Biochem 4403 - Genes And Genomes 1.2

Front 1

what are group II introns

Back 1

a self-splicing catalytic retroelement that can be mobile

Front 2

what are 2 forms of gene fusion

Back 2

- DNA based (genomic)

- transcription mediated

Front 3

what is transcription-mediated gene fusion?

Back 3

chimeric transcripts are formed by transcription of two consecutive genes into one RNA that can then undergo reverse transcription to yield new chimeric retrogenes

Front 4

what are orphan genes (ORFans)

Back 4

genes without obvious homologs in the genomes of other organisms

Front 5

what are 2 models for sequence homogenization?

Back 5

- concerted evolution

- birth and death model

Front 6

what is gene conversion

Back 6

non-reciprocal recombination where a DNA segment of a recipient gene is copied from a donor

Front 7

what is a virus

Back 7

entity whose genome has elements of nucleic acid and replicates in living cells using their cellular machinery; causing synthesis of virions to transfer the genome to other cells

Front 8

5 types of viral genes

Back 8

- genes present in a group of viruses with closely related homologs in cellular organisms
- genes conserved in a major/several group(s) of viruses with distant homologs
- ORFans
- virus-specific genes conserved in a broad group of viruses with no detectable homologs in cellular life
- viral hallmark genes

Front 9

4 ways to classify viruses:

Back 9

based on
- shape of caspid
- nature of genome
- presence/absence of envelope
- type of organism they parasitize

Front 10

viral factory

Back 10

the site of viral replication and assembly; using the host cell's metabolites and protein machinery

Front 11

what are mobile genetic elements

Back 11

DNA elements that encode proteins that mediate the movement of the element within and between genomes

Front 12

what are mobile introns

Back 12

intervening sequences capable of self-splicing and moving themselves within and between genomes (ex: group I and II)

Front 13

inteins

Back 13

proteins that carry out protein splicing and can move the gene that encodes them to other locations (internal homing endonuclease)

Front 14

what are 2 compositional features of a genome that can evolve?

Back 14

- GC content
- codon usage patterns

Front 15

what are group I introns

Back 15

- mobile, self-splicing ribozymes that catalyze their removal from RNA

- found in protein, rRNA and tRNA genes

Front 16

what is a homing endonuclease?

Back 16

HEs are nucleotide sequences that recognize and cleave 12-40 bp DNA sequence motifs. Some HEs also have a maturase function and can help the intron folding in the 3D shape required for splicing

Front 17

what is ectopic transposition

Back 17

the movement of an intron to a new genomic site

Front 18

group ____ introns are thought to be progenitors of nuclear spliceosomal introns and retrotransposons

Back 18

2

Front 19

clonal model of gene divergence

Back 19

novelty arises from mutations arising within asexual populations

Front 20

novelty arises via homologous recombination by

Back 20

recombining alleles that exist within a population/species independent of normal DNA replication.

Front 21

what affects the frequency of recombination between donor and recipient?

Back 21

the degree of sequence divergence. the further apart they are, the less likely it is for recombination to take place.

Front 22

what are IS elements?

Back 22

insertion sequence elements are small DNA segments capable of transposition and mediating recombination; found in all domains of life.

Front 23

what are virulence factors

Back 23

molecules that allow a pathogenic organism to replicate and disseminate by subverting or eluding the defence systems of the host

Front 24

what is lateral gene transfer

Back 24

movement of genetic material between different species (not by "traditional" reproduction)

Front 25

what are 3 requisites for Muller's ratchet

Back 25

- strong bottlenecks

- lack of recombination

- obligate synthesis providing a rich nutrient environment

Front 26

features of the viral genome (6):

Back 26

- no typical structure

- diverse gene expression patterns

- high gene density

- often compositionally biased

- fast evolving, divergent gene sequences

- diverse coding capacity

Front 27

what are 3 ways ectopic transposition can happen?

Back 27

- reverse splicing into another RNA

- reverse transcription by an exogenous RT enzyme

- recombination of cDNA into the genome

Front 28

what are 5 influences on gene duplication

Back 28

- rate of duplication
- intrinsic features of DNA recombination machinery
- structure of gene families
- population size of the organism
- impact of newly evolved duplicate genes on the organism

Front 29

4 factors that influence the frequency of successful gene transfer

Back 29

- physical proximity

- gene transfer mechanisms and their efficacy

- metabolic compatibility

- gene expression systems

Front 30

4 contributors to genome reduction

Back 30

- small population of endosymbionts

- host-restrictions

- there is inherent deletion bias

- A/T mutation pressure

Front 31

3 evolutionary forces on bacterial variants

Back 31

- genome reduction by deletion events

- gene acquisition by HGT

- mutations and genetic rearrangement

Front 32

what 3 things do you consider when thinking about genome reduction

Back 32

- mutational biases

- deletion biases

- population genetics

Front 33

what is reductive evolution

Back 33

- suggests that gene loss reflects relaxed selection on dispensable traits, elevated mutation pressure and even loss of beneficial functions because of genetic drift in small bacterial populations.

- a proposed model to explain the genomic commonalities seen in all obligate endosymbionts

Front 34

what is bacterial transformation

Back 34

genetic alteration in a cell whereby the recipient cell recognizes and takes up foreign DNA (from a lysed cell)

Front 35

how do compositional anomalies relate to LGT?

Back 35

over time, genomes evolve characteristic compositional features because of natural selection, drift and mutation pressure. if a donor genome differs from the recipient in this way, the transferred gene may appear anomalous

Front 36

what is amelioration?

Back 36

a change in the nucleotide composition of a laterally transferred gene/group of genes towards that of its genomic context

Front 37

integrative and conjugative elements (ICEs):

Back 37

bacterial mobile genetic elements that primarily reside in the host chromosome but can excise and be transferred to other cells via conjugation

Front 38

what is bacterial transduction

Back 38

generally virus-mediated movement of genetic material that can be general or specialized (limited to specific genes)

Front 39

what is bacterial conjugation

Back 39

the transfer of genetic material between bacterial cells by direct/physical contact between donor and recipient

Front 40

how can you identify LGT with phylogenetic incongruence?

Back 40

build a phylogenetic tree from the genome and see if it fits with known information. LGT is inferred if the resulting topology is incongruent with known/predicted relationships

Front 41

insect nutritional symbioses:

Back 41

mutual interdependence of the metabolism of the host insect and one or more bacterial symbionts

- seen in 10-15% of insects

Front 42

what is muller's ratchet

Back 42

the process by which the genomes of an asexual population irreversibly accumulate deleterious mutations and low G/C content