Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

CMMB 411 > UNIT 4 > Flashcards

UNIT 4 Flashcards

1
Q

what are the 4 components for translation

A

tRNA, mRNA, ribosome, and aminoacyl tRNA synthetase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

function of mRNA

A

consists of codons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

function of tRNA

A

provides physical interface btw amino acids being added to growing polypeptide chain and codons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

function of aminoacyl tRNA synthetase

A

couple amino acids to specific tRNAs that recognize the appropriate codon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

function of ribosome

A

composed of RNA and protein, coordinated correct recognition of mRNA by each tRNA and catalyzes peptide bond formation btw growing chain and amino acid attached to selected tRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what is open reading frame (ORF)

A

protein coding region of mRNA that is composed of contiguous, non-overlapping strings of codons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what are the start codons and their order

A

pro: AUG>GUG>UUG
euk:AUG
codes for Met

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what are the stop codons

A

UAA, UAG, UGA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

describe how many ORF’s in pro and euk

A

pro-monocistronic (single)

euk-polycistronic (multiple)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

components of prokaryotic mRNA

A
  1. ORF
  2. ribosome binding site (rbs)
  3. spacer
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what is the ribosome binding site (rbs)

A

short sequence upstream of start codon that facilitate binding of the ribosome to mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what is Shine-Dalgarno sequence

A

the ribosome binding site sequence
located on 5’ side of start codon
5’UAAGGAGGU3’ 4-8nts
purine rich

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

how does ribosome binding site work

A

complementary to Shine-Delgarno sequence is 16S rRNA

ribosome base pairs with this, aligning ribosome to beginning of ORF

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what is 5’ cap

A

a chemical modification in eukaryotes that recruits ribosome and stabilizes mRNA (joined to 5’ end of mRNA via 5’ to 5’ linkage)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what is the Kozak sequence

A

purine three bases upstream of start codon, and guanine immediately downstream (most lack but those that have, increase the efficiency of translation)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what is a 3’ poly-A tail

A

added be enzyme poly-a-polymerase to 3’ end of mRNA, results in stabilization of mRNA and more efficient translation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

how long are tRNAs

A

75-95 nts

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what does the 3’ end of tRNA have and its function

A

universally conserved CCA sequence

-absolutely required for protein synthesis because that is the site that is attached to cognate amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

describe the unusual nucleotides found in tRNA

A
  • post transcription
  • found in all 4 bases
  • more complicated modifications in purines
  • some are species specific, some are tRNA specific
  • modified by specific enzymes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

what are the three roles of modification in tRNA

A

stability, sequence diversity, anticodon-codon recognition

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Stability has a role in the modification of tRNA, describe it

A

without some of these modifications t1/2 of tRNA reduced from hours to minutes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

sequence diversity has a role in the modification of tRNA, describe it

A

offers extra recognitions for aminoacyl-tRNA synthetases to recognize the appropriate tRNA for amino acid charging

23
Q

anticodon-codon recognition has a role in the modification of tRNA, describe it

A

expansion of the capability of a tRNA to recognize multiple codons (eg 1 tRNA can possibly recognize 3 codons)

24
Q

describe the secondary structure of tRNA

A

clover leaf like structure
acceptor arm: site of attachment of the amino acid, formed by pairing between 5’ and 3’ end of the tRNA molecule; contains the 5’CCA3’ sequence
D loop: made up of dihydrouridines
Anticodon loop: contains the anticodon (3 nucleotide long sequence that is responsible for recognizing the codon by base pairing with the mRNA) on it’s 3’ end it has purine and 5’ end it has uracil
variable loop: varied from 3-21 bases
TPsi loop: contains unusual base PsiU (sequence reads 5’TPsiUCG3’

25
Q

Describe the tertiary structure of tRNAs

A

inverted L shape

26
Q

Describe the 4 steps to attach amino acids to tRNA

A
  1. Recognize acceptor arm and anticodon arm
    eg. Met/Trp
  2. Recognize specific nucleotide pair in acceptor arm
    eg. Ala and Cys
    G3-U70 pair in acceptor arm of Ala-tRNA
    C3-U70 pair on acceptor arm of Cys-tRNA
    change C3-G70 to G3-U70 in Cys-tRNA switched this mutated tRNA to be charged with Ala
  3. recognize variable loop
    eg. Serine
  4. recognize modified base
    eg. Y in Phe-tRNA
27
Q

describe a charged and uncharged tRNA

A

charged contains an amino acid

uncharged has no amino acid

28
Q

What are the two classes of enzymes (tRNA synthetases)

A

Class I enzymes: attach amino acid to 2’OH of the tRNA (generally monomeric)
Class II enzymes: attach amino acid to 3’OH of tRNA (typically dimeric or tetrameric)

29
Q

What are the function of aaRS

A

recognize different combinations of identity elements in tRNA

30
Q

Describe the modular structure of aaRS

A
  • catalytic domain
  • tRNA recognition domain
  • editing domain (may be separate subunit)
31
Q

how many aaRS are there

A

20

32
Q

Describe the 1st step rxn that is catalyzed by aaRS

A

Adenylation (transfer of AMP)-done via hydrolysis of pyrophosphate by pyrophosphatase
amino acid reacts with ATP to become adenylated (aminoacyl-AMP) and releases PPi (pyrophosphate)
RESULT: amino acid is attach to adenylic acid via high energy ester bond which the carbonyl group of amino acids is joined to the phosphorylated group of AMP
[amino acid+ATP->aminoacyl-AMP + PPi]

33
Q

Describe the 2nd step in the rnx that is catalyzed by aaRS

A

tRNA charging-
adenylated amino acid (which remains tightly bond to synthease) reacts with tRNA
RESULT: transfer of amino acid to 3’ end of tRNA via the 2’ or 3’ hydroxyl and release of AMP
[amino acid+tRNA=ATP->aminoacyl-tRNA+AMP+PPi]
[PPi->2Pi]

34
Q

What is the error frequency for the amino acid charging step
and what is the overall error rate

A

~10^-5

overall=1.67*10^-5

35
Q

What is the double sieve model

A

proposing that an amino acid larger than the correct one is rarely activated because (1) it is too large to fit into the active site of the tRNA synthetase (first sieving), and (2) the hydrolytic site of the same synthetase is too small for the correct amino acid (second sieving). Thus, an amino acid smaller than the correct one can be removed by hydrolysis.

  • Active site (AS, SS) and editing site (ES) have different shape and size
  • AS fits into cognate substrate the best (Ile doesn’t fit into editing)
  • Leu is too big to fit into AS but both Ile and Val can bind
  • ES is too small for Ile but fits Val
36
Q

Describe the proofreading function of Ile-tRNAIle synthase

A
  • with val attached to tRNAIle, the CCA tail shuttles betwen AS and ES
  • Val will be hydrolyzed from tRNAIle
  • -this is the 1st reason why the 3’ end tail of tRNA has to be single stranded
37
Q

describe the 2 subunits that make up the ribosome

A

small subunit: mRNA binding channel
-recognition of prokaryotic RBS
-decoding centre(charged tRNAs read/decode the codon units of mRNA)
-part of tRNA binding sites
-(interacts with anticodon loop)
-mRNA translocation
large subunit: peptidyltransferase centre (rRNA)(responsible for formation of peptide bond)
-nascent polypeptide exit channel
-part of the tRNA binding site
-(interacts with the acceptor arm)
-factor binding centre (GTPase associated region, GAR)

38
Q

Describe the ribosome cycle

A
  • translation begins with binding of the mRNA and initiating tRNA to a free, small subunit of the ribosome
  • small subunit - mRNA inititator-tRNA complex then recruits large subunit to create intact ribosome with mRNA sandwiched btw 2 subunits
  • protein synthesis initiated, commencing the start codon at the 5’ end of the message and progressing towards 3’ end of mRNA
  • as ribosome translocates from codon to codon, 1 charged tRNA after another is slotted into the decoding and peptidyl transferase centres of ribosome
  • when elongating ribosome encounters a stop codon, now completed polypeptide chain released and ribosome dissociates from the mRNA as separate large and small subunits
39
Q

what 3 events needs to occur for translocation initiation

A
  • ribosome recruited to mRNA
  • charged tRNA must be placed into p site of ribosome
  • ribosome must be precisely positioned over start codon
40
Q

what are 3 binding site to perform peptidyl transferase rxn

A

A-binding site for amino acylated tRNA
P-binding site for peptidyl tRNA
E-binding site for tRNA that is released after the growing polypeptide chain has been transformed to aminoacyl-tRNA

41
Q

describe mRNA binding path

A

mRNA wraps around neck of 30S subunit

42
Q

what is degeneracy

A

when one amino acid can potentially have more than one genetic code

43
Q

describe 4 features of genetic codes

A
  1. AUG is the most common translation initiation codon
  2. 2 translation termination codons
  3. mutation in the 3rd position is less likely to cause a change in amino acid at the protein level
  4. mutation in the 1st codon will give a similar amino acid in many cases
44
Q

what is third base wobble

A

there are 20 standard amino acids. These 20 standard amino acids are encoded by 61 codons, each codon containing 3 bases. If you look closely at a list of codons that encode for a single amino acid, you may notice that one amino acid is encoded by many codons, usually with the first 2 bases the same, and the third codon variable. This third codon is known as a wobble, and the bond formed between this third base on the tRNA and the ribosome is not as stable, thus its importance is diminished.

45
Q 
G
C
A
U
I
A 
U or C
G
U
A or G
A, U, or C
46
Q

which base is more flexible

A

34 compared to 35, and 36

47
Q

function of IF1, IF2, IF3

A

IF1-prevents tRNAs from binding to portion of small subunit that will become part of A site
IF2-GTPase (protein that binds and hydrolyzes GTP) that interacts with key components of initiation machinery (small subunit, IF1, and charged initiator tRNA(fMet-tRNAi)–facilitates the association of charged initiator with small subunit and prevents other charged tRNAs from associating with small subunit
If3-binds to small subunit and prevents it from reassociating with large subunit

48
Q

Prokaryotic Translation Initiation Process

A
  1. IF3 binds to 30S subunit
    - prevent the association of the 50S subunit with the 30S subunit
    - binds to the E site in the 30S subunit
  2. Binding od IF1
    - blocks the A site
    - recruits IF2-GTP
  3. Binding of IF2-GTP
    - binds close to P site
  4. Recruitment of fMet-tRNAi and mRNA
    - can be in any order
    - the initiation codon is in P site
    - fMet-tRNAi inserted at the P site by IF2
    - IF3 binds to the G-C region in the anti-codon
    - formation of 30S initiation complex
  5. Anticodon in fMet-tRNAi base pairs with the initiation codon
    - conformational change in 30S subunit
    - dissociation of IF3
  6. Formation of the 70S initiation complex
    - Binding of the 50S subunit
    - stimulation of GTPase activity in IF2-GTP
    - GTP hydrolyzed
    - dissociation of IF2-GDP and IF1
    - site is empty
    - ready to accept a charged tRNA
49
Q

Key steps in bacterial translation elongation

A
  1. Aminoacyl-tRNA binding
    - mediated by EF-Tu-GTP
    - GTP hydrolysis of EF-Tu-GTP
    - Locking step*
    - accomodation*
  2. Peptide bond formation
  3. Translocation
50
Q

How is charged tRNA delivered to A(T) site

A

EF-Tu-GTP binds to a charged tRNA
-protects the activated amino acid from hydrolysis
-delivers the charged tRNA to the assembled ribosomes (70S not 30S)
-ensures the correct codon-anticodon interaction
With proper codon-anticodon interaction
-EF-Tu interacts with the factor binding centre in the large subunit
-GTP hydrolysis
-Release of EF-Tu-GDP
Reloading of GTP to EF-Tu-GDP by EF-Ts

51
Q

Possible interactions between codons and anticodons: selection by EF-Tu-GTP

A

12, 123,23* , 13

52
Q

Possible interactions between codons and anticodons: selection by locking

A

12, 123,23

53
Q

Two other mechanisms for selection of correct aminoacyl-tRNA

A
  1. Locking
    - checking the correct pairing of the 1st two nucleotides in the codon with the anticodon by several conserved nucleotides (A 1492, A1493 and G530) in 16S rRNA
  2. Correct paring of the 1st 2 nucleotides in codon-anticodon region
    - allows hydrogen bond formation btw the 2 A nucleotides in 16S rRNA and the codon-anticodon structure in the A-site of the ribosome
    - locks the mRNA-tRNA complex to the 30S subunit (16s rRNA)

CMMB 411 (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions