Bicohem Flashcards
1
Q
Histones are rich in what two amino acids making it positively charged?
A
lysine and arginine
2
Q
What phase do DNA and histone synthesis occur in?
A
S phase
3
Q
Inactive DNA and histone morphology?
A
Heterochromatin. Deacetylated and methylated histones allows for tight association and transcriptionally inactive)
4
Q
Active DNA and histone morphology?
A
Euchromatin. Acetylated and non-methylated histones allow for loose association and transcriptionally active)
5
Q
What is methylated in promoter region that can lead to silencing and decreased transcription?
A
CpG island
6
Q
What is methylated in prokaryotic DNA replication to allow for mismatch repair enzymes to distinguish between old and new prokaryotic strands?
A
Cytosine and Adenine
7
Q
5 parts needed for purine synthesis
A
Glycine, aspartate, glutamine (“PURe girls still gag”), THF, CO2
8
Q
2 parts needed for pyrimidine synthesis
A
Carbomyl phosphate, aspartate
9
Q
What is carbomoyl phosphate derived from?
A
Glutamine + CO2
10
Q
Nucleoside vs Nucleotide?
A
Nucleoside-base + (deoxy)ribose
Nucleotide-base + (deoxy)ribose + phosphate; linked by 3’–>5’ phosphodiester bond
11
Q
Cytosine deamination–>
A
Uracil
12
Q
Thymine has a ______
A
Methyl group
13
Q
Guanine vs. Adenine?
A
Guanine has a =O and can be thought of as “OG”
14
Q
Rings in purines?
A
2 rings
15
Q
Rings in pyrimidines?
A
1 ring
16
Q
Rate limiting step for pyrimidine production
A
Glutamine+ CO2–>Carbomyl phosphate (via CPS II)
17
Q
Leflunomide inhibits…
A
Dihydroorotate dehydrogenase
18
Q
Mycophenolate and ribavirin inhibit..
A
IMP dehydrogenase
19
Q
Hydroxyurea inhibits..
A
ribonucleotide reductase
20
Q
6 MP and its prodrug azothioprine inhibits…
A
de novo purine synthesis
21
Q
5 FU inhibits
A
Thymidilate synthase
22
Q
Metotrexate, Trimethoprim, and pyrimethamine inhibit…
A
DHF reductase
23
Q
How are ribonuclotides converted to deoxyribonucleotides?
A
ribonucleotide reductase
24
Q
Draw the purine/pyrimidine synthesis pathway
A
p. 63 FA
25
What is the salvage pathway for thymidylate synthase inhibition?
Thymidine kinase requires thymidine supplementation and normally accounts for 5-10% of dTMP synthesis
26
Draw the purine salvage pathway
p. 64 FA
27
Inheritance of adenosine deaminase deficiency?
Auto recessive
28
Inheritanc of Lesch nyhan syndrome?
X-linked recessive
29
symptoms of HGPRT deficiency
Hyperuricemia, Gout, Pissed off (aggression, self mutilation) Retardation, DysTonia
30
Treatment for HGPRT?
Can't treat other symptoms but can treat hyperuricemia/gout with allopurinol and febuxostat
31
Each codon specifies only 1 amino acid
Unambiguous
32
Most amino acids are coded by multiple codons?
Degenerate/redundant
33
What are the exceptions to AA being coded by multiple codons?
Methionine (AUG)
| Tryptophan (UGG)
34
What is commaless, nonoverlappying genetic code?
Read from a fixed starting point as a continuous sequence of bases (exception: viruses)
35
What is a universal genetic code?
genetic code convserved throughout evolution (exception: mitochondria)
36
2 enzymes that increase activity of de novo purine synthesis?
PRPP synthetase (Ribose 5-Phosphate-->PRPP) and PRPP amidotransferase (PRPP-->5-phosphoribosylamine)
37
Rate limiting enzyme of purine synthesis
Glutamine PRPP amidotransferase
38
Carbon sources in purine synthesis?
Glycine, THF, CO2 (Aspartate, glutamine nitrogen sourceS)
39
Consensus sequence of base pairs in genome where DNA replication begins. Difference in prokaryotes and eukaryotes?
Origin of replication
| Multiple (eukaryotes), single (prokaryotes)
40
Y-shaped region along dna template where leading and lagging strands are synthesized
Replication fork
41
Unwinds DNA template at replication fork
Helicase
42
Prevents strands from reannealing after unwinding
Single-stranded binding proteins
43
Create a single-or double-stranded break in the helix to add or remove supercoils
DNA topoisomerases
44
How do replication forks travel?
Travel bidirectionally away from origin of replication as DNA polymerase synthesizes complementary daughter DNA strands
45
Makes an RNA primer on which DNA pol III can initiate replication
Primase
46
What is ori identified and bound by that locally allows it do dissociate from dsDNA into ssDNA?
DNA A protein. SSB proteins then bind to ssDNA and stabilize and prevent premature reannealing. Helicase then binds ssDNA at ori, moves into rep fork and proceeds to seperate and unwind DNA
47
What protein triggers DNA replication in bacteria?
DNA A
48
5'-->3' synthesis on leading and lagging strand (until reaches primer of preceeding fragment) and proofreads with 3'-->5' exonuclease
DNA polymerase III
49
5'-->3' synthesis of leading and lagging strand with 3'-->5' exonuclease and also excises RNA primer with 5'-->3' exonuclease+repair of damaged parent DNA
DNA polymerase I
50
Catalyzes formation of phosphodiester bond within a strand of dsDNA (ie. joins Okazaki fragments)-->seals
DNA ligase
51
RNA dependent DNA polymerase (reverse transcriptase) that adds DNA to 3' ends of chromosomes to avoid loss of genetic material with every duplication?
Telomerase
52
Inhibit prokaryotic enzyme topoisomerase II (DNA gyrase) and topoisomerase IV
Fluoroquinolones
53
Makes up DNA helicase and primase complex
Primosomes
54
Coes for tRNA and rRNA and resembles bacterial (prokaryotic) chromosome
Mitochondrial DNA (small circular chromosome similar to bacterial chromosome)
55
What is an exonuclease?
Removes nucleotides at the end of DNA molecule so it has a particular direction
56
Sequence added to 3' DNA ends of chromosomes
TTAGGG
57
Telomeres are expressed in what 3 types of cells
Stem cells-long telomeres and act ve telomerase, telomeres shorten with each cell division
Cancer cells-upregulate telomerase activity, preventing cell death by maintaining length of telomeres. Cancer cells immportal b/c cells continue to divide w/o aging and shortening of telomeres
Somatic cells-terminally differentiated and
58
Transversion and transition apply to which type of mutations?
Point mutations (silent, missence, nonsence)
59
Transition mutation
purine to purine or pyrimidine to pyrimidine "same"
60
Transversion mutation
purine to pyrimidine or pyrimidine to purine
61
Sickle cell disease is a type of what mutation and what happens?
Point mutation that is missence (GAG (glutamic acid) substitution with GTG (valine))
62
Where is the base change in a silent mutation?
Often base change in the 3rd position of codon (tRNA wobble)
63
What is it called if new AA is similar in structure to old in missence mutation?
Conservative
64
Duchenne muscular dystrophy is what type of mutation?
Frameshift mutation (deletion of dystrophin gene)
65
Slapped strand mispairing can lead to what?
Insertion and frameshift mutation
66
What causes the formation of a larger nonfunctional protein, but usually the immunoreactivity of normal proteins (i.e.binding to antibodies?
Splice site mutations (type of point mutation) where mutation of splice sites (not removing all introns from hnRNA in formation of mature mRNA). This is a type of point mutation
67
Eukaryotic lagging strand building
DNA pol. alpha
68
Eukaryotic leading strand building
DNA pol. delta
69
Eukaryotic DNA repair (specifically base excision repair)
DNA pol. beta
70
replicates mitochondrial DNA
DNA pol. gamma
71
Mechanism defective in xeroderma pigmentosum
nucleotide excision repair
72
Repair important in spontaneous/toxic deamination
base excision repair
73
Mechanism defective in HNPCC
Mismatch repair
74
Mechanism defective in ataxia telangiectasia; fanconi anemia
Nonhomologous end joining
75
What is an endonuclease?
Cut DNA specific DNA sequences within the molecules with no particular direction
76
When does nucleotide excision repair occur and when does base excision repair occur and when does mismatch repair occur?
G1 phase-NER
Throughout cell cycle-BER
G2 phase-Mismatch repair
77
Steps in nucleotide excision repair
Specific endonucleases release oligonucleotides by creating a nick on either side. DNA polymerase and ligase fill and reseal gap respectively.
78
Steps in base excision repair
Base-specific glycosylase (specific endo nuclease) removes base creating an AP site. Following that, one or more nucleotides are removed via AP endonuclease on 5' end and lyase and 3' end. After that DNA polymerase beta adds DNA and is sealed via ligase.
79
Steps in mismatch repair
Newly synthesized strand is recognized. Mismatched nucleotides are removed. Gap is filled and resealed.
80
Cause and symptoms of xeroderma pigmentousm?
Most commonly due to absence of UV-specific endonuclease. This is responsible for normally excising thymine dimers by nicking the strand at the thymine dimer.
Symptoms include photosensitivity, poilkiloderma, and hyperpigmentation in sun exposed areas--> increase risk of skin cancer
81
What brings together 2 ends of DNA fragments to repair ds breaks?
Nonhomologous end joining
82
DNA and RNA is synthesized in what direction?
mRNA is read in what direction?
Protein synthesis?
5'-->3'
5-->3'
N terminus-->C terminus
83
What is the mechanism behind drugs that block DNA replication?
modified 3' OH, preventing addition of next nucleotide (i.e. cant attach 5' end triphosphate)--> "chain termination"
84
Mutations in what 2 genes account for 90% of lynch syndrome?
MSH2 and MLH1 genes code for MutS and Mut L homologs. Normally, mismatch repair beings with MutS homolog detecting a mis-match on new daughter strand, which is distinguished from parent strand with occasional nicks in phosphodiester bonds. Mut L recruited slides along complex until nick is recgonized. Exonuclease I loaded onto and activated by repair complex. Daughter strand degraded. DNA pol. delta creates new strand and ligase seals
85
mRNA start codons (eukaryotes vs. prokaryotes)
Eukaryotes-codes for methionine, which may be removed before translation is completed
Prokaryotes-codes for N-formylmethionine (fMet). fMet stimulates neutrophil chemotaxis.
86
RNA pol binding?
Promoter region
87
CAP binding in lac operon (prokaryotic)
At CAP site upstream of promoter
88
lac l transcribes?
Repressor protein (known as regulatory gene)
89
lac z codes for?
B-galactosidase (responsible for hydrolysis of lactose into glucose and galactose)
90
lac y codes for?
Permease (allowing lactose to enter bacterium)
91
lac A encodes?
B galactosidease transacetylase
92
Repressor protein binds to (prokaryotic)?
operator region
93
Toxin Inhibits RNA pol II and side effect?
```
a-amanitin (found in amanita phalloides death cap mushrooms)
Severe hepatotoxicity (increase ALT, AST, bilirubin)
```
94
Inhibits RNA pol in prokaryotes
Rifampin
95
Inhibits RNA pol in eukaryotes and prokaryotes
Actinomycin D
96
What opens DNA at promoter site?
RNA pol II
97
What are specific foci involved in mRNA regulation/turnover in the cytoplasm?
P bodies
98
Antibodies to spliceosomal snRNPs
Anti-smith antibodies in SLE
99
Anti-U1 RNP antibodies
MCTD
100
Single gene coding for multiple proteins when same gene is organized differently in different tissues
Alternative splicing
101
Abnormal splicing variants implicated in what?
Oncogenesis, genetic disorders (B-thalassemia)
102
3' end of tRNA
CCA
103
D arm (dihydrouracil residues)
Recognizes specific aminoacyl tRNA synthetase for each AA
104
T arm (thymine, psuedouracil, cytosine)
Recognizes sequence necessary for tRNA-ribosome binding
105
Hsp60 in yeast is example of a?
Chaperone protein (facilitating and/or maintaining protein folding)
106
What helps incoming tRNA bind to A site?
elongation factors
107
What catalyzes peptide bond formation, transferring growing peptide to AA in A site?
rRNA ("ribozyme") mediates peptidyl transferase activity
108
How does prokaryotic protein synthesis begin and what is first step for initiation?
mRNA (Shane-Dalgarno sequence) binds to complementary to 16S rRNA (part of 30S ribosomal subunit) and this is necessary for initiation of protein translation.
109
AA linked by covalent peptide bonds
Primary structure
110
alpha helix, B-sheet
Secondary structure
111
Compact folding of secondary structure with ionic hdyrophobic hydrogen disulfide stabilizing
Tertiary structure
112
Arrangement of multiple folded protein into a multi-subunit complex
Quarternary structure
113
Constitutive and inactive regulation of cell cycle
CDKs
114
Regulatory proteins that control cell cycle events; phase specific
Cyclins
115
Phosphorylate other proteins to coordinate cell cycle progression; must be activated and inactivated at appropriate times for cell cycle to progress
Cyclin-CDK complexes
116
2 cells rich in RER
Mucus-secreting goblet cells of small intestine and antibody-secreting plasma cells
117
3 cells rich in SER
Liver hepatocytes, steroid hormone producting cells of adrenal cortex, gonads
118
Functions in lipid synthesis and carbohydrate metabolism
SER
119
Functions in synthesis of proteins (exported)
RER
120
Two subunits of ribosomes?
Small unit-binds mRNA (template for protein synthesis) and tRNA (carry amino acids)
Large unit-contains peptidyl transferase (catalyzes peptide bond formation in AA)
121
Membrane enclosed organelle involved in catabolism of very-long chain fatty acids, branched-chain fatty acids, and amino acids
Peroxisomes
122
Degrades damaged or uibiquitin-tagged proteins.
proteosome
123
Defects of ubiquitin proteoasome system in what disease?
Parkinson disease
124
N-oligosaccharides on what in post translational modification?
Asparagine amino group
125
O-oligosaccharides on what in post translational modification?
serine and threonine hydroxyl group
126
Mechanism for coarse facial features, clouded corneas, restricted joint movement, and high plasma levels of lysosomal enzymes
Failure of golgi to phosphorylate mannose residues on glyocoprotins so proteins are not delivered to lysososomes.
127
COP I
Golgi-->Golgi (Retrograde); cis golgi-->ER
128
COP II
ER-->cis-golgi (anterograde)
129
Clathrin
trans golgi-->lysosomes; plamsa membrane-->endosomes
130
Which AA can be modified by the golgi apparatus?
Asparagine, serine, threonine
131
Cyclin D binds to what?
CDK4-->phosphorylation of Rb protein-->Rb protein is released from transcription factor E2F-->w/ E2F unbound, cell is free to transcribe/synthesize components needed for progressing THROUGH S phase (DHF, cyclin E, thymidilate synthase, DNA polymerase)
132
Cyclin E binds to what?
CDK2-->allows progression INTO S phase.
133
Cyclin A binds to what?
CDK2 to allow progression from G2-->M (mitotic prophase)
134
Cyclin B binds to what?
CDK1 complex activated by Cdc 25-->breakdown of nuclear lamnins (skeletal framework) and initiation of mitosis
135
Nuclear localization signals rich in what AA?
Proline, Arginine, Lysine (PAL). Makes sense b/c histones are in nucleus and rich and lysine and arginine
136
What are the sorting centers of the cell?
Endosomes. For material from outside of cell or from Goligi, sending it to lysosomes for destruction or back to membrane/golgi for further use.
137
Stain: Vimentin
| Cell type: ?
Connective tissue (stain used to identify sarcoma)
138
Stain: Desmin
| Cell type?
Muscle (stain used to identify rhabdomyosarcoma for example)
139
Stain: Cytokeratin
| Cell type?
Epithelial cell (cell used to identify carcinoma)
140
Stain: GFAP
| Cell type?
Neuroglia (Astrocytoma)
141
Stain: Neurofilaments
| Cell type?
Neurons (specifically axons. used to identify neuroblastoma)
142
Predominant function of microfilaments?
Muscle contraction, cytokinesis
143
Predominant function of intermediate filaments?
cell structure
144
Predominant function of microtubules?
Cell division, movement
145
Drugs that act on microtubules?
Mebendazole, Griseofulvin, Colchicine, Vincristine/Vinblastine, Paclitaxel (Microtubules Get Constructed Very Poorly)
146
ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets
Axonemal dynein
147
MOA of Ouabain?
Inhibits Na+ K+ ATPase by binding to K+ site.
148
Most abundant protein in human body
collagen
149
Inhibited by scurvy?
hydroxylation of specific proline and lysine residues
150
OI has problems forming what?
problems forming triple helix (procollagen)
151
Ehlers danlos, menkes disease has problems with what?
Cross-linking tropocollagen molecules to make collagen fibrils (secondary to lysyl oxidase covalently linking lysine-hydroxylysine cross-linkage)
152
Mature collagen is synthetized in what cells?
Fibroblasts, osteoblasts, and chondroblasts
153
Most abundant AA in collagen?
Glycine
154
What catalyzes cleavage of disulfide rich terminal regions of procollagen?
Extracellular precollagen peptidases
155
2 components of bone matrix
Inorganic hydroxyapatite crystals and organic type I collagen
156
Common mutations leading to ehlers danlos phenotypes include deficiencies in what two enzymes?
Lysyl hydroxylase (characteristic of kyphoscoliosis and ocular fragility) and pro-collagen peptidase (joint laxity, loos skin, and easy bruising)
157
3 major differences between collagen and elastin?
1) Very few proline, lysine residues hydroxylated in elastin (thought of as rich in nonhydroxylated proline, glycine, and lysine
2) Triple helix in collagen. No triple helix in elastin
3) Triple helix formation in collagen is initiated by hydroxylation, glycosylation, and inter-chain disulfide bridges @ C-terminus of procollagen. These modifications not happen in elastin molecules
158
Enzyme catalyzing elastin b linking vs collagen cross linking
Lysyl hydroxylase vs lysyl oxidase
159
What is unique about elastin crosslinking?
Unique form of desmosine crosslinking between 4 lysine residues between 4 different elastin chains.
160
Southern blot
DNA sample cleaved into smaller pieces (restriction endonuclease). Electrophoresed on gel. Transferred to filter and filter soaked in denaturant, which is than labeled by DNA probe that recognizes and anneals to complementary strand
161
Northern blot
Similar to Southern blot except RNA sample is electrophoresed and recognized by DNA probe
162
Western blot
Sample protein via gel electrophoresis and labeled antibody used to bind relevant protein
163
Southwestern blot
DNA binding proteins (TF, histones, nucleases) used labeled oligonucleotide probes
164
Describe HIV confirmatory test
Western blot. Antibodies to gp41, gp120/160, p24. Two positive necessary for confirmed positive diagnosis
165
Direct ELISA used for?
Test for antigen in patient blood
166
Indirect ELISA used for?
Test for antibody in patient blood
167
Constitutive insertion
Random insertion of gene into mouse genome
168
Conditional insertion
Targeted insertion or deletion of gene thorugh recombination with mouse gene
169
Inducibly manipulate genes at specific developmental points
Cre-lox system
170
dsRNA is synthesized that is complementary to the mRNA sequence of interest. When transfected into human cells., dsRNA seperates and promotes degradation of traget mRNA, "knocking down" gene expression
RNA interference.
171
What explains variable expression in mitochondrially inherited disease
Heteroplasmy due to presence of both normal and mutated mtDNA.
172
Mccune albright syndrome is an example of
somatic mosaicims that arises from mitotic errors after fertilization and propagates through multiple tissues or organs
173
4 assumptions of hardy weinberg
No net migration, no mutation at locus, completely random mating, natural selection is not occuring
174
X-linked recessive diseases:
"Oblivious female will give her boys x-linked disorders"
Ocular albinism, fabry disease, wiskott-aldrich, g6pd deficiency, hunter syndrome, bruton agammaglobulinemia, hemophilia A+B, lesch nyhan, duchenne muscular dystrophy
175
Hypophosphatemic rickets inheritance
x-linked dominant
176
Lifraumeni syndrome commonly causes:
SBLA cancer: sarcoma, brain/breast, leukemia, adrenal gland cancers
177
Deletion of what 3 nucleotides in cystic fibrosis coding for what?
Phe at position 508
178
Quad screen Downs, Edwards, Patau?
Down: Increase B-hCG, Decrease afp, decrease estriol, increase inhibin A
Edwards: Decrease b-hCG, decrease afp, decrease estriol, decrease or normal inhibin A
Patau: decrease bCG decrease PAPPA and increase nuchal translucency in 1st trimester screening (not quad screen)
179
Chromosome 3 disorders
VHL, renal cell carcinoma
180
Chromosome 4 disorders
ADPKD with PKD2 defect, Huntington disease
181
Chromosome 5 disorder
Cri-du-chat syndrome, FAP
182
Chromosome 7 disorders
williams syndrome, cystic fibrosis
183
Chromosome 9 disorder
Fredreich ataxia
184
Chromosme 11 disorder
Wilms tumor
185
Chromosome 13 disorder
Patau syndrome, wilson disease
186
Chromosome 15 disorder
Prader-willi, angelman
187
Chromosome 16 disorder
ADPKD with PKD1 defect
188
Chromosome 17 disorder
NF1
189
Chromsome 18 disorder
Edwards
190
Chromsome 21 disorder
downs
191
Chromsome 22
nf2, digeorge
192
X chromosome
Fragil x, klinefelter, x-linked agammaglobulinemia
193
what 5 chromosome pairs do robertsonian translocation occur in?
13,14,15,21,22
194
```
Trinucleotide expanision
Fragile X
Fredreich ataxia
Hungtinton
Myotonic dystrohy
```
CGG
GAA
CAG
CTG
