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CMB > EXAM 4 > Flashcards

EXAM 4 Flashcards

1
Q

3 stages of transcription

A
  1. Initiation
  2. Elongation
  3. Termination
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2
Q

Promoter region

A

TATA box, about -25 upstream.

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3
Q

RNAPII needs ________ to recognize promotor regions

A

General Transcription Factor (GTF) proteins

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4
Q

GTF has to assemble and recruit _______ to initialte transcription

A

DNA Polymerase II

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5
Q

Mediator complex

A

Increases rate of initiation and/or assembly of PIC (Pre Initiation Complex)

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6
Q

Pre-mRNA is

A

the initial RNA molecule synthesized during transcription. Must be converted to MATURE mRNA before translation

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7
Q

Three types of mRNA

A

18s
5.8s
20s

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8
Q

45s and 32s are __________ to 28s and 18s

A

precursors

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9
Q

the precursor hypothesis test

A
  1. incubate for short period, only 45s are radioactive
  2. Add actomyosin D to prevent synthesis of 45s
  3. continue to incubate
  4. 45s gradually dissapears, 32s, 28s, and 18s appear
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10
Q

What are heterogenous nuclear RNAs?

A

hnRNAs are primary transcripts from transcription process. long, found only in nucleus. Degraged after a very short time.
Precursors to mature RNA, become mRNA after processing.

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11
Q

mRNA structure:

A

5’cap | 5’ UTR | Coding region | 3’ UTR | Poly(A) tail

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12
Q

Processing of Eukaryotic mRNA 3 steps:

A
  1. Primary RNA transcripts become associated with ribonucleoproteins as they are synthesized
  2. During processing, an 5’ cap and a 3’ polyA tail are added.
  3. Introns are removed and exons connected by RNA splicing.
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13
Q

5’ cap purpose (3)

A
  1. Protects 5’ end from degradation by nucleases (provides stability)
  2. Assists in exporting mRNA from nucleus to cytoplasm.
  3. Initiates mRNA translation (binds to ribosome)
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14
Q

3’ end Polyadenylation

A

After transcription, mRNA is capped.
AAUAAA: recognition site for 3’ polyadenylation, endonucleases cleave downstream of AAUAAA.
Poly A polymerase adds around 250 adenosines to make polyA tail, begins 10-30 bp downstream of AAUAAA.

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15
Q

PolyA tail purpose (2)

A

Prevent degradation of 3’ end

Regulate mRNA transport to cytoplasm

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16
Q

Split genes

A

Genes with intervening sequences (introns). introns are spliced out, mature mRNA’s only consist of exons.

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17
Q

mRNAs transported from nucleus to cytoplasm by ______ via _____________

A

mRNP’s (mature ribonuclearproteins), nuclear pore channels

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18
Q

Genetic code is read from ________ end of mRNA, translation proceeds along mRNA in ___________ direction.

A

5’, 5’ to 3’

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19
Q

Start codon:

A

ATG = methionine (AUG in RNA)

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20
Q

Stop codons:

A

TAA
TAG
TGA

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21
Q

The coding strand, or ________, contains the start codon, as opposed to the template strand , or __________.

A

sense strand (ATG), antisense strand (TAC)

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22
Q

tRNA does what now?

A

Helps decode mRNA sequence into amino acid. Anticodons pair up with codons.

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23
Q

SYNONYMOUS MUTATION

A

Does not change the amino acid sequence (wobble effect).

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24
Q

NONSYNONYMOUS MUTATION

A

Causes an amino acid substitution

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25
Q

NONSENSE MUTATION

A

Creates a premature termination codon

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26
Q

FRAME SHIFT MUTATION

A

Alters the normal reading frame of the mRNA

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27
Q

tRNA structure

A

~73-93 nucleotides
amino acid attached to 3’ end
andticodon complements codon of mRNA
unusual bases

28
Q

Wobble hypothesis

A

nucleotide at the 5’ end of each anticodon is capable of pairing with more than 1 nucleotide at 3’ end (3rd position) of mRNA codon.

29
Q

How do amino acids bind with tRNA

A

by carboxyl group (COOH) that must be activated by specific aaRS (amino acly tRNA synthetase)

30
Q

Amino acid activation (2 steps)

A

Step 1: Specific aaRS bind to specific amino acid. Activation requires ATP.
Step 2: aminoacyl-AMP transferred to 3’ end (acceptor stem) of specific tRNA to form aminoacyl-tRNA (charged tRNA). Charged tRNA releases from aaRS and ready for translation.

31
Q

Ribosome is

A

ribozyme (RNA enzyme)

32
Q

3 binding sites for tRNA in a ribosome

A

A - aminoacyl/acceptor site (for aminoacyl/ charged tRNA in growing protein
P - Peptidyl site (for peptidyl tRNA carrying crowing protein
E- exit site (for decylated/discharged tRNA to be released from ribosome.

33
Q

Small subunit of ribosome binds to

A

AUG (initiation/start codon)

34
Q

Shine-Dalgarno sequence

A

5-10 nucleotides before AUG, complementary to 3’ end of 16S rRNA of small subunit

35
Q

Nonsense mutations destroyed by

A

nonsense-mediated deay (NMD)

36
Q

___ can be used to detect an inappropriate stop

A

EJC (exon-junctions complex)

37
Q

Process in cells that turn the information of genes into gen products (mRNAs, proteins)

A

Control of gene expression/Gene regulation

38
Q

What is an operon?

A

A unit of genomic DNA with a cluster of genes that regulate functionally related proteins. GENETIC REGULATORY SYSTEM

39
Q

Operator

A

next to promoter, binding site for repressor. on/off switch

40
Q

Repressor

A

binds to operator, prevents RNA pol from binding.

41
Q

lac operon: an __________ which is turned on in the ________

A

inducible operon, presence of lactose

42
Q

lactose induces synthesis of ___________

A

beta-galactosidase

43
Q

Absence of inducer (lactose)

A

In absence of lactose, repressor is bound to operator region, blocking RNA pol from transcribing structural genes.

44
Q

Presence of inducer (lactose)

A

In presence of lactose, lactose binds to repressor, changing its confirmation. The repressor unbinds from the operator, and RNA pol is able to transcribe structural genes that code for enzymes that help break lactose down into a usable form of sugar. NEGATIVE REGULATION

45
Q

3 conditions where differential gene expression is found:

A

Cells at different stages of embryonic development
Cells in different tissues
Cells that are exposed to different types of stimuli

46
Q

2 functional classes of Transcription Factors:

A

GTF: bind at core promotor sites in association with RNA polymerase (pre-initiation)

Sequence Specific TF: Bind to various regulatory sites of particular genes

47
Q

2 TF domains:

A

DNA binding domain

Activation domain

48
Q

Ubiquitin

A

Attach to protein to be destroyed, feed to proteasome

49
Q

Proteasome

A

carry out the degredation of proteins

50
Q

Proliferation

A

increase in cell number by growth and division

51
Q

Carcinoma

A

Hard cancer, begins in skin or tissues that line or cover internal organs. 90% of cancer

52
Q

Sarcoma

A

Soft cancer, bone, cartilage, fat, muscle, blood vessels, connective or supportive tissues (mesodermal origin, rare)

53
Q

Leukemia

A

Blood forming tissue - bone marrow (hemapoietic)

54
Q

Lymphoma and myeloma

A

cells of immune system

55
Q

Basic properties of cancer cells (4)

A
  1. Uncontrolled cell growth (ignore stop signals)
  2. Invasive: destroy normal tissues
  3. Immortal: senescence, telomere shortening
  4. Chromosomal abnormalities: aneuploidy
56
Q

Contact inhibition:

A

A feedback mechanism which keeps cells growing into a monolayer until in contact with other cells. Cancer cells lack contact inhibition

57
Q

EMT

A

Epithelial-mesenchymal transition. loss of cell adhesion, ability to migrate.

58
Q

2 main genes implicated in cancer:

A

Tumor suppressor genes (brakes) and oncogenes (gas)

59
Q

Tumor suppressor genes encode proteins that _______ and prevent malignant cells. Keeps cells from ________. Always ____ to restrain growth. TSG casues cancer when ____________

A

restrain, dividing, on, inactivated or turned off

60
Q

50% of cancers have a mutation in ______

A

p53 gene, codes for a TSG

61
Q

________ are genes that usually help cells grow. When mutated, become _________

A

PROTO-ONCO GENES, ONCOGENES

62
Q

Oncogenes cause cancer when they are _______

A

Activated or turned on.

63
Q

Two restriction enzyme ends:

A

Sticky

Blunt

64
Q

Most common restriction enzyme

A

EcoR I

65
Q

What is a plasmid?

A

Small accessory DNA in bacteria separate from chromosomal DNA. can replicate independently.

66
Q

Why is DNA possible?

A

Because all organisms share the same chemical structures in DNA

67
Q

in PCR you need (6)

A
  1. DNA template
  2. Polymerase (Taq)
  3. Forward and reverse primers
  4. Additional nucleotides (dNTPs)
  5. MgCl2 cofactor for Taq, and helps remove phosphorylated bonds.
  6. Heating and cooling, thermocycler

CMB (5 decks)

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