Week 2 Content - Fibrous Proteins, bioenergetics, nucleic acids, DNA packaging, DNA replication, DNA transcription, RNA processing, Enzymes Flashcards
What enzyme degrades collagen? what cofactor do they need?
collagenases (MMP)
zinc!
what makes up the protein chains of collagen?
glycine, proline, lysine
what does hydroxylysine do?
residues can be glycosylated and can be used for linking of collagen
what is the catalyst for prolyl hydroxylase and lysyl hydroxylase?
Vitamin C
What does a glycine in each 3rd position do?
allows for very tight winding because of very small side chain
What does proline do?
makes kinks, disrupts the alpha helix which is good - allows close winding
what does hydroxyproline do? where it is?
on top of proline kink, many many hydrogen bonds (weak) but there are lots of them
they stablize the triple helix of 1 monomer
what does lysine do?
long positive side chains, binds more tropocollagen, cross linking
what does hydroxylysine do?
allows the addition of sugar (glucose, galatcose)
why does biosynthesis of collagen have to be with a soluble pro collagen?
because collgen is insoluble - it wouldn’t be able to leave the cell if it was made insoluble
what is ehler danlos syndrome?
mutation of type III collagen (reticular) - hereditary defect related to one of the enzymes that are needed for correct collagen synthesis
what are the symptoms of ED syndrome?
hypermobility of joints, hyperextensiblity of skin, vessels can rupture
what is osteogenesis imperfect?
less collagen or abnormal (type I collagen)
what does lysyl oxidase need as a coenzyme?why?
copper
forms allysine residues which are needed for cross linking and desmosine formation (bend and stretch)
what makes up a demo sine?
3 allysine and 1 lysine (covalently linked)
what can be a result of copper defeicienty?
aneurism
what is marfan syndrome? what are the symptoms?
autosomal dominant defect in gene that encose fibrillin-1
long limbs, aortic root dilation
what packages DNA in eukaryotes/prokaryotes?
histones / HU
What is the DNa template strand called?
antisense strand
What is the DNA strand called that is not being used and is the same as RNA in terms of base sequences?
sende strand
what direction does RNA polymerase go?
3’ to 5’
Synthesis in the 5’ to 3’
what is TFIID do?
causes distortion = recruitment of other TF
what does TFIIB do?
start site recog - DNA polymerase interactions
what does TFIIH do?
helicase
what does TFIIE do?
positioning RNA polymerase
What is in RNA polymerase I in eurkaryotes?
rRNA…#S
What is in RNA polymerase II in eukaryotes?
mRNA, some snRNA and miRNA
what is in RNA polymerase III in eukaryotes?
tRNA, ssRNA, some snRNAs
SLE lupus whats the problem>
SLE antibodies react with U1 RNA on splicesoome = anormal splicing
What is beta thalassemia?
mutation of the beta globin gene that generates the addition spice sites within mRNA
what is limb girdle MD?
mutation in the calpain 3 gene that generates new splice sites witin the 16 exon (coding sequence) = shorter calpain 3 mRNA
What is magenizium a cofactor for?
DNA polymerase
GLUT-1-5 - name type of affinity and location
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
what does polycistronic mean?
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).
why is the 5’ mRNA cap biologically important?
it is required for the efficient binding of the ribosome to the mRNA and the subsequent translation of the mRNA into protein.
what does poly-A-polymerase do?
add 200 A nucleotides to teh 3’ end of mRNA produce by cleavage
what does poly A binding proteins do?
bind to poly a tail and assist in directing translation by the ribosome
what does the branch point sequence of the intron always have?
A nucleotide
what nucleotides are at teh 5’ end and 3’ end of the introns?
GU and AG
what is the lariet structure?
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
what is alternative splicing?
producing different forms of proteins from the same gene - smooth muscle mRNA, fibroblast mRNA, etc. use the same gene to make different mRNA
what happens in Beta thallasemia?
defects in mRNA splicing of the beta golbin gene! = enemia
at what level does RNA editing take place?
mRNA level - A-I editing and C-U editing (cytidine deaminase enzyme)
what is the purpose of alternative splicing?
increase diversity and increase expressed protein - use activators and repressors
what does the branch point sequence of the intron always have?
A nucleotide
what nucleotides are at teh 5’ end and 3’ end of the introns?
GU and AG
what is the lariet structure?
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
what is alternative splicing?
producing different forms of proteins from the same gene - smooth muscle mRNA, fibroblast mRNA, etc. use the same gene to make different mRNA
what happens in Beta thallasemia?
defects in mRNA splicing of the beta golbin gene! = enemia
at what level does RNA editing take place?
mRNA level - A-I editing and C-U editing (cytidine deaminase enzyme)
what is the purpose of alternative splicing?
increase diversity and increase expressed protein
what configuration are amino acids enzymes found in, what are carbs found in?
L and R
what does km describe?
the affinity for the substrate for the enzyme
low km = high affinity
what is alkaline phosphatase?
optimal pH is 9 - refflecting the basic pH env. oin bone - its involved in bone metabolism
what does the pH influence in terms of enzymes?
velocity
when do enzymes begint o denature?
40 degrees C in humans
when the substrate is oxidized…
the coenzyme is reduced —“SOCR” = soccer
what do all oxidoreductases need?
a coenzyme
what are the coenzymes for oxidorectases?
NAD+ and FAD - get reduced
how can enzymatic reactions be measures?
NADH formation
what is teh michaelis menten equation?
v = Vmax[S]/Km + S
what type of curve do allosteric enzymes show?
sigmoidal
what happens to km and vmax with competitive inhibition?
km increases
v max does not change
ex. pravastatin
what happens to km and vmax with noncompetitive inhibition?
km is the same
vmax decreases
what is suicide inhibitor?
allopurinol - looks like comp. inhibitor but are used by the enzyme –> irreversible inhibitor (not reversible anymore) = purine degradation
what are irreversible inhibitors?
inhibitiors that bind covalently to the enzymes and inactivate it
what does DFP di-isopropyl fluorophosphate) do?
irreversible “suicide” inhibitor of acetylcholinesterase - binds covalently to the Serine in the active site !
what are isoenzymes ?
CK and LDH
what can you infer when ALP and GGT are elevated?
that ALP was released from the liver and NOT from bone
what does an increase in ALP-1 (liver) mean?
obstruction of bile ducts - liver
cirrhosis or bile duct obstruction.
what does increase in ALP-2 (bone) mean?
bone diseases = osteomalacia, Padget’s disease
what do high levels of GGT and ALP indicate?
that the bile ducts are blocked/irritated
what will increase GGT alone?
drinking alcohol in LARGE amounts
a lipase/amylasse ratio greaters than 2 is what?
ethanol related pancreatitis
sALP is normal in who?
children and pregnant mothers
when is myoglobin increased?
general damage to muscle - nonspecific to heart but absolutely can be used in conjunction with the other markers!
when is myoglobin increased?
general damage to muscle - nonspecific to heart but absolutely can be used in conjunction with the other markers!
