Molecular Flashcards
1
Q
How many times does DNA loop around histone octamer to form a nucleosome
A
2
2
Q
What charge do phosphate groups give DNA
A
Negative
3
Q
What gives a positive charge to histone
A
Lysine and arginine
4
Q
Which phase does DNA and histone synthesis occur in?
A
S phase
5
Q
Which phase does Cell Division occur in?
A
M phase
6
Q
In what way is Mitochondria’s own DNA different than ours?
A
It is circular and does not have histones
7
Q
What is heterochromatin?
A
Condensed DNA, appearing dark on EM
8
Q
Is Heterochromatin transcriptionally inactive?
A
Yes
9
Q
What are Barr Bodies?
A
Inactive X chromosomes may be visible on the periphery of nucleus
10
Q
What’s DNA methylation involved in?
A
Genetic imprinting, X chromosome inactivation, aging, carcinogenesis
11
Q
What is DNA methylation?
A
Methyl group is added to cytosine,
In CG islands
12
Q
What does DNA methylation do?
A
It prevents transcription
13
Q
What does histone acetylation do?
A
Histone acetylation makes DNA active
14
Q
What’s nucleoside ?
A
Base plus (deoxyribose sugar) Nucleoside= S
15
Q
What’s Nucleotide?
A
Base plus (deoxyribose sugar) plus phosphate, linked by 3’-5’ phosphodiester bond. NucleoTide= PhosphaTe
16
Q
What does the 5’ end of incoming nucleotide bear?
A
Triphosphate hence energy source
17
Q
Triphosphate bond is the target of?
A
3’ OH attack
18
Q
Purines are?
A
PURe As Gold—> Adenine, Guanine, 2 rings
19
Q
Pyriminides are?
A
CUT the PY——> cytosine, uracil, thymine. 1 ring
20
Q
Thymine has a?
A
Methyl group
21
Q
C-G bonds have how many h bonds?
A
Three
22
Q
Higher the C-G content, higher the?
A
Melting temp of DNA, C-G bonds___> Crazy Glue bonds
23
Q
Deamination of cytosine forms ?
A
Uracil
24
Q
Deamination of adenine forms?
A
Hypoxanthine
25
Deamination of guanine forms?
Xanthine
26
Deamination of 5-methlycytosine forms?
Thymine
27
Methylation of uracil forms?
Thymine
28
Uracil is found in?
RNA
29
Thymine is found in?
DNA
30
Amino acids necessary for purine synthesis?
Cats PUrr until they CAG—-> Glycine, Aspartate, Glutamine
31
What does unmethylated CG do?
Stimulates immune response
32
What does bacterial methylation?
Bacteria methylates cytosine and adenine
33
What does bacterial methylation do?
It protects bacteria from viruses, phages
| Non methylated DNA destroyed by endo nucleases. Restriction modification systems
34
What does histone methylation do?
It makes DNA mute
35
What is drug induced lupus?
Fever, joint pains, rash after starting drug
36
What are the lab findings in drug induced lupus
Anti histone antibodies in contrast to
| Anti dsDNA in classic lupus
37
What are the classic drugs for Drug induced Lupus?
Hydralazine, Procainamide, Isoniazid
HPI
38
What is adenosine deaminase deficiency?
Degradation of adenosine into inosine
dATP increases
Lymphotoxicity
One of the major causes of SCID
39
What is Lesch Nehan syndrome?
Absent HGPRT
Hence increased uric production
and increased de novo synthesis (prpp, imp increases)
40
What is the classic presentation of Lesch nyhan
```
H hyper uricemia (orange sand)
G gout
Pissed off (aggression, self mutilation)
Retardation
DysTonia
```
MALE
41
What is orotic aciduria?
Defective UMP synthase, increased orotic acid in urine
42
What are the symptoms of orotic aciduria?
Megaloblastic anemia, you give folate and still it doesn’t get better
43
What is treatment of orotic aciduria?
You give uridine, bypasses UMP synthase
44
What are the levels of RBC, MCV, homocysteine and MMA in folate, B12 def?
RBC increases both
MCV increases both
Homocysteine increases both
MMA, only increased in B12
45
What is the origin of replication?
It is the AT rich pair sequence (found in promotors as well)
46
Replication fork is the _________ along dna template where _____________
It is the y shaped region
where lagging and leading strands are synthesised
47
What is the role of helicase?
Unwinds dna template at replication fork
48
What are single stranded binding proteins?
Prevents strands from re annealing
| Stabilisation
49
Dna topo isomerases can create __________ stranded breaks to ______________
single or double
to add or remove super coils
50
Which drug inhibits TOP 1 in eukaryote?
Irinotecan/topotecan
51
Which drug inhibits TOP11 in eukaryote?
Etoposide/teniposide
52
Which drug inhibits TOP11 and TOP1V in prokaryotes?
Floroquinolones
53
Primase is enzyme which makes _________ on which ________ can initate replication
Rna primer
Dna polymerase 111
54
What is the role of DNA polymerase 111?
Only in prokaryotes
Has 5’-3’ synthesising activity and 3’-5’ exonuclease activity
55
How do drugs block replication?
They have modified 3’OH, thereby preventing addition of next nucleotide (chain termination)
56
What is the role of DNA polymerase 1?
In prokaryotes only
Remove rna primer, replace it w dna
And have 5’-3’ exo nuclease activity
DNA polymerase delta (in Euko)
57
What is dna ligase?
Joins Okazaki fragments
58
What are telomerases?
Eukaryotes only
TTAGGG+AACC 3’ is extended
CCUUGG (has rna template)
DNA polymerase
Fills in remaining gaps on lagging strand
59
What is the use of telomerases?
Avoids loss of genes after every duplication
60
What cells have high levels of telomerase ?
Hematopoietic cells, epidermis, hair follicles, intestinal mucosa
61
What does it mean to have genetic code be unambiguous?
One codon is specific for one amino acid
62
What does it mean to have genetic code by degenerate/redundant?
One amino acid may be specific for several codons
63
What is the Wobble hypothesis mean?
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
64
What are the exceptions of Wobble phenomenon?
Methionine (AUG)
Tryptophan (UGG)
Encoded by one codon
65
What does it mean to have a genetic code be commaless, non overlapping ?
Read from a fixed starting point as continuous sequence of bases.
Exception some virsus
66
What does it mean to have genetic code be universal?
Genetic code is conserved throughout evolution (exception: mitochondria)
67
What are point mutations?
Silent, missense, nonsense
68
What is transition and transversion of point mutations?
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
What is silent mutation?
Nucleotide substitution at 3rd position of codon (tRNA wobble), but same amino acid
70
What is missense mutation?
Nucleotide substitution resulting in changed amino acid (called conservative if new amino acid is similar in chemical structure )
71
What is example of missense mutation?
An example, is sickle cell anemia
In which 6th codon in beta chain, substitution of glutamic acid with valine.
72
What is nonsense mutation?
Nucleotide substitution resulting in early stop codon (UAG, UAA, UGA). Nonfunctional protein
73
What is frameshift mutation?
Deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream
74
What are the effects of frameshift mutation?
Shorter or longer
| Functional disruption or alteration
75
What are the examples of frameshift mutation?
Duchenne muscular dystrophy
| Tay Sachs disease
76
What are the severity of the mutations?
Frameshift
Nonsense
Missense
Silent
77
What happens in lac operon: low glucose, high lactose
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
What happens in lac operon: high glucose, low lactose
cAMP-CAP on CAP site absent and repressor protein present on operator.
Lac genes not expressed
79
What happens in lac operon: low glucose, low lactose
cAMP-CAP on CAP site present and repressor protein present on operator.
Lac genes not expressed
80
What happens in lac operon: High glucose, high lactose
Very low basal expression
81
What are the dna repair systems for single strand?
Nucleotide excision repair, base excision repair, and mismatch repair
82
What are the steps of nucleotide excision repair?
Specific endonucleases release the oligonucleotides containing the damaged bases
DNA polymerase fills the gap
DNA ligase reseals the gap
83
What does the nucleotide excision repair do?
It repairs the bulky helix distorting lesions
84
In what phase does the nucleotide excision repair work in?
It works in the G1 phase of the cell cycle
85
What are the clinical correlates of nucleotide excision repair?
Defective in xeroderma pigmentosum
Cannot repair the pyrimidine dimers caused by UV exposure
86
What are the symptoms of xeroderma pigmentosum
Dry skin, various levels of pigmentation
Sun burning easily, freckles
Children——skin cancer
87
What are the steps to base excision repair?
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
What phase in cell cycle does base excision repair occurs in?
Occurs throughout the entire cell cycle
89
Does base excision repair occurs in spontaneous/toxic deamination?
Yes
90
What are the steps to mismatch repair?
Newly synthesised strand is recognised and mismatched nucleotides are removed and the gap is filled and resealed.
91
What does mismatch repair do?
It repairs dna when proofreading misses errors
92
Does base damage occur in mismatch repair system?
No
93
Which phase in cell cycle does mismatch repair occurs in?
S/G2 phase (after dna has been synthesised)
94
What is clinical correlation of mismatch repair?
Defective in lynch syndrome, (HNPCC)
Germline MLH1 and MSH2 mutation in dna mismatch repair enzymes
Leads to colon cancer via micro satellite instability
95
What are the dna repair systems for double strand?
NHEJ and homologous recombination
96
What is NHEJ?
Brings 2 ends of dna fragments to repair double stranded breaks
97
Is there requirement for NHEJ?
No, there is no requirement of homology
98
What happens to the DNA in NHEJ?
Some of it is lost
99
____________ 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 ____________
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
What is homologous recombination?
Strand from damaged double stranded dna is repaired by using a complementary strand from the intact homologous double stranded dna as a template
101
What is the requirement for homologous recombination?
Two homologous dna duplexes
102
What happens to the dna in homologous recombination?
Restores duplexes accurately without loss of nucleotides
103
What is the clinical correlation of homologous recombination?
Defective in breast ovarian cancers with BRCA1 mutation
104
What are the types of DNA damage?
Depurination, 1000x frequency, purines are lost
Deamination,
100x
Frequency,
Cytosine loses NH2--->uracil
105
What are the single strand DNA repair systems?
Nucleotide excision repair, base excision repair and mismatch repair
106
What are the steps to nucleotide excision repair?
- specific endonucleases release the oligonucleotides containing the damaged bases
- DNA polymerase fills the gap
- DNA ligase reseals the gap
107
What are the mRNA start codons in transcription?
AUG—— AUG inAUGurates protein synthesis
108
What does AUG code for?
It codes for methionine in eukaryotes
Codes for N formylmethionine fMet—- stimulates neutrophils for chemotaxis
109
What are the mRNA stop codons?
UGA, UAA, UAG
U Go Away
U Are Away
U Are Gone
110
How many RNA polymerase does prokaryotes have and what are its function?
I rna polymerase, and its function is to make all three kinds of RNA
111
Rifampin inhibits which enzyme?
DNA dep rna polymerase in prokaryotes
112
How many rna polymerase does eukaryotes have and what are its functions?
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
Do rna polymerase need primers? What do they need?
They don’t need primers, they need promotors and transcriptional factors
114
Which enzyme does a amanitin inhibit?
Death cap mushrooms inhibits rna polymerase 11 in euk
Leads to acute liver failure
115
Which enzyme does actinomycin D inhibit?
Rna polymerase in both euk and pro
116
What way is mRNA read as?
5’ to 3’
117
What are promotors?
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
What does promotor mutation do?
It results in dramatic decrease in level of gene transcription
119
What are enhancers and what do they do?
DNA locus where the regulatory proteins called like activators bind and increase the expression of the gene on the same chromosome
120
What are silencers and what do they do?
DNA locus where regulatory proteins like depressors bind and decrease the expression of gene on the same chromosome
121
Where are enhancers and promoters located?
May be located upstream or downstream, within the intron
Due to dna coiling, they can be close to despite being many nucleotides away
122
What are the untranslated regions and what are their jobs?
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
What is hnRNA?
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
What happens to mRNA before it gets out of the nucleus?
Three key modifications happens to mRNA before it gets out of nucleus into the cytosine
125
What is the capping of mRNA?
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
What is the purpose of the 7 methyl guanosine cap?
It distinguishes mRNA from other rna
127
What is splicing?
It is one of the key modifications before the mRNA leaves the nucleus
128
What are exons?
Exons are expressed and exit the nucleus
129
What are introns?
They are intervening sequences and stay inside the nucleus
130
What is alternative splicing?
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
What are the different proteins made by alternative splicing?
Transmembrane vs secreted iG
Tropomyosin variants in muscle,
Dopamine receptors in brain
132
What are the disorders that can be generated due to defective alternative splicing ?
Oncogenesis, b thalesseniam gaucher disease, Tay sach disease, Marfan syndrome
133
What is polyadenylation?
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
What are P bodies?
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
What are micro rnas?
Non coding rna molecules that target the 3’ UTR post transcriptionally for degradation or translational repression
136
What does abnormal expression of Mi rna do?
Lead to silencing of the mRNA from a tumour suppressor gene
137
How many nucleotides does tRNA have?
75-90 nucleotides
138
What is structure of the tRNA in terms of protein structure?
Secondary structure
139
Which form does it have and why? tRNA ?
It has a cloverleaf form, and so it can fit into ribosome properly
140
What do pro and euk have in common in terms of tRNA?
They have CCA at 3’ end
141
How many arms does tRNA have?
2
142
What is the t arm of tRNA and what does it do?
T arm of the tRNA has T¥C (ribothymidine, pseudouridine, cytidine)
T arm Tethers tRNA molecule to ribosome
143
What is the d arm of tRNA and what does it do?
D arm contains the dihydrouridine
D arm Detects the tRNA by aminoacyl tRNA synthetase
144
What is the acceptor stem for amino acid in tRNA?
5’ CCA 3’
145
What is charging of the tRNA?
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
Why is amino acyl tRNA synthetase called the match maker?
Specific for one amino acid
147
What happens when the mismatched tRNA occurs? When the wrong amino acid is added after reading of usual mRNA codon?
Hydrolyic editing
Aminoacyl tRNA synthetase scrutinises the amino acid
And if incorrect bond is hydrolysed from tRNA or amp
148
What is responsible for accuracy of amino acid selection?
Amino acyl tRNA synthetase and binding of charged tRNA
149
How many steps does protein synthesis have?
Three
150
What are the steps of initiation of protein synthesis?
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
What does the process of initiation require?
GTP
GTP: Gripping and Going places
Going (translation)
ATP: Activation (charging)
152
What are the sites of ribosome?
APE
A: incoming aminoacyl tRNA
P: accommodates growing peptide
E: holds Empty tRNA as it Exits
153
What are the steps to elongation ?
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
What are the steps of termination?
Release factors recognise the stop codon and halts translation
Completed polypeptide released from ribosome. Requires GTP
155
What are the subunits of euk ribosomes?
40S +60S: 80
156
What are the subunits of pro ribosomes?
30S + 50S: 70s
157
Which way does the protein synthesis occur in?
N terminus to C terminus
158
What are the post translational modifications?
Trimming and covalent alterations
159
What is trimming?
Removal of N and C terminal propeptides from zymogen to generate mature protein, trysinogen to trypsin
160
What are the covalent alterations?
GAPHUM
glycosylation, acetylation, phosphorylation, hydroxylation, ubiquitination, methylation
161
What are chaperon proteins and what purpose they serve?
They are heat shock proteins (HSP 60)
That rise in numbers when exposed to stress, hypoxia, ph shift
Prevent denaturing and misfolding o
