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Bcem 341 > Lecture 4-6: Transcription+Translation > Flashcards

Lecture 4-6: Transcription+Translation Flashcards

1
Q

RNA is synthesized in the

A

5’-3’ direction

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2
Q

New nucleotides for RNA are added onto the —- of the growing strand

A

3’ OH

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3
Q

RNA polymerase unwinds about — of DNA at a time

A

17bp

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4
Q

DNA template strand is being read —–, RNA is made —–

A
  • 3’-5’
  • 5’-3’
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5
Q

Exon

A

Included in the mature RNA, will be transcribed into protein

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6
Q

Intron

A

Noncoding, not included in the mature RNA (spliced out)

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7
Q

Transcription starts (2)

A
  • end of promotor
  • the +1 site
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8
Q

Transcription initiation begins at

A

promotor sequences

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9
Q

Introns begins with —- and end with —

A
  • GU
  • AG
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10
Q

Upstream is

A

towards the 5’ end

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11
Q

Downstream is towards the

A

3’ end

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12
Q

The template strand is also called the (2)

A
  • antisense strand
  • noncoding strand
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13
Q

Non template strand is also called the

A
  • sense strand
  • coding strand
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14
Q

unless told otherwise, given gene= — strand

A

sense strand

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15
Q

mRNA looks exactly like the — strand but has — instead of T

A
  • Sense strand
  • U
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16
Q

Amino group is the — end

A

N-terminal

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17
Q

The carboxyl group is the —- end

A

c-terminal

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18
Q

Components of an amino acid

A
  1. amino group
  2. R group
  3. Carboxyl group
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19
Q

mRNA codon helps buffer

A

transition SNPS

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20
Q

tRNA molecule has an anticodon loop oriented

A

3’-5’

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21
Q

Amino acid is attached to the —– end of the tRNA molecule

A

3’

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22
Q

What attaches the amino acid to tRNA?

A

aminoacyl-tRNA synthetase

23
Q

Ribosome move along mRNA in the —— direction

A

5’-3’

24
Q

What catalyzes the formation of the peptide bond in amino acid chain?

A

Peptidyl-transferase center

25
Q

Shine-Dalgarno sequence

A

in prokaryote mRNA, is recognized by rRNA in the ribosome small subunit so it bind.

26
Q

Kozak Sequence (2)

relative to start codon?

A
  • in Eukaryotes and helps position the ribosome
  • upstream of start codon
27
Q

Silent mutation+ its impact on potein (2)

A
  • encodes the sae amino acid
  • Fairly small impact on protein function
28
Q

Missense mutation conservative+ex

A

Encodes a chemically similar amino acid
- makes a different amino acid
- ex: both lys and arg are + charged amino acid-> fairly minor impact on overall protein function

29
Q

Missense mutation nonconservative+ex

A
  • encodes a chemically different amino acid
  • ex: thr is not charged, lys is charged
30
Q

i

Nonsense mutation

A

encodes a stop codon

31
Q

Insertions and deletions result in

A

frameshift mutations

32
Q

When might a silent mutation not be completely silent? (2)

A
  • the mRNA sequence has changed: If the silent mutation is near the end of an exon, it can interfere with splicing
  • alterations in mRNA structure or stability (ex:G instead of C cause mRNA to fold uo on itself and be less acessible to translation machinary)
33
Q

Wetern block

A
  • used to detect a particular protein from a mixture of protein
34
Q

Steps for a western blot analysis

A
  • extract protein from cells/tissue
    • Boil the sample and add detergent to allow seperation of protein based only on number of amino acids
  • perform gel electrophoresis on a polyacrylamide gel
  • Use probes/antibody to bind to the protein or primary antibody
35
Q

Silent mutation vs SNP

A

If this occured in an intron or non-coding region, we wouldn’t use silent mutation and would instead just call it a SNP

36
Q
A
37
Q

Difference between ribose and deoxyribose

A

Ribose has an OH group on 2’ carbon

38
Q

RNA polymerase

A

A complex enzyme containing multiple subunits which promotes the formation of phosphodiester linkages between incomming ribonucletotides (ribonucleoside triphosphates)

39
Q

Characteristics of RNA synthesis (3)

Require+ uses+ does not

A
  1. Reaction requires all four ribonucleotides : ATP, GTP, CTP, UTP
  2. RNA synthesis uses DNA as a template
  3. RNA polymerase does not require a primer to begin synthesis
40
Q

How is new nucleotide attached?

A
  • 3’OH of growing strand: nucleophillic attach on the alpha phosphate of the incoming nucleotide
41
Q

Genome

A

The entire set of DNA found in cell

42
Q

Gene

A

Segments of DNA that are transcribed into RNA and then into protein

43
Q

mRNA
tRNA
rRNA

A
  • mrna codes for the protein sequence
  • tRNA are compoents of the machinery that translate mRNA into protein
44
Q

Transcription in Prokaryotes: 3 stages

A
  1. Inititation: Transcription is initiated at promoter sequences in the DNA template
  2. Elongation: RNA strand complementary to template DNA is synthesized by RNA polymerase
  3. RNA strand synthesis stops and RNA polymerase is released
45
Q

Promotor sequences

what do they do?

A
  • directs the RNA polymerase to the proper site for transcription initation
46
Q

Promotors are located — of the coding region on the —- strand

A
  • upstream
  • sense
47
Q

RNA polymerase subunits (6)

what is the entire thing called?

A
  • entire enzyme complex is called the holoenzyme
  • Alpha: required for assembly of core enzyme; interacts with regulatory factors
  • Beta: Takes part in all stages of catalysis
  • Beta prime: Binds to DNA; takes part in catalysis
  • Omega: required to restore denatured polymerase to its native form
  • Sigma 70: Takes part in promotor recognition
48
Q

Talk about the sigma subunit (5)

A
  • helps the polymerase to find the correct start site for transcription
  • Decrease affinity of RNA polymerase for general binding to DNA
  • Enables RNA polymerase to recognize promoter sites
  • sigma subunit is released after transcription is initated
  • Other sigma subunits recognize other promoter sequences (for genes that are expressed in certain environmental conditions)
49
Q

Distinct feature on the 5’ end of the newly synthesized prokaryotic RNA:

A

The 5′ end of newly synthesized RNAs bears a triphosphate derived from the first transcribed nucleotide

50
Q

In transcription, DNA strand is being —- newly synthesized RNA is being made ——

A
  • 3’-5’
  • 5’-3’
51
Q

Transcription bubble contains (3):

A
  • The RNA polymerase
  • The unwounds DNA
  • Newly formed RNA
52
Q

Rho independent Termination (3)

only in+used

A
  • only in prokaryotes
  • Terminator sequence in mRNA base pairs, coded from DNA strand pairs with itself to form a G-C hairpin as the mRNA base pairs are inverted (CCCCG-…….-GGGGC) followed by a string of U’s. This hairpin causes RNA polymerase to stall and dissociate
  • No ATP is used
53
Q

Rho Dependant Termination (3)

only in+steps (4)

A
  • only in prokaryotes
  • Rho binds to RNA on the recognition sequence
  • Move along the RNA via ATP
  • RNA polymerase pauses at terminator and Rho catch up
  • Terminator sequence in mRNA is recognized and bound by the Rho helicase which unwinds the RNA from the template DNA and RNA polymerase by breaking H bonds.
54
Q
A

Bcem 341 (32 decks)

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