Molecular Flashcards

1
Q

How many times does DNA loop around histone octamer to form a nucleosome

A

2

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2
Q

What charge do phosphate groups give DNA

A

Negative

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3
Q

What gives a positive charge to histone

A

Lysine and arginine

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4
Q

Which phase does DNA and histone synthesis occur in?

A

S phase

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5
Q

Which phase does Cell Division occur in?

A

M phase

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6
Q

In what way is Mitochondria’s own DNA different than ours?

A

It is circular and does not have histones

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7
Q

What is heterochromatin?

A

Condensed DNA, appearing dark on EM

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8
Q

Is Heterochromatin transcriptionally inactive?

A

Yes

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9
Q

What are Barr Bodies?

A

Inactive X chromosomes may be visible on the periphery of nucleus

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10
Q

What’s DNA methylation involved in?

A

Genetic imprinting, X chromosome inactivation, aging, carcinogenesis

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11
Q

What is DNA methylation?

A

Methyl group is added to cytosine,

In CG islands

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12
Q

What does DNA methylation do?

A

It prevents transcription

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13
Q

What does histone acetylation do?

A

Histone acetylation makes DNA active

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14
Q

What’s nucleoside ?

A

Base plus (deoxyribose sugar) Nucleoside= S

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15
Q

What’s Nucleotide?

A

Base plus (deoxyribose sugar) plus phosphate, linked by 3’-5’ phosphodiester bond. NucleoTide= PhosphaTe

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16
Q

What does the 5’ end of incoming nucleotide bear?

A

Triphosphate hence energy source

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17
Q

Triphosphate bond is the target of?

A

3’ OH attack

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18
Q

Purines are?

A

PURe As Gold—> Adenine, Guanine, 2 rings

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19
Q

Pyriminides are?

A

CUT the PY——> cytosine, uracil, thymine. 1 ring

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20
Q

Thymine has a?

A

Methyl group

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21
Q

C-G bonds have how many h bonds?

A

Three

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22
Q

Higher the C-G content, higher the?

A

Melting temp of DNA, C-G bonds___> Crazy Glue bonds

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23
Q

Deamination of cytosine forms ?

A

Uracil

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24
Q

Deamination of adenine forms?

A

Hypoxanthine

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25
Q

Deamination of guanine forms?

A

Xanthine

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26
Q

Deamination of 5-methlycytosine forms?

A

Thymine

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27
Q

Methylation of uracil forms?

A

Thymine

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28
Q

Uracil is found in?

A

RNA

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29
Q

Thymine is found in?

A

DNA

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30
Q

Amino acids necessary for purine synthesis?

A

Cats PUrr until they CAG—-> Glycine, Aspartate, Glutamine

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31
Q

What does unmethylated CG do?

A

Stimulates immune response

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32
Q

What does bacterial methylation?

A

Bacteria methylates cytosine and adenine

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33
Q

What does bacterial methylation do?

A

It protects bacteria from viruses, phages

Non methylated DNA destroyed by endo nucleases. Restriction modification systems

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34
Q

What does histone methylation do?

A

It makes DNA mute

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35
Q

What is drug induced lupus?

A

Fever, joint pains, rash after starting drug

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36
Q

What are the lab findings in drug induced lupus

A

Anti histone antibodies in contrast to

Anti dsDNA in classic lupus

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37
Q

What are the classic drugs for Drug induced Lupus?

A

Hydralazine, Procainamide, Isoniazid

HPI

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38
Q

What is adenosine deaminase deficiency?

A

Degradation of adenosine into inosine

dATP increases
Lymphotoxicity

One of the major causes of SCID

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39
Q

What is Lesch Nehan syndrome?

A

Absent HGPRT

Hence increased uric production
and increased de novo synthesis (prpp, imp increases)

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40
Q

What is the classic presentation of Lesch nyhan

A
H hyper uricemia (orange sand)
G gout 
Pissed off (aggression, self mutilation)
Retardation 
DysTonia 

MALE

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41
Q

What is orotic aciduria?

A

Defective UMP synthase, increased orotic acid in urine

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42
Q

What are the symptoms of orotic aciduria?

A

Megaloblastic anemia, you give folate and still it doesn’t get better

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43
Q

What is treatment of orotic aciduria?

A

You give uridine, bypasses UMP synthase

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44
Q

What are the levels of RBC, MCV, homocysteine and MMA in folate, B12 def?

A

RBC increases both
MCV increases both
Homocysteine increases both
MMA, only increased in B12

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45
Q

What is the origin of replication?

A

It is the AT rich pair sequence (found in promotors as well)

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46
Q

Replication fork is the _________ along dna template where _____________

A

It is the y shaped region

where lagging and leading strands are synthesised

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47
Q

What is the role of helicase?

A

Unwinds dna template at replication fork

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48
Q

What are single stranded binding proteins?

A

Prevents strands from re annealing

Stabilisation

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49
Q

Dna topo isomerases can create __________ stranded breaks to ______________

A

single or double

to add or remove super coils

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50
Q

Which drug inhibits TOP 1 in eukaryote?

A

Irinotecan/topotecan

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51
Q

Which drug inhibits TOP11 in eukaryote?

A

Etoposide/teniposide

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52
Q

Which drug inhibits TOP11 and TOP1V in prokaryotes?

A

Floroquinolones

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53
Q

Primase is enzyme which makes _________ on which ________ can initate replication

A

Rna primer

Dna polymerase 111

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54
Q

What is the role of DNA polymerase 111?

A

Only in prokaryotes

Has 5’-3’ synthesising activity and 3’-5’ exonuclease activity

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55
Q

How do drugs block replication?

A

They have modified 3’OH, thereby preventing addition of next nucleotide (chain termination)

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56
Q

What is the role of DNA polymerase 1?

A

In prokaryotes only

Remove rna primer, replace it w dna
And have 5’-3’ exo nuclease activity

DNA polymerase delta (in Euko)

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57
Q

What is dna ligase?

A

Joins Okazaki fragments

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58
Q

What are telomerases?

A

Eukaryotes only

TTAGGG+AACC 3’ is extended
CCUUGG (has rna template)

DNA polymerase
Fills in remaining gaps on lagging strand

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59
Q

What is the use of telomerases?

A

Avoids loss of genes after every duplication

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60
Q

What cells have high levels of telomerase ?

A

Hematopoietic cells, epidermis, hair follicles, intestinal mucosa

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61
Q

What does it mean to have genetic code be unambiguous?

A

One codon is specific for one amino acid

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62
Q

What does it mean to have genetic code by degenerate/redundant?

A

One amino acid may be specific for several codons

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63
Q

What is the Wobble hypothesis mean?

A

It means that the codons may differ in third base, and may code for the same tRNA/amino acid. Specific base pairing is usually required only in the first 2 nucleotide positions of mrna

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64
Q

What are the exceptions of Wobble phenomenon?

A

Methionine (AUG)
Tryptophan (UGG)

Encoded by one codon

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65
Q

What does it mean to have a genetic code be commaless, non overlapping ?

A

Read from a fixed starting point as continuous sequence of bases.
Exception some virsus

66
Q

What does it mean to have genetic code be universal?

A

Genetic code is conserved throughout evolution (exception: mitochondria)

67
Q

What are point mutations?

A

Silent, missense, nonsense

68
Q

What is transition and transversion of point mutations?

A

Transition: purine to purine (A to G) or pyrimidine to pyrimidine (C to T)

Tranversion: purine to pyrimidine (A to T) or pyrimidine to purine(C to G)

69
Q

What is silent mutation?

A

Nucleotide substitution at 3rd position of codon (tRNA wobble), but same amino acid

70
Q

What is missense mutation?

A

Nucleotide substitution resulting in changed amino acid (called conservative if new amino acid is similar in chemical structure )

71
Q

What is example of missense mutation?

A

An example, is sickle cell anemia

In which 6th codon in beta chain, substitution of glutamic acid with valine.

72
Q

What is nonsense mutation?

A

Nucleotide substitution resulting in early stop codon (UAG, UAA, UGA). Nonfunctional protein

73
Q

What is frameshift mutation?

A

Deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream

74
Q

What are the effects of frameshift mutation?

A

Shorter or longer

Functional disruption or alteration

75
Q

What are the examples of frameshift mutation?

A

Duchenne muscular dystrophy

Tay Sachs disease

76
Q

What are the severity of the mutations?

A

Frameshift
Nonsense
Missense
Silent

77
Q

What happens in lac operon: low glucose, high lactose

A

High AC activity, ATP——>cAMP. High cAMP:ATP ratio.

cAMP binds to the CAP, which binds to CAPsite in promoter

Which leads to RNA polymerase transcribing the three structural genes, z, y, and a

Lactose breaks into pieces, binds to repressor( lacl gene) bound to operator and leads to its inactivation

78
Q

What happens in lac operon: high glucose, low lactose

A

cAMP-CAP on CAP site absent and repressor protein present on operator.

Lac genes not expressed

79
Q

What happens in lac operon: low glucose, low lactose

A

cAMP-CAP on CAP site present and repressor protein present on operator.

Lac genes not expressed

80
Q

What happens in lac operon: High glucose, high lactose

A

Very low basal expression

81
Q

What are the dna repair systems for single strand?

A

Nucleotide excision repair, base excision repair, and mismatch repair

82
Q

What are the steps of nucleotide excision repair?

A

Specific endonucleases release the oligonucleotides containing the damaged bases

DNA polymerase fills the gap

DNA ligase reseals the gap

83
Q

What does the nucleotide excision repair do?

A

It repairs the bulky helix distorting lesions

84
Q

In what phase does the nucleotide excision repair work in?

A

It works in the G1 phase of the cell cycle

85
Q

What are the clinical correlates of nucleotide excision repair?

A

Defective in xeroderma pigmentosum

Cannot repair the pyrimidine dimers caused by UV exposure

86
Q

What are the symptoms of xeroderma pigmentosum

A

Dry skin, various levels of pigmentation

Sun burning easily, freckles

Children——skin cancer

87
Q

What are the steps to base excision repair?

A

Specific glysosylases remove the altered base and create AP site

AP nucleotides cleave the 5’ end

Lyase cleave the 3’ end

DNA polymerase beta fills the gap

DNA ligase seals it

88
Q

What phase in cell cycle does base excision repair occurs in?

A

Occurs throughout the entire cell cycle

89
Q

Does base excision repair occurs in spontaneous/toxic deamination?

A

Yes

90
Q

What are the steps to mismatch repair?

A

Newly synthesised strand is recognised and mismatched nucleotides are removed and the gap is filled and resealed.

91
Q

What does mismatch repair do?

A

It repairs dna when proofreading misses errors

92
Q

Does base damage occur in mismatch repair system?

A

No

93
Q

Which phase in cell cycle does mismatch repair occurs in?

A

S/G2 phase (after dna has been synthesised)

94
Q

What is clinical correlation of mismatch repair?

A

Defective in lynch syndrome, (HNPCC)

Germline MLH1 and MSH2 mutation in dna mismatch repair enzymes

Leads to colon cancer via micro satellite instability

95
Q

What are the dna repair systems for double strand?

A

NHEJ and homologous recombination

96
Q

What is NHEJ?

A

Brings 2 ends of dna fragments to repair double stranded breaks

97
Q

Is there requirement for NHEJ?

A

No, there is no requirement of homology

98
Q

What happens to the DNA in NHEJ?

A

Some of it is lost

99
Q

____________ is the clinical correlate of NHEJ disorders?

There is ___________ on chromosome 11

Mostly the children are healthy in the ________

Also have high risk of __________

Can develop high risk of __________

There is also ____________

A

Defective in ataxia telangiectasia

ATM gene mutation on chromosome 11

Mostly the children are healthy in the first year but begin to slow walking developers, leads to progressive motor problem, they end up in wheelchairs at age 10

Also have high risk of infections and recurrent sinuses

Can develop high risk of cancer

There is also fanconi anemia

100
Q

What is homologous recombination?

A

Strand from damaged double stranded dna is repaired by using a complementary strand from the intact homologous double stranded dna as a template

101
Q

What is the requirement for homologous recombination?

A

Two homologous dna duplexes

102
Q

What happens to the dna in homologous recombination?

A

Restores duplexes accurately without loss of nucleotides

103
Q

What is the clinical correlation of homologous recombination?

A

Defective in breast ovarian cancers with BRCA1 mutation

104
Q

What are the types of DNA damage?

A

Depurination, 1000x frequency, purines are lost

Deamination,
100x
Frequency,
Cytosine loses NH2—>uracil

105
Q

What are the single strand DNA repair systems?

A

Nucleotide excision repair, base excision repair and mismatch repair

106
Q

What are the steps to nucleotide excision repair?

A
  • specific endonucleases release the oligonucleotides containing the damaged bases
  • DNA polymerase fills the gap
  • DNA ligase reseals the gap
107
Q

What are the mRNA start codons in transcription?

A

AUG—— AUG inAUGurates protein synthesis

108
Q

What does AUG code for?

A

It codes for methionine in eukaryotes

Codes for N formylmethionine fMet—- stimulates neutrophils for chemotaxis

109
Q

What are the mRNA stop codons?

A

UGA, UAA, UAG

U Go Away

U Are Away

U Are Gone

110
Q

How many RNA polymerase does prokaryotes have and what are its function?

A

I rna polymerase, and its function is to make all three kinds of RNA

111
Q

Rifampin inhibits which enzyme?

A

DNA dep rna polymerase in prokaryotes

112
Q

How many rna polymerase does eukaryotes have and what are its functions?

A

Three

Rna polymerase 1—makes rRNA. 5.8S, 18S, and 28S
Rna polymerase 11—-makes mRNA
Rna polymerase 111—-makes tRNA, and 5S of rRNA

113
Q

Do rna polymerase need primers? What do they need?

A

They don’t need primers, they need promotors and transcriptional factors

114
Q

Which enzyme does a amanitin inhibit?

A

Death cap mushrooms inhibits rna polymerase 11 in euk

Leads to acute liver failure

115
Q

Which enzyme does actinomycin D inhibit?

A

Rna polymerase in both euk and pro

116
Q

What way is mRNA read as?

A

5’ to 3’

117
Q

What are promotors?

A

Sites (TATAAT box, CCAAT box, CG box) upstream to gene locus where the rna polymerase 11 binds along with transcription factors (TFIIB, TFIID, TFIIE). It opens the helix

118
Q

What does promotor mutation do?

A

It results in dramatic decrease in level of gene transcription

119
Q

What are enhancers and what do they do?

A

DNA locus where the regulatory proteins called like activators bind and increase the expression of the gene on the same chromosome

120
Q

What are silencers and what do they do?

A

DNA locus where regulatory proteins like depressors bind and decrease the expression of gene on the same chromosome

121
Q

Where are enhancers and promoters located?

A

May be located upstream or downstream, within the intron

Due to dna coiling, they can be close to despite being many nucleotides away

122
Q

What are the untranslated regions and what are their jobs?

A

5’UTR: may be found upstream to the coding sequence,
and recognised by ribosomes to initiate translation

3’UTR: may be found following a stop codon,
and needed for post transcription gene regulation

123
Q

What is hnRNA?

A

Initial transcript of the mRNA is called the hnRNA, heterogenous nuclear rna, hnRNA. Also called pre mRNA. It is then modified and becomes mRNA

124
Q

What happens to mRNA before it gets out of the nucleus?

A

Three key modifications happens to mRNA before it gets out of nucleus into the cytosine

125
Q

What is the capping of mRNA?

A

It is one of the key modifications before leaving nucleus,

And it involves the addition of the 7-methyl guanosine cap at 5’ end

126
Q

What is the purpose of the 7 methyl guanosine cap?

A

It distinguishes mRNA from other rna

127
Q

What is splicing?

A

It is one of the key modifications before the mRNA leaves the nucleus

128
Q

What are exons?

A

Exons are expressed and exit the nucleus

129
Q

What are introns?

A

They are intervening sequences and stay inside the nucleus

130
Q

What is alternative splicing?

A

Many proteins from single same gene

DNA: exon 1, exon 2, exon 3, exon 4, exon 5
Protein 1: exon 1, exon 3, exon 5
Protein 2: exon 2, exon 4

131
Q

What are the different proteins made by alternative splicing?

A

Transmembrane vs secreted iG
Tropomyosin variants in muscle,
Dopamine receptors in brain

132
Q

What are the disorders that can be generated due to defective alternative splicing ?

A

Oncogenesis, b thalesseniam gaucher disease, Tay sach disease, Marfan syndrome

133
Q

What is polyadenylation?

A

It is one of the key modifications before mRNA leaves the nucleus

mRNA AAUAA————————-CA 3’
(Poly adenylation signal)

          CSF binds here                               CstF binds here(trans termination)

Polyadenylation of 200As at the 3’end by PAP (does require template)

CSF: cleavage and polyadenylation specificity factor
CstF: cleavage stimulating factor

134
Q

What are P bodies?

A

They are in cytoplasm, mRNA is degraded and stored in P bodies for future translation. May contain exo nucleases, decapping enzymes and micro rnas. mRNA can be translated later

135
Q

What are micro rnas?

A

Non coding rna molecules that target the 3’ UTR post transcriptionally for degradation or translational repression

136
Q

What does abnormal expression of Mi rna do?

A

Lead to silencing of the mRNA from a tumour suppressor gene

137
Q

How many nucleotides does tRNA have?

A

75-90 nucleotides

138
Q

What is structure of the tRNA in terms of protein structure?

A

Secondary structure

139
Q

Which form does it have and why? tRNA ?

A

It has a cloverleaf form, and so it can fit into ribosome properly

140
Q

What do pro and euk have in common in terms of tRNA?

A

They have CCA at 3’ end

141
Q

How many arms does tRNA have?

A

2

142
Q

What is the t arm of tRNA and what does it do?

A

T arm of the tRNA has T¥C (ribothymidine, pseudouridine, cytidine)

T arm Tethers tRNA molecule to ribosome

143
Q

What is the d arm of tRNA and what does it do?

A

D arm contains the dihydrouridine

D arm Detects the tRNA by aminoacyl tRNA synthetase

144
Q

What is the acceptor stem for amino acid in tRNA?

A

5’ CCA 3’

145
Q

What is charging of the tRNA?

A

Amino acid + ATP—-Amino acid AMP

AMP is lopped off

Amino acid makes bond with tRNA at 3’ end with OH of adenine

Aminoacyl tRNA synthetase makes the bond

146
Q

Why is amino acyl tRNA synthetase called the match maker?

A

Specific for one amino acid

147
Q

What happens when the mismatched tRNA occurs? When the wrong amino acid is added after reading of usual mRNA codon?

A

Hydrolyic editing

Aminoacyl tRNA synthetase scrutinises the amino acid

And if incorrect bond is hydrolysed from tRNA or amp

148
Q

What is responsible for accuracy of amino acid selection?

A

Amino acyl tRNA synthetase and binding of charged tRNA

149
Q

How many steps does protein synthesis have?

A

Three

150
Q

What are the steps of initiation of protein synthesis?

A

eIFs identify either the 5’cap of mRNA or the IRES (internal ribosome entry site) of 5’ UTR

Assemble the 40s subunit with the tRNA

Released when the 60s ribosomal subunit binds with the complex

151
Q

What does the process of initiation require?

A

GTP

GTP: Gripping and Going places

Going (translation)

ATP: Activation (charging)

152
Q

What are the sites of ribosome?

A

APE

A: incoming aminoacyl tRNA
P: accommodates growing peptide
E: holds Empty tRNA as it Exits

153
Q

What are the steps to elongation ?

A

1) amino acyl tRNA binds to A site (methionine is already at P site)
It requires elongation factor 1 and 2, and GTP

2) rRNA ribozyme catalyses peptide bond formation between the growing amino acid and the amino acid incoming in A site
3) ribosome moves three nucleotides toward the 3’ end of mRNA, moving peptidyl tRNA to P site (translocation)

154
Q

What are the steps of termination?

A

Release factors recognise the stop codon and halts translation

Completed polypeptide released from ribosome. Requires GTP

155
Q

What are the subunits of euk ribosomes?

A

40S +60S: 80

156
Q

What are the subunits of pro ribosomes?

A

30S + 50S: 70s

157
Q

Which way does the protein synthesis occur in?

A

N terminus to C terminus

158
Q

What are the post translational modifications?

A

Trimming and covalent alterations

159
Q

What is trimming?

A

Removal of N and C terminal propeptides from zymogen to generate mature protein, trysinogen to trypsin

160
Q

What are the covalent alterations?

A

GAPHUM

glycosylation, acetylation, phosphorylation, hydroxylation, ubiquitination, methylation

161
Q

What are chaperon proteins and what purpose they serve?

A

They are heat shock proteins (HSP 60)

That rise in numbers when exposed to stress, hypoxia, ph shift

Prevent denaturing and misfolding o