Genetics - Basics

Question 1

1a. Define the terms genome, chromosome, and gene.

Answer 1

• 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

Question 2

1b. Describe the structure of a nucleotide (4 points)

Answer 2

• 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

Question 3

1c. Describe the differences between DNA leading and lagging strands (3 points)

Answer 3

• 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)

Question 4

1d. Describe the structure of DNA and its base pairing (2 points)

Answer 4

• 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

Question 5

1e. Name and describe the main enzymes involved in DNA replication (5 points)

Answer 5

• 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

Question 6

1f. Describe what is meant by semi-conservative replication

Answer 6

• DNA replication uses one double helix to make two double helices, each of which contains one parental strand and one nascent strand

Question 7

2. Describe the central dogma of molecular biology (4 points)

Answer 7

• 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

Question 8

3a. Describe the structure and function of chromatin (2 points)

Answer 8

• during interphase, most chromatin exists in an extended state and is active (euchromatin)
• some chromatin is highly condensed and is inactive (heterochromatin)

Question 9

3b. What are histones? (2 points)

Answer 9

• positively charged proteins that wind around negatively charged DNA
• they help form structure of chromosomes and help control the functions of DNA

Question 10

3c. Describe the structure of centromeres (3 points)

Answer 10

• 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

Question 11

3d. Describe the structure and function of telomeres

Answer 11

• 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

Question 12

4. Describe ploidy within cells (5 points)

Answer 12

• 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

Question 13

5a. Describe the differences in meiosis in men and women (3 points)

Answer 13

• 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.

Question 14

5b. Describe how meiosis gives rise to genetic diversity (2 points)

Answer 14

• independent assortment of paternal and maternal homologues, allowing 2^23 different combinations
• recombination: swapping of maternal and paternal DNA

Question 15

6a. Describe the process of transcription (4 points)

Answer 15

• 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

Question 16

6b. Describe the process of RNA splicing (and why some transcripts do not undergo splicing) (4 points)

Answer 16

• 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

Question 17

6c. Describe the five methods of alternative splicing (5 points)

Answer 17

• alternative 5’ splice site
• alternative 3’ splice site
• mutually exclusive exons: only one of a pair of exons is transcribed
• exon skipping
• intron inclusion

Question 18

7a. Describe the process of translation (5 points)

Answer 18

• 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

Question 19

7b. Describe the structure and function of codons (3 points)

Answer 19

• 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)

Question 20

7c. Describe the structure and function of tRNA (3 points)

Answer 20

• 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

Question 21

8a. Describe the molecular types of post-translational modification (6 points)

Answer 21

• 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

Question 22

8b. Describe the higher level structures formed by post-translational modification (4 points)

Answer 22

• 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

Question 23

9. Name and describe the functions of noncoding RNA (ncRNA) (4 points)

Answer 23

• 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)