nuclear RNA): has a role in mRNA splicing
– snoRNA (small nucleolar RNA) functions in rRNA splicing
– scaRNA (small Cajal body-specific RNA) functions in snRNA splicing - piwi-RNA: prevents transposable elements (transposons)
BMSc
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