CH 23 (CH 4)

Question 1

genome

Answer 1

• an organisms full set of genes as well as any non-coding regions of DNA (for some viruses it is RNA)

Question 2

The study of Molecular evolution

Answer 2

investigates the mechanisms and consequences of the evolution of macromolecules

Question 3

Ways in which genes evolve:

Answer 3

• Nucleotide substitutions which can result in amino acid replacements in
  proteins
• Changes in amino acids can result in changes in secondary and tertiary
  structures of proteins
• the longer two sequences have been evolving separately., the more differences they accumulate

Question 4

structure of protein

Answer 4

just the chain
Alpha helix or beta pleated sheet (based on the interactions of amino acids. Proline causes kinks!)
Alpha helix and beta pleated sheet together (basically, the final folding of the proteins based on r groups, charges, polarity and hydro attractions)
Multiple proteins together like hemoglobin (4 units)

Question 5

to find homologous chromosomes

Answer 5

(same series of genes in multiple organisms)

- use sequence alignment (line up the chromosomes essentially)

Question 6

similarity matrix

Answer 6

counting the number of nucleotides or amino acids that differ between two sequences
LOOK AT THE IMAGE

Question 7

multiple substitutions:

Answer 7

more than one genetic change at a given position

Question 8

Coincident substitutions

Answer 8

at a given position different substitutions occur between ancestor and each descendant

Question 9

Parallel substitutions

Answer 9

the same substitution occurs independently between the ancestor and both descendants

Question 10

Back substitutions

Answer 10

is where the ancestral form changed at a point, then changed back

Question 11

SEE DIAGRAM OF EVOLUTION OF GENES

Answer 11

PLEASE

Question 12

synonymous or silent substitution

Answer 12

unlikely to be influenced by natural selection
Occur 5x more often in proteins encoding regions than non-synonymous mutations

when amino acid isn’t changed but nucleotide is

Question 13

Non-synonymous substitution

Answer 13

nucleotide changes causes codon change
Likely to be deleterious to organism
Does not always alter protein shape and size

Question 14

much of evolution is

Answer 14

neutral

Question 15

mutations can be

Answer 15

good or bad

• if bad, they are removed through natural selection
• if good, they are fixed so no population varies

Question 16

mechanisms of molecular evolution?

Answer 16

non coding DNA, gene duplication, gene family, concerted evolution via 2 mechanisms,

Question 17

non coding DNA

Answer 17

They hold space open that can be important for the timing of genes, where things bind (transcription factors). There needs to be an amount of space between genes to activate them
Also can sometimes regulate how and when genes become active. How much unravelling of DNA occurs for transcription and translation
Adds to evolutionary potential when natural selection happens, there might be a mutation or something that can be transcribed leading to a new trait

Question 18

gene duplication

Answer 18

Two of the same gene, will yield two copies of the same protein is gene duplication
Usually, two new coding sections can evolve on their own (won’t stay identical and make the same two protein each time gene is activated)
1. both retain function
2. One gets made in neurons vs. Muscles or Time wise, one can be in development vs the other in adult years
3. You don’t need both so body deactivates it
4. Proteins both do different thing
At first, it usually does only 1 but as they evolve, it will fall into one of the three categories

Question 19

several successful rounds of duplication and mutation may result in

Answer 19

a gene family

Question 20

gene family

Answer 20

group of homologous genes with related functions

Question 21

Concerted evolution

Answer 21

multiple copies of genes within a species evolve together

happens through unequal crossing over in meiosis resulting in more copies of genes on chromosome and

biased gene conversion (damage is repaired using another homologous sequence resulting in resulting in two copies of the same chromosome.

SEE DIAGRAM

Question 22

gene tree

Answer 22

shows the evolutionary relationships of a single gene in different species or of the members of a gene family

Question 23

Homologs

Answer 23

genes that are similar as a result of a common ancestry

Question 24

Orthologs

Answer 24

genes found in different species, and whose divergence can be traced back to the speciation event that gave rise to various species

Question 25

Paralogs

Answer 25

genes in the same or different species that are related through duplication events

Question 26

Bioprospecting

Answer 26

the search for naturally occurring compounds that can be used for pharmaceutical, agricultural, or industrial purposes

Question 27

In vitro evolution

Answer 27

new molecules are produced in the laboratory to perform novel and useful functions

Question 28

To study and combat disease

Answer 28

understanding how and when viruses and bacteria have evolved and mutated

Question 29

how can genome be diverse

Answer 29

-Mistakes in DNA replication (mutations) provide material for evolutionary
change
- Genes of an organism can be looked at as interacting members of a group (different dependencies, expressions locations)
- The positions of genes and their sequences are subject to evolutionary change

Question 30

GENE FAMILY

Answer 30

group of homologous genes with a similar function