Biochemistry 2 Flashcards
the 6 enzyme classes (and their functions)
1) oxidoreductases: redox reactions
2) transferases: transfer of chemical group
3) hydrolase: lysis by water
4) lyase: cleavage reaction not using water
5) isomerase: change of molecular conformation
6) ligase: joining of 2 compounds
serine protease mechanism
Substrate binds.
Ser-195 attacks (Ser is very reactive due to His and Asp).
Transition state is stabilized.
Peptide bond is cleaved via hydrolysis.
active site specificity of chymotrypsin
bulky, hydrophobic residues
active site specificity of trypsin
positively charged residues (Arg, Lys)
active site specificity of elastase
small AAs prevalent in elastin (Gly, Ala, Val)
spontaneous reaction (in terms of Gibb’s free energy)
spontaneous if delta G < 0 (negative)
delta G and Keq at equilibrium
delta G = 0
Keq = Q
biochemical reactions vs chemical reactions
Reactions in the body are never at equilibrium.
Some processes are solid phase reactions (not in solution).
removal of product drives the reaction _________
forward
enzymes/catalysts
Stabilize the transition state (lower transition state energy).
Do NOT change delta G or Keq.
catabolism
Breakdown.
Burn fuel for storage or ATP use.
anabolism
Build-up.
Burn ATP for biosynthetic purposes, active transport, mechanical work.
velocity
The amount of product formed per unit time.
Initial velocity is equal to the linear part of the curve.
1/2 Vmax
where Km = [S]
Km
Affinity for a substrate.
Larger Km = weaker affinity.
Never changes.
Always positive.
how to measure enzymatic activity in a sample
Michaelis-Menten.
Use saturating amounts of substrate (»>Km).
how to measure substrate levels
Michaelis-Menten.
Use low substrate levels with respect to Km.
Kcat
Measures the catalytic power of an enzyme.
Kcat = Vmax/[enzyme]
Vmax
Maximal activity for a sample.
More enzyme causes a higher Vmax (up to a point).
Lineweaver-Burke Plot
1/v = (Km/Vmax) (1/S) + (1/Vmax)
slope: Km/Vmax
x-intercept: -1/Km
y-intercept: 1/Vmax
deficiency of enzyme activity: causes
Lack of enzyme.
Defective enzyme.
Lack of substrate/cofactor.
enzyme regulation by location
Enzymes are only expressed in certain tissues.
Ex: ALT (alanine transaminase): internal liver enzyme; high levels = lots of damage
Ex: alpha-1 antitrypsin: indicator of liver damage; secreted by liver and taken up by lungs
zymogen
Inactive form of the enzyme.
Proteolytic cleavage rapidly opens up the active site.
Ex: prothrombin/thrombin and fibrinogen/fibrin in blood clotting cascade.
blood clotting cascade
Damage/trauma activates an enzyme.
Cascade of proteins (1 or 2 trigger, millions activated).
Prothrombin is soluble.
Gamma-carboxylation is added to glutamates on prothrombin (vit K dependent).
Gamma-carboxylation binds Ca2+, so prothrombin can bind to the membrane.
Prothrombin is cleaved to thrombin, an active serine protease, on the membrane.
Fibrinogen is cleaved to fibrin.
Fibrin forms cross-linnked clot.
warfarin/coumadin
Vitamin K analogue.
Interferes with gamma-carboxylation of prothrombin.
Reduces over-clotting in patients that clot too readily.
heparin
Short-acting anticoagulant.
Promotes antithrombin-thrombin complex formation.
Antithrombin is an inhibitor that binds tightly to thrombin,
Once bound together, the complex is degraded, so it reduces the thrombin available for clotting.
Reduces clotting.
elastase inhibition
Elastase is released by lung neutrophils to neutralize foreign particles.
Alpha1-antitrypsin/alpha1-antiprotease inhibit elastase normally.
If alpha1-antitrypsin is defective, then unregulated elastase activity destroys elastin, causing scarring and emphysema.
Defective alpha1-antitrypsin caused by smoking (oxidation of sulfur to sulfoxide).
Treatment: intravenous alpha1-antitrypsin.
phosphorylation of protein
Phosphorylation/dephosphorylation modifies the charge of an AA residue.
Changes structure/function/activity of enzyme.
competitive inhibitors
Interact with binding site.
Same Vmax.
Increased Km (decreased affinity).
noncompetitive inhibitors
Do not interfere with substrate binding.
Decreased Vmax.
Same Km.
irreversible inhibitors
Type of non-competitive inhibitor.
Modifies the enzymatic AAs.
Decreases Vmax.
Same Km.
Ex: DIFP inhibits serine proteases
allosteric affectors
Inhibit or activate.
Usually multiple subunits (cooperativity).
Have R and T forms.
Do not follow Michaelis-Menten kinetics.
Often regulate a reaction pathway.
Highly regulatable by substrate concentration.
Ex: PFK-1: AMP activates, ATP inhibits
product inhibition
The immediate product of an enzyme binds to the enzyme and inhibits its activity.
Ex: hexokinase: G6P inhibits
feedback inhibition
The product inhibits an earlier step of the reaction.
Retinoblastoma
Rb+, Rb+ is normal
Loss of one Rb+ –> predisposed to develop tumor.
Loss of two Rb+ –> induces tumor formation.
E2F needed for transcription of genes needed for cell growth.
E2F is regulated by pRB.
Phosphorylated pRb is inactive which allows E2F to transcribe genes for S phase growth.
Phosphorylation state of pRb is regulated by cdks (cyclin D or E).
Cell growth is accelerated if pRb is lost.
p53
p53 is stabilized by phosphorylation that occurs during stress.
When DNA is damaged, p53 induces transcription of p21 gene.
p21 binds to cdk/cyclin complex and halts the cycle.
p21 binds to PCNA and inhibits replication fork.
p53 halts the cell cycle and prevents apoptosis.
Without p53, p21 is not induced, the cell cycle is not halted, and cells will replicate damaged DNA.
Rb gene suppresses
retinoblastoma
p53 gene suppresses
sarcomas, carcinomas
NFC-1 gene suppresses
neuroblastoma
APC gene suppresses
colon, stomach
BRCA gene suppresses
breast cancer
oncogenes
Activate cell division in response to growth factor stimulation.
Dominant effect: only 1 gene needs to be altered.
Signal Transduction
Signals from outside the cell affects gene expression.
Receptors penetrate cell membrane and have enzymatic activity.
Phosphorylation of Tyr residues allow interactions with other members of cascade.
Tumor cells can generate their own growth signals.
altered growth factors
Simian Sarcoma (sis) oncogene encodes PDGF molecule and can induce signal transduction.
altered growth factor receptors
Mutant forms stimulate growth even in absence of growth factor.
Ex: epidermal growth factor receptor
Family members: ErbB, HER2
Ras signalling
Ras is active when bound to GTP, and inactive when bound to GDP (switches between states by GAP).
Causes signal transduction to nucleus.
Mutant Ras is locked “on” –> excessive signal transduction.
NF1 gene
Encodes neurofibromin protein.
Neurofibromin contains a GAP domain, possibly acts through Ras.
Neurofibromatosis: benign neurofibromas on skin due to defective signal transduction.
c-Fos and c-Jun
Transcription factors.
Bind to AP1 sites.
Too much of these cause continuous growth due to too much signal transduction.
Myc gene
Myc is a transcription factor that regulates 15% of all genes (~3,000 genes).
Myc binds to enhancer sequence and recruits HATs.
Mutant Myc upregulates genes involved in cell proliferation.
Burkitt’s Lymphoma
Translocation involving chromosome 8 (encodes Myc gene) .
When translocated, Myc is constituitively expressed.
Leads to leukemia and lymphomas.
HPV (and other DNA viruses)
T-antigen sequesters Rb and p53.
Takes “brakes” off the cell cycle.
E7 targets Rb.
E6 targets p53
characteristics of cancer
Evade apoptosis. Self-sufficiency in growth signals. Insensitive to anti-growth signals. Limitless replication potential (increased telomerase activity). Angiogenesis. Tissue invasion. Metastasis.
Familial Adenomatous Polyposis Coli (APC)
Loss of APC causes colon cancer.
maltose
glucose + glucose
alpha 1,4 linkage
lactose
glucose + galactose
beta 1,4 linkage
sucrose
glucose + fructose
amylose
Linear.
Polyglucose.
alpha 1,4 linkages.
amylopectin
Branched.
Polyglucose.
Mostly alpha 1,4 linkages.
Some alpha 1,6 linkages to create branches.
cellulose
Polyglucose.
Linear.
Beta 1,4 linkages.
Humans cannot digest.
glycosaminoglycans (GAGs)
Long: 500+ sugars. Linear. Repeating disaccharides. Highly negative (carboxylates, sulfates). Highly hydrated.