Biochem Final Flashcards
mito etc
inner mito membrane, coupled to ox phos, pH gradient
bacteria etc
no mito, so its in the cell membrane. use coq or vit k, pH gradient
photosynthesis
driven by light energy, convert co2 to hexose sugars
- located in chloroplast mem
nadph
know structure
light reactions
photosys 1 generates nadph
photosys 2 splits h2o and forms o2 and reductant
- light required
dark reactions
nadph and atp take co2 to make glucose
- no light required
chlorophyll a and b
know structure
chlorophyll
alternating single adn double bonds make them good photoreceptors
- light is transferred to reaction centers that contain the etc
etc z diagram
1) split h20
2) rise in energy and go down etc
3) photosys 1
4) rise to ferodoxin
4) go down etc and back to photosys 1 OR make nadph
microsomal etc
found in ER, which does protein synth, transport and has 2 etc
p450 system
- no atp made
- reox nadph to nadp
- Oh to groups so you can pee them out in liver
- need flavorptoein, cyto p450 reductase
- oh is done by hydroxylase, monooxygenase, mixed function oxidase
- inductible so can increase if there is a toxin to quickly remove
b5 system
- adds double bonds to fa using nadph
- can add double bonds to fa but NOT past c9
- we can’t make linoleic acid (c9,12) or linolenic acid (c9,12,15)
gluconeogenesis
- liver mostly
- see pathway
- irreversible is gly to glc 6 p and gructose 6 p to fructose 16 bisp
- turns to pyruvate
- made in exercise during lactation or starvation
how pyruvate becomes PEP, biotin problems
- irreversible
- see process
- pyruvate carboxylase needs acetyl coa and biotin
- links to lysine and binds co2 to add it to pyruvate
- avidin in egg whites stops biotin from binding
pfk reverse step
takes fructose 16 to fructose 6
- fructose 6 phosphate is the enzyme
- no atp made
- positive effected by citrate and atp
- negative by amp
- ON when atp is present
pfk enzyme
positive effectgor is adp and amp
negative is citrate and atp
hexokinase reverse step
- glucose 6 phosphatase that turns it back to glucose
- found in liver and kidney only
- liver is primary source of blood glucose
glycogen synthesis
- see diagram
phosphoglucomutase
takes glucose 6 p to 16 p
- reversible
utp glucose pyrophosphatase
utp glycose + glucose 1 p to make pyrophosphate and udp glucose
- pyrophosphate makes this irriversible
glycogen synthetase
- does udp glucose + glycogen to glycogen + Udp
- adds glucose units to non reducing ends of glycogen
- makes the 1,4 link
how glycogen is elongated
- primer is 4 units
- every 8-10 it branches using branching enzyme with 1,6 bond
- more places to break
glycogen phosphorylase
- catalyzes glygocen breakdown by attacking 1,4 links
- stops 4 units from the branch point
- transferase takes 3 of the 4 sugars and makes them 1,4 bond
- debranching enzyme cuts off the last 1,6 and releases
**phosphorylase kinase is activated by ca ions during muscle contraction
glycogen synthetase control
I form is no p, active
D form is p, inactive
- d form is allosteric and is off but glucose 6 p is positive effector
glycogen phosphorylase regulation
- p is active, no p is inactive
- phosphorylase b is effected by atp, glucose 6 p negative
- adp amp turns it on
epinephrine and glycogen
MADE IN ADRENAL MEDULLA
- acts on muscle
- g protein cascade
- activates so taht we get energy when scared, make g6p
- g6p activates the synthetase to make glycogen
- epinephrine inactivates it
glucagon and glycogen
made in pancreas, acts on liver
- g protein cascade
g protein
3 subunits then alpha and beta djssociate to activate
- stimulates adenylate cyclase, then atp to amp
- camp is then hydrolyzed to amp by hydrolyase (caffeine inhibited)
camp and protein kinase a
- camp stimulates kinase a, adds p to phosphorylase kinase and synthetase kinase to activate glycogen synthetase and phsophorylase kinase
pentose shunt
cytoplasm
- make d ribose for nucleotide synthesis, nadph
- no atp made
- starts with g6p, allosteric enzyme g6p dehydrogenase which is negative by nadph
- see diagram
- if pentose needed, then ribose is used
- if nadph is needed, then ribose is converted back
transaldolase
- takes 3c fragment, needs l stereochem, forms a schiff base with lysine,
- see diagram
aldo = shoes
transketolase
- transfers 2c fragment
- l stereochem, thiamine pyrophosphate is cofactor
starch meta
forms amylose (14) and amylopectin (16) - saliva, SI, maltase breaks down last bond
cellulose meta
- b 14
- bulk in diet, no breakdown
sucrose
- sucrase breaks down to glucose and fructose
lactose
- galactose and glucose
- lactase breaks b14 bond
- bad in infants to be deficient, switch to formula
fructose entering metabolism
pfk and hexokinase turn it to aldose
- pfk deficiency means fructose in pee
galactose entering metabolism
- galactose kinase, transferase, epimerase
- udp galactose and atp needed
- epimerase needs nad+
udp glucose and feeding
can be made into lactose for nursing mothers, modified by lactalbumin
galactosemia
- disease that causes catacts and liver problems
- tranferase block: galactose and galactose 1 p build up
- withold milk
- can still make udp galactose through epimerase reaction
kinase deficienci=y
- only galactose accumulates
- onyl cataracts
- galatitol is made, clouds the lens
blood sugar level regulation
- insulin after you eat, targets white muscle and fat
- take up glucose in tissues
- glucose level drops then glucagon
- liver then does g6p to g breakdown
insulin how it works
inhibits synthetase kinase so glycogen synthetase stays active (increase glycogen synthesis)
hypoglycemia
- low blood sugar
- overproduction of insulin so too much sugar uptake
hyperglycemia
- glucose in pee, muscles are depleted in glucose, too much thirst and pee, rapid weight loss
- ketosis from too much fat breakdown
type 1 diabetes
0 insulin is bad
- inject insulin
type 2 dia
- less insulin receptors so glcucose stays high
- eat less sugar
glucose 6 phosphatase deficiency
- can’t do g6- to glucose
- hypoglycemic
- glucagon released so high glycogen
- increase in pyruvate and lactate
- acidosis
- TEST: give person glucagon and monitor levels
- treatment: give small meals of carbs
pfk deficincy in muscle
- can’t do fructose 6 p to fructose 16
- can’t take sugar thru gkycolysis
- can’t meta glycogen during exercise fast enough
- test: no increase in lactate after exercise
- can be given fructose
glycogen phosphorylase deficiency
- hard to break down glycogen
- can’t do exercise
- no rise in pyruvate and lactate levels
- can give glucose
oxidation of fats location
mito then cyto
neutral lipid breakdown
- hydrolysis in cyto of adipose
- regulated by hormones: gluc and epi turn on camp
- camp turns on protien kinase, adds p to hormonse sensitive lipase
- also starvation, stress, esercise and growth
- glycerol is made and oxidised to dhap to enter glycolysis
insulin and fat breakdown
- unsulin inhibits adenylate cyclase so no tg breakdown
phospholipid breakdown
- broken by phospholipase
- snake venom destroys it
fatty acid breakdown - outer mito membrane
- coa is attached to the fa, hydrolysis of ppi makes it irreversible
how does fa get into the inner mito
the long fa chain must be transfered to carnitie (transferase)
- this is inhibited by malonyl coa
- then the fa is remade inside
fatty acid oxidation process
- uses fad to oxidize
- trans double bond is formed
- then add h20
- use nad to oxidize
- cleave to make acetyl coa
- if 16c then need 7 turns to get 8 acetyl coa
unsaturated fatty acid ox
- will keep oxidizing until u reach the double bond, then add water to make it l configuration and trans
diabetes, insulin and fa breakdown
- unsulin can’t stop hsl in dia, so you get lots of acetyl coa, form ketone bodies, acetoacetate
what is needed to fa synthesis
- citrate, co2
- done in cytoplasm
how to make pyruvate for fa synthesis
- oxaloacetate to malate then malate goes through malate asp a shuttle OR is converted to pyruvate through malic enzyme
acetyl coa carboxylase
- malonly coa is made from co2 + acetyl coa
- this is done by acetyl coa carboxylase (needs biotin)
- citrate is positive effector
- it is a tetramer where one unit binds biotin, one does the co2 and biotin rxn, one transfers co2 to acetyl coa and one binds citrate
- citrate causes polymerization
fatty acid synthetase complex
- malonyl coa binds, found in cyto
- the fa chain is attached to acyl carrier protein with a phosphopantetheine group
- see card
- keeps it from diffusing until palmitate is made
how much atp to make fa
- 1 atp for each malonyl coa so 7 atp to make a 16c fa
- nadph comes from pentose shunt and malic enzyme
fa breakdown vs synthesis 4
- synthesis in cytoplasm, breakdown in mito
- acp in synthesis, coa carrier in breakdownn
- malonyl needed for synth
- d stereo in synthesis, l in oxidation
- need nadph for synth, nad and fad for breakdown
- palmitate is end product for synthesis
tg and phospholipid synthesis
- dhap to phosphatidyl serine and phosphotidyl choline
inositol lipids
- involved in cascade
- makes phospho inositol
sphingolipids
- makes sphingomyelin and cerebroside from palmitoyl coa and serine
gangliosides
- formed from cerebrosides + sugars
lipid storage disease
- overproduction of lipds (overactive enzymes)
- defected degrading enzymes
tay sachs
- defect in enzyme
- increase in ganglioside gm2
- can’t do cleavage of n acetyl galactosamine
niemann pick
- increase in sphingomyelin because u can’t break it to ceramide and phosphocholine
prostaglandin description
- not true hormone since they act on tissue they are made in
- synthesis from linoleic acid to arachidonic acid by cyto b5
pge and pgf
made from eicosatrienoc acid (pge1 and pgf1)
arachidonic acid makes the 2a
prostaglandin synthetase complex
- called cox
turns the arachidonic to pgh2, pge2, pgf2, thromboxne a2 and prostacyclin (pgi2) and endoperoxide
biological effects of prostagalndin
- increase camp levels in cell types
- inflammatory reaction
- fever
- muscle contraction
- platelet aggregation
- aspirin stops inflammation
blood clot mech
- cut, endo is exposed, platelets bind, prostaglandins inhibit this, thromboxanes allow
- zymogen so not active until cut
cholesterol synthesis
2 acetyl coa –> reductase to mevalonic acid and acetoacetate
*cholesterol blocks mevalonic acid
mevalonic then goes to dimethylallylpyrophos and condense to farnesyl
then go to squalene (need 02) then lanosterol and cholesterol
lanosterol and vit d
lanosterol makes vit d by cyto p450
vit d effects
- increases ca abs in bones and teeth?
calcium is involved in
troponin c helps ca bind
- calmodulin bidns ca
cholesterol fates 7
membranes, excretion product, bile salts, progestagens, glucocorticoids, mineralcorticoids, sex hormones
bile salts
- made in liver, store in gall
- emulsify fats
- polar so lots of OH groups added by cyto p450
- from choles, needs nadph, coa to turn into glycine then glycocholate
steroid hormones
- found in endocrine tissue
- chols modified by p450 then pregnenolone and progesterone
glucocorticoids
- progesterone to corisol
- uses p450 and 21 hydroxylase
glucocorticoid roles
- increase in g6p activity
- increase gluconeo
- aa/ nuc synthesis
- controls life of fibroblasts and lymphocytes
mineralcorticoids and what they do
- progesterone using p450 and 21 hydro to make aldosterone
- ## reabsorption of na, cl and hco3
androgens and estrogens
- progesterone goes to andosterone and then estrone
testosterone then estradiol
defect in 21 hydroxylase enzyme
- means early puberty
- can’t make gluco and mineral so there is too mich sex hormones
where do fa go after breakdown
- go from intestine into mucosal cells
- cholesterol goes in and some is amde into cholesterol esters
- they clump together and form chylomicron
chylomicron composition and structure
- 2 protein, 85 tg, 13 cholesterol
- tg and ester are in the core, polar lipis and proteins are outside
chylomicrons into liver
- some tg is removed here by lipase
- lp is then secreted with 2 new proteins of liver origin
- called vldl
10 protein, 50 tg, 40 cholesterol
lipase digestion
- attacks tg and chylomicrons and vldl
- complexed to serum albumin then broekn down or adipose
lecithin cholesterol acyl transferase
cholesterol + phosphotidyl choline are turned to cholesterol ester and lysolecithin
- toxic in high amts
- combins in serum to form hdl
hdl proteins
- goes to liver to make phospho
- 50 protein, 50 lysophospho
LDL protein
- made from IDL, which looses a protein and becomes LDL
- takes up by most tissues as a source of cholesterol (take receptor and ingest it)
- the ones not taken up are picked up by macrophages
familial hypercholesterolemia
- heterozygous is 300-400 mg cholestol
- risk of heart attack in 30s or 40s
- homozygs is 600+ choles and heart in childhood
- homo has no funcitonal receptors
transamination
- first step in AA breakdown
- reversible
- AA + Alpha ketoglutarate –> a keto acid + glutamate
- need pyridoxal phosphate as cofactor (vit b6)
- doesn’t happen unless low energy state
- other transaminase can cut using aldolase and decarbo
urea cycle
- liver
- urea goes to kidney
glutamate dehydrogenase
- first step in urea
- take glutamate + NAD to make alpha keto glu
gtp and atp are -
adp and gdp are + - in mito matrix
- reverse reaction is very toxic
other ways to get nh4+
- ugh see card
nh3 poisoning
- drunken behavior
- give less protein and more ketoacid
biotin
- needed when co2 is added
s adenyosyl methionine
- transfers methyl groups
- uses n as an acceptor and methionine
thfa
- carbon in various oxidation states
- needs folic acid to become thfa by reduction
vit b12
- transfers alkyl groups from one carbon to another
vit b12 problems
- usually absobred in intestine
- intrinsic factor binds it
- pernicious anemia is when low intrinsic factor so no b12
- treatment is b12 shots
pyruvate AA pathways
- ala, cys, thr,
oxaloacetate pathway AA
- asp a, asparagine
path to alpha keto glu
- glutamic acid, glutamine, argnine, proline, his,
path to succinyl coa
- met, threo, valine, iso leu and leu make using vit b12
- do oxidative deamination
- this leads to maple syrup disease if def
phenylalanine + tyros
turns to acetoacetate
leucine
ketogenic (acetyl coa + acetoacetate)
tryptophan
gluco and keto
lysine
ketogenic
simple feedback
products blocks start
sequential feedback
- a has two paths where product of path inhibits start
concerted feedback
- a has two paths where the product blocks path AND a-
- need both to block a
enzyme multiplicity
- enzymes of pathways inhibit the pathway and the start of pathway
cumulative feedback
- lots of products made, and each increasingly inhibits the start
covalent modification (glutamine synthetase)
- amp binds to tyros
- gln synthetase without p is actie, when bound to amp it is less active
aa uses
- proteins, cofactors, hormones, porphyrins and heme, nucleotides, nt, pigments
making porphyrin
- start with delta aminolevulinate and condense using nh4+
- heme is negative effector???
hemoglobin
- 120 days
- degraded by bilirubin, goes to liver to secrete with bile
- high biliriubinn is jaundice
acute intermittent porphyria
- overactive aminolevulinate synthetase
- high levels in liver
- red pee
- light sensitive
hepatoerythropoeitic porphyria
- one aa change for enzyme in heme to make unstable
variegate porphyria
- block in enzye leading to heme, so not enough negative effector heme
- high levels of intermediates b4 blockage
- need blood transfusions
- light sensitive
serotonin
- made from tryp and pyrodoxal phos
- sleep and memory
- lsd thing
dopamine and norpei
- tyros
- catecholamines
- see card
parkinsons
- low dopamine
- broken down by monoamine oxidase
melanin
- dopa to red pigment then black
pku
- bad conversion from phenyla to tyros
- converted to a phenyl pyruvate instead using transaminase
- deficient in pigment
, no protein formation
