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

Question 1

What enzyme degrades collagen? what cofactor do they need?

Answer 1

collagenases (MMP)

zinc!

Question 2

what makes up the protein chains of collagen?

Answer 2

glycine, proline, lysine

Question 3

what does hydroxylysine do?

Answer 3

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

Question 4

what is the catalyst for prolyl hydroxylase and lysyl hydroxylase?

Answer 4

Vitamin C

Question 5

What does a glycine in each 3rd position do?

Answer 5

allows for very tight winding because of very small side chain

Question 6

What does proline do?

Answer 6

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

Question 7

what does hydroxyproline do? where it is?

Answer 7

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

Question 8

what does lysine do?

Answer 8

long positive side chains, binds more tropocollagen, cross linking

Question 9

what does hydroxylysine do?

Answer 9

allows the addition of sugar (glucose, galatcose)

Question 10

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

Answer 10

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

Question 11

what is ehler danlos syndrome?

Answer 11

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

Question 12

what are the symptoms of ED syndrome?

Answer 12

hypermobility of joints, hyperextensiblity of skin, vessels can rupture

Question 13

what is osteogenesis imperfect?

Answer 13

less collagen or abnormal (type I collagen)

Question 14

what does lysyl oxidase need as a coenzyme?why?

Answer 14

copper

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

Question 15

what makes up a demo sine?

Answer 15

3 allysine and 1 lysine (covalently linked)

Question 16

what can be a result of copper defeicienty?

Answer 16

aneurism

Question 17

what is marfan syndrome? what are the symptoms?

Answer 17

autosomal dominant defect in gene that encose fibrillin-1

long limbs, aortic root dilation

Question 18

what packages DNA in eukaryotes/prokaryotes?

Answer 18

histones / HU

Question 19

What is the DNa template strand called?

Answer 19

antisense strand

Question 20

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

Answer 20

sende strand

Question 21

what direction does RNA polymerase go?

Answer 21

3’ to 5’

Synthesis in the 5’ to 3’

Question 22

what is TFIID do?

Answer 22

causes distortion = recruitment of other TF

Question 23

what does TFIIB do?

Answer 23

start site recog - DNA polymerase interactions

Question 24

what does TFIIH do?

Answer 24

helicase

Question 25

what does TFIIE do?

Answer 25

positioning RNA polymerase

Question 26

What is in RNA polymerase I in eurkaryotes?

Answer 26

rRNA...#S

Question 27

What is in RNA polymerase II in eukaryotes?

Answer 27

mRNA, some snRNA and miRNA

Question 28

what is in RNA polymerase III in eukaryotes?

Answer 28

tRNA, ssRNA, some snRNAs

Question 29

SLE lupus whats the problem>

Answer 29

SLE antibodies react with U1 RNA on splicesoome = anormal splicing

Question 30

What is beta thalassemia?

Answer 30

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

Question 31

what is limb girdle MD?

Answer 31

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

Question 32

What is magenizium a cofactor for?

Answer 32

DNA polymerase

Question 33

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

Answer 33

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

Question 34

what does polycistronic mean?

Answer 34

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).

Question 35

why is the 5' mRNA cap biologically important?

Answer 35

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

Question 36

what does poly-A-polymerase do?

Answer 36

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

Question 37

what does poly A binding proteins do?

Answer 37

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

Question 38

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

Answer 38

A nucleotide

Question 39

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

Answer 39

GU and AG

Question 40

what is the lariet structure?

Answer 40

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

Question 41

what is alternative splicing?

Answer 41

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

Question 42

what happens in Beta thallasemia?

Answer 42

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

Question 43

at what level does RNA editing take place?

Answer 43

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

Question 44

what is the purpose of alternative splicing?

Answer 44

increase diversity and increase expressed protein - use activators and repressors

Question 45

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

Answer 45

A nucleotide

Question 46

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

Answer 46

GU and AG

Question 47

what is the lariet structure?

Answer 47

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

Question 48

what is alternative splicing?

Answer 48

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

Question 49

what happens in Beta thallasemia?

Answer 49

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

Question 50

at what level does RNA editing take place?

Answer 50

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

Question 51

what is the purpose of alternative splicing?

Answer 51

increase diversity and increase expressed protein

Question 52

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

Answer 52

L and R

Question 53

what does km describe?

Answer 53

the affinity for the substrate for the enzyme | low km = high affinity

Question 54

what is alkaline phosphatase?

Answer 54

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

Question 55

what does the pH influence in terms of enzymes?

Answer 55

velocity

Question 56

when do enzymes begint o denature?

Answer 56

40 degrees C in humans

Question 57

when the substrate is oxidized...

Answer 57

the coenzyme is reduced ---"SOCR" = soccer

Question 58

what do all oxidoreductases need?

Answer 58

a coenzyme

Question 59

what are the coenzymes for oxidorectases?

Answer 59

NAD+ and FAD - get reduced

Question 60

how can enzymatic reactions be measures?

Answer 60

NADH formation

Question 61

what is teh michaelis menten equation?

Answer 61

v = Vmax[S]/Km + S

Question 62

what type of curve do allosteric enzymes show?

Answer 62

sigmoidal

Question 63

what happens to km and vmax with competitive inhibition?

Answer 63

km increases v max does not change ex. pravastatin

Question 64

what happens to km and vmax with noncompetitive inhibition?

Answer 64

km is the same | vmax decreases

Question 65

what is suicide inhibitor?

Answer 65

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

Question 66

what are irreversible inhibitors?

Answer 66

inhibitiors that bind covalently to the enzymes and inactivate it

Question 67

what does DFP di-isopropyl fluorophosphate) do?

Answer 67

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

Question 68

what are isoenzymes ?

Answer 68

CK and LDH

Question 69

what can you infer when ALP and GGT are elevated?

Answer 69

that ALP was released from the liver and NOT from bone

Question 70

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

Answer 70

obstruction of bile ducts - liver | cirrhosis or bile duct obstruction.

Question 71

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

Answer 71

bone diseases = osteomalacia, Padget's disease

Question 72

what do high levels of GGT and ALP indicate?

Answer 72

that the bile ducts are blocked/irritated

Question 73

what will increase GGT alone?

Answer 73

drinking alcohol in LARGE amounts

Question 74

a lipase/amylasse ratio greaters than 2 is what?

Answer 74

ethanol related pancreatitis

Question 75

sALP is normal in who?

Answer 75

children and pregnant mothers

Question 76

when is myoglobin increased?

Answer 76

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

Question 76

when is myoglobin increased?

Answer 76

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