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82 Cards in this Set

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DNA is ________-charged because of ______.
DNA is negatively charged bc of Phosphate groups
Purines vs Pyrimidines
PURe As Gold: PURine
A,G

CUT the PY (pie): PYrimidines
C, T, U
This nucleotide is found exclusively in RNA.
Uracil
Which nucleotide bonds have two bonds? Which have three?
TA: 2 bonds
GC: 3 bonds
Which amino acids are essential to PURINE synthesis?
GAG
Glycine
Aspartate
Glutamine
What is required for PYRIMIDINE synthesis?
ATP, CO2, Glutamine
What is the rate limiting enzyme of pyrimidine synthesis?
Carbamoyl phosphate synthetase II (CPSII)
Carbamoyl phosphate synthetase I vs II:
Location
Pathway
Nitrogen Source
I:
Location--mitochondria
PW: Urea cycle
Nitrogen Source: ammonia

II
Location--cytosol
PW: pyrimidine synthesis
Nitrogen Source: glutamine
Orotic aciduria:
Pathophys
Presentation
Treatment
Inability to convert orotic acid to UMP (de novo pyrimidine synthesis PW) due to defect in either orotic acid phosphoribosyltransferase or orotidine 5'-phosphate decarboxylase

Will find inc'd orotic acid in urine, megaloblastic anemia that does n't improve with admin of B12 or folic acid, no hyperammonemia

Tx: Oral uridine
Ribonucleotide reductase:
Role
Relevant drug
Ribonucleotide reductase:
UDP-->dUDP

Inhibited by hydroxyurea, thus, no more pyrimidine synthesis
Thymidylate synthase:
Role
Relevant Drug
Thymidylate synthase:
dUMP-->dTMP

REQUIRES FOLIC ACID

Inhibited by 5-fluorouracil (dec'd dTMP, dec'dp pyrimidine synthesis)
Dihydrofolate reductase:
Role
Relevant Drug
Dihydrofolate reductase:
DHF-->THF (trihydrofolate = active folic acid)

Active folic acid then feeds into thymidylate synthase for dTMP production

Methotrexate (in eukaryotes) and Trimethoprim (in bacteria)both inhibit dihydrofolate reductase, causing dec'd dTMP and dec'd pyrimidine synthesis
PRPP Synthetase:
Role
Relevant Drug
PRPP synthetase
Ribose 5-P-->PRPP

Required for PURINE synthesis

Inhibited by 6-mercaptopurine; blocks de novo purine synthesis
What is the rate-limiting step in purine synthesis?
Glutamine PRPP aminotransferase (comes right after Ribose 5-P-->PRPP)
What is the rate-limiting step in pyrimidine synthesis?
CPS II
What are the sources of carbons in the formation of purines?
CO2
Glycine
THF

(aspartate and glutamine provide nitrogens)
What are the sources of carbon in pyrimidine synthesis?
Aspartate
CO2

Glutamine for nitrogen
What accounts for the positive charge of histones?
Lysine
Arginine
What accounts for the negative charge of DNA?
Phosphate groups
How many adenine residues are found in a molecule of DNA if one strand contains A=2000, G=500, C=1500, and T=1000?
A pairs to T, one strand of DNA is double-strand

3000 adenine residues
What strand of DNA nucleotides opposes this DNA strand:
5'-ATTGCGTA-3'
5'-TACGCAAT-3'
Which drug:
Inhibits ribonucleotide reductase
Hydroxyurea
Which drug:
Inhibits DHF reductase
Trimethroprim
MTX
Which drug:
Inhibits thymidylate synthase
5-FU
Which drug:
Inhibits inosine monophosphate dehydrogenase
Mycophenylate
Which drug:
Inhibits PRPP synthetase
6-MC
What are the characteristic features of orotic aciduria?
Orotic acid in urine
Megaloblastic anemia not correctable by B12 or folate
Failure to thrive
No elevation of ammonia level
Lesch-Nyan Syndrome:
Pathophys
Presentation
Treatment
Defective purine salvage (breakdown) owing to absence of HGPRT, which converts hypoxanthine to IMP and guanine to GMP

results in excess uric acid production

Findings: retardation, self-mutilation (lip biting), aggression, hyperuricemia, gout

Tx: Allopurinol
Adenosine deaminase deficiency:
Pathophys
Presentation
Excess ATP and dATP-->negative feedback-->inhibits ribonucleotide reductase (UDP-->dUDP)-->prevents DNA synthesis and thus dec'd lymphocyte count

Major cause of SCID (severe combined immunodef dz--happens to kids)
What is a silent mutation?
Same aa, often change in 3rd position of codon (tRNA wobble)
What is a missense mutation?
Changed aa (conservative--new aa is similar in chemical structure)
What is a nonsense mutation?
Change results in EARLY STOP codon--STOP THE NONSENSE
How does UV light damage DNA?
Creates thymine dimers on same strand of DNA
Topoisomerase:
Role
Relevant drug
Creates nick in helix to relieve supercoils created during replication


Fluoroquinolones inhibit DNA gyrase--a specific prokaryotic topoisomerase

Etoposide inhibits eukaryotic topoisomerase (cancer drug)
Which eukaryotic DNA polymerase:
Repicates lagging strand
alpha
Which eukaryotic DNA polymerase:
Synthesizes RNA primer
alpha
Which eukaryotic DNA polymerase:
Replicates mitochondrial DNA
gamma
Which eukaryotic DNA polymerase:
Replicates leading strand DNA
delta
Which eukaryotic DNA polymerase:
Repairs DNA
beta, epsilon
Label
1. Primosome (lays down RNA primer); composed of DNA helicase and Primase
2. DNA Helicase
3. Primase
4. RNA primers made by 6
5. Okazaki frag
6. DNA polymerase
7. ssBP stabilizing DNA while complementary strand synthesized
8. DNA polymerase on leading strand
Xeroderma pigmentosum:
Pathophys
Presentation
Lack nucleotide excision repair; can't repair thymidine dimers

Hypersensitive to UV light-->1000x inc'd risk of skin cancer
Hereditary nonpolyposis colorectal cancer:
Pathophys
Inability to perform mismatch repair--unmethylated, newly synthesized string is recognized, mismatched nucleotides are removed, and gap is filled and resealed
How is double-stranded DNA repaired?
Nonhomologous end joining--brings together 2 ends of DNA fragments; no requirement for homology
Everything is synthesized __' to __'.
5' to 3' ALWAYS
Start codons
AUG
Stop codons
You are away
Yo go away
You are gone
UAA
UGA
UAG
What is an operon?
Structural genes that are transcribed + promoter region + all regulatory genes
What are transcription factors?
Factors that must bind PROMOTER region (TATA box) in order for transcription to occur
What is an operator region?
Region of gene that binds repressor (stops transcription) or inducer (starts transcription) located between promoter region and start site
lac operon:
Role
Regulation
Controls expression of beta-galactosidase, which breaks down lactose into glucose and galactose

In presence of glucose, lac operon is turned off because lac repressor is bound

In absence of glucose, CAP binds, but transcription of beta-galactosidase will only begin in presence of lactose

Only when lactose is present and glucose is absent, will lac repressore release from lac operon.
RNA polymerase I vs II vs III:
Role
RNA pol I: makes rRNA
II: makes mRNA
III: makes tRNA

No proofreading function; ONLY present in eukaryotes
rRNA is synthesized in the ______.
Nucleolus
mRNA is synthesized in the ______.
Nucleoplasm
tRNA is synthesized in the _______.
Nucleoplasm
What events must occur for RNA to leave the nucleus?
5' capping
3' poly A
Splicing out of introns
What structures removes introns from pre-mRNA?
Spliceosome!
Aminoacyl-tRNA synthetase:
Role
"Matchmaker"; 1 per amino acid--scrutinizes aa before and after it binds to tRNA, then delivers it to ribosome
What are the steps of elongation in protein synthesis?
1. Aminoacyl-tRNA binds A site of ribosome (PREVENTED BY TETRACYCLINE)

2. Ribosomal rRNA catalyzes peptide bond formation via PEPTIDYL TRANSFERASE, transfers growing polypeptide to amino acid in A site of ribosome

3. Ribosome advances 3 nucleotides toward 3' end of RNA, moving peptidyl RNA to P site (translocation)
How do eukaryotic ribosomes structurally differ from prokaryotic ribosomes?
Eukaryotes: 40S + 60S-->80S (EVEN EUK)

PrOkaryotes: 30S + 50S-->70S (ODD prO)
Aminoglycosides:
MOA
-micins

Inhibit formation of initiation complex (assembly of euk ribosome?)
Chloramphenicol:
MOA
Inhibits 50S peptidyltransferase (this enzyme catalyzed peptide bond formation in growing polypeptide being synthesized)
Macrolides:
MOA
Bind 50S and block translocation
Clindamycin:
MOA
Binds 50S and blocks translocation
Ribosomes are synthesized in the ______.
Nucleus (and then exported to cytoplasm)
Role of ubiquitin.
Attaches to defective proteins to tag them for breakdown (Proteasomal degradation)
Which antibiotic:
Inhibits 50S peptidyltransferase
Streptogrammins
Chloramphenicol
Which antibiotic:
Binds 50S, blocking translocation
Macrolides
Lanezolide (sp?)
Which antibiotic:
Binds 30S, preventing attachment of tRNA
Tetracyclines
Which antibiotic:
Inhibits prokaryotic RNA polymerase
Rifampin
Which antibiotic:
Inhibits prokaryotic topoisomerase
Fluoroquinolones
Which antibiotic:
Inhibits prokaryotic dihydrofolate reductase
Trimethoprim
What are the 3 mechanisms cell employ to break down proteins?
Ubiquitin mechanism
Lyososmal degradation mech
Calcium-dependent enzyme mech
What enzyme catalyzes peptide bond formation during protein synthesis?
Peptidyltransferase--a type of ribozyme
What enzyme matches amino acids to tRNA?
AMinoacyl tRNA synthetase
What are the mRNA stop codons?
UGA
UAA
UAG
What are the different RNA polymerases in eukaryotes?
RNA pol I: codes for rRNA
II: transcribed mRNA
III: transcribes tRNA
What amino acid frequently has more coding sequences in the mRNA than are represented in the peptide that is created from that mRNA?
Methionine--more AUG than methionine in a protein because AUG is the start sequence and it is commonly cleaved off
How is hnRNA processed before it leaves the nucleus?
5' cap
3' poly-A tail
Splice out introns
What is the characteristic sequence of the promoter region? What does a mutation in the sequence cause?
-25 TATA box
-75 CAT box

Mutation-->dec'd amount of gene transcribed
What enzyme is deficient in Lesch-Nyhan Syndrome?

What is the treatment?
HGPRT

Tx: allopurinol
What structural motifs allow for proteins to bind DNA?
Helix turn helix
helix loop helix
Leucine zippers
Zinc fingers
Which drugs cause gynecomastia?
Some Drugs Create Awesome Knockers

Spironolactone
Digitalis
Cimetidine
Alcohol
Ketoconazole