1A: Dt 9-3

Front 1

DNA is ________-charged because of ______.

Back 1

DNA is negatively charged bc of Phosphate groups

Front 2

Purines vs Pyrimidines

Back 2

PURe As Gold: PURine
A,G

CUT the PY (pie): PYrimidines
C, T, U

Front 3

This nucleotide is found exclusively in RNA.

Back 3

Uracil

Front 4

Which nucleotide bonds have two bonds? Which have three?

Back 4

TA: 2 bonds
GC: 3 bonds

Front 5

Which amino acids are essential to PURINE synthesis?

Back 5

GAG
Glycine
Aspartate
Glutamine

Front 6

What is required for PYRIMIDINE synthesis?

Back 6

ATP, CO2, Glutamine

Front 7

What is the rate limiting enzyme of pyrimidine synthesis?

Back 7

Carbamoyl phosphate synthetase II (CPSII)

Front 8

Carbamoyl phosphate synthetase I vs II:
Location
Pathway
Nitrogen Source

Back 8

I:
Location--mitochondria
PW: Urea cycle
Nitrogen Source: ammonia

II
Location--cytosol
PW: pyrimidine synthesis
Nitrogen Source: glutamine

Front 9

Orotic aciduria:
Pathophys
Presentation
Treatment

Back 9

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

Front 10

Ribonucleotide reductase:
Role
Relevant drug

Back 10

Ribonucleotide reductase:
UDP-->dUDP

Inhibited by hydroxyurea, thus, no more pyrimidine synthesis

Front 11

Thymidylate synthase:
Role
Relevant Drug

Back 11

Thymidylate synthase:
dUMP-->dTMP

REQUIRES FOLIC ACID

Inhibited by 5-fluorouracil (dec'd dTMP, dec'dp pyrimidine synthesis)

Front 12

Dihydrofolate reductase:
Role
Relevant Drug

Back 12

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

Front 13

PRPP Synthetase:
Role
Relevant Drug

Back 13

PRPP synthetase
Ribose 5-P-->PRPP

Required for PURINE synthesis

Inhibited by 6-mercaptopurine; blocks de novo purine synthesis

Front 14

What is the rate-limiting step in purine synthesis?

Back 14

Glutamine PRPP aminotransferase (comes right after Ribose 5-P-->PRPP)

Front 15

What is the rate-limiting step in pyrimidine synthesis?

Back 15

CPS II

Front 16

What are the sources of carbons in the formation of purines?

Back 16

CO2
Glycine
THF

(aspartate and glutamine provide nitrogens)

Front 17

What are the sources of carbon in pyrimidine synthesis?

Back 17

Aspartate
CO2

Glutamine for nitrogen

Front 18

What accounts for the positive charge of histones?

Back 18

Lysine
Arginine

Front 19

What accounts for the negative charge of DNA?

Back 19

Phosphate groups

Front 20

How many adenine residues are found in a molecule of DNA if one strand contains A=2000, G=500, C=1500, and T=1000?

Back 20

A pairs to T, one strand of DNA is double-strand

3000 adenine residues

Front 21

What strand of DNA nucleotides opposes this DNA strand:
5'-ATTGCGTA-3'

Back 21

5'-TACGCAAT-3'

Front 22

Which drug:
Inhibits ribonucleotide reductase

Back 22

Hydroxyurea

Front 23

Which drug:
Inhibits DHF reductase

Back 23

Trimethroprim
MTX

Front 24

Which drug:
Inhibits thymidylate synthase

Back 24

5-FU

Front 25

Which drug:
Inhibits inosine monophosphate dehydrogenase

Back 25

Mycophenylate

Front 26

Which drug:
Inhibits PRPP synthetase

Back 26

6-MC

Front 27

What are the characteristic features of orotic aciduria?

Back 27

Orotic acid in urine
Megaloblastic anemia not correctable by B12 or folate
Failure to thrive
No elevation of ammonia level

Front 28

Lesch-Nyan Syndrome:
Pathophys
Presentation
Treatment

Back 28

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

Front 29

Adenosine deaminase deficiency:
Pathophys
Presentation

Back 29

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)

Front 30

What is a silent mutation?

Back 30

Same aa, often change in 3rd position of codon (tRNA wobble)

Front 31

What is a missense mutation?

Back 31

Changed aa (conservative--new aa is similar in chemical structure)

Front 32

What is a nonsense mutation?

Back 32

Change results in EARLY STOP codon--STOP THE NONSENSE

Front 33

How does UV light damage DNA?

Back 33

Creates thymine dimers on same strand of DNA

Front 34

Topoisomerase:
Role
Relevant drug

Back 34

Creates nick in helix to relieve supercoils created during replication


Fluoroquinolones inhibit DNA gyrase--a specific prokaryotic topoisomerase

Etoposide inhibits eukaryotic topoisomerase (cancer drug)

Front 35

Which eukaryotic DNA polymerase:
Repicates lagging strand

Back 35

alpha

Front 36

Which eukaryotic DNA polymerase:
Synthesizes RNA primer

Back 36

alpha

Front 37

Which eukaryotic DNA polymerase:
Replicates mitochondrial DNA

Back 37

gamma

Front 38

Which eukaryotic DNA polymerase:
Replicates leading strand DNA

Back 38

delta

Front 39

Which eukaryotic DNA polymerase:
Repairs DNA

Back 39

beta, epsilon

Front 40

Label

Back 40

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

Front 41

Xeroderma pigmentosum:
Pathophys
Presentation

Back 41

Lack nucleotide excision repair; can't repair thymidine dimers

Hypersensitive to UV light-->1000x inc'd risk of skin cancer

Front 42

Hereditary nonpolyposis colorectal cancer:
Pathophys

Back 42

Inability to perform mismatch repair--unmethylated, newly synthesized string is recognized, mismatched nucleotides are removed, and gap is filled and resealed

Front 43

How is double-stranded DNA repaired?

Back 43

Nonhomologous end joining--brings together 2 ends of DNA fragments; no requirement for homology

Front 44

Everything is synthesized __' to __'.

Back 44

5' to 3' ALWAYS

Front 45

Start codons

Back 45

AUG

Front 46

Stop codons

Back 46

You are away
Yo go away
You are gone
UAA
UGA
UAG

Front 47

What is an operon?

Back 47

Structural genes that are transcribed + promoter region + all regulatory genes

Front 48

What are transcription factors?

Back 48

Factors that must bind PROMOTER region (TATA box) in order for transcription to occur

Front 49

What is an operator region?

Back 49

Region of gene that binds repressor (stops transcription) or inducer (starts transcription) located between promoter region and start site

Front 50

lac operon:
Role
Regulation

Back 50

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.

Front 51

RNA polymerase I vs II vs III:
Role

Back 51

RNA pol I: makes rRNA
II: makes mRNA
III: makes tRNA

No proofreading function; ONLY present in eukaryotes

Front 52

rRNA is synthesized in the ______.

Back 52

Nucleolus

Front 53

mRNA is synthesized in the ______.

Back 53

Nucleoplasm

Front 54

tRNA is synthesized in the _______.

Back 54

Nucleoplasm

Front 55

What events must occur for RNA to leave the nucleus?

Back 55

5' capping
3' poly A
Splicing out of introns

Front 56

What structures removes introns from pre-mRNA?

Back 56

Spliceosome!

Front 57

Aminoacyl-tRNA synthetase:
Role

Back 57

"Matchmaker"; 1 per amino acid--scrutinizes aa before and after it binds to tRNA, then delivers it to ribosome

Front 58

What are the steps of elongation in protein synthesis?

Back 58

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)

Front 59

How do eukaryotic ribosomes structurally differ from prokaryotic ribosomes?

Back 59

Eukaryotes: 40S + 60S-->80S (EVEN EUK)

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

Front 60

Aminoglycosides:
MOA

Back 60

-micins

Inhibit formation of initiation complex (assembly of euk ribosome?)

Front 61

Chloramphenicol:
MOA

Back 61

Inhibits 50S peptidyltransferase (this enzyme catalyzed peptide bond formation in growing polypeptide being synthesized)

Front 62

Macrolides:
MOA

Back 62

Bind 50S and block translocation

Front 63

Clindamycin:
MOA

Back 63

Binds 50S and blocks translocation

Front 64

Ribosomes are synthesized in the ______.

Back 64

Nucleus (and then exported to cytoplasm)

Front 65

Role of ubiquitin.

Back 65

Attaches to defective proteins to tag them for breakdown (Proteasomal degradation)

Front 66

Which antibiotic:
Inhibits 50S peptidyltransferase

Back 66

Streptogrammins
Chloramphenicol

Front 67

Which antibiotic:
Binds 50S, blocking translocation

Back 67

Macrolides
Lanezolide (sp?)

Front 68

Which antibiotic:
Binds 30S, preventing attachment of tRNA

Back 68

Tetracyclines

Front 69

Which antibiotic:
Inhibits prokaryotic RNA polymerase

Back 69

Rifampin

Front 70

Which antibiotic:
Inhibits prokaryotic topoisomerase

Back 70

Fluoroquinolones

Front 71

Which antibiotic:
Inhibits prokaryotic dihydrofolate reductase

Back 71

Trimethoprim

Front 72

What are the 3 mechanisms cell employ to break down proteins?

Back 72

Ubiquitin mechanism
Lyososmal degradation mech
Calcium-dependent enzyme mech

Front 73

What enzyme catalyzes peptide bond formation during protein synthesis?

Back 73

Peptidyltransferase--a type of ribozyme

Front 74

What enzyme matches amino acids to tRNA?

Back 74

AMinoacyl tRNA synthetase

Front 75

What are the mRNA stop codons?

Back 75

UGA
UAA
UAG

Front 76

What are the different RNA polymerases in eukaryotes?

Back 76

RNA pol I: codes for rRNA
II: transcribed mRNA
III: transcribes tRNA

Front 77

What amino acid frequently has more coding sequences in the mRNA than are represented in the peptide that is created from that mRNA?

Back 77

Methionine--more AUG than methionine in a protein because AUG is the start sequence and it is commonly cleaved off

Front 78

How is hnRNA processed before it leaves the nucleus?

Back 78

5' cap
3' poly-A tail
Splice out introns

Front 79

What is the characteristic sequence of the promoter region? What does a mutation in the sequence cause?

Back 79

-25 TATA box
-75 CAT box

Mutation-->dec'd amount of gene transcribed

Front 80

What enzyme is deficient in Lesch-Nyhan Syndrome?

What is the treatment?

Back 80

HGPRT

Tx: allopurinol

Front 81

What structural motifs allow for proteins to bind DNA?

Back 81

Helix turn helix
helix loop helix
Leucine zippers
Zinc fingers

Front 82

Which drugs cause gynecomastia?

Back 82

Some Drugs Create Awesome Knockers

Spironolactone
Digitalis
Cimetidine
Alcohol
Ketoconazole