Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Mol. Cell Bio > Ch 11: Expression of Genetic information > Flashcards

Ch 11: Expression of Genetic information Flashcards

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

Central dogma of molecular biology

A

DNA -> RNA -> protein

not necessarily true, RNA -> DNA is possible through reverse transcriptase

and RNA can have catalytic function i.e. Ribozymes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Alkaptonuria

A

A disease studies by Garrod in 1908 that is characterized by dark urine.

Trait is ingerited (genetic basis)

Affected indiciduals are deficient for enzyme responsivle for oxidizing homogentisic acid (part of the pheylalanine breakdown pathway)
enz = homogentisic acid oxidaseq

invented term “inborn error of metabolism”

one gene-one enzyme hypothesis is derived

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Beadle and Tatum experiment

A

irradiated neurspora spores to induce mutations

gre irradiated neurospora on complete medium

Gre individual spores on minimal medium to identify mutants

mutant smaples tested on minimal medium supplemented with specific vitamins

by growing on minimal medium, wwyou can see which enzyme // metabolite is missing, or cannot be converted

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Vernon Ingram and sickle cell anemia (1956)

A

used proteolytic enzymes = trypsin to cleave normal and sickle cell hemoglobin polypeptides (hemoglobin A vs S)

identified fragments with two dimensional paper chromatography (seperation via charge [left-right] and molecular size [up-down])

one fragment migrated differently

sequenced fragment and identified mutation

one gene-one protien/// polypeptide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Sickle cell Beta Globin Protein

A

Glu (-ve charge) to Val (neutral) aa sub

results in sticky patches on moleucle

form crystals that distort rbc

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

flow of genetic informaiton

A

use of mRNA separates storage of genetic information form information utalization

also permits amplification of gene information

proteins translated from mRNA on ribosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

types of RNA

A

mRNA

rRNA

tRNA

tRNA and rRNA form secondary structures

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

mRNA

A

transcribed form DNA template

code for protien

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

rRNA

A

structural and catalytic RNA in ribosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

tRNA

A

carries aa ro ribosome and mRNA transcript

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Groupo II self-splicing intron

A

RNA secondary strucutre

has selfsplicing activity

hairpin loop exhibits ribozyme acticity

proximiy effects increase rate

hydroxy group acts as a nucleophile (A) to attack (G)
then 3’ end hydroxy group acts as a nucleophile to push off the intron= leaving group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Basics of transcription

A

RNA transcribed by DNA dependent RNA polymerase (DNA template to make their transcripts)

Polymerase binds to promoter (upstream of the gene coding region) with aid of transcription factors

DNA temporarily unwound as polymerase moves along (by the aqid of helicases and topomerases)

Mg2+ is required in the active site as a cofactor

RNA is trancribed in the 5’ to 3’ direction

transcription bubble is 35 bp of DNA, DNA-RNA hybrid is 8 bp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Transcription elongation

A

DNA clamped down by RNA pol

(and twisted???? see slide 24) ch 11

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Direction of RNA transcription

A

RNA synthesized in the 5’ to 3’ direction

pyrophosphate is hydrolyzed to make the overall process favourable

3’ OH of nucleotide at the end of the growing strand attack 5’ alpha phosphate of the incomping nucleotide triphosphate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Experimental system for studying RNA transcripton

A

RNA ligated to glass surface by a his tag

fluorescent bead is on the upstream end of DNA, can measure wobble

fluoresent bead is on the downstram end of DNA, can measure the force produced by the enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

RNA has high processivity

A

stays associated with DNA remplate with high efficiency

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

RNA produces force while transcribing

A

force produced by RNA pol is twice that of myosin moleucle

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

How is energy supplied to RNA pol

A

energy derived from the hydrolysis of NPPP = ribonucleotide precursors

pyrophosphate is hydrolyzed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

RNA pol movement

A

movement is not cts

polymerase may stall
=fix mistakes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

RNA pol has high fidelity

A

RNApol backtracks to correct errors, and cleaves the mishap

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Look at the video of RNA pol backtracking

A

on nexus website

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

sense strand

A

coding strand

in ds DNA that carries the translatable code i the 5’ to 3’ direction

this strand has the same sequence of mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

anti-sense strand

A

responsible for the RNA that is later translated to protein (is the template during transcription)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Initiation of transcription in prokaryotes

A

core enz + sigma factor to help increase the core enzymes affinity for the promoter active site

this does not stay associated during transcription once RNA pol starts, sigma factor leaves.

-35, -10 upstream of the initiation site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Bacterial promoters

A

located in the region preceding transcription initiation
35 bases upstream TTGACA consensus sequence
=recognized by sigma factor

10 bases upstream TATAAT\
=pribnow box, is important for proper alignment, such that it can start transcription aty the start site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Comparison of RNApol

A

archeal and eukaryotic RNA pol are more similar to each other than either is to bacterial polymerase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Eukaryotic RNA pol

A

RNA pol I

RNA pol II

RNA pol III

RNA pol IV

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

RNApol I

A

synthesizes large rRNA transcripts

28s, 18s, 5.8s

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

RNApol II

A

synthesizes mRNA and small nuclear RNA (snoRNA and snRNA)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

small nucleolar RNA

A

snoRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

small nuclear RNA

A

snRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

RNApol III

A

synthesizes tRNA and small rRNA

5s rRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

RNApol IV

A

synthesizes siRNAs

plants only

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Nucleolus, the site of Ribosome assembly

A

darker bodies with in the nucleus

gc = granular component = ribosomal subunits in process of assembly

fc = fibrillar component = DNA (genes) coding for rRNA (ribosomal RNA)

dfc = dense fibrillar component = rRNA nascent transcripts

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Synthesizing rRNA precursor

A

rRNA genes in oocytes are amplified during development

increase number of nucleoli

expand tandem arrays of rRNA genes via rolling circle replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

Rolling circle replication

A

making RNA transcripts

circular DNA makes many linear copies

can re-insert themselves back into the genome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

rRNA transcription unit

A

5s in a differnet part of the genome
but these three = 18s, 5.8s and 28s are transcribed together

needs to be processed

post transcriptional processing (much different than RNA pol II which is one gene, one transcript)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

kinetic analysis of rRNA synthesis and processing

A

pulse chase exp

I have no fucking clue

see lec jan 25

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

what is the first mature transcript ot be seen in the cytoplasm with mammalian rRNA

A

18s

this is later followed by by the 28s and the 5.8s

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

modification of mammaliam rRNA

A

large number of methylated nucleotides and pseudouridine residues in processed rRNA (post translation modification are conserved, that is, they are always on the same residue)
=posttranscriptional modificaiton
= conserved regions

ex =- methylation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Roles of modified residues in the modification of mammalian rRNA

A

protect from cleavage

promote folding

promote interactions with other molecules (proteins)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

role of snoRNAs

A

small nucleolar RNAs complex with protein to form snoRNPs (a RNA/ protein combintion)

Antisense snoRNAs =

U3

BOX C/D

BOX H/ACA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Antisense snoRNAs

A

bind to RNA

help modification enzymes recognize rRNA (methylase)

44
Q

BOX C/D snoRNAs

A

= methylation

guide RNA thats responsible for methylating uracil residures

bind to RNA and helps modificaiton enzymes (methylase) recognize rRNA

antisense snoRNA

45
Q

5s rRNA processing

A

genes are seperate from other rRNA genes (unlike the other rRNA transcripts)

located outside the nucleolus

organized in tandem arrays

transcribed by RNA pol III
=> promoter is internal (w/ in the gene, not upstream)

5s rRNA transported back io nucleolus following processing

5s rRNA is first to be seen because it doesn’t have the extra processing the other transcripts have

46
Q

tRNA processing

A

~50 different species of tRNA (b/c need redundancy)
=> many codons for the same aa (helps with silenct mutations??)

found in clusters throughout genome

transcribed by RNA pol III
=> internal promoter

Pimary transcript is processed (RNase P)

47
Q

Bacterial tRNA processing

A

Ribonuclease P is needed for proper post translation modifivations of tRNA

good example of the RNA being catalytic// ribozyme

cleaves off the 5’ end

48
Q

mRNA transcription

A

mRNA transcripts transcribed by RNA pol II

initiation depends on transcripiton factors

promoters are upstream of coding sequence
=> core promoter element between 24 and 32 bases upstream
=> TATA box is the site of formatio of initiation complex

49
Q

Know the formation of the preinitiation complex

A

know it

many general transcription factors (GTFs)

cause all genes use these for the pre-initiation complex (which is before RNA pol II transcribes)

TAF
DPE
TBP

TFIIB
TFIIF
TFIIH

help align and dock RNApolII so it aligns at the proper start site

50
Q

TAF

A

TATA binding protein associated factors

51
Q

DPE

A

downstream promoter element

52
Q

TBP

A

TATA binding protein

bends DNA approx 80 degrees and allows TFIIB to bind

does this via insertion into the minor groove of DNA helix

53
Q

TFIIB

A

provides bindng site for RNA pol II

54
Q

TFIIF

A

contains subunit homolgous to bacterial sigma factor

55
Q

TFIIH

A

is a multisubunit protien with enzymatic proterties (kinases)

phosphorylation of RNA pol II promotes the uncoupling of enzyme from the promoter

region of RNA pol II rich in serine is phosphorylated = CTD = C terminal domain

56
Q

CTD of RNA pol II

A

C terminal domain

is rich in serine and is phosphorylated by TFIIH which can allow it to be uncoupled form TFs and begin transcription

57
Q

mRNA structure

A

encode a specific polypeptide

found in cytoplasm

attached to ribosomes

contain noncoding segments (Untranlated UTR = untranslated region)

eukaryotic mRNAs are modified
= 5’ methyl guanosine cap
= 3’ poly A tail

58
Q

Discovery of split genes

A

proposed that hnRNA =heterogenous RNA was processeed to form mRNA

discovered that mRTTNA is transcribed form segmetns of DNA

Discovered intervening sequences in adenovirus genome = introns

R-loop formation experiments used to locate intervening sequences

59
Q

U3 snoRNA

A

binds to the 5’ terminus and helps to catalyze the removal of 5’ end of transcript

60
Q

Box H/ACA snoRNA

A

conversion of uridine to pseudoeuridine

align themselve and form a hairpin opposite of the nucleotide to be modified

61
Q

hnRNA

A

nacent RNA from DNA transcription
=primary RNA transcript

done associated with ribosomes, ribosomes only associated with mature RNA =mRNA

hnRNA is much longer than mRNA and is extremely variable in size.
-> this is opposed to the average size of mRNA trancscripts ~2kb

62
Q

Restriction map changes

A

allows us to tell if RNA is modified

smaller transcripts = modifications

have to look at cDNA because you can use restriciton enzymes on RNA

63
Q

visualizing introns

r-loop formaiton experiments

A

Displaced single stranded DNA implies mRNA exon. Sense strand binds and displaced antisense-template strand of DNA.

Displaced dsDNA implies introns have been removed. Thus, there is no complimentary strand for the mRNA to displace so the DNA bulges out and forms a loop.

64
Q

TIming of mRNA transcript processing

A

co-transcriptionally

Pre-mRNA transcripts are processed as they are synthesized

65
Q

mRNA modificaton

A

Capping and polyadenylation

For capping, the removal of the last of the three phosphates on the 5’ end by RNA triphosphatase is performed first. Then, a guanine is added on its 5’ end by guanylyltransferse by a tri-phosphate bridge. The 2’ positon of guanine is then methylated by RNA methyltranserase
=Methylguanosine cap

For polyadenylation, the 3’ end is first cleaved, and then Poly(A) polymerase can add adenosines redidues via non-template addition for about 250 residues.

66
Q

intron types

A

Group 1

Group 2

Spliceosomal intron

67
Q

Group 1 introns

A

self-splicing introns first discovered in tetrahymena

these form complex sencondary structures

68
Q

Group 2 introns

A

self splicing introns

found in fungal mitochondria and plant chloroplasts

use a lariate intermediate for splicing

also have that branch point adenine
-> performs a nucleophilic attack via its 3’ hydroxyl towards the 5’ end of the intron. This makes the lariet, which then will perform a secondary nucleophilic attack on the 3’ splice site.

Ribonuclease activity

69
Q

Spliceosomal introns

A

found in animal cells

use a lariate intermediate + nuclear snRNAs

U1 snRNP attaches at the 5’ branch site (btwn exon and intron). U2 is recruited by U2AF, and attaches at the adenine branch site.

U1 is displaced by U6 (which has ribozyme activity), and U4 dissociated from the U4/5/6 complex. Together U6 and U5 have catalytic helicase activity.

cleavage of the 5’ splice site by U2/ U6 while U5 holds the exons in proximity.

Second cleavae reaction at the 3’ splice site frees intron, and exons are ligated together.

70
Q

Ribonuclease P

A

processign of tRNA precursors in bacteria

pTyr -> Tyr and 5’ Tyr

23 S rRNA of prokaryotic ribosomes

71
Q

Spliceosomal vs. self-splicing introns

A

conformationally and mechaninally similar.

Spliceosome evolved from a self splicing intron?

72
Q

CTD of RNApol 2

A

CTD serves as a scaffold (when is serines are phos) for splicing, caping and polyadenylation.

recall, modificaitons of RNA transcripts begin before transcription ends

73
Q

Origin of introns

A

see introns early vs introns late article on nexus

introns introduced by endosymbionts

introns became self splicing

exons (catalytic portions) became snRNA genes

introns become variable in size

74
Q

Advantages of introns

A

alternative splicing adds diversity to genes

snoRNAs encoded in ribosomal protien introns

Exon shuffling

  • > introms are potential recombinations sites = genetic varation
  • > recombination increases b/c more DNA exists
  • > Better shuffling
75
Q

Alternative splicing

A

depends on snRNA avalible in the tissue

exon skipping/ inclusion

alternative 3’ spice sites

alternative 5’ splice sites

mutally exclusive exons

intron retention (intron is left in, can occur in the intron is in the reading frame)

76
Q

PLC and exon shuffling

A

PLC is a parts bin

exons code for individual protien domains, and PLC is compled of components of four distinct proteins

77
Q

RNA interference

A

double stranded RNA sequences capable of destructon of select mRNAs
-> recoignize mRNA with complementary sequence

may be a primitive immune system

Double stranded RNA cleaved into small interfering RNAs (siRNA) by DICER enz.

antisense strand incorperated into protein complex RISC

leads to destruction of complementary mRNA by RNAi

See slide 107????

78
Q

Process of siRNA

A

dsRNA synthesized

DIcer enzyme cleaves dsRNA (chops up with little overhangs ->dsRNA fragments)

This is incorperated into RISC complex associates

RISC complex associates and unwinds RNA in ssRNA (antisense to target mRNA)

siRNA binds to mRNA target

mRNA cleaved (endonuclases avtivty)

79
Q

micro RNAs (miRNA)

A

small RNA sequence complementary to 3’ UTR of specific mRNA (first discovered in C. elegans)
-> sequence is highly conserved, miRNAs conserved btwn divergent organsims

synthesized at specific times during development

  • > may turn genes on and off
  • > translational inhibitors (instead of degredation, they inhibit ribosomal association)
80
Q

process of miRNA

A

single stranded RNA folds back on itself

cleaved by dicer enzyme

RISC complex associates

miRNA binds to mRNA target

block translation

81
Q

role of miRNAs

A

developmental programming

patterning of nervous system

control of cell proliferation and cell death

cell differentiation

82
Q

Lin-4

A

in 1993 it was discovered that C. elegans lacking lin-4 gene was unable to develop normally

lin-4 encodes small RNA complementary to 3’ UTR of mRNA encoding the protien LIN-14

lin-4 mutants possess high level of LIN-14 protien

83
Q

Let-7

A

highly conserved

found in both worms and humans

let-7 mutant animals die by bursting through the vulva at the L4 to adult moult

84
Q

siRNAs vs miRNAs

A

siRNAs derived from double stranded product of virus of synthetic dsRNA

miRNAs encoded by genomic region

miRNAs target specific mRNA transcripts

miRNAs primary role is to regulate gene expression

85
Q

si-RNA from run on gene transcription

A

si can be produced in vivo when run-on transcription occurs

extra mRNA transcripts can hybridize to form dsRNA

86
Q

piwi RNA

A

expressed in germ cells

suppress movement of transposable elements

associate with PIWI protiens

required for successful gamete formaiton
-> transposible elements SHOULD NOT be allowed to be active in germline cells

Deletion of PIWI protiens leads to failure in gamate formaiton

87
Q

CRISPER

A

found in bacteria, clustered repeats are remnants of bacteriophage genomes

CRISPER RNA transcript cut into smaller guide sequences

associate with cas9 protein
-> targett and cleave DNA with homology to guide RNA (primitive immune system)

can use to edit genes

88
Q

transcriptome

A

at least 2/3 of the mouse and human genome is transcribed

this is way more than would be expected, since lots of it is non-coding

transcripts overalap and originate from both sense and antisense strands

debate between wheiter they are junk or functional transcripts

89
Q

junk transcripts

A

loss of regions coding for transcripts does not seem to affect development

90
Q

functional transcripts

A

have reproducible patterns of tissue specific distribution

91
Q

Deciperhign the code of DNA/RNA

A

nirenberg and philip leder developed a technique using ribosome-bound transfer RNAs (tRNAs)

synthesized short 3 nucleotide mRNAs

incubated with ribosomes and labeled charged tRNAs

identified with tRNA/ aa bound to syntheic mRNA

92
Q

third position degeneracy

A

tRNA wobble

93
Q

Purpose of clustering codons for AA

A

single base mutation will not always cause the change of codon (synonymous mutation)

nonsynonymoys mutations change AA coding

excess of nonsynonymoys to synonymous mutations suggests a selective advantage

similar AA clustered together in chart

94
Q

three phases of translation

A

initiation

elongation

terminaiton

95
Q

Translation initiation

A

ribosome attaches at initiation codon (AUG), this helps to establish a readign frame

Step 1 = small ribosomal subunit associated with initiation codon, aligned by -25 shine dalgarno sequence GGAGGA on mRNA

96
Q

step 1 of prokaryotic translation initiation

A

this is the process of bringing small subunit to initiation codon

IF2: required fo rthe attachment of the first aminoacyl-tRNA

IF3: prevents large subunit (50s) from joining. Facilitates entry of the intial aa-tRNA

IF1: facilitates attachemnt of 30s subunit to mRNA and prevents aa-tRNA from entering wrong area

97
Q

step 2 of prokaryotic translation initiation

A

bringing first aa-tRNA into the ribosome

enters P site and binds to AUG codon and IF2 initiation factor

IF3 and IF1 releases

98
Q

step 3 of prokaryotic translation initiation

A

assemblind the comple initiation complex

large subunit joins the complex and GTP bound to IF2 is hydrolyzed

99
Q

Translation initiation in in eukaryotes

A

eIF2-GTP
=> associates with initiator tRNA

eIF4G
=> links 5’ cap and the poly A tail

eIF4E
=> binds to the 5’ cap

eIF4A
=> removes double stranded regions

100
Q

step 1 of prokaryotic translation elongation

A

aminoacyl-tRNA selection

aminoacyl tRNA enters the A site

101
Q

step 2 of prokaryotic translation elongation

A

peptide bond formaiton

peptidyl transferase activity in large subunit

amino group of aa-tRNA reacts with carbonyl group of P site

102
Q

step 3 of prokaryotic translation elongation

A

translocation

deacylated tRNA moves to E site

binding of EF-G and hydrolysis of GTP results in translocation of ribosome

103
Q

step 4 of prokaryotic translation elongation

A

releasing the deacylated tRNA

104
Q

Ribosome oscilatates between two states during the process of elongation

A

hybrid stats of transslocation observed by cryo-microscopy

tRNA anticodons still reside in A and P sites of small subunit while acceptor ends move to P and E sites (A/P and P/E)

EF-G stabilizes ratcheted state and prevents movement back of tRNAs back to A/A and P/P conformation
GTPhydrolysis causes conformational change that moves mRNA and tRNAs to E/E and P/P sites

105
Q

Translation termination

A

termination codons
=> UUA, UAG, UGA

Requires release factors

in prokaryotes, the release factors are:

  • > RF1 recognizes UAA and UAG
  • > RF2 recognizes UAA and UGA
  • > RF3 not codon specific

in eukaryotes:
-> eRF1 and eRF3 combine and recognize all termination codons

106
Q

mRNA survaillance

A

looks for mRNA with premature stop codons

nonsense mutations detected by specific process
=> aka nonsense mediated decay pathway

exon-junction complex normally displaced by advancing ribosomes
=> these complexes remain on transcripts with premature stop codons since they will not be knocked off my RNA polymerase

(ribosome reaches stop codon and falls off before it reachs the EJC protiens complex)

107
Q

Polyribosomes

A

more than one ribosome associated with a transcript

this helps to increase the rate of protien synthesis

Mol. Cell Bio (6 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions