Skildum/ Prunuske Week 1 Flashcards
Which are the nonpolar, aliphatic amino acids?
Glycine (G, R= H) Alanine (A, R= CH3) Proline (P, R= ring structure) Valine (V, R= CH with 2 CH3 groups) Leucine (L, R= CH2-CH with 2 CH3 groups) Isoleucine (I, R= C bound to a CH3 and CH2-CH3)
Which are the aromatic amino acids?
Phenylalanine (F, R= Ch2-benzene)
Tyrosine (Y, R= CH2- benzene with para OH)
Tryptophan (W, R= big structure with 2 rings)
Which are the polar, uncharged amino acids?
Asparagine (N, R= CH2- C=O-NH2)
Glutamine (Q, R= CH2-CH2-C=O-NH2)
Serine (S, R=CH2OH)
Threonine (T, R= CH bonded to OH and CH3)
Which are the sulfur containing amino acids?
Methionine (M, R= CH2-CH2-S-CH3)
Cysteine (C, R= CH2-SH)
Which are the negatively charged (acidic) amino acids?
Aspartate (D, R= CH2, COO-)
Glutamate (E, R= CH2-CH2-COO-)
Which are the positively charged (basic) amino acids?
Arginine (R, R= CH2-CH2-CH2-NH-C=NH2+ and NH2 on last carbon
Lysine (K, R= CH2-CH2-CH2-CH2-NH3+)
Histidine (H, R= CH2- ring structure)
What is a peptide bond and how is it formed?
bond in amino acids between carbonyl carbon and nitrogen
-formed through dehydration reaction (releases H2O)
What are the 2 main structures in secondary proteins?
Alpha helix- R groups stick on outside
beta sheets- R groups stick up and down
What is Creutzfeldt Jakob’s disease caused by?
prion disease, increases in protein beta sheets which leads to amyloid fibers
Normal = PrP^c
Abnormal = PrP^sc
Where does ubiquitin tag bring misfolded proteins?
To the proteasome to be destroyed
What are the components of hemoglobin?
2 beta and 2 alpha subunits
Cooperatively binds oxygen (sigmoidal curve)
What are hemoglobin T and R states?
T state- promoted by 2,3-BPG (allosteric modulator) promotes O2 dissociation
R state- relaxed, easier for O2 to bind
What is the blood test to test for diabetes? (glycosylation on hemoglobin)
HbA1C
The base pair mutation of what to what amino acid causes sickle cell anemia?
From glutamate (negatively charge) to valine (nonpolar) on position 6 of beta subunit
What do these problems with Hb mean? HbS HbSS HbAA HbSA HbC
HbS- glu6val, sickle cell HbSS- alpha 2 beta 2^s- sickle cell HbAA- alpha2 beta 2^a normal HbSA- sickle cell trait HbC- Glu6Lysine -lysine in the spot of glutamate
What is thalassemia?
altered ratio of alpha beta hemoglobin, usually 1 is not produced
What is deltaS in the Gibbs free energy equation and what does increase or decrease mean?
Entropy.
deltaS > 0 is order decreasing (more randomness)
deltaS < 0 is order increasing (less randomness)
What does it mean if the Michaelis-Menten constant (Km) decreases?:
Takes less concentration for enzyme to reach Vmax so:
The enzyme is more active
What is a competitive inhibitor and does Km or Vmax change?
It competes at substrate binding sites
-increases Km but does not change Vmax
What is a noncompetitive inhibitor and does Km or Vmax change?
Molecules which bind an enzyme and inhibit its activity without inhibiting substrate binding (ex: suicide inhibitors)
-decreases Vmax but does not change Km
What is an allosteric inhibitor?
a molecule that binds an enzyme away from active substrate binding site and causes conformational change to prevent substrate binding
- cannot be described by Michaelis- Menten
- hyperbolic to sigmoidal curve)
Why do people with sickle cell have jaundice?
Sickle red blood cells turnover faster than normal RBCs
-heme breaks down into bilirubin and liver is overwhelmed–> causes discoloration
What are treatments for sickle cell?
only cure is a bone marrow transplant
- Hydroxyurea- drug that increases production of fetal (gamma) Hb subunits
- blood transfulsion
What are the oxidation/ reduction cofactors?
NADH, NADPH, PAD, metals, ascorbic acid
What are the activation transfer reaction cofactors?
TPP, Biotin, Lipoate, PLP, Cobalamin, Coenzyme A
What is the difference between an apoenzyme and holoenzyme?
An apoenzyme needs to be bound by a cofactor and a holoenzyme is functional
-the apoenzyme cannot bind the substrates transition state
What is it called when a cofactor binds permanently to its enzyme?
prosthetic group, ex) FAD binding succinate dehydrogenase
What is the reusable cofactor for alcohol dehydrogenase?
NADH
enzyme oxidizes ethanol to acetaldehyde
What are the 3 functions of redox reactions?
fuel oxidation (ex: succinate dehydrogenase)
detoxification (ex: alcohol dehydrogenase)
biosynthesis (ex: HMG CoA reductase)
Which enzyme converts pyruvate + NADH –> lactate + NAD+
lactate dehydrogenase
What is niacin used for and where is it found?
Dietary precursor for NADH and NADPH
Found in meat, whole grains, and fortified cereals
What is niacin deficiency?
Pellagra
What are the symptoms of pellagra?
3Ds - dermatitis, diarrhea, and dementia (also glossitis- bright red and smooth tongue)
What is the dietary precursor for FAD and FMN?
riboflavin (vitamin B2)
What is riboflavin (vitamin B2) found in?
eggs, milk, organ meats, legumes, mushrooms
What does riboflavin deficiency cause?
cheiosis (sores at corners of mouth), glossitis, keratitis, seborrheic dermatitis, anemia (fewer RBCs but they look normal)
How is riboflavin deficiency diagnosed?
Erythrocyte glutathione reductase assay
- collect and lyse blood, incubate with substrates (NADPH, gludathione) and +/- extra FAD
- NADPH absorbs light at 340nm and NADP+ is lower- use to compare ratio before and after more FAD was added
- > 1.4 indicates riboflavin deficiency
What are the 2 functions of ascorbic acid (vitamin C)?
1) redox cofactor for hydroxylase enzymes in collagen synthesis, neurotransmitter synthesis, and oxygen sensing
2) non-enzymatic antioxidant
What is the deficiency in ascorbic acid (vitamin C) called? What are the symptoms?
Scurvy
- Slow wound healing, irritability/ apathy, anemia, enlarged junctions between ribs, petichiae (rash with bumps)
- x-ray has white plate at ends of bones
What metals are used in redox reactions? And what are their basic features?
iron, cobalt, copper, manganese, molybdenum
-need 2 stable oxidation states
What are the main functions of pyruvate dehydrogenase?
Regulates glycolytic substrate oxidation in mitochondria
-converts pyruvate to acetyl CoA
What main functions are associated with TPP, NAD+ and FAD, lipoate and CoASH?
TPP = decarboxylation
NAD+ and FAD = reduction and oxidation
lipoate and CoASH = transfer acyl groups
What is thiamine found in? What causes deficiency?
- meat, legumes, whole grains, cereals
- Deficiency from malnutrition, alcoholism, monotonous diet
What 3 conditions are caused by thiamine deficiency?
Beri beri- “I can’t I can’t” headache, malaise, peripheral neuropathy, and heart failure
Wernike encephalopathy- confusion, mental status changes, abnormal eye movements, ataxia
Karsokoff psychosis- amnesia and confabulation
What enzymes is biotin a cofactor for?
acetyl CoA carboxylase (FA synthesis)
pyruvate carboxylase (gluconeogenesis)
propionyl CoA carboxylase (branched chain FA metabolism)
methylcrotinyl CoA carboxylase (branched chain amino acid metabolism)
What symptoms are from biotin deficiency?
Rare, but scaly dermatitis, thinning hair, and alopecia
What protein in raw egg whites binds biotin permanently and can cause deficiency?
avidin
What is the cofactor pyridoxal phosphate (PLP) used for?
- enzymes that metabolize amino acids
- ex) transaminases
What is pyridoxal phosphate deficiency?
in infants causes seizures, diarrhea, anemia
in adults causes peripheral neuropathy
-Diagnose by measuring erythrocyte transaminase activity with and without exogenous PLP
What is antiquitin deficiency (PDE)?
epilepsy caused by sequestration of PLP so not available
in infants
What is cobalamin (vitamin B12) used for?
to transfer and rearrange methyl groups
-2 forms: deoxyadenosine cobalamin and methylcobalamin
Where can cobalamin be found in diet?
in bacteria
What are the symptoms of cobalamin (vitamin B12) deficiency?
How is it diagnosed?
pernicious anemia, megaloblastic anemia, weakness, fatigue, seizures, sensory deficits
Diagnose- blood smear, methylmalonic acid in blood and urine
