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Medical Biochemistry > Week 2 Content - Fibrous Proteins, bioenergetics, nucleic acids, DNA packaging, DNA replication, DNA transcription, RNA processing, Enzymes > Flashcards

Week 2 Content - Fibrous Proteins, bioenergetics, nucleic acids, DNA packaging, DNA replication, DNA transcription, RNA processing, Enzymes Flashcards

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USMLE® Step 1 flashcards
1
Q

What enzyme degrades collagen? what cofactor do they need?

A

collagenases (MMP)

zinc!

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2
Q

what makes up the protein chains of collagen?

A

glycine, proline, lysine

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3
Q

what does hydroxylysine do?

A

residues can be glycosylated and can be used for linking of collagen

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4
Q

what is the catalyst for prolyl hydroxylase and lysyl hydroxylase?

A

Vitamin C

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5
Q

What does a glycine in each 3rd position do?

A

allows for very tight winding because of very small side chain

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6
Q

What does proline do?

A

makes kinks, disrupts the alpha helix which is good - allows close winding

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7
Q

what does hydroxyproline do? where it is?

A

on top of proline kink, many many hydrogen bonds (weak) but there are lots of them
they stablize the triple helix of 1 monomer

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8
Q

what does lysine do?

A

long positive side chains, binds more tropocollagen, cross linking

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9
Q

what does hydroxylysine do?

A

allows the addition of sugar (glucose, galatcose)

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10
Q

why does biosynthesis of collagen have to be with a soluble pro collagen?

A

because collgen is insoluble - it wouldn’t be able to leave the cell if it was made insoluble

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11
Q

what is ehler danlos syndrome?

A

mutation of type III collagen (reticular) - hereditary defect related to one of the enzymes that are needed for correct collagen synthesis

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12
Q

what are the symptoms of ED syndrome?

A

hypermobility of joints, hyperextensiblity of skin, vessels can rupture

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13
Q

what is osteogenesis imperfect?

A

less collagen or abnormal (type I collagen)

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14
Q

what does lysyl oxidase need as a coenzyme?why?

A

copper

forms allysine residues which are needed for cross linking and desmosine formation (bend and stretch)

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15
Q

what makes up a demo sine?

A

3 allysine and 1 lysine (covalently linked)

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16
Q

what can be a result of copper defeicienty?

A

aneurism

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17
Q

what is marfan syndrome? what are the symptoms?

A

autosomal dominant defect in gene that encose fibrillin-1

long limbs, aortic root dilation

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18
Q

what packages DNA in eukaryotes/prokaryotes?

A

histones / HU

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19
Q

What is the DNa template strand called?

A

antisense strand

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20
Q

What is the DNA strand called that is not being used and is the same as RNA in terms of base sequences?

A

sende strand

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21
Q

what direction does RNA polymerase go?

A

3’ to 5’

Synthesis in the 5’ to 3’

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22
Q

what is TFIID do?

A

causes distortion = recruitment of other TF

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23
Q

what does TFIIB do?

A

start site recog - DNA polymerase interactions

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24
Q

what does TFIIH do?

A

helicase

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25
Q

what does TFIIE do?

A

positioning RNA polymerase

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26
Q

What is in RNA polymerase I in eurkaryotes?

A

rRNA…#S

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27
Q

What is in RNA polymerase II in eukaryotes?

A

mRNA, some snRNA and miRNA

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28
Q

what is in RNA polymerase III in eukaryotes?

A

tRNA, ssRNA, some snRNAs

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29
Q

SLE lupus whats the problem>

A

SLE antibodies react with U1 RNA on splicesoome = anormal splicing

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30
Q

What is beta thalassemia?

A

mutation of the beta globin gene that generates the addition spice sites within mRNA

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31
Q

what is limb girdle MD?

A

mutation in the calpain 3 gene that generates new splice sites witin the 16 exon (coding sequence) = shorter calpain 3 mRNA

32
Q

What is magenizium a cofactor for?

A

DNA polymerase

33
Q

GLUT-1-5 - name type of affinity and location

A

Glut 1 is high affinity found in brain and rbcs
Glut 2 is low affinity found in intestinal mucosa near portal vein
Glut 3 is high affinity found n neurons
Glut 4 is high affinity found in fat and muscle cells also they store inside the cell!
Glut 5 is low affinity found in intestinal lumen …fructose

34
Q

what does polycistronic mean?

A

This means that the mRNA contains more than one protein-coding region (ie. More than one protein will result from the translation of a polycistronic mRNA).

35
Q

why is the 5’ mRNA cap biologically important?

A

it is required for the efficient binding of the ribosome to the mRNA and the subsequent translation of the mRNA into protein.

36
Q

what does poly-A-polymerase do?

A

add 200 A nucleotides to teh 3’ end of mRNA produce by cleavage

37
Q

what does poly A binding proteins do?

A

bind to poly a tail and assist in directing translation by the ribosome

38
Q

what does the branch point sequence of the intron always have?

A

A nucleotide

39
Q

what nucleotides are at teh 5’ end and 3’ end of the introns?

A

GU and AG

40
Q

what is the lariet structure?

A

when the cut 5’ G binds to the branch point A in the middle of the intron and forms a loop - simply a ring of intron segments

41
Q

what is alternative splicing?

A

producing different forms of proteins from the same gene - smooth muscle mRNA, fibroblast mRNA, etc. use the same gene to make different mRNA

42
Q

what happens in Beta thallasemia?

A

defects in mRNA splicing of the beta golbin gene! = enemia

43
Q

at what level does RNA editing take place?

A

mRNA level - A-I editing and C-U editing (cytidine deaminase enzyme)

44
Q

what is the purpose of alternative splicing?

A

increase diversity and increase expressed protein - use activators and repressors

45
Q

what does the branch point sequence of the intron always have?

A

A nucleotide

46
Q

what nucleotides are at teh 5’ end and 3’ end of the introns?

A

GU and AG

47
Q

what is the lariet structure?

A

when the cut 5’ G binds to the branch point A in the middle of the intron and forms a loop - simply a ring of intron segments

48
Q

what is alternative splicing?

A

producing different forms of proteins from the same gene - smooth muscle mRNA, fibroblast mRNA, etc. use the same gene to make different mRNA

49
Q

what happens in Beta thallasemia?

A

defects in mRNA splicing of the beta golbin gene! = enemia

50
Q

at what level does RNA editing take place?

A

mRNA level - A-I editing and C-U editing (cytidine deaminase enzyme)

51
Q

what is the purpose of alternative splicing?

A

increase diversity and increase expressed protein

52
Q

what configuration are amino acids enzymes found in, what are carbs found in?

A

L and R

53
Q

what does km describe?

A

the affinity for the substrate for the enzyme

low km = high affinity

54
Q

what is alkaline phosphatase?

A

optimal pH is 9 - refflecting the basic pH env. oin bone - its involved in bone metabolism

55
Q

what does the pH influence in terms of enzymes?

A

velocity

56
Q

when do enzymes begint o denature?

A

40 degrees C in humans

57
Q

when the substrate is oxidized…

A

the coenzyme is reduced —“SOCR” = soccer

58
Q

what do all oxidoreductases need?

A

a coenzyme

59
Q

what are the coenzymes for oxidorectases?

A

NAD+ and FAD - get reduced

60
Q

how can enzymatic reactions be measures?

A

NADH formation

61
Q

what is teh michaelis menten equation?

A

v = Vmax[S]/Km + S

62
Q

what type of curve do allosteric enzymes show?

A

sigmoidal

63
Q

what happens to km and vmax with competitive inhibition?

A

km increases
v max does not change
ex. pravastatin

64
Q

what happens to km and vmax with noncompetitive inhibition?

A

km is the same

vmax decreases

65
Q

what is suicide inhibitor?

A

allopurinol - looks like comp. inhibitor but are used by the enzyme –> irreversible inhibitor (not reversible anymore) = purine degradation

66
Q

what are irreversible inhibitors?

A

inhibitiors that bind covalently to the enzymes and inactivate it

67
Q

what does DFP di-isopropyl fluorophosphate) do?

A

irreversible “suicide” inhibitor of acetylcholinesterase - binds covalently to the Serine in the active site !

68
Q

what are isoenzymes ?

A

CK and LDH

69
Q

what can you infer when ALP and GGT are elevated?

A

that ALP was released from the liver and NOT from bone

70
Q

what does an increase in ALP-1 (liver) mean?

A

obstruction of bile ducts - liver

cirrhosis or bile duct obstruction.

71
Q

what does increase in ALP-2 (bone) mean?

A

bone diseases = osteomalacia, Padget’s disease

72
Q

what do high levels of GGT and ALP indicate?

A

that the bile ducts are blocked/irritated

73
Q

what will increase GGT alone?

A

drinking alcohol in LARGE amounts

74
Q

a lipase/amylasse ratio greaters than 2 is what?

A

ethanol related pancreatitis

75
Q

sALP is normal in who?

A

children and pregnant mothers

76
Q

when is myoglobin increased?

A

general damage to muscle - nonspecific to heart but absolutely can be used in conjunction with the other markers!

76
Q

when is myoglobin increased?

A

general damage to muscle - nonspecific to heart but absolutely can be used in conjunction with the other markers!

Medical Biochemistry (17 decks)

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