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Biochemistry I > Final > Flashcards

Final Flashcards

1
Q

PTransM: function of enzyme peptidases or proteases

A

cleavage of peptide bond

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2
Q

PTransM: functions of disulfide cross linking

A

joining to Cysteine groups together S-S to make cystiene

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3
Q

Process of preproinsulin to insulin

A

after membrane transport (from ribosomes), the leader sequence is cleaved by protease then the resulting proinsulin is folding using disulfide bonds and lastly, the connecting sequence gets cleaved resulting in the final mature insulin

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4
Q

Does proinsulin or insulin run faster on polyacrmylamide gel?

A

insulin runs faster because it has a lower MW so it will be at bottom while the pro insulin will be at the top (heaviest MW)

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5
Q

PTransM: acetylation of histone tails

A

lysine w/ histone tail + Acetyl CoA + HAT = opening of the double helix which allows enzymes to come in for transcription
Reverse you use HDAC to put back together

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6
Q

PTransM: GPI anchors

A

GPI anchors proteins into the cell membranes at the C terminus

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7
Q

PTransM: Vit C Dependent

A 
example being the hydroxylation
Vit C (acts as an antioxidant) is required so it can convert Fe3+ to Fe2+ so it can be used in the proline --> hydroxylproline reaction (IMPORTANT in SCURVY disease, aka lack of vit C disease)
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8
Q

PTransM: function of kinases

A

phosphorylation of hydroxyl groups (SER, THR, TYR)

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9
Q

PTransM: function of phosphotases

A

removal of PO4 group from a phosphorylated side chain

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10
Q

PTransM: Phosphorylation of CTD in RNA 2 poly (EUK) is a form of PTM and regulation. What is the protein that acts as a kinase?

A

TFIIH

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11
Q

PTransM: N linked glycosylation

A

occurs on ASN side chains, occurs in ER during synthesis, occurs b/w the amide N of the ASN and the C-1 of the amino sugar residue

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12
Q

PTransM: O linked glycosyaltion

A

occurs on SER and THR side chains, bond occurs b/w OH of the SER and THR and the amino sugar of the sugar residue

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13
Q

PTransM: zinc finger

A

zinc finger is bound to 2 CYS and 2 HIS residues. ZFD interact with the major groove with 3 consecutive bases from one strand of B-DNA

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14
Q

PTransM: Chaperonin

A

assists in protein folding, have to have hydrolysis of ATP molecules

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15
Q

PTransM: Ubiquitin

A

mostly highly conserved protein known in PRO and EUK, last form of PTM used to degrade protein, requires energy and LYS in target proteins, proteasome recognizes the polyubiquitinated protein that catalyzes the degradation of that protein

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16
Q

Biotechnology: basic cloning process

A

mRNA + reverse trancriptase = cDNA which is joined to the plasmid, that newly synthesized plasmid is then inserted into the E coli

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17
Q

Biotechnology: basic step in recombinant DNA experiment

A

1) Preparation of DNA
2) Cleavage of DNA in particular sequences
3) Ligation of DNA fragments
4) Introduction of recombinant DNA into compatible host cells
5) Replication and expression of recombinant DNA in host cells
6) Identification of host cell that contain the recombinant DNA of interest

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18
Q

Biotechnology: endonucleases are needed for

A

for reconstruction, they have to cut vector and pop in the target of the gene to that region

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19
Q

Biotechnology: Ligase is needed for

A

joining the cDNA into the plasmid

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20
Q

Biotechnology: Restriction enzymes

A

cut DNA at highly specific sequences, they have to be palindromic sequences (inverted repeats)

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21
Q

Biotechnology: in order to replicate, a plasmid MUST be

A

circular AND must contain a replicon

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22
Q

Biotechnology: what do you NOT want to have in your target DNA?

A

you do NOT want to have introns, thats why you use cDNA

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23
Q

Biotechnology: preparation of cDNA

A

mRNA + oligo (T) primer + reverse transcriptase = cDNA and mRNA (next the mRNA is degraded and TTTT is attached at the 3’ end of the cDNA, next DNA poly is added and made into a double stranded cDNA, next you will insert that into vector into plasmid

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24
Q

Biotechnology: Are probes used to screen?

A

probes are used to scan cDNA library for particular DNA sequences

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25
Q

Biotechnology: 3 possibilities of the experiment findings

A

1) no transformation
2) blue colonies cells were transformed but they did not contain the inserts
3) white colonies cells were transformed and they DID contain the inserts

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26
Q

Biotechnology: ampicillin

A

cells that are resistant to this will be white or blue colonies

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27
Q

Biotechnology: Dideoxy method

A

contain an H at the 3’ position where there is normally a OH. These are chain terminators, if you incorporate one of these, it will not attack incoming nucleotides and will not create a phosphodiester bond, terminates at that point where this is incorporated, done through a machine, makes exponential copies of the target sequences.

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28
Q

Translation: initiation in PRO

A

recognized by shine delgrano’s sequence in mRNA by 16S rRNA

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29
Q

Translation: formulated MET

A

only found in PRO, this recognizes AUG (start codon)

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30
Q

Translation: methionine’s found in PRO

A

both formulated MET external (Fmet-tRNA) and regular MET internal

31
Q

Translation: Methionine’s found in EUK

A

ONLY regular MET, no formulated MET

32
Q

Translation: formylmethionyl

A

form of post translational modification, after tRNA gets transcribed, formyl group attaches to the amino group

33
Q

Translation: Steps of initiation of PRO

A

30S will tract for AUG and position itself w/ 3 codons in place to position tRNA’s, anticodon will be complimentary of codon mRNA, 16S of the 30S will find the shine delgrano’s sequence, once found the IF’s come in and recruit 50S resulting in the whole 70S complex

34
Q

Translation: Initiation factors in pro and euk

A

pro (3)

euk (8 or more)

35
Q

Translation: Elongation factors (pro) and their process

A

EF-Tu: bring in amino acid and position on codon , GTP gets hydrolyzed to GDP
EF-Ts: recycle GDP and turn back into GTP so EF-Tu can use it again for another cycle
Peptidyl transferase comes in to attach the amino acids creating a peptide bond
EF-G: once created, EF-G will move peptidyl-tRNA to the P site and allow the A site to be open for another amino acid

36
Q

Translation: peptidyl transferase

A

catalyzes peptide bond formation

37
Q

Translation: 3 steps for chain elongation

A

1) positioning correct amino aicd tRNA in the A site
2) Formation of the peptide bond
3) Shifting mRNA by one codon

38
Q

Translation: Termination are caused by what

A

Termination factors

39
Q

Translation: Termination steps

A

e coli releases termination factors, the TF will come in and bind to stop codons (UAA, UAG, UGA), once bound the polypeptide chain will be released by activating hydrolysis of the peptidyl-tRNA

40
Q

Translation: Differences b/w PRO and EUK, ribosomal structure

A

same process, PRO: 70S– 50S + 30S (16S recognizes shine delgrano)
euk: heavier in weight 40S + 60S = 80S

41
Q

Translation: Differences b/w PRO and EUK, Initiator tRNA

A

pro: n-formylmethionyl-tRNA
euk: methionyl-tRNA, 5’ cap site is recognized as the origin of translation, 40S will find the cap, tracks for the 1st AUG, MET binds to the codon, recruting the 60S resulting in whole complex 80S

42
Q

Translation: Differences b/w PRO and EUK, initiation factors

A

pro: IF 1, 2, 3
euk: 8 or more

43
Q

Translation: Differences b/w PRO and EUK, Elongation

A

pro: EF-Tu, EF-Ts, EF-G (3)
euk: EF1 and EF-Ts (2)

44
Q

Translation: Differences b/w PRO and EUK, Termination

A

pro: RF 1 and RF 2
euk: eRF1 (1)

45
Q

Translation: Differences b/w PRO and EUK, mRNA

A

For EUK, the 5 capping and poly A tail aid in stability

46
Q

Translation: Differences b/w PRO and EUK, Protein synthesis

A

pro: cytoplasm
euk: nucleus

47
Q

Streptomycin

A

inhibits translation only attacks PRO system, treats bacterial infection

48
Q

Purocycin

A

dont ever use to treat, kills protein synthesis

49
Q

Genetic code:
overlapping or non-overlapping
punctuation or no punctuation
Degenerate or not?

A

non overlapping, NO punctuation, and DEGENERATE

50
Q

Genetic code: How many different codons are there for 20 amino acids?

A

64 codons

51
Q

Genetic code: Stop codons

A

UAA, UAG, UGA

52
Q

Genetic code: Start codons

A

AUG which is the only codon for Methionine

53
Q

Genetic code: Some tRNA molecules can recognize more than one codon. The recognition of the 3rd base in the codon by the anticodon is called

A

the wobble

54
Q

Genetic code: On the CCA acceptor stem, there is an aminoacyl-tRNA attached via

A

ester linkage

aminoacyl-tRNA is an amino acid ester of tRNA

55
Q

Genetic code: function of aminoacyl tRNA synthetase

A

attaches amino acid to CCA acceptor stem on tRNA

56
Q

Genetic code: Aminoacyl-tRNA sythetase reaction, what does it have to have

A

needs ATP for reaction to occur

57
Q

RNA processing: what are the 3 steps of EUK PTranscM

A

1) 5’ppp capping
2) poly A tail
3) splicing

58
Q

RNA processing: For the capping of the 5’ end of euk mRNA, what is the linkage called b/w the GTP molecule and precursor mRNA?

A

5-5 triphosphate linkage

1 PO4 on the GTP and 2 PO4 on the precursor mRNA

59
Q

RNA processing: function of S-adenosyl methionine

A

the enzyme that caps and methylates CAP 0 at N-7

60
Q

RNA processing: What begins/synthesizes polyadenylation? And at what end of the mRNA precursor?

A

RNA poly 2!! and at the 3’ end of the mRNA precursor

61
Q

RNA processing: CPSF forms a complex containing what enzyme? This helps catalyze the cleavage of the transcript downstream

A

RNA endonuclease

62
Q

RNA processing: After the endonuclease dissociates, the new 3’ end of the precursor is polyadenylated with what enzyme?

A

poly A polymerase

which results in the polyadenylated mRNA precursor

63
Q

RNA processing: What do the splice sites contain as well as the branch site? These splice sites are also called what?

A

5’ splice site is GU, branch site is an A, and the 3’ splice site is an AG
—introns

64
Q

RNA processing: What is the spliceosome?

A

a RNA protein complex that catalyzes splicing reactions

65
Q

RNA processing: During the removal of the intron, what group attaches the 2’OH group on the 5’ splice site?

A

the branch site, A

66
Q

RNA processing: After the 2’OH group is attacked by the A, what is the resulting linkage called? what is this overall process called? How is the newly OH group oreinted?

A

2-5 phosphodiester linkage, transesterfication, hanging 3’ OH group from the 5’ splice site

67
Q

RNA processing: The newly 3’OH group hanging off of the 5’ splice site attacks what next?

A

The 3’ splice site

68
Q

RNA processing: After the 3’OH from the 5’ splice site attacks the 3’ splice site, what does it result?

A

mature mRNA and lariat shaped molecule

69
Q

Thalassemia is caused by ______ mutation which causes degradation of the alpha and beta cells

A

splicing

70
Q

tRNA processing: which endonuclease cleaves the primary transcript?

A

RNase P

71
Q

tRNA processing: what enzyme adds the CCA sequence to the 3’ end

A

tRNA nucleotidyl transferase

72
Q

Rifampicin

A

inhibits transcription by blocking the RNA poly from binding

73
Q

Actinomycin

A

prevents DNA to be used as a template

74
Q

Cisplatin

A

inhibitor of replication and transcription

Biochemistry I (7 decks)

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