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Bio 107 > Lecture 12 > Flashcards

Lecture 12 Flashcards

1
Q

The central dogma refers to:

which is ___directional

A

the flow of information in the cell

unidirectional

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2
Q

Define a gene

A

a gene is a region of DNA that directs the synthesis of an RNA molecule
- it’s a unit of heredity

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3
Q

What’s a promoter?

A

a DNA sequence that directs/ regulates transcription

- site of RNA polymerase assembly

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4
Q

the first nucleotide to be transcribed is at ____[number] on the ____
(start site of transcription- where there’s a start codon)

A

+1

double stranded DNA

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5
Q

A common promoter in prokaryotes is the _______

  • the ___ sequence is A/T rich. Why?
  • the ___ sequence orients ___ ____
A
  • the minus 10 and minus 35 combo
  • minus 10. Because A and T is a weaker base pair (so it’s easier to pull apart the DNA)
  • minus 35. orients RNA polymerase
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6
Q

What are the -10 and -35 sequences?

A

specific 6 base pair sequences common to most bacterial promoters
(the -10 and -35 combo)

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7
Q

mRNA is synthesized in what direction?

A

5’ to 3’

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8
Q

Directions:

Transcription occurs __ to ___ by reading the template strand __ to ___

A

5’ to 3’

template is read 3’ to 5’

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9
Q

True/ false

There are multiple genes on each chromosome

A

True

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10
Q

What is transcription?

A

the process of copying a segment of DNA into RNA

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11
Q

Describe the template strand

A

the strand of DNA that’s used in transcription

- runs 3’ to 5’ away from the promoter

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12
Q

Describe the coding strand

A

complementary and antiparallel to the template strand

  • runs 5’ to 3’ away from the promoter
  • NOT used in transcription
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13
Q

Define “transcript”

A

a piece of RNA that’s the product of transcription

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14
Q

How does RNA pol “know” where a gene is?

A

it’s recruited to a promoter by transcription factors

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15
Q

compare DNA polymerase and RNA pol.

list 3 differences

A

DNA:

  1. takes part in DNA replication
  2. requires a primer
  3. useful for both strands of DNA

RNA:

  1. takes part in transcription
  2. does not require a primer
  3. acts only on the template strand of DNA
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16
Q

Transcription vs. translation?

A

Transcription is DNA –> RNA
Translation is RNA –> protein

*transcription comes first

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17
Q

define genetic code

A

Genetic code is the term we use for the way that the four bases of DNA–the A, C, G, and Ts–are strung together in a way that the cellular machinery, the ribosome, can read them and turn them into a protein. In the genetic code, each three nucleotides in a row count as a triplet and code for a single amino acid.

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18
Q

which experiment helped determine the universal genetic code?

A

Nirenberg experiment

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19
Q

what are the 3 post-transcriptional modifications? Where do they occur?

A
  1. Addition of a methyl-guanosine cap at the 5’ end
  2. addition of 100-200 adenosines to the 3’ end, known as the poly-A tail
  3. Splicing

They occur in the nucleus of eukaryotes

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20
Q

what’s the function of the first 2 post-transcriptional modifications?
(meG cap and poly-A tail)

A

they both function to increase stability of mRNA in cytoplasm
- they prevent/ delay exonuclease digestion (of our own mRNA!)

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21
Q

what’s an exonuclease?

A

evolved from an antiviral response- degrades any foreign RNA (like covid!)

  • our own RNA is protected from exonuclease digestion by the post-transcriptional modifications: meG cap and poly-A tail
  • eukaryotes only
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22
Q

Fill in the blank (RNA Polymerase)

  1. RNA pol is part of a transcription initiation complex that assembles at the _____
  2. RNA pol synthesizes RNA ___’ to __’ (by reading DNA __’ to __’)
  3. RNA pol “knows” where a gene is because it’s recruited to a promoter by ____ _____
  4. RNA pol ____(does/ does not) require a primer and has its own “____” activity.
A
  1. promoter
  2. RNA: 5’ to 3’ by reading DNA 3’ to 5’
  3. transcription factors
  4. does not
    helicase activity (can open DNA on its own)
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23
Q

template strand is chosen based on the direction of the ____

A

promoter

if it’s on the right, the bottom strand is the template

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24
Q

As mRNA is elongated, the area that’s unwound is called the ____ ____

A

transcription bubble

25
Q

RNA splicing removes ____, which are _________

A

introns= “intervening sequences (non-coding)”

26
Q

What is a spliceosome?

A

a complex of snRNPs (protein/ RNA complex; recognizes sequences at intron/ exon boundaries). In the splicing of mRNA, snRNPs bind intron/ exon boundaries and loop out the intron (into the lariat).

27
Q

Explain alternative splicing

A

mix and matching of exons; makes similar but non identical proteins from the same gene.
This is the reason splicing has survived evolutionarily.
- eg. can splice intron 1, exon 2, and intron 2= creates muscle protein
OR splice just the 2 introns= creates neural protein

28
Q

why is RNA single stranded?

A

because of the 2’ OH: it provides more reactivity, therefore the RNA molecule likes to be alone

29
Q

transcription initiation ends after ________

A

the first phosphodiester bond is catalyzed.

30
Q

Ingredients for translation

A

A) tRNAs (the translator)
B) Aminoacyl tRNA synthetases
C) Ribosomes (the “machine”)

31
Q

Aminoacyl tRNA synthetase is required to attach ___ to an ___ ___

A

the tRNA to an amino acid

32
Q

4 steps of translation in prokaryotes

A
  1. pre-initiation (charging)
  2. initiation
  3. elongation
  4. termination
33
Q

Aminoacyl tRNA synthetases pairs the correct amino acids based on the ____ sequence
(covalently links a.a. to tRNA in sequence dependent manner)
- results in a ____ tRNA which associates with the appropriate a.a.

A

anticodon

  • charged tRNA
34
Q

Ribosomes are large protein complexes with ___s associated.

  • they catalyze the formation of ____ ____
  • they facilitate the specific coupling of ___ ____(codons/ anticodons) with mRNA ____ (codons/ anticodons) during protein synthesis
A

rRNAs

  • peptide bonds
  • tRNA anticodons with mRNA codons
35
Q

proteins are synthesized __ to __ by reading mRNA __’ to __’

A

N to C

5’ to 3’

36
Q

3 important sites in a ribosome

A 
A= "approach" (furthest right)
P= "polymerization"
E= exit (furthest left)
37
Q

compare and contrast small/ large ribosomal subunits

A

small: contains rRNA
- recognition of mRNA

large: contains rRNA
- catalytic site

*functions are provided by the associated rRNAs

38
Q

define the rbs (ribosomal binding site)

A

a sequence in the mRNA that’s recognized by base pairing with rRNA in the small ribosomal subunit

  • binds to the ribosome to position the message correctly for the initiation of translation. The RBS controls the accuracy and efficiency with which the translation of mRNA begins.
39
Q

In prokaryotes, translation occurs in the ___

A

cytoplasm

40
Q

In the inititaion phase of ____, the rbs positions the small subunit such that the start codon sits in the __ site

A

translation

- P-site

41
Q

In elongation, what happens?

What’s the phrase?

A

BIND- BOND- SHIFT

  • various elongation factors escort the next tRNA into the A site of the ribosome
  • peptidyl transferase catalyzes the formation of a peptide bond b/w the F-met and 2nd amino acid
42
Q

Describe what happens in the “BIND” phase of elongation

A

tRNA carrying the correct amino acid approaches the A-site and binds to the mRNA (codon-anticodon specificity)

43
Q

Describe what happens in the “BOND” phase of elongation

A

a peptide bond forms b/w tRNA #1 and tRNA #2 and the growing chain moves to the tRNA in the A-site (tRNA #2)

44
Q

after the “bond” phase of elongation, the whole a.a chain is in the __ site
(so tRNA #__ is empty)

A 
A-site
#1 empty (the tRNA in the P-site)
45
Q

Describe what happens in the “SHIFT” phase of elongation

A

ribosome shifts down mRNA (to 3’ end) in a one codon step

therefore the A-site becomes available again

46
Q

In the termination phase of translation, what happens when a stop codon is read?

A

When a stop codon is read, a release factor (which recognizes the stop codon) moves into the A site
- the polypeptide is then released from the tRNA, and all the ribosome components seperate and dismantle (they’re recycled)

47
Q

release factor allows the a.a. chain to dissociate from the __ in the __-site

A

tRNA

P-site

48
Q

transcription and translation coupling occurs in ___only

A

prok

49
Q

Define mutation

A

a heritable change in base sequences that modify the info content of DNA

50
Q

what is “wild type (WT)” DNA?

A

the “normal” sequences (generally the alleles that dominate in a wild population

51
Q

Which mutation is at the DNA level? What can this cause?

A

base-pair substitutions= the replacement of one nucleotide & its partner with another pair
-This can cause mutations at protein level

52
Q

Which mutations are at a protein level? What causes them?

A
  1. Silent mutations
  2. missense mutations
  3. nonsense mutations
  4. frameshift mutations

they’re caused by mutations at the DNA level (base pair substitutions)

53
Q

Define a silent mutation

A

no change in the primary sequence

- because of the redundancy in the genetic code

54
Q

Define a missense mutation

A

encode the wrong amino acid

  • change in the primary sequence
  • MAY affect protein function
55
Q

define a nonsense mutation

A

premature stop codon

  • shortened protein
  • MAY affect protein function
56
Q

define a frameshift mutation

A

single base pair added or deleted that changes the reading of a protein

57
Q

If you change the primary sequence of a protein, you MAY change the ____ and thus the ___ of the protein

A

folding

function

58
Q

Sickle cell anemia is a ___ mutation which causes _____

A

missense

causes: aggregation of hemoglobin and misshapen red blood cells

59
Q

Muations can be spontaneous (DNA replication errors) or induced. Give some examples of induced mutations

A
  • caused by mutagens such as:
    x-rays
    gamma rays
    base analogs (mimic bases but don’t pair correctly)
    oxidizing agents (damage bases, so they don’t pair properly)
    benzene

Bio 107 (12 decks)

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