Cell Bio Chapter 7

Front 1

Not all is transcribed. non coding (Junk) is just as important. The polymorphisms are in the noncoding regions. Non code shows where protein goes etc and can be lost in disease.

Back 1

polymorphisms

Front 2

Why could gene A make more DNA than gene B?

Back 2

The coding regions

Front 3

RNA helix has diff geometry and has a hole down the middle and is ______ than DNA.

Back 3

Narrower

Front 4

The RNA backbone has ribose and the 2 prime carbon with hydroxyl group which gives it . A-U has two hydrogen bonds.

Back 4

its diff shape

Front 5

What can cause nonconventional binding?

Back 5

RNA can form hairpin, and single stranded loop

Front 6

Loss of function and gain of function for protein: genetically you can manipulate the protein. Manipulate genes for knock out, using _______ to silence genes.

Back 6

mRNA

Front 7

RNA chain is displaced does not remain __________ to DNA. Only ____________ is transcribed : RNA are single stranded

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hydrogen-bonded

one strand

Front 8

complementary base pairing happens during?

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transcription

Front 9

Many RNA copies can be made from ______ gene in short time.Average gene of ______ nucleotides ~ 50 sec

Back 9

same

1500

Front 10

Transcripts: fine threads (rRNA) : used as components ofRibosomes they do not?? The goal is to make?

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translate to proteins.

ribosomes

Front 11

RNA: some will make proteins and some will be _______

Back 11

regulators

Front 12

tRNA:

Back 12

Connects mRNA and the amino acids used to make the protein

orm adaptors that select a.a. and hold them in place on ribosomes for incorporation into proteins

Front 13

rRNA

Back 13

rRNA form ribosomes on which mRNA is translated

form the core of the ribosomes structure. (Ribosome:structure used to form RNA)

catalyzes protein synthesis.

Front 14

mRNA

Back 14

codes for proteins

Front 15

miRNA

Back 15

regulates gene expression

Front 16

Other coding RNA's

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RNA splicing, telomere maintenance, gene regulation

Front 17

Once transcription begins

Back 17

sigma factor is released.

Front 18

Chain elongation continues until .

Back 18

polymeraseencounters a termination signal in DNA

Front 19

Enzyme halts and releases bothRNA polymerase then

Back 19

DNA template andnewly made mRNA.

re-associates with sigma factor

Front 20

RNA polymerase contains called sigma factor that

Back 20

recognizes the promoter on DNA.

Front 21

Signals in sequence of gene tells

Back 21

RNA polymerase where to start and stop transcription

Front 22

Promoter ________________. _____________ binds and recognizes start sequence. Polymerase clamps and starts copying it, and when it senses the stop signal it stops. The process uses a______________protein. The cofactor is the sigma factor and it recognize_______________. The polymerase finds the sigma factor. When transcription starts the cofacter comes off and it will be __________________

Back 22

regulates gene expression

Polymerase

integral (cofactor)

s where the promoter is

recycled and used for another time.

Front 23

Promoters and terminators have specific nucleotide sequencesthat are recognized by

Back 23

RNA polymerase

Front 24

Start site is first nucleotide transcribed

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designated +1

Front 25

________________ orients the polymerase and determines direction of transcription.

Back 25

Asymmetry of promotor

Front 26

All bacterial promoters contain DNA sequences at

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-10 and -35

Front 27

DNA is double stranded: promoter could direct synthesis of However promoter is asymmetrical and binds

Back 27

2 different RNA transcript one left to right & other rightto left.

polymerase in only one orientation.

Front 28

Once positioned, RNA polymerase has only one choice to transcript appropriate DNA strand only in

Back 28

5’ to 3’ direction

Front 29

bacteria have ___ RNA polymerase.Eukaryotic cells have ____ RNA polymerase

Back 29

one, three

Front 30

RNA polymerase 1

Back 30

most rRNA genes

Front 31

RNA polymerase 2

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all protein coding genes, noncoding RNA (splicesomes), miRNA genes

Front 32

RNA polymerase 3

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tRNA (not coding), 5s rRNA genes, genes for other small RNAs

Front 33

TATA box is recognized by _____. The sequence promotes the binding of the next transcription factor ______.

Back 33

TFIID

TFIID

Front 34

TFIIH TFIIH also phosphorylates

Back 34

pries apart the double helix at transcription start point using energy of ATP hydrolysis exposing template strand.

RNA polymerase II to allowtranscription: releases enzymes from transcription factors.

Front 35

Site of phosphorylation is a

Back 35

long polypeptide ‘tail’ that extends from polymerase molecule.

Front 36

Once transcription begins most general factors are released from

_____

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DNA

Front 37

TATA-binding protein (TBP)

Back 37

binds to TATA box sequence and distorts the DNA

Front 38

TBP Sits on top and attaches to TATA to change

Back 38

the DNA structure and then will attract other transcription factors when unwound.

Front 39

TBP is subunit of

Back 39

TFIID that recognizes & binds TATA box sequence (letters).

Front 40

Unique DNA bending caused by TBP

Back 40

two kinks in double helix separated by unwound DNA helps attract other transcription factors.

Front 41

TBP is a

Back 41

single polypeptide chain folded into 2 similar domains (blue & green). Sits on top of DNA helix like saddle

Front 42

The initiation of transcription is the most common way organisms

Back 42

control gene expression.

Front 43

Eukaryotic mRNA is processed in the

Back 43

nucleus

Front 44

Eukaryotic RNAs must be processed in the _________ and exported to ________

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nucleus, cytoplasm

Front 45

Transcription occurs in ________, translation occurs in _________. This export of RNA occurs via ________________.

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nucleus, cytoplasm, pores in the nuclear envelope

Front 46

Prior to nuclear export, _________________.

Back 46

RNA processing occurs

Occurs as RNA is being made. Synthesizing RNA and proofreads at same time. (not in bacteria)

Front 47

RNA processing occurs as _______________, it is processed. The tail is phosphorylated.Machinery sits on the “tail” of the eukaryotic _________________. There are variations, it is not conservedDifferent types of processing occurs depending of what type of RNA is being made.

Back 47

RNA is being made

RNA polymerase

Front 48

Eukaryotic mRNA processing

Back 48

Involves adding 5’-caps and 3’-polyadenylation tails (poly-A tails) and splicing.

Front 49

5’-caps and poly-A tails do?

Back 49

Increase stability of RNA.Identifies the molecule as mRNA.Marks the mRNA as being complete.

Front 50

Usually gets trimmed back first before few hundred “a” added.

Back 50

Poly A tail

Front 51

Phosphorylation of RNA polymerase II allows

Back 51

RNA processing proteins to assemble on its tail

Front 52

Polymerase transcribes

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DNA into RNA.

Front 53

Polymerase also carries

Back 53

RNA-processing proteins that act on newly formed RNA.

Front 54

Proteins bind to RNA polymerase tail when

Back 54

it is phosphorylated late in the process oftranscription initiation.

Front 55

Capping, polyadenylation, and splicingare

Back 55

modification made to RNA during thisprocess.

Front 56

mRNA are modified by _________. Once it is methylated_____________.

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capping and polyadenylation

It is viewed as processed RNA

Front 57

Ends modified by addition of cap at _________ & cleavageof _______________ & addition of _________________.The unusual 5’ to 5’ linkage of 7-methyl G to remainderof RNA.In eukaryotes cap contain additional modification2’-hydroxyl group on 2nd ribose sugar is methylated.

Back 57

5’ end, primary transcript, poly-A tail at 3’ end

Front 58

In Eukaryotes, Protein-Coding Genes Are Interrupted by

Back 58

Noncoding Sequences Called Introns

Front 59

Eukaryotic mRNA processing also involves

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RNA splicing

Front 60

Eukaryotic genes are often interrupted by _____________

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noncoding sequences (introns). So they are spliced out

Front 61

Exons-Introns-

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(coding) expressed sequences

(noncoding) intervening/nonexpressed sequences

Front 62

Bacterial gene consists of Eukaryotic genes (Exons) are

Back 62

single stretch of uninterrupted nucleotide sequence that encodes the a.a. sequence of a protein.

are interrupted by noncoding sequences (Introns).Exons are shorter; Introns are longer : can be up to 10,000 nucleotides.Some no introns, others few, most have many.

Front 63

β-globin gene encodes Factor VIII gene encodes

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one of the subunits of oxygen carrying protein hemoglobin : contains 3 exons.

a protein Factor VIII that functions in clotting pathway : contains 26 exons.

Front 64

Introns Are Removed From _____________ by RNA Splicing

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pre-mRNAs

Front 65

Only nucleotides shown are required to remove an intron. These sequences are recognized by ___________________________ which cleave RNA intron-exon borders and covalently link exon sequence together.

Back 65

small nuclear ribonucleoproteins (snRNPs)

Front 66

A lariat structure forms and the hydroxyl group

Back 66

will bind to 5 prime side

Front 67

An intron forms a

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branched structure during splicing

Front 68

1. Branch point adenine in intron

2. The cut 5’ end of intron becomes covalently linked

2. The cut 5’ end of intron becomes covalently linked

3. 3’-OH end of exon sequence then

4. Forms continuous coding sequence & releases introns in form of

Back 68

1. attacks the 5’ splice site and cuts sugar-phosphate backbone of RNA.

2: to 2’-OH group of ribose of A to form branched structure.

3. reacts with start of next exon sequence, joining the two exons together.

4.lariat structure which is degraded.

Front 69

snRNPs come together and assemble to the site that shows

THe 5 core snRNPs are _____________

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the beginning and end of splicing.

U1, U2, U4, U5 and U6.

Front 70

Alternative splicing leads to

RNA splicing enables

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greater protein diversity from single gene.Can produce distinct proteins.

increases coding potential of their genomes.

Front 71

Alternative splicing, so ________________

The alternative splicing comes from ______________________ allowing more diversity of proteins for survivability. Creates different functions.

ex:

Back 71

not every RNA is spliced the same way.

alpha tropomyosin gene

Coiled-coil Muscle contraction

Front 72

The Nuclear Pore Complex

Back 72

recognizes and exports only completed mRNAs

Front 73

Nuclear Pore Complex: Transport out of nucleus is _________Nuclear pore complex recognizes _______________ only.Must be bound to appropriate proteins: signal correct.Includes ______________________________

Back 73

highly selective.

completed mRNAs

polyA binding proteins, cap-binding complex, completed RNA splice protein (EJC: exon junction complex).

Front 74

(Nuclear Pore complex) Waste mRNAs digested by _________ and then reused for transcription.Sequences in the __________ help determine how much protein synthesized. Stability of mRNA:________mRNA with long lifetimes (3’UTR) high levels of proteins:________.

Back 74

RNAse, 3’-UTR, 3’-UTR, β-globin

Front 75

NPC: mRNA binds to proteins __________ to leave the nucleus

Back 75

Poly A tail

Front 76

Eventually all mRNA molecules are degraded into nucleotides via ________ in the ________. Sequences in the _________ help determine stability.

Back 76

RNases, cytosol, 3’-UTR

Front 77

The Earliest Cells May Have Had ________ in Their Genes

Back 77

Introns

Front 78

RNA linear polymer of 4 different nucleotides: so how many possibilities? combinations of three nucleotides: ex

ex

Back 78

64, AAA, AUA, AUG etc.

Front 79

tRNA molecules are adaptors that link _________

_________

Back 79

a.a. to codons

Front 80

Anticodon recognizes __________________ to start ______________

Back 80

complementary strand, replication

Front 81

More than________ for many AAs.Some tRNAs recognize > 1 codon, this is called theUnpaired nucleotides: ____________Anticodon bind complementary codon in __________

Back 81

1 tRNA, wobble phenomenon, anticodon, mRNA

Front 82

Genetic code is translated by means

Back 82

of 2 adaptors that act on one another

Front 83

Aminoacyl-tRNA synthetase

Back 83

couples a particular a.a. to its corresponding tRNA : Charging.

Front 84

Anticodon of tRNA forms

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base pair with codon on mRNA: Charging.

Front 85

There are 20 synthetases that

Back 85

catalyze amino acid to tRNA

Front 86

Synthtase catalyzed reactions attach _________ uses ATP later used to link _______________

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a.a. to tRNA , a.a. to polypeptide chain.

Front 87

the mRNA message is decoded by

Back 87

ribosomes

Front 88

RNA message is decoded on

Back 88

Ribosomes

Front 89

Protein is synthesized in the

Back 89

ER

Front 90

80 ribosomal proteins; several RNA molecules (ribosomal RNA) form ribosome.Eukaryotic and prokaryotic ribosome are very different.___________________ form ribosome.Two subunits come together on ____________, near ________ to begin protein synthesis.As mRNA moves through it, ribosome translates nucleotide sequence into a.a. sequence one codon at a time using _________

Back 90

One large and one small subunit: together form ribosome.

mRNA molecule, 5’end, tRNAs as adaptors.

Front 91

A ribosome is a large complex of _______ and more than ______ proteins

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4 RNAs, 80

Front 92

Each ribosome has __ binding site for mRNA and ______ binding sites for tRNA

Back 92

one, three (EPA)