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Biochemistry 1 > Replication, Transciption, Translation (Exam 1) > Flashcards

Replication, Transciption, Translation (Exam 1) Flashcards

1
Q

In DNA replication, is the whole genome duplicated, or just part of it?

A

whole genome

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2
Q

How is DNA shape different between prokaryotes and eukaryotes?

A

Prokaryotes have circular DNA, whereas eukaryotes have linear DNA

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3
Q

How is the starting point of DNA replication in prokaryotes compared to eukaryotes?

A

Origin of replication in prokaryotes is only 1, whereas in eukaryotes there’s multiple

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4
Q

Prokaryotes and eukaryotes have similar mechanisms of replication. How are they the same?

A

-semi-conservative replication (1 old and 1 new strand in daughter cell)
-bi-directional replication (the fork advances in both directions)

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5
Q

How is DNA replication initiated? What 3 enzymes play a role in initiation?

A

origin(s) of replication are in TA rich regions

note: prokaryotes have only one origin, eukaryotes have multiple

3 enzymes
-DNA helicases separates strands of a DNA double helix by breaking up hydrogen bonds at the replication fork
-topoisomerases unwind DNA (relaxes and unwinds DNA from its super-coiled nature)
-SSBP binds to single strands and holds DNA open during replication (prevents it from re-annealing)

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6
Q

What happens during elongation of DNA replication?

A
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7
Q

What does DNA polymerase 1 do?

A

replaces RNA primer with complementary DNA during DNA replication

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8
Q

What enzyme in DNA replication joins okazaki fragments (of the lagging strand)?

A

DNA ligase

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9
Q

What creates an RNA primer?

A

primase creates a short RNA sequence primer during DNA replication for DNA polymerase 3 to begin synthesis

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10
Q

What strand in DNA replication is being synthesized in fragments and is not continuous?

A

okazaki fragments (of the lagging strand)

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11
Q

What strand in DNA replication has continuous replication and is in the same direction as the replication fork?

A

leading strand

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12
Q

What does DNA polymerase 3 do?

A

reads old strand to copy bases and put down complementary new bases

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13
Q

DNA polymerases are the major enzyme/workhorse of DNA replication. Why?

A

they create DNA polymer!

Also, they both have proofreading 3’-> 5’ ability to check for mutations/errors (this is known as exonuclease activity as well, which cuts from the end of the sequence)

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14
Q

What enzyme during DNA replication reads from 3’->5’ and adds nucleotides in 5’->3’ direction?

A

DNA polymerase

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15
Q

Which DNA polymerase replaces the RNA primer with DNA?

A

1

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16
Q

What are the 2 strands called in transcription?

A

template and coding strand

note: the template strand is always from 3’->5’ because it can be read and synthesized continuously! Its the easiest

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17
Q

What helps a specific gene be found at the beginning of transcription/helps it to initiate transcription?

A

promoter! It helps promote gene expression

each gene has its own promoter, info is fragmented

it will appear with a “+1”

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18
Q

What are exons? What are introns?

A

exon= sequence that will eventually be expressed in proteins

intron= will be removed/not expressed in protein

note- this happens in eukaryotic transcription

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19
Q

Where does transcription occur?

A

nucleus

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20
Q

What does RNA polymerase do?

A

opens up dsDNA and transcribes DNA-> RNA

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21
Q

What are the other names for post transcription modification?

test q

A

RNA processing or RNA maturation

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22
Q

Is eukaryotic transcription monocistronic or polycistronic?

A

monocistronic (1 promoter for each gene in eukaryotes)

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23
Q

What 3 major steps happen during post transcription modification?

A

1) splicing (introns removed)
2) capping (add 7’ Me- Guanosine cap)
3) poly-A tail

this is needed to protect RNA so it won’t degenerate when it leaves nucleus (mRNA is only one leaving once its mature)

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24
Q

Are transcription and translation coupled in eukaryotes?

A

no! only coupled in prokaryotes

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25
Q

What are the differences between DNA and RNA synthesis?

A

DNA replicates, RNA transcribes
Primer is DNA exclusive
Polymerase differs between DNA and RNA
Subunits differ (ATCG vs AUCG)
RNA has no proofreading ability since it is short

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26
Q

The complementary mRNA strand that would be synthesized from the DNA base sequence of CTGAC would be….

A

3’ GACUG 5’

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27
Q

T/F: The synthesis of mRNA is called translation

A

false

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28
Q

T/F: synthesis of a new strand of mRNA is in the 5’ -> 3’ direction

A

true

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29
Q

What are the 3 types of RNA found in eukaryotes?

A

mRNA, rRNA, tRNA

30
Q

protein is linked together by what bonds?

A

peptide bonds

31
Q

What are ribosomes made of?

A

ribosome protein and rRNA

ribosomes are the major workhorse proteins in translation

32
Q

What are the subunits of a prokaryotic ribosome?

A

large subunit= 50S

small subunit= 30S

together= 70S

33
Q

What are the subunits of a eukaryotic ribosome?

A

large subunit= 60S

small subunit= 40S

together= 80S

34
Q

Which ribosome subunit has peptidyl transferase activity? What is this?

A

large subunit of eukaryotic ribosome (60S) and large subunit of prokaryotes (50S) has peptidyl transferase activity

this enzyme forms peptide bonds between amino acids

35
Q

Which ribosome subunit recognizes shine delgarno sequences of mRNA (mRNA cap)?

A

small subunit of prokaryotic ribosome (30S)

36
Q

Which ribosome subunit recoginizes the 7-Me-cap of mRNA?

A

small subunit of eukaryotic ribosome (40S)

37
Q

What are the 3 things needed for translation?

A

-mRNA
-ribosome
-tRNA

38
Q

What shape is tRNA?

A

clover leaf structure

39
Q

Which RNA picks up amino acids?

A

tRNA

40
Q

Which RNA recognizes codon on mRNA?

A

tRNA

41
Q

If the codon is AUG, what is the anticodon?

A

5’ CAU 3’

42
Q

A codon is made up of how many nucleotides?

A

3

43
Q

How many codons are there in the codon table? How many code for amino acids?

A

64 codons, 61 code for amino acids (stop codons are the ones that dont)

44
Q

What does the start codon AUG code for?

A

methionine

note: ATG would also code for this

45
Q

What are the 3 stop codons?

A

-UAG
-UGA
-UAA

46
Q

How does translation begin?

A

when mRNA and tRNA bind and the starting codon is AUG

47
Q

What are the 3 sites within a ribosome?

A

A= attachment site
P= peptidyl binding site
E= free tRNA/exit site

48
Q

Ribosome synthesizes protein from what terminal to what terminal?

A

N terminal to C terminal

N is free amino group in polypeptide
C is free carboxyl group

49
Q

What is the end product of translation?

A

protein

50
Q

What is post translational modification modifying?

A

protein

51
Q

Where does post translational modification occur?

A

ER and golgi

52
Q

What happens during post translational modification?

A

-oxidation reaction to help protein fold
-protein will be cleaved
-1 active protein is made (and in the case of insulin there will also be C-peptide)

during post translational modification, there can be folding, cutting, and other processes such as glycation (addition of a sugar molecule to a protein)

53
Q

Is insulin a protein or lipid hormone?

A

protein hormone

54
Q

Where is insulin secreted?

A

pancreatic B cells in the islets (alpha cells in this islets will secrete glucagon)

55
Q

Does insulin increase or decrease blood sugar?

A

decrease

56
Q

Does glucagon increase or decrease blood sugar?

A

increase

57
Q

What does insulin have that helps it to fold during post-translational modification?

A

3 disulfide bonds (1 disulfide bond looks like this: -S-S-, which comes from thiol -SH + -SH)

58
Q

What is a marker for endogenous insulin?

A

c-peptide

59
Q

What are the 2 sources of insulin?

A

1) endogenous (from pancreas)
2) exogenous (from insulin injection)

60
Q

Genes are DNA. What are the causes of damage to DNA?

A

-spontaneous aging
-deamination (removal of amino group in amino acids)
-oxidation (damages cell membrane/DNA with oxygen, note that antioxidants can decrease oxidation)
-UV light (makes a thymine thymine dimer on DNA)
-X-ray and gamma rays cause DNA fragmentation (damages the backbone)
-nitrites accelerate deamination of bases

61
Q

What does it mean if a mutation is a “selective force”?

A

its advantageous

62
Q

What does an excision endonuclease do?

A

enzyme that cuts out the damaged region out of the bubble, usually the T-T dimer and its in the middle of the chain

T-T dimers form in DNA when there is overexposure to UV light

and then DNA polymerase and ligase will rebuild new strand what was cut out and glue it

63
Q

Can mutations occur in both DNA and RNA?

A

Yes, but DNA is permanent whereas RNA is not

64
Q

What are the 3 types of point/substitution mutations?

A

1) silent (usually affects 3rd position of the codon)
2) nonsense (early stop codon, will be relatively short protein and non-functional)
3) missense (a nucleotide change results in a different AA, reduces the function)

65
Q

What is frameshift mutation?

A

deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream

usually results in a truncated non-functional protein

66
Q

What is xeroderma pigmentosum?

A

its an excision endonuclease deficiency (T-T dimers will build up and not get cleaved like they’re supposed to)

will result in hyperpigmentation of the skin, the sun is very dangerous to these people

67
Q

What is denaturation in DNA?

A

breaking of the intra chain of H bonds in DNA creates single stranded nucleic acids

68
Q

Tertiary and secondary structures of nucleic acids can be “melted” by moist heat and…

A

high pH

69
Q

DNA/RNA with a high content of G/C base pairs will require more harsh denaturation conditions, which means…

A

higher melting temperatures

(DNA with a higher percentage of A/T and RNA with A/U will melt under less harsh conditions A/T and A/U base pairs have just 2 H bonds between them)

70
Q

Denatured DNA/RNA will ____________ when returned to normal conditions. If this is done in the presence of foreign DNA or RNA then hybrid duplex strands will result

A

renature

71
Q

Formation of hybrid duplex can have 3 different doubles stranded molecules. What are they?

A

-DNA/DNA
-RNA/DNA
-RNA/RNA

note: hybrid duplexes form where 2 different nucleic acid molecules have regions of complementarity

the more complementarity- the more stable the hybrid

the more mismatches- the more unstable and easier to denature

Biochemistry 1 (12 decks)

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