Lecture 01

Question 1

a. What is the genome central to?(1)

b. What is genomics central to?(1)

Answer 1

a.Genome is central to individuals

b.genomics is central to the science of
biology

Question 2

a. What is at the epicenter of genomics?(1)

b. What 2 things does the human genome do?(2)

Answer 2

a.At the epicenter of genomics - the human genome

b. -no other data sets command curiosity and imagination
- no others offer hope to improve human health

Question 3

a. When was the genome first sequenced?(1)
b. How many base pairs does it have?(1)
c. How many chromosomes does it contain?(2)
d. How many protein coding genes does it have?(1)
e. What is the microbiome?(2)
f. What kind of component is the genome? what does this mean?(1)

Answer 3

a.First sequenced in 2001
b. approximately 3.2 × 109 base pairs (bp)
c. 22 pairs of chr’s as well as two X chr’s in females or X and Y in males; mitochondrial DNA (separate genome!)
d. about 23,000 protein-coding genes (compare to 1012 – 1016 antibodies!)
e.microbiome: popu of bacteria occupying microenviron’s on and within our
bodies - all static component of genome
f. dynamic component: complex network of regulatory interactions, which integrates activities of individual components

Question 4

a. Give the equation of a phenotype(1)
b. Define phenotype(1)
c. Define genotype(1)
d. Define environment(1)
e. Define life history(1)
f. Define epigenetic factors(1)
g. What is NB to note?

Answer 4

a. P = G + E + LH + (GxE)
b. Phenotype – observable features, e.g., eye, hair or skin colour; some traits govern susceptibility to disease/drug efficacy  pharmacogenomics
c. Genotype – DNA sequence, i.e. genome; both nuclear + mitochondrial (chloroplast in plants)

d.Environment – its effect can be window specific (e.g. sex determination in reptiles; aromatase: converts androgens to estrogens); humans? (see
McLachlan & Storey 2003 J Theor Biol 222:71–72)

e.Life history – in utero, physical, nutritional and psychological environments

f.Epigenetic factors – genome x life experience (e.g. ‘Project Ice Storm’; see
Cao-Lei et al 2016 Curr Mol Biol Rep 2:16–25)

g.NOTE:
interactions among these factors to determine a phenotype differs from
trait to trait (alleles are also key!)

Question 5

Does a genome dictate features of an organism?(1)

-explain and give an e.g (2)

Answer 5

A genome constrains, but do not dictate features of an organism

-environment and surroundings lead organisms to explore different states in line with their genomes, e.g. lactose or tryptophan operons in E. coli

Question 6

Give 2 examples of science providing several means of interposition between G and P.(2)

Answer 6

Science has provided several means of interposition between G and P
- change in hair colour, tanning, cosmetic surgery, ‘cosmetic endocrinology’, enhancing athletic performance with drugs

-clustered regularly interspaced short palindromic repeats (CRISPR)-associated system (Cas) - genome editing; Chinese ‘designer babies’ (2018)

Question 7

Given all factors (thus, P, G, En, LH and Ep), how can we measure the relative importance of each?(2)

Answer 7

In humans, monozygotic twin studies- for example, twins reared apart (same genes; diff. environ’s)

In plants, breeding trials using clones
- beware ‘dead cow syndrome’; replicates

Question 8

Compare the feautres of a prokaryotic and eukaryotic cell.

a. size
b. subcellular division
c. state of major component of genetic material
d. internal differentiation
e. Cell division

Answer 8

Prokaryotic cell 
-Size 10 µm
-No nucleus
-Circular loop, few proteins
permanently attached
- No organized subcellular structure
-Fission

Eukaryotic cell

• size ~0.1 mm
• Nucleus
• Complexed with histones to form chr’s
• Nuclei, mitochondria, chloroplasts,cytoskeleton, endoplasmic reticulum, Golgi apparatus
• Mitosis (or meiosis)

Question 9

Describe Genes – after sequencing, structural and functional characterization

Answer 9

• protein-coding genes occur as open reading frames (ORFs) – DNA
  sequence of “reasonable length” that begins with an initiation (ATG) codon
  and ends with a stop codon (TAA, TAG or TGA); exon (1.3%) vs introns
• non-protein-coding regions – exhibit local self-complementarity
  corresponding to hairpin loops, e.g., transfer RNA (tRNA, Fig. 1.3)
• targets of regulatory interactions (motifs, e.g., TATA, GC, CAAT, Y patch)

Question 10

Discuss gene identification
a. Easier in?(1)

b. Describe gene identifiation in prokaryotes(2)
c. Describe gene identification in eukaryotes(2)

Answer 10

Identification
a. easier in prokaryotes vs eukaryotes

b. Prokaryotes: smaller genomes, contain fewer genes, contiguous genes that lack introns and small intergenic regions-> e.g. E. coli genome is 90% coding, high seq conservation

c. for eukaryotes
- very challenging: sparsely distributed genes with most having introns; alternative splicing further complicates gene ID
- lower vs higher eukaryotes, e.g., yeast genome is 67% coding and < or =4% genes have introns

Question 11

List 3 approaches towards gene identification (3)

Discuss each(2)(2)

Answer 11

Approaches toward gene identification
1. a priori methods – recognize sequence patterns within expressed genes and the regions flanking them (e.g., codon statistics and no stop codons)

2. ‘been there, seen that’ methods – recognize regions corresponding to previously known genes (e.g., expressed sequence tag (EST) matching; see
   Box 1.3)
3. combination of both methods