Gene Structure and Chromatin Flashcards

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1
Q

3 components defining a gene (in eukaryotes)

A

1) transcribed section of DNA molecule and its
2) CIS regulatory elements
3) this section of DNA sequence contributes to a phenotypic trait (influences structure/function of organism)

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2
Q

what does the translated or “protein coding” portion of the gene consist of? how long is it?

A

average 1200 bp; consists of exons (some exons have UTRs also)

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3
Q

what does the transcribed part of the gene include? average size?

A

all exons and introns; 27,000 bp

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4
Q

what do exons contain?

A

protein-coding regions and untranslated sequences (5’ and 3’ UTRs)

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5
Q

what do introns contain?

A

start with splice donor sites and end with splice acceptor sites

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6
Q

two consequences of alternative splicing

A

1) can cause some exons to be removed with introns
2) can cause some introns to be used as exons

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7
Q

are CREs (cis-regulatory elements) transcribed?

A

no

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8
Q

where is the promoter located?

A

right next to transcriptional start (beginning of exon 1); where the pre-initiation complex forms

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9
Q

how many promoters per gene?

A

one

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10
Q

characteristics of promoters

A

binding site for RNA pol, binding site for “general” transcription factors, often have TATA boxes, around 100-1000 bp

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11
Q

where are enhancers located?

A

often far (100 kbp) from transcriptional start and first exon; can be in introns of same gene, in adjacent gene or downstream

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12
Q

purpose of enhancers

A

needed for expression in specific tissues/ cell types at specific time

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13
Q

how many enhancers per gene?

A

several

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14
Q

characteristics of enhancers

A

bind cell-type specific transcription factors, have transcription factor binding sites (TBSs), around 100-1000 bp long

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15
Q

role of shadow enhancers

A

redundant, back-up enhancer (functionally equivalent to enhancers)

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16
Q

role of silencers

A

prevent transcription in particular cell types; bound by “repressing” transcription factors

17
Q

4 CREs

A

promoters, enhancers, shadow enhancers, silencers

18
Q

why are CREs hard to find?

A

TBSs are short and “degenerate” (their sequences are not very strict), and the rules in which they are ordered and spaced are unknown, located up to 500,000 bp away from promoter

19
Q

approximate size of an average eukaryotic “gene” (including space between CREs and exons)

A

100,000-1,000,000 bp

20
Q

given the average size of a eukaryotic gene and the fact that we have 3.1 billion bp, how do we have so many different “genes”?

A

1) genes can overlap; all or parts of adjacent genes can be present between Exons and CREs
2) genes can be on either strand, with transcription oriented in different directions
3) genes can share enhancers

21
Q

define nuclear genome

A

all DNA in your nucleus

22
Q

in eukaryotic cells, the nuclear genome is made of..

A

individual, linear, double stranded DNA molecules called chromosomes

23
Q

genes are sequences on…

A

chromosomes

24
Q

how long are human chromosomes

A

57-250 million bp long

25
Q

how many genes do human chromosomes have?

A

200-2000 genes each

26
Q

what does the word “chromosome” technically refer to?

A

DNA molecules with their associated proteins

27
Q

what are chromosomes made of?

A

chromatin (any sequence of DNA + associated proteins)

28
Q

what are the proteins associated with DNA called?

A

histones

29
Q

basic unit of chromatin

A

nucleosome

30
Q

define nucleosome

A

147 bp of DNA wrapped around 8 histone proteins (histone octamer)

31
Q

what happens to nucleosomes during transcription?

A

RNA polymerase pushes off histones then nucleosome reforms behind it

32
Q

open, loosely wrapped and actively transcribed chromatin

A

euchromatin

33
Q

tightly wrapped, generally inactive and untranscribed

A

heterochromatin

34
Q

location of euchromatin

A

unwrapped and free in nucleus

35
Q

location of heterochromatin

A

attached to nuclear envelope (membrane)