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Biochem 2 > Final Exam Study Guide > Flashcards

Final Exam Study Guide Flashcards

1
Q

Define mRNA

A
  • Messenger RNA is the main player in genetic information transfer. Sends instructions from genome to ribosome. From there, ribosomes make proteins.
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2
Q

Define RNA polymerase

A
  • Enzymes that synthesize mRNA from a DNA template
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3
Q

What does “expressed” mean in genomics?

A

When a gene is transcribed into mRNA. Only when a gene makes a protein does it become an active gene.

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4
Q

Define Transcriptional Control

A

Process of transcription can be up regulated or down regulated to control the level of expression, which controls how much of a certain protein is made. Control when genes actually become functional

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5
Q

Describe the importance of the promoter region

A
  • The promoter region is where transcription by RNA polymerase is initiated by a conserved DNA sequence.
  • Recruits RNA polymerase and tells when it needs to be transcribing.
  • It is a conserved DNA sequence
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6
Q

Explain the structure and mechanism of RNA polymerase.

A
  • RNA polymerase mechanism is similar to DNA polymerase. Same synthesis process: synthesizes mRNA 5’ –> 3’ direction. Uses -OH and PPP.
  • Requires: nucleotide triphosphates (ATP, CTP, GTP, and UTP), divalent cations, and DNA template
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7
Q

Compare and contrast DNA and RNA polymerases.

A

Both:
- Synthesize mRNA in the 5’ –> 3’ direction
- Both use OH and PPP
Different:
- Only one strand of DNA is being copied by RNA polymerase.
- When synthesizing RNA, there is no thymine; uracil is used instead

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8
Q

What are the two mechanisms for termination of transcription?

A

1) Sequence-based (sequence-dependent)

2) Rho-factor (gene-dependent)

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9
Q

Describe sequence-based termination of transcription

A

Transcription is terminated at specific sites through a complex process. Sequences of A/T rich region and beta hairpin signal the end of transcription. This tells the RNA polymerase to terminate by falling off the DNA and start transcribing.

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10
Q

Describe the Rho-factor termination of transcription

A
  • Rho factor ( a RNA-DNA helicase) is a lockwasher architecture.
  • Associated with the end of transcription
  • ATP dependent
  • ATPase domains resemble F1 ATPase (6 homologous subunits to this)
  • Helicase attaches to mRNA, slides down the RNA and knocks off the RNA polymerase from the gene.
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11
Q

Explain the chemical importance of uracil being used in RNA and thymine being used in DNA

A
  • Cytosine in the presence of acid becomes uracil. If DNA used uracil, the DNA damage repair mechanisms wouldn’t be able to tell if uracil was supposed to be there or if it was a damaged cytosine. The extra methyl group on thymine allows the DNA repair mechanism to differentiate between the uracil of damaged DNA and the thymine of the correct DNA.
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12
Q

The name of the DNA strand that is directly read by RNA polymerase is the __________ strand. The name of the DNA strand that has the same sequence as the mRNA is called the ________ strand.

A

Template strand / antisense / non-coding ; Non-template strand/ sense / coding

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13
Q

What sections of the DNA are recognized by prokaryotic RNA polymerase? What sections are recognized by eukaryotic RNA polymerases?

A

Prokaryotic polymerase: -35 and -10 regions

Eukaryotic polymerase: upstream and downstream of initiation site

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14
Q

What is meant by the term “DNA foot printing”? What key question can this technique answer?

A
  • Uses agarose electrophoresis to determine where proteins interact with DNA.
  • Gives you an idea where proteins interact with DNA
  • Smaller pieces of DNA move slower through the gel (closer to the bottom) than larger pieces
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15
Q

Inactive Rho-Factor

A
  • open RNA-DNA helicase.

- Rho-factor is wrapped around ssRNA

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16
Q

How does the RNAP holo complex differ from the core complex?

A
  • A large complex; 450 kDa
  • Six subunits : α2ββ’ωσ
  • Inactive complex
  • About a 10 A opening between the two “claws”, the β’ and β proteins.
  • Not a strong affinity for dsDNA but a high affinity for the promoter regions
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17
Q

What is the biochemical role of the sigma cofactor?

A
  • On activation ( once the RNA polymerase finds a gene it wants to transcribe), the σ subunit leaves to form α2ββ’ω (core complex). Claw opens to active form. Starts transcribing mRNA.
  • Lays along the β’ and makes interactions with the -35 and -10 regions of the gene sequence.
  • Makes interactions with the promoter sequences of a specific gene.
  • Without the σ present there is a strong affinity for dsDNA but a low affinity for the promoter regions
  • Part of recruitment for RNA polymerase
  • About a 25 A opening when absent
  • USED AS AN ADAPTER TO HAVE RNA POLYMERASES LOOK FOR DIFFERENT GENES OR DIFFERENT PROMOTERS.
  • GIVES SPECIFICITY WHEN GENES ARE TURNED ON OR OFF
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18
Q

Why is it ok for RNA polymerase to have lower fidelity in nucleotide synthesis compared to DNA polymerase?

A

1) RNA is used to make proteins, which are then recycled to AA. Not as permanent of a mistake as DNA
2) Codes are redundant. Multiple codons code for the same AA. When converted into protein, it still makes the same protein ( read the same way)

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19
Q

What is meant by “nascent RNA”?

A

This is RNA produced directly by RNA polymerase ( transcribed 5’ –> 3’)

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20
Q

Genes in prokaryotic organisms are often organized into ______________.

A

operons

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21
Q

Define operons

A

genes related by function

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22
Q

E. coli use lactose as primary ______ source

A

carbon

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23
Q

Prokaryotes tend to have _________ genes on one mRNA transcript. This is called ___________.

A

multiple ; polycistronic

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24
Q

Eukaryotes tend to have ______ genes on one mRNA transcript. This is called _________.

A

one ; monocistronic

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25
Q

What is the transcription bubble?

A

In DNA being read by RNA polymerase, the dsDNA is separated into two single strands. This allows RNA polymerase to bind to them and have a place to read and synthesize from the code.

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26
Q

What is the initiation site?

A

-Place where RNA polymerase is going to start making the transcripts of mRNA.
-This is the first set of nucleotides incorporated into mRNA
-Where transcription is initiated
+1 nucleotide where mRNA starts being made

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27
Q

Gene expression can be controlled using different _________ specific for different promoters.

A

sigma factors

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28
Q

The actual sequence of a promoter can be used to ______________.

A

Recruit different types of sigma factors that give binding to specific promoters which gives bacteria control when genes are turn on or off at certain times

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29
Q

DNA polymerase is _______ than RNA polymerase.

A

faster

30
Q

RNA polymerase doesn’t use an additional ______ like DNA polymerase.

A

clamp protein

31
Q

These are “housekeeping” genes. They are always being transcribed.

A

Constitutive genes

32
Q

These genes are expressed only when needed.

A

Inducible genes

33
Q

As 1st RNA polymerase leaves, a space opens up and allows another RNA to start _________.

A

transcribing

34
Q

Define “transcription factors” in regards to eukaryotic transcription.

A

Proteins that are required to initiate transcription in eukaryotes. Help RNA polymerase form the pre-initiation complex

35
Q

Define “enhancer region” in regards to eukaryotic transcription.

A
  • act at long distances to regulate gene expression

- 100 to 1000s of nucleotides upstream away from gene and promoter region. Affects how much gene is expressed

36
Q

Eukaryotic transcription involves multiple RNAP enzymes. What are the 3 classes?

A

1) RNAP I - rRNA (ribosomal RNA) : Transcribes the genes involved w/ rRNA synthesis
2) RNAP II - mRNA (constitutive and inducible): APPLIES TO MOSTLY METABOLIC AND SIGNAL TRANSDUCTION GENES. Main RNA polymerase for transcribing messenger RNA of constitutive and inducible genes
3) RNAP III - tRNA (transfer RNA) and 5s rRNA

37
Q

How is the core structure of eukaryotic RNA polymerase differ from prokaryotic?

A
  • Same structure just 9 extra subunits

- Rpb1 (β’) has an important C-terminal domain (CTD) that prokaryotes don’t.

38
Q

Eukaryotic promoters are _________ than prokaryotic sites

A

more complex

39
Q

Upon recognition of upstream -35 and -10 promoter regions, RNAP and Transcription factors assemble to form ___________ at the promoter region. What do they do?

A

pre-initiation complex (PIC); Proteins are coming in to make a happy binding site for RNA pol II. PIC is set for phosphorylation of the C-terminal’s serine. This recruits other transcription factors to activate the actual transcription steps.

40
Q

What does the DNA bending protein do?

A

Helps the DNA to fold back and interact with RNA polymerase to regulate its function. Able to interact with all proteins in PIC or active complex.

41
Q

There is no __________ in eukaryotes. In this case, RNA polymerase keeps going until _______. This is because eukaryotes have ___________ and prokaryotes don’t. mRNA is not recognizable by ribosome until___________.

A

Termination signal ; it falls off ; post-translational processing for mRNA ; it gets processed

42
Q

Describe the three steps of eukaryotic mRNA processing.

A

1) 5’-cap: Added to pre-RNA. Helps identify the translation initiation site. Protects the 5’ end of mRNA transcript. Gives info to ribosome when mRNA is ready to start being processed
2) 3’ poly-A tail: Protects 3’ end of pre-mRNA from random nucleases that would chew up gene from 3’ end.
3) Splicing events: pre-mRNA contains expressed (exon) and unexpressed (intron) regions. Splices out specific portions of mRNA to create a mature mRNA. Removes parts of the mRNA that was just transcribed. The exons are connected and introns are removed.

43
Q

With splicing, exons are connected by ________. This is the final piece that will be read by the _______.

A

phosphodiester bonds ; ribosome

44
Q

Cells use diff. collection of exons to code for different _________ for different __________. This is important for multicellular organisms.

A

polypeptides ; proteins

45
Q

Some pre-mRNA molecules are self-splicing (no proteins required)

A

Ribozymes

46
Q

Define translation. ________ helps catalyze the formation of polypeptide chain so that AA are in the correct order. (corresponding to the codons inside the mRNA)

A

the process of converting mRNA sequence into the amino acid sequence of a protein. Ribosomes.

47
Q

How many nucleotides does it take to make one amino acid? This is called _______.

A

3 ; triplet codons

48
Q

Are triplet codons read in overlapping or sequential manner? How can we test this?

A

Overlapping ; Crick and Brenner used bacteriophage infected with a virus to show that insertion with sequential method cause the code to become gibberish = non-virulent. With insertion and deletion near each other = bacteriophage was virulent. Only one codon was messed up.

49
Q

What number of closely spaced insertions or deletions could also be tolerated?

A

3

50
Q

Mismatch in tRNA means = can’t read any _______ correctly

A

mRNA

51
Q

The ________ is a massive organelle responsible for polypeptide synthesis

A

Ribosome

52
Q

What are the jobs of ribosomes (5)?

A
  • bind mRNA
  • bind tRNA
  • bind additional proteins ( regulation)
  • catalyze peptide bond formation between AA to make polypeptide chains
  • Translocation along mRNA strand
53
Q

Ribosomes are ribonucleotide proteins containing ______.

A

rRNA

54
Q

Prokaryotic Ribosome is a _______S ribosome with a ____ S large subunit and a _______ S smaller subunit.

A

70 ; 50 S ; 30 S

55
Q

Eukaryotic ribsome is a _____ S ribosome with a ____ S large subunit and a ______ S smaller subunit.

A

80 S ; 60 S; 40 S

56
Q

Because the eukaryotic ribosome is bigger than the prokaryotic ribosome, it is able to have ______ function and __________.

A

more ; regulation

57
Q

What is the start codon?

A

Methionine (AUG), tells ribosome this is a new polypeptide chain beginning

58
Q

Changes to the first base tend to code for _____________. Safety at first position is so that ______ don’t mess up the protein.

A

similar types of amino acids; mutations

59
Q

The identity of the second base tends to be conserved for either _____ or _____ substitution

A

purine or pyrimidine. Purine for purine or pyrimidine for pyrimidine

60
Q

Why is the 3rd position of the codon called the wobble position?

A

This is because changes in the third position of the codon usually code for the same base

61
Q

What do stop codons do?

A

Signal the end of translation for the ribosome. Tell ribosome this is the end of the polypeptide chain.

62
Q

What is codon bias?

A

Not all codons are created equal. Organism specific and due to different levels of tRNAs

63
Q

What is the 2D structure of tRNA

A

Clover-leaf structure; acceptor stem is where amino acids are attached. Anticodon arm will base pair with mRNA on ribosome

64
Q

What is the 3D structure of tRNA?

A

L-shaped. Acceptor stem on one end( where AA attaches) and anticodon on the other end. No direct interaction between the mRNA and the AA.

65
Q

Aminoacyl-tRNA synthetases (aaRS) attach ________ to the ___ OH of tRNAs through an __ -dependent reaction. ATP is used to activate ______.

A

Amino acids ; 3’ , ATP ; carboxylic acid

66
Q

Several proteins associated with the ribosome exhibit similar architecture. Tails of these structures are rich in _____________. The amino acid sequence of the tails is _______.

A

basic residues ; evolutionarily conserved

67
Q

Tails of proteins that associate with the ribosome insert into the ribosome to maintain _____________________.

A

Positive charges to balance negative charges of phosphodiester backbone and provide stability.

68
Q

The interface where mRNA and tRNA will be joined is made up almost entirely of ________.

A

rRNA

69
Q

Peptides are synthesized from _____ to _____.

A

N (amino) to C (carboxyl) direction

70
Q

Peptide growth occurs by linkage to the ________.

A

incoming tRNA

71
Q

There are many AUG codons. The _______ in the small subunit directs ribosome to the correct initiation site.

A

16S rRNA

72
Q

How would you characterize the size of the following items relative to the size of the human genome?

a. amount of DNA in the genome of E. coli
b. amount of DNA that is converted to protein in humans
c. amount of DNA that is converted to RNA in humans

A

a) Almost 700 x’s smaller

b)

Biochem 2 (4 decks)

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