Protein Biochem 1 Flashcards
number of aa
20 (have specific tRNAs
about 300 overall
2 aa into collagen
hydroxyproline (Hyp)
hydroxylysine (Hyl)
Hyp: used in collagen for H-bonding that increases collagen strength. Prolyl hydroxylase converts Pro to Hyp.
Hyl: use in collagen for interchain crosslinks. Lysyl hydroxylase converts Lys to Hyl
-interstrand cross links between Lys and Hyl–covalent interaction (lysyl oxidase)
collagen is most abundant protein in human body
- triple helix
- tensile strength
What to prolyl hydroxylases and lysyl hydroxylase need?
Vit C (ascorbate) as coenzyme -Lack of Vit C leads to scurvy (reduced collagen strength)
Scurvy
- reduced strength of collagen fibrils due to deficiency in Vitamin C
- reduced vascular strength
- hemorrhages
- loss of red blood cells
- bruising
- anemia
- swollen gums
Gamma carboxyglutamate (Gla)
- Glutamic acid modified by gamma glutamylcarboxylase (a transmembrane protein)
- makes gamma carboxyglutmate (Gla) which has 2 negative charges
- Vit K dependent
Effect: chelate Ca2+ leads to conformational changes
- Prothrobin uses Gla to target membranes.
- N-terminal domain of prothrombin is “Gla domain”
- Gla domain contains 10 Gla residues that bind Ca
- Partially embeds into membrane
2 ways for protein degrdations
Ubiquination pathway: ATP dependent
-targets enzyme to proteasome after cross linking protein to ubiquitin
Lysosome engulfs extracellular proteins to mix with digestive enzymes
Ubiquitin proteasome mechanism
-Shuttling mech:
E1, E2, E3
-Allows covalent bond b/t ubiquitin and substrate
-Step 1: ATP dependent: Conjugate E1 to ubiquitin, through cysteine
-Pass from one enzyme to next (E1 to E2)
-E2 and E3 complex decide which substrate will get marked for degradation
-E2 modulates how active E3 is by binding to it
Know E1 to E2 to E3
-can get one or many ubiquitins
Ubiquitin structure
7 lysine residues
- C terminus has glycine
- Gly Gly will be bound to chain
Ubiquitin put on protein thru lysines and protein gets cut up in proteasome
-Ub recycled
Lysosome
-engulfs extracellular proteins to mix with digestive enzymes
-Can engulf larger material like bacteria
-Contains hydrolytic enzymes that include aspartic proteases
Ex: mac and granulocytes
Enzymatic degradation of proteins
-In stomach: pepsin (pepsinogen cleaved by HCl)
-In intestine:
enteropeptidase (cleaves trypsinogen to trypsin)
-trypsin produced in pancreas, goes to small intestine: cleaves all other zymogens in SI (chymotrypsinogen, procarboxypeptidase)
Trypsin cleaves after
arginine or lysine
Chymotrypsin cleaves after
aromatic residue
Aspartic Protease
Pepsin: hydrolyzes N terminal of aromatic residues (phe, trp, tyr)
Serine proteases
Trypsin: hydrolyzes C terminal side of basic amino acids (arg, lys)
Chymotrypsin: hydrolyzes C terminal side of aromatic and some hydrophobic residues (phe, trp, typr and leu, met)
Metallocarboxypeptidases
Carboxypeptidase A: hydrolyzes C terminal of hydrophic aa (Ala, Ile, Leu, Val)
Carboxypeptidase B: hydrolyzes C terminal of basic residues aa ( arg, lys)
Aminotransferases
(transaminases) transfer amino groups
- point is to get rid of nitrogen
- catalyze rxn of an alpha keto acid and an amino acid to another alpha keto acid and amino acid
- reversible rxn & Keq 1
- goal: produce Asp, NH3 for urea cycle
- hundreds of aminotransferases within our genome
- mostly in cytosol of cells and especially abundant in liver, kidney, intestine, muscle
- **increased lvls in blood indicate liver damage/disease
Alanine aminotransferase (ALT)
alanine + alpha ketoglutarate pyruvate + glutamate
Aspartate aminotransferase (AST)
aspartate + alpha ketoglutarate oxaloacetate + glutamate
Glutamate from AST and ALT rxns
- ALT path: glutamate turned into NH3+ that is incorporated into urea cycle by Glu dehydrogenase
- AST path: use bidirectionality to make aspartate that feeds into urea cycle
Transamination requires
Vitamin B6 (derivative is pyridoxal phosphate PLP)
- holds amino group during transfer
- waits for other ketoacid to transfer it to
Schiff base
In the resting state, PLP forms a Schiff Base with the aminotransferase.
-Covalent linkage holds PLP in resting enzyme
Control points for protein catabolism
- The directionality of transamination (by ALT and AST) is regulated by the relative concentrations of “substrates and products”
- N-acetylglutamate is a required activator of carbamoyl phosphate synthetase I that kick starts the urea cycle (ie protein degradation)
- The directionality of oxidative deamination by Glu dehydrogenase depends on the relative conc of GLU, alpha-ketoglutarate, NH3
- ATP and GTP are allosteric inhibitors of Glu dehydrogenase while ADP and GDP are activators
Urea Cycle
purpose:
get rid of ammonia by forming something less toxic (urea)
Why? ammonia is toxic, body cannot store aa (hyperammonemia)
-cerbral edema, coma, death can come from hyperammonemia
Entry points for nitrogen in urea cycle
- aspartic acid (aspartate)
2. free ammonia
Overall sum of urea cycle
3ATP + HCO3- + NH4+ + aspartate –>
2ADP + AMP + 2Pi + PPi + fumarate +urea
