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70 terms

Biochem Study Guide Terms- Proteins

Terms mentioned on study guide related to proteins.
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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.