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BIOL 213 > Exam 4 Study Guide > Flashcards

Exam 4 Study Guide Flashcards

1
Q
  1. What does the central dogma of molecular biology state?
A

a. Genetic information follows a flow from DNA which is transcribed into RNA which is translated into proteins

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2
Q

What is transcription? Where does it take place?

A

DNA sequence (3’ to 5’ template strand) is copied to a complementary mRNA sequence (5’-3’)

Nucleus

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3
Q

What is translation? Where does it take place?

A

mRNA is translated into polypeptides by tRNA

Cytosol

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4
Q
  1. What is a promoter and what’s its function?
A

A specific sequence on DNA (like the TATA box) that shows the RNA Polymerase II where to start and which part of DNA to transcribe.

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5
Q

What are consensus sequences? Where are they found?

A

Site where transcription factors can bind (TATA, CAAT box, GC box) that are found upstream of the promoter regions

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6
Q

What is a transcription initiation complex comprised of?

A

RNA Pol II
Transcription Factors
RNA Transcript

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7
Q
  1. What’s a transcription factor?
A

Proteins that bind to DNA sequences and to the initiation complex which facilitate transcription.

Examples include Transcription Binding Protein (TBP) binding to the TATA Box

TFIIE (helicase minor) which recruits TFIIH to unwind DNA and phosphorylates RNA Pol II

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8
Q

What are the three phases of transcription?

A
  1. Initiation
  2. Elongation
  3. Termination
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9
Q

Describe initiation and its key components

A

Initiation: RNA pol binds to promoter; promoter has an initiation site where transcription begins

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10
Q

Describe elongation and its key components

A

Elongation: RNA pol unwinds DNA about 10 bps at a time; reads template in the 3’ to 5’ direction; transcript is antiparallel to DNA template strand; RNA pol does NOT proofread and correct mistakes

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11
Q

Describe termination and its key components

A

Termination: in eukaryotes, RNA pol continues for hundreds of nucleotides past terminator sequence (AAUAAA)

then another enzyme cuts RNA 10-15 bases past terminator sequence on RNA

Prokaryotes, transcript forms a loop and falls away from DNA; or a helper protein binds to transcript and causes to detach from DNA

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12
Q

In which direction is the DNA sequence read? In which direction is the pre-mRNA strand created?

A

3’ to 5’ DNA reading

5’ to 3’ pre-mRNA

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13
Q
  1. How are eukaryotic pre-mRNAs processed before they can be used?
A
  1. 5’ Cap with abundance of guanine added
  2. Poly A tail at 3’ end
  3. Excision of introns
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14
Q

What is the purpose of a 5’ cap?

A

The cap is modified GTP which facilitates mRNA binding to a ribosome; also protects mRNA from being digested by ribonucleases

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15
Q
  1. What does a 3’ poly A tail do?
A

AAUAAA sequence after last codon is a signal for an enzyme to cut the pre-mRNA; then another enzyme adds 100 to 300 adenines—the “poly A tail”; the tail assists in export from the nucleus and is important for stability of mRNA

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16
Q

What is RNA splicing? Which protein facilitates this?

A

RNA splicing is a process that removes the intervening, non-coding sequences of genes (introns) from pre-mRNA and joins the protein-coding sequences (exons) together in order to enable translation of mRNA into a protein

Spliceosomes

17
Q
  1. What is a spliceosome? What is it comprised of?
A

A large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs (snRNA) and numerous proteins; they remove introns

18
Q

What is a snRNP?

A

Small nuclear ribonucleoproteins that have several protein molecules and a small nuclear RNA molecule (snRNA); they bind to consensus sequences in RNA; combine with unmodified pre-mRNA and various other proteins to form a spliceosome

19
Q
  1. How many different codons are possible? How many actually code for amino acids?
A

There are 64 codons and 20 amino acids; 61 actually code for amino acids because there are 3 stop codons

20
Q
  1. What are the three characteristics of the genetic code that we discussed in class?
A

For most amino acids, there is > one codon: the genetic code is redundant
Not ambiguous; each codon specifies only one amino acid
Correct reading frames

21
Q

How are codons read (5’ to 3’ or 3’ to 5’)? Which end of the polypeptide are the amino acids added (N or C terminus)

A

Codons are read 5’ to 3’ with the first amino acid being added at the N-Terminus of the polypeptide

22
Q
  1. What’s a tRNA? What does it do? What does it look like?
A

A type of RNA that links mRNA codons with specific amino acids; stem and loop structure that forms a three-leaf clover

23
Q
  1. What is the Wobble Hypothesis?
A

Specificity for the base at the 3’ end of the codon is not always observed; allows cells to produce fewer tRNA species, but does not allow the genetic doe to be ambiguous

This allows for amino acids to be produced with UCA, UCG, UCU

24
Q

How many different tRNAs could exist? How many do exist?

A

61, 20-40

25
Q
  1. What’s aminoacyl tRNA synthetase? What does it do?
A

Enzyme is specific for one amino acid and its corresponding tRNA; a high-energy bond forms between the amino acid and the tRNA—it is later used to form the peptide bond; its what charges the amino acid

26
Q
  1. How does translation initiate?
A

Begins with the formation of an initiation complex; in prokaryotes, the small ribosomal subunit binds to the Shine-Dalgarno sequence; in eukaryotes, it binds to 5’ cap

27
Q
  1. How does the translational process proceed in terms of steps?
A

Small ribosomal subunit binds first to mRNA

  1. A tRNA charged w/ methionine (anticodon UAG) binds to complete the initiation complex
  2. First amino acid is always Methionine and is added to CCA at the 3’ end

APE

  1. The large subunit joins the complex; the charged tRNA is now in the P site
  2. The A site is aligned with the second mRNA codon
  3. Initiation factors are responsible for assembly of the initiation complex
28
Q
  1. What are the three different “sites” on a ribosome?
A
  1. A (aminoacyl tRNA) site binds with anticodon of charged tRNA
  2. P (peptide tRNA) site where tRNA adds its amino acid to growing chain
  3. E (exit) site where tRNA sits before being released from ribosome
29
Q
  1. How does a ribosome “know” which tRNA to bring in next?
A

Ribosomes have a fidelity function: when proper binding occurs, hydrogen bonds form between the base pairs of the anticodon and the mRNA codon

-small subunit rRNA validates the match—if hydrogen bonds have not formed between all three base pairs, the tRNA must be an incorrect match for that codon and the tRNA is rejected

30
Q
  1. What is a “charged” tRNA?
A

tRNAs are charged by aminoacyl-tRNA synthetases; charging requires ATP; a high-energy bond forms between the amino acid and the tRNA—it is later used to form the peptide bond

31
Q
  1. What does a release factor do?
A

Stop codons bind a protein release factor which hydrolyzes bond between the polypeptide and the tRNA in the P site; the polypeptide then separates from the ribosome

32
Q
  1. What are polyribosomes?
A

A strand of mRNA with associated ribosomes; several ribosomes can work together to translate same mRNA, producing multiple copies of polypeptide

33
Q
  1. What’s the difference between attached ribosomes and free (cytosolic) ribosomes in terms of function and structure?
A

Attached ribosomes: found attached to the exterior of the rough ER; are responsible for generating proteins which will be part of a membrane or which will be stored in units called vesicles. Bound ribosomes also translate mRNA for proteins which will be moved outside the cell

Free ribosomes: located in the cytosol and can move about the cell; synthesize proteins that are released into the cytosol and used within the cell

34
Q
  1. What’s the purpose of signal peptide or signal sequence?
A

A signal sequence binds to a receptor protein on the surface of an organelle; a channel forms in the organelle membrane and protein enters

35
Q
  1. Which organelles employ the use of signal sequences to target protein delivery to them?
A

Rough ER, Golgi apparatus

36
Q
  1. What is a signal recognition particle? What does it do?
A

A signal sequence that stops translation and send the ribosome to the ER; SRP is looking for a large ribosomal subunit that is searching for a particular sequence

37
Q
  1. Describe some post-translational modifications that some proteins will undergo before becoming functional.
A

Proteolysis: polypeptide is cut by proteases

Glycosylation: addition of sugars to form glycoproteins; the sugars can act as signals; others help form membrane receptors

Phosphorylation: addition of phosphate groups catalyzed by protein kinases; the charged phosphate groups change conformation and may expose active sites or binding sites

BIOL 213 (8 decks)

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