Chp 7 Lec 3 + 4

Question 1

Genome information in eukaryotes is divided between?

Answer 1

The nuclear genome and cytoplasmic organelles {mitochondria(mt) and chloroplasts(cp’s) }

Question 2

State two facts about the nucleus (nuclear genome):

Chromatin remodeling is an important component of?

Answer 2

1. DNA is complexed with proteins to form chromosomes
2. The amount of nuclear DNA per cell is constant in all cells of an organism except for gamete(multiple vs half)

Regulation of gene expression

Question 3

State the facts about the cytoplasmic organelles (mt and cp’s)

Answer 3

1. DNA forms nucleoprotein complexes (similar to bacterial nucleoids, reflecting endosymbiont origin of organelles)
2. Contain a circular, double-stranded DNA molecules(dsDNA) ,whereas some species contain more than one DNA molecule.
3. Both vary in no.of DNA copies they contain, also cells of different tissues contain different no.of organelles:
   - mt are more numerous in cells that consume large amounts of energy (e.g. brain, heart and eye- about 10000 mt/cell), than in skin cells( only a few hundred); cells of parasites have no mt at all.
   - in plants, (1)a leaf cell may contain up to 100 cp’s (there is species variability); (2)leaves may have 10⁶ per mm²; (3) root cells have none(becoz no photosynthesis)
4. Both genomes vary in size among species
5. 1.- human mt= 16 569 bp
   - yeast mt= 75kb
   - whereas protozoa (Cryptosporidium) has no DNA in the mt organelle
6. 2. • plant mt’s are larger (e.g. muskmelon =2.4 Mbp
7. 3 - cp genome range from about 110 to 160 kb, larger than animal mtDNAs

Question 4

1. Mt and cp’s each carry out their own____; nuclear DNA encode ____ mt proteins.
2. In plant’s, cp’s and mt translate their DNA using ____, but animal mt use ____.(near-universality of code)
3. Between organelle and nuclear genomes there is ____.
4. About ~90% of cp proteins are encoded by ___and __(still continues e.g. slugs feeding on algae)
5. But then, differences in genetic code___(nuclear transfer in animals)
6. In A.thaliana genome=___, in nuclear chromosome 2 contains much of the ___ including some ___.
7. With full mt genome is ?

Answer 4

1. Protein synthesis, almost all
2. Standard genetic code, variants
3. Active molecular traffic
4. Nuclear Gene’s and gene transfer
5. Inhibit mt
6. 620 kb insertion of mtDNA, duplicated material
7. 366 924 bp

Question 5

1. Where do similarities and differences among genome sequences appear at?
2. What can happen to a gene(during evolution)?

Answer 5

1. 1. Nucleotide level
2. 2. Gene level
3. 3. Larger-scale blocks
4. 4. Level of whole genomes that have undergone complete duplications
5. 1. May be passed to descendants, accumulating favorable (or unfavorable) mutations or drifting neutrally.
6. 2. May be lost
7. 3. May be duplicated, followed by divergence or by loss of one of the pair
8. 4. May undergo horizontal transfer to an organism of another species
9. 5. May undergo complex patterns of fusion, fission, or rearrangement, perhaps involving regions encoding individual protein domains

Question 6

1. Closely related genomes tend to contain regions encoding ____.
2. Sequence alignments of homologous Gene’s will reveal differences, mostly in the form of___or___and___.
3. There is___ between overall species divergence and divergence of individual gene sequences and the corresponding proteins.
4. Note the observations in gene sequence alignment:

Answer 6

1. Closely related proteins
2. Single-site mutations (SNPs), insertions, deletions
3. Correlation
4. • intron
   • asterisks, indicate positions containing the same base in all 3 genomes (human,chicken and staphylococcus)
   • colons, indicate positions containing two identical bases among the 3, in most cases 2 common bases in chicken and human seq,even in non-coding regions.
   • frequent occurrence of patterns ‘:’ and ‘-blank’ ,the likely reason for this pattern is degeneracy of the genetic code.

Question 7

1. Where can duplications occur?
2. Since when duplications are an important mechanism of evolution?
3. Duplications have been seen in which 3 domains?
4. True/false - Estimates of duplication levels vary, but generally it is substantial, ranges from 17-65% in different genomes.

Answer 7

1. -In individual genes
   
   • regions containing many genes
   • or even entire genomes
2. Since the duplications are a prolific source of variation, the raw material of both selection and genetic drift.
3. Archaea, bacteria and eukaryotes
4. True

Question 8

1.Duplications of genes affects organisms in all 3 domains, after duplication, both copies of a gene may___ and___. One copy may turn into a ____or be ___leaving only one functional copy.

2. 1. S. Ohno proposed in 1970 that ?
3. 2. He then put forward that?
4. During evolution, proteins descending from a common ancestor will___, depending on whether they___or ___.

Answer 8

1. Survive and diverge. Psuedogene, deleted
2. 1. Duplications followed by divergence is an important source of proteins with novel functions.
3. 2. It’s easier to recruit and adapt an already active molecule to a new function than to invent a new protein from scratch.
4. Differ, retain or change functions.

Question 9

Define the following terms:

1. Homologues
2. Paralogues
3. Orthologues

Answer 9

1. Regions of genomes, or portions of proteins, that are derived from a common ancestor
2. Related genes (i.e. homologues ) that have diverged to provide separate functions within the same species. E.g. alpha and beta chains of human haemoglobin
3. Homologues that perform the same function in different species. E.g. human and horse myoglobin

Question 10

Other related sequences may be psuedogenes, which may have arisen by____or by___from mRNA, followed by the_____to the point of ____or___.

Answer 10

Duplication or retrotransposition, accumulation of mutations, loss of function or expression.

Question 11

Explain the following terms:

1. Nonfunctionalization
2. Neofunctionalization
3. Subfunctionalization

Answer 11

1. Following duplication, one copy simply become silenced by degenerative/deleterious mutations, while the other copy retains the original function.
2. Following duplication, one copy may acquire a novel, beneficial function and become preserved by natural selection, while the other copy retains the original function.
3. Following duplication, both copies may become partially compromised by mutation accumulation to the point at which their total capacity is reduced to the level of the single-copy ancestral gene.
   E.g haemoglobin genes; ancestral gene = alpha and beta ; none can function independently to produce a monomeric protein molecule (i.e. 2alpha or 2beta vs 2aplha2beta)

Question 12

In analyzing the divergence of related genes, how can we distinguish between the effect of selection from genetic drift?

Answer 12

(Natural) selection - process that progressively eliminates individuals whose fitness is lower and chooses individuals of higher fitness to survive and produce the next generation.

(Random) genetic drift - a change in the gene pool of a small population that takes place strictly by chance.

Question 13

What can one calculate given the two aligned gene sequences?

Answer 13

Ks - the no.of synonymous substitutions

Ka - the no.of non-synonymous substitutions

Question 14

True/false
All synonymous substitutions are changes in the 3rd position of codons.

What does the calculation of Ks and Ka involve?

Answer 14

False , most but not all synonymous….

More than simple counting because of the need to estimate and correct for possible multiple changes.

Question 15

Define the following terms:

1. Synonyms

2. Non-synonymous

Answer 15

1. Nucleotide change that does not change the amino acid.

2. Nucleotide change that changes the amino acid.

Question 16

1. The role of Ka/Ks distinguishes the role of?
2. What do the following imply:
3. 1. Ka/Ks = 1
4. 2. Ka/Ks&raquo_space;1
5. 3. Ka/Ks «1

Answer 16

1. Selective pressure and drift in the divergence of genes after duplication
2. 1. Implies neutral evolution - silent and substitution mutations have occurred to approximately equal extents.
3. 2. Implies positive (adaptive) selection - substitution mutations are more prevalent than silent mutations, implying that selective pressures are active and the substitutions are advantageous.
4. 3. Implies purifying (negative) selection - substitution mutations are underrepresented, implying that the sequence is optimized fairly rigidly, with relatively little tolerance for mutation.

Question 17

Provide examples of duplication and divergence.

Answer 17

1. Clusters on chr 11 and 16 (alpha and beta) + other globins (neuro- , cyto- and myo- )
2. Closely linked genes suggest recent divergence
3. Temporal expression patterns imply divergence in control of expression
4. Dating the divergence of globin genes