Flashcards
Amino Acids
Cards in this deck (36)
- 1What is the function of an amino acid?- cell signaling
- "building blocks" for proteins (metabolites --> energy!)
- precursors for other molecules - 2What makes up an amino acid?- alpha carbon
- chiral
- exists as L (CCW) or D (CW) isomers
- carboxylic acid group (COO-)
- amino group (NH3 +)
- R group "side chain" - 3What isomer is more abundant in nature, L 0r D?L-isomer is more abundant in nature
- 4What is a Zwitterion?a molecule that has both positively and negatively charged groups at a neutral/physiological pH (pH ~7)
- 5What happens to a Zwitterion at very low pH's?Everything will be protonated therefore the amine group will have a positive charge, and the carboxylic acid group will become neutral COO- --> COOH
- 6What happens to a Zwitterion at very high pH's?Everything will be deprotonated therefore the carboxylic acid group will have a negative charge, and the amine group will become neutral NH3+ --> NH2
- 7How many amino acids exist?20 different amino acids
- 8What are the different groups we classify amino acids by?- hydrophobic. non-polar (a lot of hydrocarbons)
- negatively charged
- positively charged
- polar, neutral (overall), charge not evenly distributed - 9Amino Acids: hydrophobic, non-polar- Glycine (Gly, G): hydrogen
- Alanine (Ala, A): methyl
- Valine (Val, V): v-shape carbons
-Leucine (Leu, L): valine + 1 carbon
- Isoleucine (Ile, I): isomerize leucine
- Methionine (Met, M): 4 "things" including S
-Proline (Pro, P): side-chain forms two-carbon ring
- Phenylalanine (Phe, F): phenyl + alanine
- Tryptophan (Trp, W): phenyl + 5-C ring = W shape - 10Amino Acids: negatively charged- Aspartate (Asp, D): 1 hydrocarbon chain
- Glutamate (Glu, E): 2 hydrocarbon chains
* A before D *
- at pH 7: functional group of side chain (carboxyl) group turns negative - 11Amino Acids: polar neutral (overall)- Cysteine (Cys, C): methyl + S
- Aspargine (Asn, N): aspartate + amine
- Glutamine (Gln, Q): glutamate + amine
* N comes before Q *
- Serine (Ser, S): Cysteine sub S to OH
- Threonine (Thr, T): Valine + term. OH
- Tyrosine (Tyr, Y): hydroxylated phenylalanine - 12Amino Acids: positively charged- Lysine (Lys, K): 4 hydrocarbons + term. amine
- Arginine (Arg, R): 3 hydrocarbons + Guanidinium (+ve charged shared)
- Histidine (His, H): Alanine + Imidazole (gets protonated) - 13Non-essential (humans can synthesize these) * single letter abbreviation *SPY DANGER QC
Serine, Proline, Tyrosine, Aspartic acid Alanine, Aspargine, Glycine, Glutamic acid, Arginine, Glutamine, Cysteine - 14Essential (must consume in our diet) * amino acid name *"Freedom Voice WITH MLK"
Phenylalanine, Valine, Tryptophan, Isoleucine, Threonine, Histidine, Methionine, Leucine, Lysine
* Arginine: depending on whether or not our body has produced enough * - 15What are the seven amino acids that have an ionizable side chain (besides the terminal carboxyl group & terminal amine)?DR. CHEKY
Aspartate (COO-), Arginine (Guanidinium), Cysteine (S-), Histidine (imidazole), Glutamate (COO-), Lysine (NH3+), Tyrosine (-OH) - 16pKa values of ionizable groups in proteins (DO NOT NEED TO MEMORIZE)
- 17Isoelectric pH (pI)the pH at which the molecule is neutral in charge (no net electrical charge)
- 18How to find the isoelectric "range"* only with amino acids that have an ionizable side chain "DR CHEKY" *
1. Identify ionizable groups (what groups can be protonated/ unprotonated)
2. Find pH "range" where molecule is isoelectrically neutral (no net charge)
3. Average. two pKa of the "range" - 19Protein structures- primary: amino acid sequence
- secondary: alpha helices and beta pleated sheets
- tertiary: considers 3D shape - 20What links amino acids?Linked by peptide bonds
- condensation reaction
- carboxyl carbon AA1 ("residue 1") forms a covalent bond with amino nitrogen group of AA2 ("residue 2") - 21What are the "start" and "end" groups in an amino acid?Start: N-terminus (a-amino group)
End: C-terminus (carboxylic acid group)
* Pattern: nitrogen - a-carbon - carbonyl * - 22Peptide bond characteristics- distance: 1.32 A
- uncharged
- two a-carbon configurations (cis & trans) - 23Torsion angles- phi: nitrogen - a-carbon (-80 degrees) (look at relative position of carbonyl groups)
- psi: a-carbon - carbonyl carbon (+ 85 degrees) (relative position of amine groups)
* size of R-chain will determine torsion angle *
* Glycine (H-group) will have a very large torsion angle * - 24Ramachandran DIagramfavorable torsion angles in due to steric hinderance (darker green more favorable)
* disfavored *
- phi: 90
- psi: -90 - 25Disulfide bonds: oxydation & reduction reaction- Chains can be covalently linked by cysteine "residues" forming disulfide bridges [oxidation reaction]
- these bonds can also be broken using b-mecaptoethanol [reduction] - 26Oligopeptide (simply "peptide")> 25 residues
- 27Polypeptide~ 25 - 50 residues
- 28Protein~ 50 - 2000 residues
- 29Relationship between 1 residue and g/mol (Da)1 residue = ~110 g/mol (Da)
* therefore 50 residues is 5500 g/mol (5.5 Da) - 30Primary sequence(and doing Ramachandran plots) Determines the 3D structure of a protein
- 31Secondary structure: alpha helices- coiled backbone (mostly right-handed, can be left-handed)
- R-groups directed outward
- stabilized by H-bonds (between carbonyl oxygen and amide hydrogen four residues away)
- 3.6 residues per turn (one complete revolution)
- 1.5 A pero amino acid or 5.4 A per helical turn
- usually less than 45 A long - 32Secondary structure: alpha helices * special case: Proline *- proline does not have a free hydrogen therefore they are no good in alpha helices
- 33What groups are NOT common in alpha helices?- branched chain amino acids: Valine, Threonine, Isoleucine
- H-bonding side chains: Serine, Aspargine, Aspartic acid
- PROLINE lacks "free" NH groups - 34Secondary structure: beta sheets- planar structure
- consists of two or more beta-sheets which can be in parallel or anti-parallel orientation - 35Parallel vs anti-parallelanti-parallel: C -> N / N -> C (perpendicular H bonds, shorter and more stable)
parallel: N -> C / N -> C (diagonal H bonds, longer and less stable - 36—
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- MCAT Exam 1: Biochemistry (Exam 1) Flashcards on Amino Acids, created by Arantxa Martinez on 27/09/2021.
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- Arantxa Martinez
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