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MCAT Biochemistry > RNA and the Genetic Code > Flashcards

RNA and the Genetic Code Flashcards

Ch 7

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MCAT flashcards
1
Q

central dogma

A

states that DNA is transcribed to RNA, which is translated to protein

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2
Q

degenerate code

A

allows for multiple codons to encode for the same amino acid
-allows for mutations in DNA that do not always result in altered protein structure or function

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3
Q

initiation (start) codon

A

AUG

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4
Q

termination (stop) codon

A

UAA: U Are Annoying
UGA: U Go Away
UAG: U Are Gone

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5
Q

wobble

A

third base in the codon

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6
Q

what allows for mutations to occur without effects in the protein?

A

redundancy and wobble

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7
Q

point mutations can cause

A

they are often called expressed mutations:
nonsense mutations (truncation)
missense mutations

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8
Q

silent mutations

A

mutations with no effect on protein synthesis

these tend to be in mutations in the wobble position

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9
Q

nonsense mutations (truncation)

A

mutations that produce a premature stop codon

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10
Q

missense mutations

A

mutations that produce a codon that codes for a different amino acid

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11
Q

messenger (mRNA)

A

messenger of genetic information

  • carries message from DNA in the nucelus via transcription of the gene
  • travels into the cyptoplasm to be translated
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12
Q

DNA codes for

A

codes for proteins but cannot perform any of the important enzymatic reactions that proteins are responsible for in cells

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13
Q

where does the creation of the primary protein structure occur?

A

ribosomes

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14
Q

transfer RNA (tRNA)

A

responsible for converting the language of nucleic acids to the language of amino acids and peptides

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15
Q

ribosomal RNA (rRNA)

A

synthesized in the nucleolus, makes up ribosome
used during protein assembly in the cytoplasm
helps catalyze the formation of peptide bonds
important in splicing out its own introns within the nucleus

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16
Q

frameshift mutations

A

result from nucleotide addition or deletion, and change the reading frame of subsequent codons

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17
Q

RNA is similar to DNA except

A
  • substitution of a ribose sugar for deoxyribose
  • substitution of uracil for thymine
  • it is single stranded instead of double stranded
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18
Q

there are three types of RNA in transcription

A

transfer RNA
messenger RNA
ribosomal RNA

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19
Q

transcription

A

the creation of mRNA from a DNA template

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20
Q

RNA translation

A

changes the language from nucleotides to amino acids

it’s translating for us!

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21
Q

helicase

A

unwinds the DNA double helix

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22
Q

RNA polymerase II

A

binds to the TATA box within the promoter region of the gene
-25 base pairs upstream from first transcribed base
does nor require a primer to start generating a transcript

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23
Q

what is RNA synthesized by

A

a DNA-dependent RNA polymerase

locates genes in promotor regions

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24
Q

TATA box

A

high concentration of thymine and adenine bases

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25
Q

what do transcription factors help with

A

help the RNA polymerase locate and bind to its promoter region of the DNA
help establish where transcription will start

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26
Q

RNA polymerase I

A

located in the nucleolus and synthesizes rRNA

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27
Q

RNA polymerase II

A

located in the nucleus and synthesizes hnRNA (processed mRNA) and some small nuclear RNA (snRNA)

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28
Q

RNA polymerase III

A

located in the nucleus and synthesizes tRNA and some rRNA

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29
Q

hnRNA is synthesized from

A

heterogeneous nuclear RNA

the DNA template (antisense) strand

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30
Q

what is significant about hnRNA

A

mRNA is derived from hnRNA via posttransciptional modifications

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31
Q

post-transcriptional processing includes

A
  • intron/exon splicing
  • 5’ cap
  • 3- poly-A tail
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32
Q

what is significant about posstransciptional processing?

A

before the hnRNA can leave the nucleus and be translated into protein, it must undergo process to allow it to interact with the ribosome and survive the conditions of the cytoplasm
DNA - parents
hnRNA - child
the child must mature if he/she is to survive

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33
Q

mnemonic for introns and extrons

A

INtrons stay IN the nucleus

EXtrons will EXit the nucleus as part of the mRNA

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34
Q

intron/exon splicing in posttranscriptional processing

A
  • removes the noncoding sequences of the intron and the ligate coding sequences of the exon
  • splicing is done by snRNA and snRNPs in the spliceosome
  • introns are remove in a lariat structure
  • exons are ligated together
35
Q

5’cap in the posstranscriptional processing

A

a 7-methylguanylate triphosphate cap is added

  • protects the mRNA from degeneration in the cytoplasm
  • added during the transcription process and recognized by the ribosome as the binding site
36
Q

3’ Poly-A Tail in posttranscriptional processing

A

a polyadenosyl (poly-A) tail is added to the 3’ end

  • protects the message against rapid degradation
  • the “time bomb” for the mRNA transcript: the longer the poly-A tail, the more time the mRNA will be able to survive before being digested in the cytoplasm
37
Q

polycistronic genes

A

starting transcription in different sites within the gene leads to different gene products
-prokaryotic cells can increase the variability of gene products from one transcript

38
Q

alternative splicing

A

combining different exons in a modular fashion to acquire different gene products
-eukaryotic cells can increase variability of gene products

39
Q

tRNA does what

A

translates the codon into the correct amino acid

40
Q

what are the factories where translation (protein synthesis) occur?

A

ribosomes

41
Q

what are the three stages of translation?

A
  • initiation
  • elongation
  • termination
42
Q

initiation (in translation)

A

in prokaryotes, occurs when the 30s ribosome attaches to the Shine-Dalgarno sequence and scans for the AUG start codon
-lays down N-formlymethionine in the P site of the ribosome

43
Q

DNA to DNA term

A

replication

new DNA synthesized in 5’ to 3’ direction

44
Q

DNA to RNA term

A

transcription

new RNA synthesized in 5’ to 3’ direction

45
Q

RNA to protein

A

translation

mRNA read in 5’ to 3’ direction

46
Q

comparison of the prokaryotic ribosome to the eukaryotic ribosome

A

prokaryotic ribosome: 50S + 30S = 70S

eukaryotic ribosome: 60S + 40S = 80S

47
Q

when does initiation (in translation) happen in eukaryotes?

A

occurs when the 40S ribosome attaches to the 5’ cap and scans for a start codon
it lays down methionine in the p site of the chromosome

48
Q

elongation (in translation)

A

involves the addition of a new aminoacyl-tRNA into the A site of the ribosome and transfer of the growing polypeptide chain from the tRNA in the P site to the tRNA in the A site
-uncharge tRNA pauses in the E site before exiting the ribosome

49
Q

order of sites in the ribosome during translation

A

APE

50
Q

termination

A

when the codon in the A site is a stop codon

51
Q

release factor

A

places a water molecule on the polypeptide chain and thus releases the protein

52
Q

posttranslational modifications include

A
  • folding of chaperones
  • formation of quaternary structure
  • cleavage of proteins or signal sequences
  • covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)
53
Q

phosphroylation

A

addition of a phosphate (PO4^2-) by protein kinases to active or deactivate proteins
-in eukaryotes, most commonly seen with serine, threonine, and tyrosine

54
Q

carboxylation

A

addition of carboxylic acid groups

-usually to serve as calcium-binding sites

55
Q

glycosylation

A

addition of oligosaccharides as proteins pass through the ER and golgi apparatus to determine cellular destination

56
Q

prenylation

A

addition of lipid groups to certain membrane-bound enzymes

57
Q

operon

A

a cluster of genes transcribed as s ingle mRNA

  • include bother inducible and repressible systems
  • offer a simple on-off switch for gene control in prokaryotes
58
Q

Jacob-Monod model

A

explains how operons work
-repressors and activators
two systems: inducible and repressible systems

59
Q

inducible systems

A

ex: lac operon
allow for gene transcription only when an inducer is present to bind the otherwise present repressor protein
-negative control: the binding of a protein to DNA stops transcription
the system is normally “off” but can be made to turn “on” given a particular signal

60
Q

repressible systems

A

allow constant production or a protein product

  • continually allow gene transcription unless a corepressor binds to the repressor to stop transcription
  • the system is normally “on” but can be made to turn “off”, given a particular signal
    ex: trp operon
61
Q

positive control

A

the binding of a protein to DNA increases transcription

62
Q

negative control

A

the binding of a protein to DNA stops transcription

63
Q

transcription factors

A

search for promoter and enhancer regions in the DNA

-two recognizable domains: a DNA-binding domain and an activation domain

64
Q

promoters

A

within 25 base pairs of the transcription start site

65
Q

enhancers

A

more than 25 base pairs away from the transcription start site

66
Q

modification of chromatin structure affects what

A

the ability of transcriptional enzymes to access the DNA through histone acetylation (increases accessibility) or DNA methylation(decrease accessibility)

67
Q

what is the difference between DNA regulatory base sequences and transcription factors

A

DNA regulatory ase sequences are known as cis because they are in the same vicinity as the genes they control
transcription factors are trans because they have to be produced and translocated back to the nucleus

68
Q

DNA binding domain

A

binds to specific nucleotide sequence in the promoter region or to a DNA response element

69
Q

activation domain

A

allows for the binding of several transcription factors and other important regulatory proteins

70
Q

what role does peptidyl transferase play in protein synthesis?

A

it catalyzes the formation of a peptide bond between the incoming amino acid in the A site and the growing poly peptide chain in the P site

71
Q

what stage of protein synthesis does not require energy?

A

THEY ALL REQUIRE LARGE AMOUNTS OF ENERGY

72
Q

topoisomerase are enzymes involved in what?

A

DNA replication and transcription

73
Q

enhancers are transcriptional regulatory sequences that function by enhancing the activity of

A

RNA polymerase at a single promoter site

specific transcription factors bind to a specific DNA sequence, such as an enhancer, and to a RNA polymerase at a single promoter sequence. They enable the RNA polymerase to transcribe the specific gene more efficiently

74
Q

frameshift mutation

A

when some number of nucleotides are added to or delted from the mRNA sequece
-this will shift the rading frame and usually resulting in changes in the amino acide sequence or premature truncation of the protein

75
Q

signal molecules

A
  • enhancer in transcription factors

- ex: cyclic AMP, cortisol, estrogen, bind to specific receptors

76
Q

at high ph, what happens to the amino acid

A

protons are scarce
rip off the protons
negative charge on the AA
deprotonate

77
Q

at low pH, what happens to the amino acid

A

abundance of protons
load them on the AA
protonate
positive charge on the AA

78
Q

oxidation

A

less bonds to H

79
Q

reduction

A

more bonds to H

80
Q

primary level of organization

A

amino acid sequence

81
Q

Secondary level of organization

A

alpha helices
beta sheets
short range interactions
H bonds between backbone

82
Q

tertiary structure

A

long range interactions

disulfide bonds, H bonds b/w R groups, salt bridge, hydrophobic interactions

83
Q

quaternary

A

2 or more subunits

MCAT Biochemistry (8 decks)

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