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Biology 121 > Sheet 12-Test 4 > Flashcards

Sheet 12-Test 4 Flashcards

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1
Q

How do we know that DNA specifies the primary structure of a protein?

A

Defective instructions cause insertion of wrong amino acids (s) in protein that the gene codes for.

–incorrect genes=incorrect amino acids=incorrect gene

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2
Q

What is “in vitro trnslation” and why is it useful

A

in-lab production of protein used to “crack” genetic code

  • -which codon codes for which amino acid
    ex. AUG for methionine
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3
Q

why do we know there must be an intermediate between DNA and protein synthesis?

A

can make protein without DNA

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4
Q

what is the central dogma?

A

flow of genetic information

DNA–> Transcription–>RNA–> translation–> protein

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5
Q

what is gene expression and what are the two stages of gene expressions?

A

Gene expressionL the use of genetic information to produce a protein
involves:
1) transcription
2) translation

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6
Q

what are transcription and translation?

A

Transcription: making an RNA copy of a portion of DNA (portion=gene)

Translation: using an RNA copy to make a protein

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7
Q

what are ribosomes and what do they do?

A

organelles (complex) that makes proteins

protein= large chain of amino acids assembled in a certain order

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8
Q

what are the 3 roles of RNA in protein synthesis?

A

rRNA– component of ribosome, ribosomal RNA

mRNA– Messenger RNA, copy of a gene takes message to ribosome; message used to make a prtein

tRNA– transfer RNA, transports an amino acid to the ribosome

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9
Q

what are the sequences of the DNA and mRNA strands make from the template 5’AGCTTGACTA-3’

A

DNA 3’-TCGAACTGAT-5=’

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10
Q

what is a promoter and what is a terminator

A

Promoter– forms a recognition and binding site for RNA polymerase; binding of RNA polymerase to promoter is first step of transcription

Terminator– signal to RNA polymerase to end transcription

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11
Q

what is a transcription factor

A

proteins that bind to regulatory sequences and tell RNA polymerase where to start transcription

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12
Q

what are the 4 main differences between DNA replication and transcription?

A

1) differnt substrates: nucleo tides differ
- -sugars: ribose vs deoxyribose
- -bases: U vs T
- -replication requires DNA nucleotides transcription requires RNA nucleotides
2) only transcribe one strand replicate both strands

3) must be told when to stop transcription
4) transcription starts from scratch and starts in a region thats not important

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13
Q

What are the 3 post transcriptional modifications to eukaryotic mRNA?

A
  1. Cap 5’ end with 7 methyl G (identifies it as mRNA)
  2. Splice–remove introns and splice together exons (intron–intrusion, get rid of)
  3. Polyadeoylation– 3’ end replaced with ~250 adenines (identifies it as mRNA)
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14
Q

why do all eukaryotic mRNA molecules have a 5’ methyl G cap?

A

identifies molecules as mRNA

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15
Q

why are most eukaryotic mRNA’s much shorter than the gene which encodes them?

A

take out introns and splice together exons.

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16
Q

What are introns and exons?

A

Intron– section of mRNA that is removed from hn RNA

Exon– segments of mRNA spliced together as actual coding sequence.

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17
Q

what is spliceosome and what does it do?

A

complex that takes out introns and splices together exons.

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18
Q

what is polyadenylation and what functions does it serve?

A

polyadenylation– replace 3’ end of mRNA with 250 adenines; identifies it as mRNA and prevents degradation
–regulates rate of translation

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19
Q

what is a frame shift mutation?

A

add or remove 1 or 2 bases from DNA

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20
Q

what is a codon?

A

sequence of 3 bases on mRNA that corresponds to one amino acid

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21
Q

why do we know that genetic code consists of nucleotide triplets with no punctuation?

A

adding 1 or 2 bases affects entire message

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22
Q

why does in vitro translation of 5’-CCCCCCCCCCC-3’ give a protein that is all prolines?

A

CCC is codon for proline

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23
Q

What is a triplet binding assay, and how was it used?

A
  • -mixture of 3 bases of RNA
  • -add charged tRNAs and ribosomes and see what amino acids are used.
  • -used to crack genetic code
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24
Q

why do we say that the genetic code is degenerate by unambigous?

A
  • -each codon stands for one amino acid

- -there is more than one codon for some amino acids

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25
Q

what is tRNA and what does it do?

A
  • -transfer RNA
  • -translates nucleotide sequences into amino acid sequences
  • -transports an amino acid to the ribosome
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26
Q

what is an anticodon, and what is the sequence of the anticodon which binds to the codon 5’-GCA-3’

A

3 bases on tRNA corresponing to codon on mRNA
Codon: 5’-GCA-3’
anticodon: 3’-GCA-5’
Answer: 5’-UGC-3’

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27
Q

which proteins actually read the genetic code?

A

activating enzymes that attach appropriate amino acid to tRNA

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28
Q

how can a single activating enzyme add serine to all serine tRNAs given that there are 6 serine codons?

A

us anticodon, structure of D loop and variable arms

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29
Q

how do cells translate the genetic code?

A
  • -Ribosome binds to 5’ end of mRNA and scans for Shine-dalgerno sequence (prok) or Kozak sequence (euk) next AUF is start
  • -Formation of initiation complex: fMet positioned at P site of ribosome, corresponding to AUG start of mRNA on small ribosomal subunit
  • -Large ribosomal subunit binds, forming E,P, and A sites
  • -Ribosome reads next codon; tRNA brinds in secured amino acid which binds to first
  • -Fmet in prokaryotes
  • -Met in eukaryotes
  • -Continues reading message and building protine= elongation
  • -Terminate at stop codon
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30
Q

what are the 3 stages of protein synthesis?

A

1) initiation
2) elongation
3) termination

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31
Q

how do cells know where to start translating an mRNA?

A
  • -scan for shine dalgerno sequence–prokaryotes
  • -scan for Kozak sequence–eukaryotes
  • -once found…next AUG is “start”

**you can have AUG before this sequence but without shine or kozak it is not recognized

32
Q

how do cells know where to stop translating mRNA?

A

stop codon is recognized by release factors

33
Q

how do cells ensure that the correct amino acid is inserted at each position?

A

anti codon must be complementary to codon

34
Q

why do cells need a special initiator tRNA?

A
  • -unlike other tRNA’s it occupies P site
  • -all other tRNA’s enter A site
  • -initiator tRNA is P site, ribosome things theres a growing protein on there
  • -can only add amino acids to peptide in the P site
35
Q

what is translocation?

A

rearrangements of chromosomes between non-homologs chromosomes.

36
Q

why doesnt that large ribosomal subunit attach until after the initiator tRNA is bound to the start codon?

A

Dont want to start until start codon is in position

37
Q

what are elongation factors?

A

escort charged tRNAs into A site

–ribosome catalyzes bind between amino acid in A site and growing peptide in P site

38
Q

what is a nonsense codon? what is a release factor

A

release factor– stop, bind to nonsense codon in A site, release peptide from P site

Nonsense codon– does not code for an amino acid or tRNA, recognized by release factors signals ‘stop’

39
Q

what are the main differences between protein synthesis in prokaryotes and eukaryotes?

A
  1. Eukaryotes ribosomes are longer and use different initiation and elongation factors as well as termination factors.
  2. DNA is in nucleus of Euk; Euk has complicated RNA processing
    - —-no RNA processing in prokaryotes
  3. Prokaryotes can start translating before transcription is finished
    - ——in eukaryotes transcription and translation are completely separate.
  4. Prokaryotes have polycistronic mRNA’s with more than one protein/mRNA
    - —–eukaryotes have 1 protein/ mRNA
40
Q

why dont antibiotics such as chloramphenicol which poison bacterial protein synthesis harm human?

A

–protein synthesis in prokaryotes is much different from protein synthesis in eukaryotes

41
Q

how can proteins bind to a specific DNA sequence without opening the double helix?

A
  • -proteins bind to speficif DNA sequences without opening helix because each base pair forms unique pattern in major and minor grooves
  • –proteins move along outside of DNA until they find correct pattern
42
Q

what is the goal of regulating gene expression?

A
  • -control amount of activity of proteins
  • -which proteins make what
  • -how much of each make
43
Q

what is the most important step in regulation gene expression, and why is it the most important?

A
  • -control transcription

- –dont copy a gene until you need its product which is a protein

44
Q

what is the primary purpose of gene regulation in prokaryotes?

A

Prokaryotes:

  • -exploit transient resources
  • -need correct proteins to grow on avaible food source
  • -regulates gene expression to fit enviroment
  • -general strategy is to keep all genes waiting in reserve
45
Q

what is an operon?

A
  • -gene for all enzymes in a pathway

- -transcribed as a single unit, producting a single mRNA

46
Q

what are promoters, operators, repressors?

A

Promotor– part of operon to which RNA polymerase binds

  • –located on first part of gene
  • –promotes transcription by allowing RNA polymerase to bind

Operator– part of promotor

  • –regulatory site
  • – if repressor binds to operator, keeps RNA polermerase off

Repressor
– protein that binds to operatory (within promotor) and prevents binding of RNA polymerase.

47
Q

what is the TRP operon and how is it regulated?

A

its used to make tryptophon “on” only when there is NO tryptophon in enviroment

YES: TRP in enviroment– TRP lands on repressor, repressor blocks and TRP repressor complex binds to operator–> no transcription because RNA polymerase cannot bind

No: TRP not in enviroment–No TRP on repressor so it is off the operator–> transcription occurs because RNA polymerase can bind.

48
Q

What is CAP protein, and how is it regulated?

A

global regulator and catabolite activator protein–it senses if glucose is present

[cAMP] increases then [glucose] is low
cAMP binds to CAP and changes its shape
–CAP binds DNA near promotors; promotors activated, genes are transcribed other sugars are metabolized.

49
Q

What is the LAC operon and how is it regulated?

A

uses combination of on and off swithes
transcription occurs if there is (1) no glucose and (2) if lactose is present.–LAC repressor turns transcription off
–CAP protein and cAMP turns transcription on

In order to transcribe genes:
1) no glucose– increases cAMP;cAMP binds to CAP, CAP changes shape and binds to DNA; activates transcription

2) yes lactose– lactose binds repressor; repressor off operator RNA polymerase can proceed to transcribe

–only bacteria

50
Q

what happens if the lac operator is mutated so that the repressor cant bind?

A

will have transcription because repressor cant bind as long as [glucose] is low

51
Q

what are the main reasons that projaryotes and eukaryotes regulate gene expression differenetly?

A

Eukaryotes use activation, not repression–because theres not enough room in nucleus to make all genes available all the time; also need an initiation complex

repressors arent used to regulate eukaryotes genes since gens are off unless activated not enough room in nucleus to make all genes avabile at once.

52
Q

what is ‘chromatin remodeling’ and why is it necesary?

A

large complexes of proteins that modify histones and DNA and also change chromatin structure itself.
Functions–make DNA more accessible to regulatory proteins this affects gene expression.

53
Q

why are eukaryotic promotors larger than eukaryotic promotors?

A

.

54
Q

what are the two parts of a eukaryotic promotor?

A

.

55
Q

what is the core promoter and what is the TATAA box?

A

binding site for TATA binding protein

The TATA box is a DNA sequence that is the primary promotor

56
Q

what are basal factors and what is their function?

A

basal factors bind to core promotor and RNA polymerase 2 binds to basal factors

57
Q

what are enhancers?

A

the binding site of the specific transcription factors
–DNA bends to form a loop so the enhancer can be positioned closer to promotor.

–increase rate of transcription

58
Q

what are transriptional activators, co activators, and what is mediator?

A

Transcriptinoal activators and coactivators act by binding the transcription factor and then binding to another part of the transcription apparatys.
mediator–

59
Q

what is the sequence of events in activating and transcribing a eukaryotic gene?

A

.

60
Q

what are seven post transctiptional mechanisms for regualting gene expression in eukaryotes?

A

.

61
Q

which controls over gene expression in eukaryotes are nuclear and which are cytoplasmic?

A

.

62
Q

what is alternative splicing and why is it important?

A

,

63
Q

gene expression includes which of the following processes?

A

transcription and translation

64
Q

the tRNA nucleotide sequence that pairs with the mRNA is called?

A

anticodon

65
Q

what is the sequence of the anticodon which binds to the mRNA codon 5’-CAU-3’

A

5’-AUG-‘3

66
Q

what do transcription, translation, and DNA replicatoin have in common?

A

all of the above

67
Q

why dont antibiotics which poison bacterial protein synthesis affect humans?

A

bacterial ribosomes and translation factors are different from eukaryotic ribosomes and translation factors.

68
Q

in eukaryotes, mRNA processing includes which of the following events?

A

capping the 5’ end and adding a poly A tail to the 3’ end

69
Q

how do regulatory proteins bind to specific DNA sequences?

A

by forming H-bonds with specific combination of H-bond donors and acceptors exposed in the the major groove by each base pair

70
Q

transcriptional control is exerted by means of

A

DNA sequences that are not transcribed

71
Q

how is the trp operon regulated?

A

trp operon is only transcribed if [trp] is low because trp repressor senses the [trp] and binds to the operator with [trp] is high

72
Q

what will happen if you mutate the trp repressor so that it can no longer bind ot DNA?

A

trp operon will be transcribed whenever [trp] is high.

73
Q

What are small interfering RNAs and what do they do?

A
  • -short strand of RNA complementary to a section of mRNA
  • -sticks to complementary RNA
  • -this double stranded RNA targets the RNA for destruction
74
Q

what are micro RNAs and what do they do?

A

bind some mRNA and block translation; has mismatched to target unlike small RNAs which are complementary to target RNA

75
Q

why is protein degradation important and how are proteins marked for destruction?

A
  • -undergo proteolytic cleavage and covalent modifications (ex. phosphorylation)
  • -lifespans of protein vary
  • -once their function is completed, need to remove them

Biology 121 (9 decks)

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