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Terms mentioned on study guide related to proteins.

Zymogens

inactive protein that requires extra peptides attached to it to be cleaved before it becomes active. Released in the stomach to digest proteins.

Stomach

Proteins go into ______ Interacts with => HCl + Mucus + Pepsinogen + Gastrin => final product (chyme).

HCl

Maintains stomach pH around 2, kills bacteria, denatures protein structures held together by 'weak bonds', provides ideal environment for certain enzymes to function properly.

Mucus

protects inner lining of stomach from acidic pH and corrosion.

Pepsinogen

a zymogen protein that is converted to pepsin by HCl (due to low pH).

Gastrin

peptide hormone controlling acid secretion and gastric motility.

Chyme

the final product of digested enzymes in the stomach. Mixture of partially digested proteins, enzymes, and HCl which enters the small intestine.

Lumen, Trypsinogen, Chymotrypsinogen, Procarboxypeptidase.

pancreatic enzymes released as zymogens into ____ of the small intestine: _____, ______, ______ => trypsin, chymotrypsin, carboxypeptidase.

enteropeptidase

converts trypsinogen to trypsin in the lumen of the small intestine

trypsin

converts chymotrypsinogen and procarboxypeptidase => chymotripsin and carboxypeptidase.

Lumen zymogens

trypsinogen, chymotrypsinogen, procarboxypeptidase.

aminopeptidase dipeptidase enteropeptidase

SI Brush Border (BB) enzymes present are ____ ____ ____

Amino Acids

Alpha carbon w/ 4 arms: carboxyl gourp, amino group, hydrogen atom, distinct R group.

Glycine

simplest AA has a hydrogen as the R group.

Peptide bond

bond formed by the condensation of the carboxyl group of one AA with the amino group of another AA. Strongest bond in protein structure. One water molecule is removed in the process.

Primary

____ protein structure: Linear order of amino acids from N terminis to C terminis formed using mRNA.

Secondary

_____ protein structure: alpha helices and beta sheet formation. Provides functional site for proteins

Alpha helix

stabilized by h bonds between amide nitrogen and carbonyl carbon of peptide bonds; essential for globular proteins. All R groups are sticking out.

Beta sheet

stabilized in adjacently opposed stretches of the poly peptide backbone; can be parallel or antiparallel ( based on N terminis).

Tertiary

_____ protein structure: complete 3-d structure of the polypeptide chain; relationship of different domains to one another w/in a protein. Often final protein structure.

tertiary forces

hydrogen bonds, hydrophobic, electrostatic, van der waals (weakest) (all weak bonds)

Quaternary

two or more different polypeptide chains are stabilized by the same non-covalent forces. EX Hemoglobin (2 alpha and 2 beta chains) Not all proteins have this structure

Denaturation

_____ is the alteration of a protein's 3-d structure caused by either ph, heat, enzymes, or agitation (stirring). Doesn't affect primary structure (except enzymes)

Renaturation

restoration of protein 3-d structure

Transamination

transfer of amino group to an alpha-keto acid. OAA as an acceptor to produce Aspartate. Pyruvate as an acceptor to produce Alanine.

Deamination

removal of an amino group from an amino acid. Glutamate + Glutamate dehydrogenase => a-ketoglutarate + NH3 + NADH

Urea cycle

Starts from NH3 +HCO3+ aspartate. Uses 3 ATP and results in Urea and Fumarate.

Urea

one amino group comes from ammonia and the other amino group comes from aspartate.

Metabolic Bicycle

linkage of Urea cycle to citric acid cycle. Fumarate (from Urea cycle) => CAC => OAA => transanimation => aspartate => Urea cycle => Fumarate

Glucogenic AA

(GNG) conversion to pyruvate or CAC intermediates to make glucose.

Ketogenic AA

direct conversion to Acetyl CoA to enter CAC or undergo FA synthesis. Carbons never make it to glucose via GNG (2 carbons lost in CAC).

Branched chain AAs

Isoleucine, Leucine, and Valine (40 percent of skeletal muscle AAs). Significant energy source in skeletal muscles, heart, kidney, and brain. Turned into BCKA by BCKD.

Maple syrup disease

BCKD (branched a-keto acid dehydrogenase) defective. Autosomal recessive disease. Accumulation of BCAAs (branched chain amino acids) and their corresponding BCKAs.

Aromatic AAs

Consist of phenylalanine, tryptophan, and tyrosine. All contain ring structures. Phenylalanine are considered essntial AAs. Ring structures absorb light near the UV spectrum. Found in lens of eye to filter out UV radiation.

tyrosine metabolism

____ is the synthesis f catecholamines from tyrosine. Results in epinephrine, norepinephrine, dopamine, and DOPA.

(Phenylketouria) PKU

most common clinically encountered inborn error of amino acid metabolism. Autosomal recessive. Hyperphenylalaninemia (plasma Phe > 1000 um) resulted from defective phenylalanine metabolism => impaired cognitive development and function => lack of tyrosine => lack of neurotransmitters => mental retardation, seizure, microcephaly, growth retardation.

Alkaptonuria

Autosomal recessive disease resulted from defective homogentisic acid oxidase (catabolism of Phe and Tyr). Charactarised by homogenistic aciduria (black urine), ochronosis, and arthritis. Not life threatening

Sulfur containing AAs

Cysteine and Methionine

Cysteine

Sulfur containing AA which Forms disulfide bond by interacting with itself, important role in protein stabilization. Tertiary structure is most likely stabilized by this bond.

Methionine

sulfur containing AA that is a major methyl donor.

Collagen

triple helix structure. Repeating sequence (Gly-x-y). X often proline; y often hydroxyproline or hydroxylysine. Hydroxylation by prolyl hydroxylase and lysyl hydroxylase and VITAMIN C cofactor. glycine, proline, and Lysine needed for _______ formation

Ehlers-Danlos

heterogeneous group of generalized connective tissue dissorders. Skine hyperelasticity and joint hypermotility.

Ocular sclerotic

________ ehlers-danlos syndrome (type 6) is an autosomal recessive disease w/ a deficiency in pro-collagen lysyl hydroxylase. Occular problems: more fragile, high myopia, retinal detachment, keratoconus.

Heme

protoporphyrin IX has a Fe2+ center. Most common prosthetic group for hemoglobin, myoglobin, cytochromes, and catalase.

Jaundice

accumulation of bilirubin in the body => yellowing of skin and sclera. Caused by increased production (hemolysis => sickle cell) or decreased excretion due to liver damage (cirrhosis, heparitis) or bile duct obstruction (regurgitation into bloodstream).

Kwashiorkor

High starch diet with low amount of protein.

Marasmus

Low protein and caloric uptake.

pKa > pH

When _____ the AA will be protonated.

pKa < pH

When _____ the AA will be deprotonated.

zwitterion

term meaning electrically neutral concentration with both COO- and NH3+ present.

pK1, pK2

____ pKa for COOH ~ 2, and ____ = pKa for NH2 ~ 9

Blood buffering

pH is maintained around 7.4. This is done by the absorption of CO2 by hemoglobin => H2CO3 <=> H+ HCO3- <=> H+ buffered by Hb => lowers the affinity for oxygen in the peripheral tissues; increasing affinity in lungs. Alternate is Formation of Hb-carbamate (15 percent) (both pathways do this). Hb acts as the buffer for blood.

Bohr effect

______ happens when HB buffers H+ after CO2 absorption causing a lowered affinity for oxygen and therefore release.

Metabolic acidosis

accumulation of ketone bodies or lactic acids => increased H+ => increased CO2 => have to breath more.

respiratory acidosis

if the lungs fail to expel CO2 => increased CO2 => have to breath more

Respiratory alkalosis

during hypervention (decreased CO2) => not enough H+ => have to breath less (brown bag).

Induced fit model

substrate bindin induces a conformational change in the active site leading to further enzyme substrate interactions and brings catalytically active groups to the substrate.

Transition state

structurally unstable requiring higher free energy state. The formation of the _______ is rate-limiting in the overall reaction.

Activation energy

the free energy difference between substrate and transition state.

vmax

maximum velocity of the reaction acheived by the system after it has reached a certain amount of substrate. Part of Michaelis-Menton model

Km (Michaelis constant)

amount of substrate to reach half of vmax

LB Plot

inverse of Michaelis-Menton model which makes it linear.

Competitive

______ inhibitors are structurally related to the normal substrate. Binds to the active site, non covalent, reversible. Vmax unchanged; Increases Km

Non-competitive

_____ inhibitors binds to a site other than the active site of an enzyme. Has equal affinity for free enzyme or enzyme substrate complex. Substrate binding is unaltered, but ESI complex cannot form products. Non covalent, reversible. Reduces vmax. Km unchanged.

oxidoreductase

transfer hydrogen between a substrate and coenzyme

transferase

enzyme that transfers a group from one molecule to another

hydrolase

cleaves bonds by the addition of water

lyase

remove a group non hydrolytically, forming a double bone

isomerase

interconvert positional, geometric or optical isomers

ligase

couple the hydrolysis of a phosphoanhydride bond to the formation of a bond.

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