BIOCHEM--Molecular Flashcards
p 34-45 FA2018
1
Q
_____ give DNA a neg (-) charge
A
phosphate groups
2
Q
_____ and _____ give histones a pos (+) charge
A
lysine and arginine
3
Q
DNA and histone synthesis occur during ___-Phase
A
S-phase
4
Q
describe the structure of a nucleosome
A
DBA loops twice around a histone octamer forming “beads on a string”
5
Q
____ binds to the nucleosome and ____ to stabilize the chromatin fiber
A
H1 binds to the nucleosome and linker DNA
6
Q
what bits make up the histone octamer
A
two of each of the following: H2A, H2B, H3, and H4
7
Q
describe heterochromatin
A
“HeteroChromatin = Highly Condensed”
transcriptionally inactive, sterically inaccessible
increased methylation, decreased acetylation
8
Q
- how does heterochromatin appear on EM
2. how does euchromatin appear on EM
A
- dark
2. lighter
9
Q
What is a Barr body
A
inactive X chromosome made of heterochromatin
maybe visible on the periphery of nucleus
10
Q
describe Euchromatin
A
“Eu=true, truly transcribed”
“Euchromatin is Expressed”
Transcriptionally active, sterically accessible
11
Q
- what is DNA methylation
2. what is the result of DNA methylation
A
- direct methylation of DNA itself; does not change the sequence of DNA
- “CpG Methylation Makes DNA Mute.”
12
Q
where are gene promoters located
A
CpG islands
13
Q
examples of events in which DNA methylation takes place
A
genomic imprinting x-chromosome inactivation repression of transposable elements aging carcinogenesis
14
Q
- what is histone methylation
2. what is the result of histone methylation
A
- methyl groups attached to histones, NOT DNA
- usually causes reversible transcriptional suppression, but can also cause activation depending on location of methyl groups
“Histone Methylation Mostly Makes DNA Mute”
15
Q
Histone Acetylation causes what…
A
relaxation of DNA coiling»>allow for DNA transcription
“histone Acetylation make DNA Active”
16
Q
what is a nucleoSide
A
base + deoxyribose (Sugar)
17
Q
what is a nucleoTide
A
base deoxyribose + phosphaTe
18
Q
what kind of bond links a phosphate to deoxyribose?
A
3’-5’ phosphodiester bond
19
Q
which end of the nucleotide has the triphosphate?
A
5’ end
20
Q
name the purines and their basic structure
A
Adenine and Guanine
2 rings
“PURe As 2 Gold rings”
21
Q
Name the pyrimidines and their basic structure
A
Cytosine, Uracil, and Thymine
1 ring
“CUT the PY(pie)”
22
Q
Thymine has a ____
A
“thymine has a meTHYl”
23
Q
Which nucleotide bonds are stronger and why?
A
G-C bonds have 3 H bonds and are stronger that A-T bonds that only have 2H bonds
Increased G-C content= increased melting temperature of DNA.
“C-G bonds are like Crazy Glue”
24
Q
Which amino acids are necessary for purine synthesis
A
Glycine, Aspartate, and Glutamine
“cats Purr until they GAG”
25
Deamination of cytosine forms ___
Deamination of cytosine forms *Uracil*
26
Deamination of adenine forms ___
Deamination of adenine forms *hypoxanthine*
27
Deamination of guanine forms ___
Deamination of guanine forms *xanthine*
28
Deamination of 5-methylcytosine forms ___
Deamination of 5-methylcytosine forms thymine
29
what is the difference between Uracil and thymine?
Uracil is found in RNA, Thymine is found in DNA
30
Methylation of uracil forms ___
Methylation of uracil forms *thymine*
31
Draw out De novo pyrimidine and purine synthesis
I don't have Brainscape Pro, so I can't add a picture
| Check Page 36 in FA 2018
32
Drugs that interfere with Pyrimidine synthesis and their MOA
1. Leflunomide- inhibits dihydroorotate dehydrogenase
2. methotrexate (MTX)-HUMAN
trimethoprim (TMP)- BACTERIA
pyrimethamine-PROTOZOA
these inhibit dihydrofolate reductase (which leads to a decrease in deoxythmidine monophosphate [dTMP] in specified organisms
3. 5-fluorouracil (5-FU) and its prodrug capecitabine- form 5-F-dUMP which inhibits thymidylate synthase (leading to decrease in dTMP)
33
drugs that interfere with purine synthesis and their MOA
1. 6-mercaptopurine (6-MP) and its prodrug azathioprine- inhibit denovo purine synthesis
2. Mycophenolate and ribavirin- inhibit inosine monophosphate dehydrogenase
34
drug that interferes with both purine and pyrimidine synthesis and its MOA
hydroxyurea- inhibits ribonucleotide reductase
35
which amino acid is required for pyrimidine base production?
aspartate
36
where are the carbamoyl phosphate synthetase enzymes located?
```
CPS1= in the m1tochondria (urea cycle)
CPS2= in the cyTWOsol
```
37
Draw purine salvage pathway
I don't have Brainscape Pro, so I can't add a picture
| Check Page 36 in FA 2018
38
Explain Biochem of Adenosine Deaminase (ADA) Deficiency
```
Adenosine Deaminase (ADA) is required for degradation of adenosine and deoxyadenosine.
in ADA Deficiency increased dATP leads to lymphotoxicity
```
39
___ is the major cause of AR SCID
Adenosine Deaminase (ADA) Deficiency
40
how is ADA deficiency inherited
AR
41
Explain Biochem of Lesch-Nyhan Syndrome
defective purine salvage bc absent HGPRT which converts hypoxanthine >>> IMP and guanine >>>GMP.
without HGPRT >>>excessive uric acid production and de novo purine synthesis
42
how is Lesch-nyhan syndrome ingerited?
X-linked recessive
43
Clinical Findings: Lesch-Nyhan Syndrome
| *Remember: HGPRT pneumonic*
- Hyperuricemia (orange "sand" [sodium urate crystals] in diaper)
- Gout
- Pissed off (aggression, self-mutilation)
- Retardation (intellectual disability)
- dysTonia
44
tx for Lesch Nyhan Syndrome
1st: allopurinol
2nd: febuxostat
45
Genetic code features: unambiguous
each codon specifies only 1 amino acid
46
Genetic code features: Degenerate/redundant
most amino acids are coded by multiple codons bc of the wobble position; exceptions: Methionine (AUG) and tryptophan (UGG) encoded by only 1 codon.
47
describe the wobble position and how it relates to the degenerate/redundant feature of genetic code
codons that differ in the 3rd "wobble" position may code for the same tRNA/amino acid.
specific base pairing is usually required only in the first 2 nucleotide positions of mRNA codon.
48
Genetic code features: commaless, nonoverlapping
read from a fixed starting point as a continuous sequence of bases.
exceptions: some viruses
49
Genetic code features: Universal
genetic code is conserved throughout evolution.
| exception in humans: Mitochondria
50
DNA replication is ___, involves both ___ and ___ synthesis, and occurs in the ___ direction
DNA replication is *semiconservative*, involves both *continuous* and *discontinuous* synthesis, and occurs in the *5'-3'* direction
51
Origin of DNA replication
may be single (prokaryotes) or multiple (eukaryotes).
| AT-rich sequences (TATA box regions) found in promoters and origins of replication
52
what is the replication fork?
y-shaped region along DNA template where leading and lagging strands are synthesized
53
Role of Helicase in DNA replication
unwinds DNA template at replication fork
| "Helicase Halves DNA"
54
Role of Single-stranded binding proteins in DNA replication
prevent DNA stands from reannealing
55
Role of DNA topoisomerases in DNA replication
create single- or double-stranded break in helix to add or remove supercoils
56
Topoisomerases inhibited by drugs in eukaryotes vs prokaryotes
In Eukaryotes:
-Topoisomerase (TOP) I: inhibited by irinotecan/topotecan
-TOP II: inhibited by etoposide/teniposide
In Prokaryotes:
-TOP II (DNA gyrase) and TOP IV: inhibited by fluoroquinolones
57
Role of primase in DNA replication
make RNA primer for DNA polymerase III to bind and initiate replication
58
Role of DNA polymerase III in DNA replication
IN PROKARYOTES ONLY
elongate leading stand by adding deoxynucleotides to 3' end.
elongate lagging strand until reach primer of preceding fragment.
3'-5' exonuclease activity "proofreads"
59
Role of DNA polymerase I in DNA replication
Prokaryotic ONLY
| degrade RNA primer, replace with DNA, + all functions of DNA polymerase III
60
Role of DNA Ligase in DNA replication
joins Okazaki fragments with phosphodiester bond
| "Ligase Links DNA"
61
Role of Telomerase in DNA replication
EUKARYOTES ONLY
a reverse transcriptase (RNA dependent DNA polymerase) that adds DNA (a TTAGGG sequence) to the 3' ends of chromosomes to avoid loss of genetic material with every duplication
often fucked up in cancer cells >>> unlimited replication
"Telomerase TAGS for Greatness and Glory"
62
Mutations in DNA ranked from least sever to most severe
silent << missense < nonsense < frameshift
63
which types of mutations are point mutations?
silent
missense
nonsense
64
what is a transition mutation
purine to purine
or
pyrimidine to pyrimidine
65
what is a transversion mutation
purine to pyrimidine
or
pyrimidine to purine
66
What is a silent mutation?
nucleotide substitution, but codes for same/ synonymous amino acid
67
What is a missense mutation?
nucleotide substitution that leads to a different amino acid.
Called "conservative" if the new amino acid is similar in chemical structure
68
example of missense mutation leading to disease
Sickle Cell Disease
| substitution of glutamic acid with valine
69
What is a nonsense mutation
nucleotide substitution results in early stop codon.
Usually results in nonfunctional protein
"Stop the Nonsense"
70
what are the stop codons?
UAA "u are annoying"
UGA "u go away"
UAG "u are gone"
71
What is a frameshift mutation?
deletion or insertion of a number of nucleotides not divisible by 3. results in misreading of all nucleotides downstream.
protein might be shorter or longer, and its function may be disrupted or altered.
72
Examples of diseases caused by frameshift mustations
Duchenne muscular dystrophy
| tay-sachs disease
73
What is a splice site mutation?
| These mutations are rare causes of what?
mutation at splice site causes retained introns in the mRNA that lead to the productino of a protein with impaired or altered function
Rare causes of cancer, dementia, epilepsy, and some types of beta-thalassemia
74
What are the two situations in which the Lac operon will be activated to switch to lactose metabolism?
What happens in each?
1. Low glucose >>> increased adenylate cyclase activity>>> increased generation of cAMP from ATP >>> acitvation of catabolite activator protein (CAP) >>> increased transcription of Lac-Z,-Y, and -A
2. High lactose>>> unbinds repressor protein from repressor/operator site >>> increased transcription
75
What are the 3 single stranded DNA repair mechanisms
1. nucleotide excision repair
2. base excision repair
3. mismatch repair
76
What kind of lesions are repaired by Nucleotide Excision Repair?
bulky, helix distorting lesions
77
Explain Nucleotide Excision Repair
Specific Endonucleases cut out the oligonucleotides containing the damaged bases.
DNA Polymerase fills gap and ligase reseals the cut.
78
When does Nucleotide excision repair occur in the cell cycle?
G1 phase
79
Nucleotide excision repair is defective in what condition?
Xeroderma Pigmentosum
80
Explain Base Excision Repair
Base-specific glycosylase removes altered base and creates an AP site (apurinic/apyrimidinic)
one or more nucleotides removed by AP-Endonuclease which cleaves 5' end.
Lyase cleaves 3' end.
DNA polymerase-beta fills the gap
DNA ligase seals it
81
When does base excision repair occur?
occurs throughout cell cycle
82
In what specific instance in base excision repair important?
repair of spontaneous/toxic deamination
83
Explain Mismatch Repair
newly synthesized strand recognized as fucked up.
mismatched nucleotides are removed.
gap is filled and resealed
84
when does mismatch repair occur?
predominantly in S phase
85
Defective mismatch repair mechanisms are found in what syndrome?
Lynch Syndrome (hereditary nonpolyposis colorectal cancer [HNPCC])
86
What are the 2 Double stranded DNA repair mechanisms
1. non-homologous end joining
| 2. homologous recombination
87
explain non homologous end joining
bring together 2 ends of DNA fragments
| does not require homology.
88
in what disorders will you find defective nonhomologous end joining?
ataxia telangiectasia
| fanconi anemia
89
what sucks about non homologous end joining?
you might lose some DNA
90
explain homologous recombination
need two homologous DNA duplexes.
a strand from the damaged dsDNA is repaired using a complementary strand from the intact homologous dsDNA as a template.
restores duplexes accurately w/o loss of nucleotides
91
where will you find defective homologous recombination?
breast and ovarian cancers with BRCA1 mutations
92
mRNA start codon
AUG (rarely GUG) "aye u, GO"
codes for...
-eukaryotes: methionine
-prokaryotes: N-formylmethionine (fMet)
93
fMet stimulates ___.
neutrophil chemotaxis
94
What is a promoter?
site where RNA polymerase II and other transcription factors bind to DNA upstream from gene locus.
AT-rich upstream sequence w/ TATA and CAAT boxes
95
what happens if a promoter is mutated?
dramatic decrease in level of transcription of that gene
96
What is an enhancer?
DNA locus where activators bind to increase the expression of a gene on the same chromosome
97
What is a silencer?
DNA locus where repressors bind to decrease expression of a gene on the same chromosome
98
Where are enhancers and silencers located with respect to the gene they regulate?
can be close to, far away from, or within (like in a intron) the gene it regulates.
99
RNA polymerase I makes ___
rRNA
100
Where is RNA polymerase I located?
only in the nucleolus
101
RNA polymerase II makes ___
mRNA
102
RNA polymerase III makes ___
tRNA
103
Which type of RNA is most common?
rRNA
104
___ is the smallest RNA, and ___ is the largest.
```
tRNA = tiny
mRNA = massive
```
105
Besides making RNA, what does RNA polymerase II do?
opens DNA at the promoter site.
106
True or false: RNA polymerases have proof-reading function.
False
107
the initial ___ is modified and becomes mRNA
heterogeneous nuclear RNA (hnRNA)
108
How and where does hnRNA become mRNA?
the following processes occur in the nucleus:
1. capping of 5' end (by adding 7-methylguanosine cap)
2. polyadenylation of 3' end (~200 A's)
3. splicing out of introns.
Once all three actions are complete, it is now mRNA
109
where is mRNA translated
cytosol
110
what the fuck is a P-body?
A "processing body" in the cytoplasm that contains exonucleases, decapping enzymes, and microRNAs.
mRNA may be degraded or stored in the P-body for future translation
111
what is the polyadenylation signal
AAUAAA
112
What are microRNAs
small, conserved, noncoding RNA molecules that posttransciptionally regulate gene expression by targeting the 3' untranslated region of specific mRNA for degradation or translational repression.
113
Where do animo acids bind on a tRNA?
at the Acceptor stem with the CCA 3' end
| "Can Carry Amino acids"
114
What is the function of the T-arm of tRNA
necessary for ribosome binding
| "T-arm Tethers tRNA to ribosome"
115
What is the function of the D-arm of tRNA?
has dihydrouridine residues that are necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase
116
Steps of Protein Synthesis
1. initiation
2. Elongation
3. termination
117
Protein Synthesis: Initiation
1. Eukaryotic initiation factors (eIFs) identify the 5' cap or an internal ribosome entry site (IRES)
2. eIFs help assemble 40S ribosomal subunit with the initiator tRNA. released when mRNA and 60S subunit assemble with the complex.
Needs GTP
118
What is the energy source for protein synthesis initiation?
GTP
119
Protein Synthesis: Elongation
1. Aminoacyl-tRNA bind to A site, require elongation factor + GTP
2. rRNA catalyzes peptide bond formation, transfers growing polypeptide to aminoacid in A site.
3. ribosome advances 3 nucleotides toward 3' end of mRNA, moving peptidyl tRNA to P site (translocation)
120
___ is required to "charge" the tRNA
ATP
121
Protein Synthesis: Termination
1. Release factor recognizes stop codon and halts translation
2. completed polypeptide is released from ribosome
Requires GTP
