Biochem Flashcards
(112 cards)
1
Q
What is the only protein subunit of histones that is not found in the core protein?
A
H1
2
Q
What is heterochromatin?
A
Highly condensed, inaccessible DNA
3
Q
What is euchromatin?
A
Available chromatin
4
Q
DNA methylation results in silencing or upregulation?
A
Silencing
5
Q
What are the two nucleotides that are methylated?
A
Cytosine and adenine
6
Q
Histone acetylation causes activation or silencing of DNA?
A
Activates
7
Q
What are the two purines? Do these have one or two ring structures?
A
A
G
Two rings
8
Q
What are the two pyrimidines?
A
C
T
U
9
Q
What is the difference between thymine and uracil?
A
Thymine has a meTHYl
10
Q
How many hydrogen bonds do purines have?
A
two
11
Q
Base + (deoxy)ribose = ?
A
Nucleoside
12
Q
Base + (deoxy)ribose + phosphate = ?
A
Nucleotide
13
Q
What is the MOA of 5-fluorouracil?
A
Inhibits thymidylate synthase
14
Q
What is the MOA of hydroxyurea?
A
inhibits ribonucleotide reductase
15
Q
What is the effect of adenosine deaminase deficiency?
A
SCID d/t decreased cell proliferation with dATP buildup
16
Q
What is Lesch-Nyhan syndrome?
A
Defective purine salvage pathway d/t a loss of HGPRTase (leads to MR and finger biting)
17
Q
What are the symptoms of Lesch-Nyhan syndrome? (HGPRT)
A
Hyperuricemia Gout Pissed off Retardation DysTonia
18
Q
Deficiency of the HGRPTase results in the build up of what metabolite? What disease is this?
A
GMP and IMP, Lesch-Nyhan syndrome
19
Q
How is the genetic code unambiguous?
A
One codon = one amino acid
20
Q
How is the genetic code redundant?
A
More than one codon for one amino acid
21
Q
What is the one part of the body in which the genetic code has not been preserved throughout evolution?
A
Mito
22
Q
What is the enzyme that is responsible for unwinding the DNA template?
A
Helicase
23
Q
What are the proteins that prevent a DNA strand from coming back together, once unwound?
A
SSBPs
24
Q
What is the enzyme that creates a single or double stranded break in DNA to allow for unwinding of supercoils?
A
Topoisomerase
25
What is the enzyme that that makes an RNA primer?
Primase
26
What is the enzyme that adds nucleotides to a growing fragment?
Pol II
27
What is the function of DNA ligase?
Ligates Okazaki fragments together using a phosphodiester bond
28
What is the function of telomerase?
RNA dependent DNA polymerase that adds DNA to the 3' end of chromosomes to avoid loss of genetic material with every duplication
29
Sickle cell disease is the result of a missense, nonsense, frameshift, or silent mutation?
Missense
30
What is the nonsense mutation?
A mutation in which there is a premature stop codon
31
What is the MOA of nucleotide excision repair? (two steps)
Endonucleases remove damaged segment
| DNA pol and lig repair
32
What are the steps of base excision repair (what is the enzyme that is utilized)?
Glycosylases recognize and remove incorrect bases
33
What is cause of xeroderma pigmentosum?
Defect in nucleotide excision repair with pyrimidine dimers
34
What are the steps of non-homologous end joining?
Bringing together of two ends of DNA
35
What is the DNA repair mechanism that is mutated in ataxia telangiectasia? Which enzyme?
non-homologous end joining of double stranded end breaks
Enzyme = ATM
36
What is the start codon (triplet sequence)?
AUG
37
What does AUG code for in eukaryotes? Prokaryotes?
```
Eukaryotes = met
Pro = Formylmethionine
```
38
What are the three sets of triplets that code for stopping replication?
UGA (U go away)
UAA (U are away)
UAG (U are Gone)
39
What is the TATA box? CAAT box?
Promoter regions of DNA
40
Which are expressed: exons or introns?
Exons
41
What is the function of pol I in eukaryotes?
makes rRNA
42
What is the function of pol II in eukaryotes?
makes mRNA
43
What is the function of pol III in eukaryotes?
makes tRNA
44
What is the protein, found in the death-cap mushroom, that inhibits RNA pol II?
alpha-amanitin
45
True or false: DNA pol I, II, and III are all utilized in eukaryotes
False--only II is. I and III are for prokaryotes
| note this is DNA pol, **not** RNA pol
46
What is the precursor form of mRNA?
hnRNA (heterogenous RNA)
47
What are the steps of maturation for mRNA?
1. capping w/ 7-methylguanosine
2. Polyadenylation (poly A tail)
3. Splicing out introns
48
Where in the cell is mRNA translated?
Cytosol
49
What are the proteins that are added to mRNA prior to splicing?
snRNPs
50
What is the structure that is formed during the splicing process?
Lariat structure
51
What are anti-smith antibodies, and what diseases are they associated with?
Antibodies to spliceosomal, snRNP.
Associated with autoimmune disorders.
52
What is the genetic basis for beta thalassemia?
Abnormal splice site
53
What is the codon sequence for the tRNA?
CCA (Can Carry AAs)
54
What is the enzyme that "charges" tRNA, and loads AAs?
Amino-acyl tRNA synthetase
55
What are the ribosomal subunits for eukaryotes? Prokaryotes?
Eukaryotic: 40s + 60s =80s (Even)
Prokaryotic: 30s + 50s = 70s (Odd)
56
What is the enzyme responsible for catalyzing the peptide bond formation between AAs in a ribosome?
ribozyme
57
What energy chemical (ATP or GTP) is needed to initiate the binding of AAs to a ribosome? Which is needed to elongate the growing chain?
ATP for initiation (Activation)
| GTP for elongation (Going places)
58
What is Li-fraumeni syndrome?
Mutation in p53 tumor suppressor protein, leading to aberrant cell growth
59
What are nissl bodies?
Organelles in neurons that synthesize neurotransmitters
60
What is the signal for trafficking proteins from the Golgi apparatus, to lysosomes?
mannose-6-phosphate
61
What is added to serine and threonine amino acid in the Golgi?
O-linked oligosaccharides
62
What is added to asparagine amino acid in the Golgi?
N-linked oligosaccharides
63
What is the cause of I cell disease?
Defect in phosphotransferase, causing protein to be secreted extracellularly, rather to lysosomes
64
What are signal recognition proteins?
Proteins that direct proteins from the ribosomes to the RER (mutation leads to inclusion disease)
65
What is the protein that directs proteins from the golgi to the ER (retrograde transport)?
COP I
66
What is the protein that directs proteins from the ER to the Golgi (anterograde transport)?
COP II
67
What is the function of peroxisomes?
Degrades long chain fatty acids
68
Defects in proteasomes have been associated with what disease?
Parkinson's
69
What are the two components of microtubules?
alpha and beta tubulin heterodimers
70
Which way does dynein transport proteins: retrograde or anterograde?
retrograde (+ to - end)
71
Which way does kinesin transport proteins: retrograde or anterograde?
Anterograde (- to + end)
72
What are the 5 drugs that act on microtubules? (Microtubules Get Constructed Very Poorly)
```
Mebendazole
Griseofulvin
Colchicine
Vincristine
Paclitaxel
```
73
9 + 2 arrangement of microtubules = ?
cilia
74
What is kartagener syndrome?
Immotile cilia d/t a dynein arm defect, causing infertility
75
What are actin and myosin involved in?
muscle contraction, microvilli, cytokinesis
76
What is the main function of microtubules?
Movement
77
What is the main function of intermediate filaments?
Structure
78
What does vimentin stain for?
CT
79
What does desmin stain for?
Muscle
80
What does cytokeratin stain for?
Epithelial cells
81
What does GFAP stain for?
Neuroglia
82
What is the chemical that inhibits K binding to the Na/K ATPase?
Ouabain
83
What is the MOA of digoxin and digitoxin?
directly inhibits that Na- K ATPase, leading indirectly to Ca exhange
84
What is the type of collagen in bone?
I
85
What is the type of collagen in Cartilage?
II
86
What is the type of collagen in blood vessels, organ casing, and nucleus pulposus?
III
87
Which type of collagen in also known as reticulin?
III
88
What type of collagen is found in the basement membrane, and lens of the eye?
IV
89
What is the cause of marfan's syndrome?
Defective elastin (fibrillin 1)
90
What is the cause of Ehlers danlos syndrome?
Defective collagen IV
91
What is the amino acid sequence in collagen?
Gly-X-Y (with X any Y usually being P or K respectively)
92
What is vitamin C needed for in the synthesis of collagen?
Hydroxylation of proline and lysine residues
93
What is the underlying defect in osteogenesis imperfecta?
Defect in glycosylation of pro-alpha-chain hydroxylysine (no triple helix)
94
Which comes first in the synthesis of collagen: hydroxylation or glycosylation?
Hydroxylation
95
What is the proteolytic processing of collagen?
Removal of disulfide rich terminal regions of procollagen
96
What are the two amino acids that are crosslinked in collagen?
Lysine and hydroxylysine
97
Problems with cross linking collagen is found in what disease?
Ehler's-danlos syndrome
98
The classic type of Ehlers danlos syndrome is caused by a defect in the cross linking of what collagen type?
V
99
The vascular type of Ehlers-danlos syndrome is caused by a defect in what type of collagen?
III
100
What is Menkes disease, and what is the enzyme affected?
X-linked recessive CT disease caused by impaired copper absorption-decrease activity of lysyl oxidase
101
What is the function of alpha-1-antitrypsin, and defects in this cause what?
Inhibits elastase.
| Defects lead to emphysema
102
Wrinkles of aging are caused by what?
Decreased collagen and elastin production
103
What is the goal of PCR?
Amplification of a DNA segment, then running in a gel to determine size of fragment.
104
What is the process involved in a southern blot? What type of genetic material does it analyze (DNA, RNA or proteins)?
Radiolabeled DNA run on a gel
105
What is the process involved in a northern blot? What type of genetic material does it analyze (DNA, RNA or proteins)?
RNA is electrophoresed and radiolabeled
106
What is the process involved in a western blot? What type of genetic material does it analyze (DNA, RNA or proteins)?
Protein run in a gel and antibodies used to identify the protein
107
What is the process involved in a southwestern blot? What type of genetic material does it analyze (DNA, RNA or proteins)?
DNA binding proteins identified using labeled oligonucleotides
108
What is an indirect ELISA vs a direct ELISA?
```
Indirect = uses a test antigen
Direct = uses a test antibody
```
109
Indirect ELISA is used to detect antigen or antibodies to an antigen?
Antibodies to an antigen
110
What is the cloning method used in biochemistry (hint: think production of insulin)?
Take mRNA, reverse transcriptase it, and insert into plasmid
111
What is the Crex-lox system?
Manipulating genes at specific developmental points
112
What is RNA interference?
dsRNA synthesized the is complimentary to mRNA of interest. Once inserted into cell, causes destruction of mRNA.
