Amino acids and HW 1
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| Four groups of biomolecules | 1. Protein
2. Carbohydrates
3. Nucleic Acids
4. Lipids
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| zwitter ions | ions that have both a positive and negative charge-- ex. all amino acids
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| Chiral carbon | carbon with 4 different substituents bound to it
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| enantiomers | a stereoisomer that is a mirror image of the other structure
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| 2 laws of thermodynamics | 1. you can't create or destroy energy
2. entropy tends to increase
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| 4 non-covalent (weak) interactions in aqueous solution | 1.Ionic bonds
2. hydrogen bonds
3. Hydrophobic interactions
4 Van Dar Waals forces
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| 5 groups of the 20 amino acids | 1. non polar, aliphatic
2. polar, uncharged
3. aromatic
4.Positively charged
5. Negatively charged
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| Nonpolar, aliphatic R groups (biggest group) (7) | 1) glycine
2) alanine
3) proline
4)Valine
5)leucine
6) Isoleucine
7)methionine
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| Nonpolar, aliphatic R group characteristics | 1) mostly hydrophobic in nature
2) like hydrophobic interactions most of the 4 interactions
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| Polar, uncharged R groups (aa) (5) | 1) serine
2) Threonine
3) Cysteine
4) Asparagine
5) Glutamine
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| 2 amino acids that have sulfur in them | 1) cysteine
2) Methionine
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| Aromatic R groups (aa) (3) | 1) phenylalanine (non polar)
2) Tyrosine (polar)
3) Tryptophan (non polar)
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| Positively charged R groups (aa) (3) | 1) lysine
2) arginine
3) Histidine
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| Negatively charged R groups (aa) (2) | 1) aspartate (aspartic acid)
2) Glutamate (glutamic acid)
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| 4 processes to change a.a. structure | 1) methylation
2) Phosphorylation
3) Carboxylation
4) Hydroxylation
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| Selenocysteine | -sometimes called the 21st a.a.
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| Citrulline and Ornithine | metabolites that are intermediates in the urea cycle
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| Carnitine | metabolite that transports fatty acids to the mitochondria
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| Creatine | metabolite that is an intermediate energy storage compound in skeletal muscle
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| Isomer | any two molecules with the same molecular formula but a different arrangement of molecular groups
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| Conformation | A spatial arrangement of substituent groups that are free to assume different positions in space, without breaking any bond, because of freedom of rotation
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| Stereoisomer | Compounds that have the same composition and the same order of atomic connections but different molecular arrangements
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| Configuration | The spatial arrangement of an organic molecule that is conferred by the presence of either (1) double bonds, about which there is no freedom of rotation, or (2) chiral centers, around which substituent groups are arranged in a specific sequence.
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| Diastereomers | stereoisomers that are not mirror images of one another
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| Glycine Characteristic | only aa that is not chiral
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| Proline characteristic | R and alpha aimno group form a ring---impacts conformation of protien.
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| Polar uncharged R group characteristics | important for hydrogen bonding
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| Aromatic R group characteristics | large, bulky aa that have aromatic rings---absorption maximum at 280nm---important for Protien biochemistry
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| Tyrosine and Tryptophan characteristic | both absorb ultra-violet light
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| Positively charged R group characteristics | Basic aa that can form Ionic bonds
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| Lysine and Arginine characteristic | pKr > 7.0
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| Histidine characteristic | pKr close to 7.0--- plays a major role in enzyme function
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| Negatively charged R group characteristics | Acidic (pKr low) aa that form ionic bonds--- "-ate": deprotonated organic acid
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| 4 abbreviations that are not the first 3 letter of the aa | 1) Isoleucine (Ile)
2) Tryptophan (trp)
3) Asparagine (Asn)
4) Glutamine (Gln)
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| How do you find neutral aa pI? | pK1 + pK2 / 2
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| How do you find Acidic aa pI? | pK1 + pKr / 2
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| How do you find Basic aa pI? | pKr + pK2 / 2
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| condensation | putting together --- catalyzed by ribosomes --- produces water
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| Hydrolysis | pulling apart --- catalyzed by proteases/ peptidases
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| Amide bond | formed through condensation of carboxyl and amino groups --- called peptide bone on amino acid polymers
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| Peptide bond | condensation between the alpha carboxyl group and alpha amino group
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| oligopeptide | polymers of a few amino acids (building blocks)
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| Polypeptide Mw? | Mw < 10,000 g/mol
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| Protien Mw? | Mw > 10,000 g/mol
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| #1 amino acid in polypeptide? | amino acid that is next to the N-terminus
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| Tripeptide mad up of? | 3 amino acids and 2 peptide bonds
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