Proteins and AAs Flashcards
Why does proline differ from other AAs?
- peptide bonds take specific shape (has a secondary amino group and side chain causes rigid ring). Leads to bends in the protein chain. Interrupt alpha helical xture. Proline is an alpha helix breaker
- Collagen is rich in proline residues
AAs with nonpolar, aliphatic, non branched side chains
Glycine, alanine, proline
AAs with non polar, aliphatic, branched side chains
Valine, leucine, isoleucine
AAs with aromatic side chains
- Phenylalanine - no UV light absorbance
- Tryptophan- absorb UV light 4x better than tyr
- Tyrosine
all non polar but slightly increase in polarity (1 –> 3)
AAs that contain sulfur
Methionine (met) - also non polar
Cysteine (cys) - uncharged, polar. 2 cysteins orms disulfide bond to form CYSTINE
AAs polar, uncharged
Asparagine (asn) - derivative of aspartate
Glutamine (gln) - amine group added to glutamate
Polar, uncharged
Serine
Threonine
Both contain -OH group that can be phosphorylated and glycosylated
Which AAs have -OH group
Serine and threonine
AAs with negative (acidic) side chains
Aspartate (asp)
Glutamate (glu)
AAs with positive (basic) side chains
Arginine (Arg)
Lysine (lys)
*Histidine – sometimes, dependent on exact pH
Amphoteric
Can act as either acid or base
Histidine side chain buffer
- has imidazole ring (pKa 6) which allows buffering of possible drop in intracellular pH (pH 7)
- pKa of his may be shifted in proteins to 6-7 due to local chem envir of the protein
Why is hb a good buffer?
Rich in his
What are the the main blood buffer systems?
phosphate
Hb
bicarb
biologically active amines and mech
AAs are precursors for many biological active amines
- Amino group is retained and alpha-carboxyl group is enzymatically removed as CO2 (decarboxylation)
ex) GABA, histamine, serotonin
How is GABA formed
decarboxylation of glutamate (also alpha carbon is now gamma)
How is histamine formed
decarboxylation of histidine
How is serotonin synth
Tryptophan is hydroxylated to 5-hydroxy tryptophan
5 hydroxy tryptophan is decarboxylated to serotonin
Catecholamine synth
Tyrosine hydroxylated to DOPA
Dopa decarboxylated to dopamine
dopamine –> norepi –> epi
Where are catecholamines synth
adrenal medulla
What is not synth by normal translation?
glutathione
Characteristics of peptide bond
- partial (40% double bond character)
- rigid and planar
- uncharged but polar
- can form H-bonds –stabilizes alpha helical and beta sheet xtures
Which configuration of peptide bond minimizes steric hindrance?
trans
Where on peptide bond is rotation possible?
alpha carbons
Which bond does not break during denaturation of proteins?
peptide bond
General functions of proteins
Regulatory: repressors and activators
Defernse: antibiotics, blood clotting
Where do polar AAs cluster on the soluble proteins?
On the surface
Where do non polar AAs cluster on membrane proteins?
Embedded in the membrane
AA primary xture
-determines the 3D xture of the protein
Covalent bonds
- Strong ( >50 kcal mol-1)
- Not meant to be broken other than during protein degradation
- Ex) peptide bonds, disulfide bonds
Non covalent bonds
- Weaker than covalent ( 1-7 kcal mol-1)
- These “weak attractive forces” specify protein folding and conformational changes. Additive, so in aggregate they may provide strong stabilizing force
- Hydrophobic forces- water excludes cmpds that don’t form H-bonds (formed bw 2 non polar AAs)
- H-bonds- formed bw polar uncharged side chains (ex- ser or asn) or bw one charged side chain and one polar (ex -OH or COO-) (also called ion dipole)
- ionic bonds– 2 opp charged side chains
- Van der Waals (london) forces
Secondary xture
- Stabilized by H bonds involving atoms of the peptide bond
- Alpha helix – SPECIAL HELIX, tightly packed and right handed helix. H-bonds parallel to axis, side chains stick out (may lead to constraints, but dep on primary xture)
- Beta sheet- perpendicular H-bonds bw peptide atoms and AA side chains alternatiec above and below the plane of the pleated sheet. Parallel or anti parallel
H-bond
non covalent
-stabilizes secondary xture (H-bonds of atoms of peptide bond)
Interruption of the alpha helix
- electrostatic repulsion bw successive AAs with charged R groups
- Bulkiness of adjacent R groups
- Helix disruption by specific residues – proline (bend, kink), glycine (rotation)
tertiary xture? How is it stabilized
- refers to 3D conformation of a protein
- water soluble protins hold into #D xture with non polar side chains to inside – “hydrophobic core”
- stabilized by AA side chains –non covalent associates, S-S (covalent), ionic interactions
H bonds can be formed bw _____ or _____
polar uncharged side chains or bw one charged side chain and one polar
Which type of proteins often have several S-S bonds?
extracellular
-intracellular proteins usually lack S-S
Insulin xture
2 inter-chain disulfide bonds hold A & B chains together
Intra-chain disulfide bond in A chain holds the peptide and needed for receptor recognition
Why is c peptide needed?
needed for proper formation of disulfide bonds in insulin
Myoglobin xture
- described in terms of tertiaty xture
- contains 80% alpha helix secondary xture
- devoid of beta sheet
Monomeric proteins lead to ____ xture
tertiary
multimeric proteins lead to ____ xture
how do the subunits assoc?
quaternary xture
-subunits assoc via NON COVALENT attractive forces
Ex) Hb, some enzymes
Chaperones
Facilitate proper folding
- Hsp70 – prevent aggregation of unfolded protein
- Hsp60 – proteins have BARREL SHAPE and are req for correct folding of proteins that don’t fold spontaneously. Also help refold protein after crossing cellular membrane
Defective proteins are tagged by _____ and degraded in the ______
ubiquitin, proteasome
ATP dep
Protein misfolding diseases
- Alzheimers, prion disease (Transmissible Spongiform Encephalopathy, TSE)
- the diseased protein is very stable
- abnormal proteins accumulate
- damage the brain
Transmissible Spongiform Encephalopathy
- Prion disease
- 3 routes to acquire: sporadic, infection, genetic predisposition
- diseased brain develops holes
- Symptoms include dementia and loss of coordination, leading to death.
Prion
Proteinaceous infectious agent
- infectious agent is a single protein names PrP
- PrP is normal constituent of cells in brain
- PrP-SC (scrapie) is abnormal form. PrP-SC acts like template and leads to conversion of PrP to large aggregates of PrP-SC. Abnormal protein is highly infective and not destroyed by sterilization
To get from PrP to PrP-SC, the _____ is changed to _______
alpha helix, beta sheet
Denaturing proteins in the lab
- Heat urea, salt to break H-bonds
- Strong acids/bases to break ionic bonds
- SDS detergent to break hydrophobic interactions
- Thiol containing compounds to red S-S
- Beta-mercaptoethanol
- 2-mercaptoethanol
Creutzfeldt-Jakob disease
prion disease
