Chmy123 Exam 6 amino acids
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a "few" amino acids held together with peptide bondsgenerally referred to as "peptides" for short
many amino acids held together with peptide bondsgenerally referred to as proteins
have both acidic and basic groups
Describe acid base behavior
- Carboxyl group: avg pKa 2.3. mostly -COO- at pH 7.4q
- Amine group: avg pKa 9.7. mostly -NHr* at pH 7.4
- Hist. pKa of 6
How do proteins make good buffers?
lots of ionizable groups with different pKas ranging from 1.8-12.5can buffer (absorb excess H* or OH-) over a wide range
unbranched chains of covalently bonded amino acids held together with amide linkages
what does every Amino Acid have?
amine and carboxyl group
- sequence of amino acids
- held together by peptide bonds
- describe full structural formula
- folds into single lowest energy conformation that has biological activity
how is amino acid sequence of a protein dictated?
- by the sequence of nucleotides in the DNA (by the gene)
- therefore the biological activity is dictated by the gene.
specific pattern of 3-D structures that are stabilized by hydrogen bonds between N-H and C=O
α - helix and β plated sheets
- types of 2nd structure
- α: right-handed helix, L-amino acids when linked w/peptide bond tend to form this.
- is stabilized by H-bonds between N-H and C=O
- amino acids with bulky side chains destabilize α-helix
- β: close packing of the "zig-zag" peptide backbone can pack closely together that is stablized by hydrogen bonding between peptide bond N-H and C=O
- Left handed helix
- unusual amino acid sequnce
- 1/3 = glycine 1/3 = proline
- *proline disrupts α-helix
- 4° = 3 subunits, H-bonds
- H-bonds can break down and reform
- distinctive conformation of a protien
- for any given primary structure there is one preferred, low energy conformation
- Major Driving Force: need for nonpolar amino acid side chains to minimize contact with water
- Also stabilized by: H-bonding, salt bridges, disulfide bonds
How do polypeptide chains keep non-polar groups away from water?
- nonpolar R groups in differnt parts of the chain are brought closet together
- creates pockets of hydrophobic groups that are away from water
Amino acid interactoins:
- Salt Bridges: between + and - charged R groups in different parts of the polypeptide
- Disulfide Bonds: two sulfides bonded between cysteine residues
- H-bonding: --
- nonpolar interactions: --
- each polypeptide chain is called a subunit.
- multiple subunits that are held together by interactions.
- intact at 1°,2°,3°,and 4° when relevant
- full biological activity
- way the protein wants to fold up at a ph of 7
- proteins that assist with protein folding
- prevent newly synthesized proteins from getting tangled w/eachother
- provide an environment that allows each new protein to fold rapidly and w/out interference
- 1° stays intact
- 2°,3°,4° are lossed
- loss of biological activity
Causes: heat, low/hi pH, less polar solvent, detergent, high salt concentration......
- spontaneous re-folding when denaturation conditions are removed and protein is back in physiological conditions
- only works when protein has been gently denatured
1960s Chris Anfinsen Experiment
1° structure has all the information needed to fold into biological active conformation
- most proteins
- compact shape
- mixed 2° structure
- organized as sheets or strands or filaments
- extremes of one type of 2° structure
- structural proteins
- extensive alpha-helix
- major structural protein in: Hair, Claws, scales, feathers, wool, nails, fur, hoofs, horns
- Extensive β-pleated sheets
- "silk protein"
- webs, cacoons.
'' '' '' '' -leu
- activity depends on binding to a receptor
- morphine binds to enkephalin receptor which is not a oligopep.
- Does it have 1? yes
- does it have 2? no, too small to have 2,3 and no 4 b/c only one chain
- does it have 1,2,3,4 structures?
- 1-yes 2-no, too small 3-yes, can form disulphide bonds 4-no only one chain
- stimulates urine contraction, delivery, muscle contractions, lactation and pair-breeding
- water retention and blood vessel constriction
- copies of the receptor for vasopressin inserted into brain of meadow voles
- became more interested in 1 partner and groomed offspring more
- made by red blood cells
- 2 α-subunits
- 2 β-subunits
- required for protein activity
- Fe2+ in the center
- oxidation of fuel molecules produces carbon dioxide
- more CO2 causes pH to drop
- carrier needed for O2
histidine side chain
- slight drop in pH protonates histidine
- cb (deprotonated his) = carrying O2
- ca (protonated his) = releasing O2
- resulting in the delivery of O2 where needed
Sickle cell anemia
- normal glu at position 6 = polar and forms h-bonds to watet
- SCA = val at position 6, np, vals stick together and distort cells
characteristics of plants, mammals, bacteria for amino acids
- Plants - make 0 amino acids, can synthesize all 20 of them
- mammals - 9-10 essential amino acids
- bacteria- varies (lactobacillus: have all 20 being in gut)
smallest amino acid, lack chiral carbon
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