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Genetics > Exam 2: Recombinant DNA, Transcription, Translation and all that jazz > Flashcards

Exam 2: Recombinant DNA, Transcription, Translation and all that jazz Flashcards

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1
Q

What is Recombinant DNA Technology?

A

techniques for synthesizing, amplifying, purifying and working with DNA

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2
Q

What is Genetic Engineering?

A

Application of recombinant DNA technology to specific biological, medical and agricultural problems.

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3
Q

What is Genomics?

A

Using recombinant DNA tech to analyze the total DNA present in a cell, organism or populations.

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4
Q

What is a Cloning Vector?

A

A piece of DNA that will allow for the amplification of the insert in a host.

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5
Q

What is a Plasmid?

A

A circular piece of DNA (ex. plasmid vector)

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6
Q

What are some Vector differences?

A

-size of foreign DNA fragments that can be cloned into them
- process by which these vectors are introduced into cells
- Mechanism by which the vectors replicate in the cell

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7
Q

What are some Vector similarities?

A

-Must have mechanism to replicate autonomously
-Must have a selectable marker such as resistance to antibiotic and B-galactose

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8
Q

What is required for PCR in a tube?

A

-Template DNA
-dNTPs (deoxyribonucleotides)
-DNA primers
-Taq polymerase
-Buffer for enzyme
-Thermocycler

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9
Q

What is used in Topo TA Cloning?

A

-Topoisomerase 1
-Pre-cut vector with a single deoxythymine (T) overhang
-PCR product with a 3’ deoxyadenine (A)

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10
Q

What does BGal do?

A

shows that the wanted piece of DNA is not in that specific colony “Blue makes you blue”

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11
Q

What is the role of restriction enzymes?

A

-Molecular scissors
-in bacteria, they protect against viral infection, cut up viral DNA, recognize 4-8 NT long specific sequences

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12
Q

Why was RBCL the gene that was used in lab?

A

-every plant has it
-Important function= highly conserved
-Chloroplast gene=”ancient structure”
-circular DNA with no introns
-well studied, rich database

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13
Q

What are the differences between prokaryotes and eukaryotes?

A

Prokaryotes:
-circular DNA
-No nucleus and cytoplasm

Eukaryotes:
-Linear DNA
-Nuclear and cytoplasm

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14
Q

What is Transcription?

A

Creation of an RNA using a specific sequence of DNA as a template

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15
Q

What is a gene?

A

the nucleotide sequence that stores the information which specifies the order of the monomers in a final functional polypeptide/RNA

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16
Q

What are the types of RNA?

A

Messenger, Transfer, Ribosomal, Small Nuclear, Micro and Small Interfering

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17
Q

What is the NONCODING DNA strand?

A

The TEMPLATE strand
COMPLEMENTARY to RNA

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18
Q

What is the CODING DNA strand?

A

It matches the original DNA strand

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19
Q

Where does RNA polymerase bind?

A

Promoter

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20
Q

What is a Promoter?

A

it is at the beginning of the gene, ‘promotes’ gene expression, ‘promotes’ transcription

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21
Q

What are the basic steps of transcription?

A

-Pol binding
-Activation
-Initiation
-Elongation
-Termination

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22
Q

How do you stop Transcription? (rho dependent)

A

Requires rho protein and a specific DNA structure, makes a stem loop structure, followed by U’s in RNA

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23
Q

How do you stop Transcription? (rho independent)

A

Requires a specific DNA structure

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24
Q

What is an example of a start Codon?

A

AUG- translation start

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25
Q

What are some examples of stop codons?

A

UAA, UGA, UAG

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26
Q

What is the ORF?

A

open reading frame, the segment to be translated

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27
Q

How does tRNA undergo major processing?

A

From primary, to intermediate to mature tRNA, the ends are clipped and an acceptor site is added.

28
Q

What are the similarities between Prok. and Euk Transcription?

A

-promoters required
-RNA polymerase required
-5’->3’ direction

29
Q

What are the differences between Prok and Euk. Transcription?

A

-Specific RNA polymerases for different gene types
-Increased promoter sequence complexity
-mRNA processing
-Separation of Transcription and Translation (coupled in Prok.)

30
Q

What is the function of RNA polymerase 1?

A

Transcribes most rRNA genes

31
Q

What is the function of RNA polymerase 2?(MAIN FOCUS)

A

Transcribes mRNAs and most snRNAs

32
Q

What is the function of RNA Polymerase 3?

A

Transcribes tRNAs, 5s rRNA, U6 snRNA

33
Q

What is the function of TATA-less promoters?

A

they are used during development for genes expressed in all cell types

34
Q

What is InR?

A

Initiator region, contains start site

35
Q

What is DPE?

A

Downstream promoter element

36
Q

What needs to occur for RNA Pol2 to function

A

General Transcription Factors
1. Tata binding protein binds to tata box, tbp associated factors bind to form preinitiation complex
2. RNA polymerase binds to promoter
3. RNA polymerase is phosphorylated

37
Q

What does the Preinitiation complex (PIC) do?

A

stabilizes and activates RNA polymerase

38
Q

How can transcription’s efficiency be increased?

A

Activator proteins bind enhancer sequences

39
Q

How can transcription be repressed?

A

Repressor proteins bind silencers

40
Q

Describe Initiation of Transcription

A
  1. Preinitiation complex
  2. Phosphorylation of RNA polymerase
  3. DNA strand are separated
  4. RNA polymerase begins to transcribe
41
Q

Describe Elongation of Transcription

A

5’ –> 3’
Disruption of histone
Proofreading

42
Q

Describe Termination of Transcription

A

RNA Pol1 and 3: sequences similar to rho-independent mechanism

Pol2: more complex, similar to mRNA processing

43
Q

What is the 5’ cap in the processing of RNA polym 2

A

5’ 7-methylguanosine cap

44
Q

What is the 3’ Tail in the processing of RNA polym 2?

A

A 3’ Poly A tail, which is added by poly A polymerase

45
Q

How does one remove introns?

A

Spliceosome (protein complex)

need 5’ and 3’ end of intron, makes loop that disconnects

46
Q

Why do introns have to be removed?

A

If they are not removed or protein can be damaged, which can be lethal

47
Q

What are the advantages of introns?

A

Exon shuffling over times can produce novel gene products, with resulting exons allow for perfect code to be read

48
Q

Fill in diagram.

A

A. mRNA
B. Ribosome
C. Polypeptide chain
D. Amino Acid
E. Codon
F. Anticodon
G. tRNA

49
Q

What is translation?

A

The process by which the ribosome, mRNA and tRNA translate genetic code into amino acids

50
Q

What does degeneracy mean in genetic code?

A

The third position is variable, multiple sequences can code for the same protein

51
Q

How many different amino acids, different enzymes and different tRNAs are there

A

20

52
Q

What are the DNA polymerase requirements?

A

-Bind to double stranded piece
-Extend along a single stranded piece
-add to 3’ OH group

53
Q

what do normal dNTPs do?

A

They extend DNA strands

54
Q

what do ddNTPS do?

A

They terminate synthesis at certain points
ddATP: leaves A behind
ddTTP: Leaves T behind
etc

55
Q

What is another method instead of using 4 lanes of ddNTPS and a huge electrophoresis gel?

A

Use colors! Each ddNTP is labeled with a color, do reaction in 1 tube, and everything separates by size, and computer assigns ATCG.

56
Q

What is a codon?

A

3 Bases that call for specific amino acid

57
Q

What is an anticodon?

A

Matching 3 base piece on a tRNA

58
Q

What does Translational Initiation require?

A

-Small subunit of ribosome
-5’ Cap mRNA
-Initiator tRNA
-GTP

59
Q

Describe Translation Initation

A

-tRNA enters (MET)
-Ribosome small subunit binds to the cap and Scans to the AUG (start)

60
Q

What are the sites on a ribosome

A

A, P, and E

61
Q

What is the A site?

A

Aminoacyl site- where incoming charged (has aa) tRNA binds ribosome (reading the codon in mRNA)

62
Q

What is the P site?

A

Peptidyl site- where tRNA w/ growing polypeptide chain is positioned

63
Q

What is the E site?

A

Exit Site- where tRNA leaves the ribosome

64
Q

Describe Elongation in Translation

A
  1. charged tRNA binds to A site
  2. peptide is transferred from tRNA in P site to tRNA in A site
  3. Ribosome translates along mRNA
  4. New charged tRNA enters empty route
65
Q

Describe Termination in Translation

A

Release factor binds stop codon, complex dissociated

66
Q

What is done with a completed polypeptide chain?

A

correct folding of proteins, cleavage of amino terminus, phosphorylation of polypeptides, addition of sugars/carbohydrates and lipids

Genetics (4 decks)

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