Z Boards Biochem 1

Front 1

carbamoyl phosphate is used in...

Back 1

urea cycle

de novo pyrimidine synthesis

Front 2

difference between purine & pyrimidine synthesis

Back 2

purines: built on a PRPP "scaffold"

pyrimidines: orotic acid (~ a base) is built, then PRPP is added to it

Front 3

5 drugs that interfere with nucleotide synthesis, and what they inhibit

Back 3

hydroxyurea: - ribonucleotide reductase
6-mercaptopurine: purine analog; - de novo purine synthesis
5-fluorouracil: - thymidylate synthase
methotrexate: - dihydrofolate reductase
trimethoprim: - dihydrofolate reductase

Front 4

aa's used in purine synthesis

Back 4

glycine
aspartate
glutamine

Front 5

components of pyrimidine synthesis

Back 5

carbamoyl phosphate
aspartate

Front 6

two bases have two interesting functional groups

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guanine: ketone
THYmine: meTHYl

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deamination of _ --> _

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cytosine-->uracil

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3 ways euchromatin differs from chromatin

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less condensed
transcriptionally active
sterically accessible

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orotic aciduria may be caused by...

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1. defective orotic acid phosphoribosyltransferase

3. defective orotidine 5'-phosphate decarboxylase

(1) and (2) --> inability to convert orotic acid to UMP

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orotic aciduria may be caused by 2 enzyme defects

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orotic acid phosphoribosyltransferase

orotidine 5'-phosphate decarboxylase

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findings of orotic aciduria

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^ orotic acid in urine

megaloblastic anemia (does not improve with B12 or folate)

failure to thrive

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OTC deficiency

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ornithine transcarbamoylase deficiency
--> accumulation of carbamoyl phosphate
--> ^ orotic acid

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orotic aciduria vs.

OTC deficiency

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^ orotic acid, no hyperammonemia

^ orotic acid with hyperammonemia

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treatment for orotic aciduria

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oral uridine

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Lesch-Nyhan syndrome mecahnism (3)

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defective purine salvage

2^ HGPRT absence

--> excess uric acid production

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Lesch-Nyhan syndrome symptoms (6)

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his ARS has hCG written on it

aggression
retardation
self-mutilation

hyperuricemia
choreoathetosis
gout

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methionine: what codon?

Back 17

AUG

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example organisms that have exceptions to the universal genetic code

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mitochondria, archaebacteria, mycoplasma, some yeasts

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primase does...

Back 19

makes an RNA primer

on which DNA polymerase III can initiate replication

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DNA polymerase I does...

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degrades RNA primer

fills in the gap with DNA

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DNA polymerase III directions in which it works

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synthesis: 5' --> 3'

exonuclease (proofreading):
3'-->5'

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two prokaryotic DNA polymerases

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DNA pol III
DNA pol I

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exonuclease in DNA pol III and DNA pol I

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pol III: 3'-->5'

pol I: 5'-->3'

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4 types of DNA repair

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nucleotide excision repair
base excision repair
mismatch repair

double strand nonhomologous end joining

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_ DNA repair is mutated in _

(2)

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nucleotide excision repair: xeroderma pigmentosum

mismatch repair: HNPCC

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nucleotide excision repair vs.

base excision repair enzymes

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endonucleases vs.

--glycosylases
--AP endonuclease (cuts at AP site)
---------------------------------
(DNA polymerase
DNA ligase)

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mismatch repair is...

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recognition of mismatched bases

in the newly synthesized strand (which is recognized e.g. in proks because it's unmethylated)

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xeroderma pigmentosum sxs and a molecular defect

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dry skin
melanoma
other cancers

thymidine dimers

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DNA & RNA are synthesized from

_' to _'. what is the energy source?

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5' to 3'

5' triphosphate of the incoming nucleotide

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mRNA is read from _ to _; protein synthesis is from _ to _

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5' to 3'

N to C

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start codon

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AUG; rarely GUG

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the promoter is bound by...

describe the promoter

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RNA polymerase
transcription factors

AT-rich
CAAT and TATA boxes

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_ binds transcription factors, but _ binds _

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enhancer

silencer binds repressors aka negative regulators

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euks vs. proks:

RNA polymerase

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euks: RNA polymerase I makes rRNA

II: mRNA
III: tRNA

proks: there's one RNA polymerase

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_ opens DNA at promoter site

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RNA pol II

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RNA polymerase lacks _ ability but has _ ability

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proofreading

can initiate without a primer

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_ is found in death cap mushrooms

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alpha-amanitin

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alpha-amanitin (3)

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found in death cap mushrooms

inhibits RNA pol II

causes liver failure

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5' cap =

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7-methylguanosine

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polyadenylation signal =

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AAUAAA

Front 41

_ disease makes antibodies to spliceosomal snRNPs

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lupus

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intron hnRNA goes where?

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stays IN the nucleus

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_ disease is notable for having mutations affecting splicing of its hnRNA

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beta-thalassemia

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mechanism of tetracyclines

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bind 30S subunit

prevent attachment of
aminoacyl-tRNA

Front 45

there are _ aminoacyl-tRNA synthetases per aa

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1 per aa

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where does energy for peptide bond come from?

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aa-tRNA bond

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Back 47

Front 48

wobble is all about the 3rd position in the _

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mRNA's codon

Front 49

initiation of protein synthesis involves 5 things

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GTP hydrolysis
eIFs that help assemble the
40S subunit with the
initiator tRNA

... then the eIFs are released

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protein synthesis:

stop codon is recognized by

Back 50

release factor

Front 51

aminoglycosides MOA

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inhibit formation of the initiation complex

--> misreading of mRNA

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chloramphenicol MOA

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inhibits 50S peptidyltransferase

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macrolides and clindamycin MOA

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bind 50S and block translocation

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posttranslational modifications include

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trimming

covalent alterations

proteasomal degradation