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Flashcards in molecular Deck (100):
1

nucleosome

H2A, H2B, H3, H4 - two of each.
POSITIVELY CHARGED.

negative DNA loops twice around each octamer. octamer subunits are mainly LYS and ARG.

2

histone H1

ties nucleosome "beads" together.
ONLY histone that is not in nucleosome core.

3

HeteroChromatin

Highly Condensed.
transcriptionally inactive.
sterically inaccessible.

4

methylation

template strand CYTOSINE and ADENINE are methylated during DNA replication, allowing mismatch repair enzs to distinguish old and new strands

5

HYPERmethylation

inactivates DNA transcription

6

euchromatin

less condensed.
transcriptionally ACTIVE.
sterically accessible.

7

histone acetylation

relaxes DNA coiling,
allows for transcription.

8

deamination of what base makes uracil?

cytosine

9

guanine contains?

ketone

10

thymine contains?

methyl

11

which bonds are stronger?

G-C (3 H bonds)
vs. A-T (only 2 H bonds)

12

increased G-C content means..?

increased melting temp

13

AA needed for PURINE synth?

Glycine
Aspartate
Glutamine

14

nucleotides linked together by?

3'-5' phosphodiester bonds

15

AA needed for pyrimidine synth?

aspartate
(only other component is carbamoyl phosphate)

16

purine process

1. start with sugar + phosphate (PRPP).
2. add base.

17

pyrimidine process

1. make temporary base (OROTIC ACID).
2. add sugar + phos.
3. modify base.

18

ribonucleotide reductase

convert ribonucleotides to deoxyribonucleotides

19

carbamoyl phosphate

2 uses:
1. de novo pyrimidine synth.
2. urea cycle.

20

if carbamoyl phosphate can't be used for urea cycle...

due to deficiency of ornithine transcarbamoylase (OTC), carbamoyl phosphate ACCUMULATES and is converted to OROTIC ACID of pyrimidine pathway

21

orotic aciduria

auto recessive inability to convert orotic acid to UMP (de novo pyrimidine synth).

due to defect of:
1. orotic acid phosphoribosyltransferase (adds PRPP).
2. orotidine 5'-phosphate decarboxylase (removes CO2 to form UMP.

22

orotic aciduria FINDINGS

increased orotic acid in urine.
megaloblastic anemia.
failure to thrive.

23

orotic aciduria vs OTC deficiency

no hyperammonemia in orotic aciduria

24

TX of orotic aciduria

oral uridine

25

what is significant about megaloblastic anemia of orotic aciduria?

does NOT improve with admin of B12 or folic acid

26

adenosine deaminase

convert adenosine to inosine in purine salvage pathway

27

adenosine deaminase deficiency

excess ATP and dATP imbalance via feedback inhib of ribonucleotide reductase
= prevent DNA synth and thus, decrease lymphocyte count

28

adenosine deaminase deficiency causes what disease?

SCID:
B and T cells die off.
occurs in kids.
1st to be treated with experimental human gene therapy (retroviral vector).

29

Lesch Nyhan syndrome

defective purine salvage due to absent HGPRT.

results in excess uric acid prod and de novo purine synth.

X-linked recessive.

30

HGPRT

converts hypoxanthine to IMP,
guanine to GMP.

31

Lesch Nyhan syndrome FINDINGS

retardation.
self mutilation.
aggression.
hyperuricemia.
gout.
choreoathetosis.

32

what is the only base that can be salvaged in Lesch Nyhan syndrome ?

adenine

33

genetic code feature: unambiguous

each codon specifies only ONE AA

34

genetic code feature: degenerate/redundant

more than 1 codon may code for SAME AA

35

genetic code feature: commaless, nonoverlapping

read from a fixed starting point as a continuous sequence of bases

36

AA that are NOT degenerate/redundant

methionine (AUG) and tryptophan (UGG) are encoded by only ONE codon

37

genetic code feature: universal

genetic code is conserved throughout evolution (except: mito DNA)

38

severity of DNA mutations

nonsense > missense > silent

39

what do frameshift mutations often result in?

truncated, nonfunctional protein

40

where does DNA replication begin in prokaryotes?

at consensus sequence of base pairs

41

where does DNA replication begin in eukaryotes?

multiple consensus points (origins of replication)

42

helicase

unwinds DNA template at replication fork

43

single-stranded binding proteins

prevent strands from reannealing

44

DNA topoisomerases

create nick in helix to relieve supercoils created during replication

45

DNA gyrase

PROKARYOTIC
topoisomerase II.

*inhibited by fluoroquinolones

46

primase

DDRP.
makes RNA primer on which DNA pol III can initiate replication.

47

DNA polymerase III

PROK ONLY.
1. elongates leading strand by adding deoxynucleotides to the 3' end (5'-3' synth).
2. elongates lagging strand until it reaches primer of preceding fragment.
3. 3'-5' exonuclease activity to proofread each added nucleotide.

48

DNA polymerase I

PROK ONLY.
1. degrades RNA primer with 5'-3' exonuclease.
2. fills in gap with DNA (5'-3' synth).
3. proofreads with 3'-5' exonuclease activity.

49

DNA ligase

seals

50

telomerase

adds DNA to 3' end of chromosomes to avoid loss of genetic material with each duplication

51

nucleotide excision repair

single strand.

specific ENDONUCLEASES release oligonucleotide-containing damaged bases.

DNA pol fills gap, ligase reseals.

52

xeroderma pigmentosum

endonuclease deficiency.

UV light causes THYMINE DIMER formation.
UV endonuclease needed to excise dimer.
deficiency = inability to repair.

53

features of XP

photosensitivity.
poikiloderma.
hyperpigmentation.
increased risk for skin cancer.

54

base excision repair

single strand.

specific GLYCOSYLASES recognize and remove damaged bases.

AP endonuclease cuts DNA at apurinic or apyrimidinic site, empty sugar removed.

gap filled and resealed.

55

base excision repair is important for?

repair of spontaneous or toxic deamination

56

mismatch repair

single strand.

unmethylated, newly synthesized string is recognized. EXONUCLEASE removes mismatched nucleotides.

gap filled and resealed.

57

mutated mismatch repair

HNPCC: hereditary nonpolyposis colorectal cancer

58

nonhomologous end joining

double strand repair.
brings 2 ends of DNA fragments together.
homology not required.

59

mutated nonhomologous end joining

ataxia telangiectasia

60

rRNA

made by EUK RNA pol I.
most abundant type.
"Rampant"

61

mRNA

made by EUK RNA pol II.
longest type.
"Massive"

62

tRNA

made by EUK RNA pol III.
smallest type.
"Tiny"

63

mRNA start codon

AUG:
codes for methionine in EUK.
formyl-methionine (f-Met) in PROK.

*starts PROTEIN synth.

64

mRNA stop codons

UGA
UAA
UAG

65

promoter

site where RNA pol and multiple other TFs bind DNA upstream of gene locus.

AT-rich sequence with TATA and CAAT boxes.

66

mutated promoter

dramatic decrease in amount of gene transcribed

67

enhancer

stretch of DNA that alters gene expression by binding transcription factors

68

silencer

site where negative regulators (repressors) bind

69

where are enhancers and silencers located?

anywhere....
close to, far from, or even within the gene whose expression is being regulated

70

RNA polymerases

no proofreading.
can initiate chains.

71

PROK RNA pol

only 1 type. multisubunit complex.
makes all 3 kinds of RNA.

72

which EUK RNA pol opens DNA at promoter site?

RNA pol II

73

what toxin can inhibit RNA pol II?

alpha-amanitin (amatoxin) in death cap mushrooms - stops mRNA synth.

cause liver failure if ingested.

74

hnRNA

heterogeneous nuclear RNA (initial transcript) - must be processed before it can leave nucleus

75

RNA processing

1. 5' cap (7-methylguanosine).
2. 3' polyadenylation (200 A's).
3. splicing of introns.

= mRNA

76

Abs to spliceosomal snRNP

lupus

77

lac operon: allolactose

inhibits repressor

78

lac operon: glucose

inhibits activator

79

exons

contain actual genetic info coding for protein

80

introns

intervening noncoding segments of DNA

81

alternative splicing

combines diff exons to make unique proteins in different tissues

ex: beta thal (abn splicing)

82

tRNA structure

75-90 nucleotides.
secondary structure: cloverleaf.

83

tRNA 3' aminoacyl end

contains CCA and high #chemically modified bases.

AA covalently binds to 3'OH of CCA tail.
"Can Carry Amino acids"

84

tRNA charging

aminoacyl-tRNA synthetase (uses ATP) examines AA before and after it binds to tRNA

85

what happens if AA-tRNA bond is incorrect?

bond is hydrolyzed

86

where does energy for peptide bond formation come from?

AA-tRNA bond

87

what blocks attachment of aminoacyl-tRNA to ribosome?

tetracyclines - bind 30S subunit

88

tRNA wobble

accurate base pairing only required for FIRST 2 nucleotide positions of codon.

3rd WOBBLE position can code for same tRNA/amino acid.

89

protein synth: initiation

activated by GTP hydrolysis.
initiation factors help.

90

initiation factors (eIFs)

help assemble 40S subunit with initiator tRNA.

released when mRNA and ribosomal subunit assemble with complex.

91

EUK ribosomal subunits

40S + 60S = 80S (Even)

92

PROK ribosomal subunits

30S + 50S = 70S

93

protein synth: elongation

1. charged tRNA binds A site.

2. ribosomal rRNA (RIBOZYME) catalyzes peptide bond formation, transferring growing polypeptide TO CURRENT AA in A site.

3. ribosome advances 3 nucleotides toward 3' of mRNA, moving growing peptidyl RNA to P site (translocation).

94

protein synth: termination

stop codon recognized by RELEASE FACTOR.
completed protein released from ribosome.

95

posttranslational modification: trimming

remove N or C-terminal PROpeptides from zymogens to create mature proteins

96

posttranslational modification: covalent alterations

phosphorylation,
glycosylation,
hydroxylation

97

posttranslational modification: proteasomal degradation

attachment of UBIQUITIN to defective proteins to tag them for breakdown

98

aminoglycosides

bind 30S and inhibit formation of INITIATION COMPLEX.

cause misreading of mRNA.

99

chloramphenicol

inhibit peptidyltransferase (ribosomal rRNA/ribozyme), AKA peptide bond formation.

binds 50S.

100

macrolides

block translocation (A to P site)- prevent release of uncharged tRNA after it has donated its AA