Genome Structure

Question 1

what is the correlation between total genome size and organism size

Answer 1

• ## very weak correlation between total genome size (# of genes) and organism size/complexity (# of cells)

Question 2

what is the correlation between noncoding sequences and organism complexity

Answer 2

• positive correlation between noncoding sequences and organism complexity

Question 3

composition of human genome

Answer 3

• exons (1.5%)
• introns & regulatory sequences (24%)
• unique non-coding DNA (15%)
• repetitive DNA (59%)

Question 4

how are genomes organized/distributed (2)

Answer 4

• gene-rich regions or gene-deserts

- biological significance of these regions is unknown

Question 5

gene-rich regions

Answer 5

• chromosomal regions that have many more genes than expected from average gene diversity over entire genome
• GC rich regions

Question 6

gene deserts (3)

Answer 6

• regions of >1 Mb that have no identifiable sequences
• AT rich regions
• 3% of human genome is comprised of gene deserts

Question 7

how do genome sequence studies affirm evolution from a common ancestor (3)

Answer 7

• genetic components of the basic cellular machinery of all living organisms are remarkably similar
• this suggests that all living organisms are descendants of a single, life-producing biology
• this means that analysis of model organisms can provide biological insight into the corresponding human systems

Question 8

why would a nematode have so many more genes than a single-celled yeast

Answer 8

• nematode is multi-cellular and needs to encode genes necessary for organism-specific functions
• eg. muscles, nerves, etc

Question 9

what might experiments might yeast be a good model organisms for

Answer 9

• cell cycle experiments

Question 10

what might experiments might nematodes be a good model organisms for

Answer 10

• neuron or muscle experiments

Question 11

protein structure

Answer 11

• relationship between amino acid sequence, secondary structure, motifs, domains, and overall tertiary structure

Question 12

secondary structure

Answer 12

• beta sheets and alpha helixes

Question 13

protein motif (2)

Answer 13

• short conserved amino acid sequence (<20 aa), that codes for a structure of biological significance
• simple combinations of secondary structure elements

Question 14

protein domain (3)

Answer 14

• region of a protein that folds into a stable 3D structure independently of the rest of the protein chain
• typically combinations of secondary structures and motifs that are organized into a characteristic structure that is shared between other protein family members
• can be used in combination in many types of proteins

Question 15

SH2 domain (2)

Answer 15

• protein domain of ~100 aa
• first identified as a conserved sequence found in oncoproteins
• recognize phosphorylated tyrosine motifs and found in many proteins involved in tyrosine kinase signalling

Question 16

SH2 function (2)

Answer 16

• connect other functional domains to phosphorylated proteins
• eg. dock to phosphorylated proteins or act in a signalling pathway

Question 17

notes on domain size (2)

Answer 17

• domains have a limit on size

- majority of domains (90%) have less than 200 residues, and are usually ~100 residues

Question 18

domains and forms of life

Answer 18

• they are common material used by nature to generate new sequences as many domain families are found in all three life forms

Question 19

what do domains tell us about the origin and evolution of proteins (2)

Answer 19

• majority of genomic proteins are multidomain proteins created as a result of gene duplication and domain shuffling/mixing
• suggests that new sequences are adapted from pre-existing sequences rather than invented

Question 20

what domains are shared between yeasts and nematodes

Answer 20

• domains that are shared pertain to basic conserved functions WITHIN cells

Question 21

what domains are not shared between nematodes and yeasts

Answer 21

• likely pertain to multicellular function/specialized cells that nematodes have, but yeasts don’t have

Question 22

how are proteins involved in core processes related to those involved in multicellularity

Answer 22

• virtually all biological processes characteristic of multicellular life are performed by proteins that are not close variants of proteins responsible for the core processes, even though they might share some domains

Question 23

what can we infer from knowing that “protein domains can be found in many combinations within proteins”

Answer 23

• most proteins have evolved as a result of gene duplication, domain shuffling, and mixing

Question 24

what can we predict by comparing genomes of different species (3)

Answer 24

evolutionary trends:

• evolution of new regulatory or signalling domains
• evolution of new domain architectures from shared (presumably preexisting) domains
• expansion of particular domain families by a series of duplications

Question 25

between DNA sequences, mRNA sequences, and amino acid sequences, where would you expect to find the greatest sequence similarity (2)

Answer 25

• amino acid sequences

- diff nucleotide sequences can produce the same amino acid sequence and DNA still includes introns