Biochemistry Ch. 1 Flashcards
List the aromatic amino acids
1) Phenylalanine
2) Tryptophan
3) Tyrosine
List the acidic amino acids
1) Aspartic acid
2) Glutamic acid
List the basic amino acids
1) Arginine
2) Histidine
3) Lysine
List the aliphatic amino acids
1) Alanine
2) Glycine
3) Isoleucine
4) Leucine
5) Proline
6) Valine
List the hydroxylic amino acids
1) Serine
2) Threonine
List the sulfur-containing amino acids
1) Cysteine
2) Methionine
List the amidic amino acids
1) Asparagine
2) Glutamine
List the essential amino acids
1) Isoleucine
2) Leucine
3) Valine
4) Phenylalanine
5) Tryptophan
6) Histidine
7) Lysine
8) Serine
9) Threonine
___ side chains have high pI’s while ___ side chains have low pI’s
Basic, acidic
What is a peptide bond?
Condensation/dehydration/acyl substitution/type of amide bond that forms between the COO- and NH+ group of two amino acids to form a -C(O)NH- group
How do trypsin and chymotrypsin catalyze hydrolysis?
Break apart amide bond by adding H to amide N and OH to carbonyl C
The __ terminus is the amino end
N
The __ terminus is the carboxyl end
C
Define primary protein structure
A linear arrangement of amino acids that is stabilized by the peptide bonds between adjacent amino acids
___ protein structure has no subtypes
primary
Define secondary protein structure
A local structure of neighboring amino acids stabilized by intramolecular H bonding between different residues of amino acids
List the two subtypes of secondary protein structures
Alpha helix and beta sheet
Define alpha helix
A secondary protein structure of a peptide chains and side chains
Describe the structure of an alpha helix
Coil of peptide chains, side chains point away from core, H bond is formed between residues of the same peptide
Define beta sheet
A secondary protein structure of parallel and antiparallel rows of peptide chains
Describe the structure of a Beta sheet
Parallel and antiparallel rows of peptide chains, R groups point above and below the plane, H bonds are formed between residues of different peptide chains
A beta sheet has H bonds formed between residues of ___ peptide chains
Different
An alpha helix has H bonds formed between residues of ___ peptide chains
Same
How does proline affect the secondary structure of a protein?
Introduces kink in alpha helix and turn in beta sheet
Where is proline typically found in a secondary protein structure?
In the turns between chains of beta sheets and as reside at start of alpha helix
List the types of proteins
1) Fibrous
2) Globular
What stabilizes/forms tertiary structures?
1) The shuffling of hydrophobic side groups to the inner core of a protein and the shuffling of hydrophilic groups (N-H and C=O) to the outside
2) Disulfide bonds between cysteine molecules
3) Salt bridges between amino acids with charged R groups
Define solvation layer
The organization of solvent around solute
Salt bridges form between ___
Amino acids with charged R groups
Cystine is formed from what? what type of reaction is this?
From the disulfide bonds between two cysteine molecules
Oxidation reaction
Quaternary structures only occur when?
For proteins with more than 1 polypeptide chain
List the functions of forming a quaternary protein structure:
1) Stabilizes protein by reducing surface area
2) Reduces amount of DNA needed to encode protein complex
3) Bring catalytic sites closer together so intermediates from 1 reaction can be directly shuttled to 2nd reaction
4) Induce cooperativity/allosteric effects
Conjugated proteins have ___ly attached ___ groups
Covalently attached; prosthetic
List the conjugated proteins and their prosthetic groups
1) Lipoproteins: have lipid as prosthetic group
2) Glycoproteins: have carbohydrate as prosthetic group
4) Nucleoproteins: have nucleic acid as prosthetic group
___ proteins can’t catalyze reactions
Unfolded
List the 2 main causes of denaturation
1) Heat
2) Solutes
How can heat cause denaturation of a protein?
Breaks hydrophobic interactions holding protein together
How can solutes cause protein denaturation?
Directly interfere with the forces holding a protein together (i.e. break disulfide bridges and side chain interactions on alpha helices and beta sheets)
How do you determine the pI value of an amino acid with a non-ionizable side chain?
Average the pka values of the terminal alpha carboxyl and amino groups
How do you determine the pI value of an amino acid with an ionizable and acidic side chain?
Average the pka values of ther terminal alpha carboxyl group and the side chain
Define isoelectric point
The point at which the positive and negative charges on a protein are equal so that the net charge is zero
How do you determine the pI of an amino acid with a basic side chain?
Average the pka values of the terminal alpha amino group and the side chain
How do you determine the pI of an amino acid with a side chain that is ionizable but neither basic nor acidic?
Determine the median pka value is (of the pka values of the terminal alpha carboxyl group, terminal alpha amino group, and side chain) and add it with the pka value of the terminal alpha carboxyl group, then average it (divide by 2)
If the pH of solution is greater than the pKa, the group is in the ____ form.
conjugate base form (deprotonated).
If the pH of solution is less than the pKa, the group is in the ___ form
conjugate acid form (protonated).
