Molecular Structure of Genes and Chromosomes 1 (L8)

Question 1

simple transcription unit - what can a mutation in an intron region cause?

Answer 1

affects splicing

Question 2

simple transcription unit - what can a mutation in a regulatory region cause?

Answer 2

gene not expressed when and where it should be

Question 3

complex transcription unit - what can a mutation cause?

Answer 3

different outcomes in multi-exon genes

Question 4

what is the origin of exon duplication?

Answer 4

unequal crossing over

Question 5

what are transposons?

Answer 5

segments of DNA that can move around to different positions in the genome of a single cell

Question 6

effects of transposons

Answer 6

• can cause mutations

- can increase or decrease amount of DNA in genome of a cell

Question 7

movement of DNA transposons? what enzyme do they require?

Answer 7

“cut and paste” - require transposase

Question 8

functional significance of alternative splicing and example

Answer 8

different final product from genes in same DNA segment - rearrange exons to make variety of end products
-example: dscam and down syndrome

Question 9

example of functional significance of gene duplication

Answer 9

beta-globin gene cluster

Question 10

homolog

Answer 10

gene related to a 2nd gene by descent from a common ancestral DNA sequence

Question 11

ortholog

Answer 11

gene in different species that evolved from a common ancestral gene by speciation - have same function

Question 12

paralog

Answer 12

genes related by duplication within a genome - evolve new functions

Question 13

tubulin example of gene duplication

Answer 13

2x copies of same gene with some sequence variation -> eventually give rise to multiple species

Question 14

hox clusters

Answer 14

duplications of same sequences

Question 15

BLAST

Answer 15

basic local alignment search tool - tells you which bases or sequences are similar or identical; measured in %

Question 16

example of sequence alignment and clinical problems

Answer 16

NF1

Question 17

non-coding RNAs

Answer 17

don’t code for protein, but have physiological fxn:

-rRNA, tRNA, snRNA, miRNA, telomerase RNA

Question 18

microsatellites

Answer 18

short tandem repeats of nts - repeating sequences of 2-5 bp of DNA

Question 19

mechanism of microsatellite expansion

Answer 19

backward slippage during replication (get n+1)

Question 20

retrotransposons

Answer 20

“copy and paste” - the copy made is RNA, not DNA - copies then transcribed back into DNA by reverse transcriptase

Question 21

end result of DNA transposons vs. retrotransposons

Answer 21

same end result but different methods of insertion

Question 22

origin of DNA transposon duplication

Answer 22

one copy of transposon before S phase -> S phase: DNA replication and DNA transposition -> after S phase, one daughter molecule has two copies of transposon

Question 23

two types of retrotransposon

Answer 23

with and without LTR - a direct repeat

Question 24

what is LTR a characteristic of?

Answer 24

integrated retroviruses

Question 25

what do retrotransposons encode for in retroviruses?

Answer 25

all proteins except envelope proteins

Question 26

non-LTR retrotransposons

Answer 26

don’t have long terminal repeats like most A/T rich regions

Question 27

non-LTR retrotransposon steps

Answer 27

1. Nicking
2. Priming of reverse transcription by chromosomal DNA
3. Reverse transcription of LINE RNA by ORF2
4. Copying of chromosomal DNA by ORF2
5. Insertion completed by cellular enzymes
   DNA now contains LINE DNA b/w direct repeats

Question 28

what are LINE?

Answer 28

long interspersed elements

Question 29

ORF1

Answer 29

RNA binding protein

Question 30

ORF2

Answer 30

DNA endonuclease and reverse transcriptase

Question 31

examples of LINE in humans

Answer 31

L1, L2, L3

Question 32

SINE

Answer 32

short interspersed elements - bare bone LINE, don’t encode proteins

Question 33

what do SINE depend on?

Answer 33

LINE protein machinery

Question 34

examples of SINE in humans

Answer 34

Alu elements

Question 35

exon and promoter shuffling via..

Answer 35

homologous recombination (double crossover b/w Alu elements)

Question 36

when can transposase recognize two transposons?

Answer 36

when they are close enough together

Question 37

origin of mitochondria

Answer 37

endosymbiosis

Question 38

mitochondrial genome

Answer 38

have own genome that uses atypical codons

Question 39

mitochondrial inheritance

Answer 39

cytoplasmic

Question 40

heteroplasmy

Answer 40

presence of a mixture of more than one type of an organellar genome w/i a cell or individual - factor in severity of mitochondrial diseases

Question 41

maternal inheritance

Answer 41

traits of offspring are maternal in origin due to expression of extranuclear DNA present in ovum during fertilization

Question 42

one example of a mitochonrial disease

Answer 42

LHON