Chapter 1: Amino Acids and Protein Structure Flashcards
1
Q
L - amino acid chemical classifications
A
- Aliphatic
- Aromatic
- Sulfur-containing
- Alcohols
- Bases
- Acids
- Amides
2
Q
Post-translational modifications
A
- Modified amino acids
- Occurs after they have been incorporated into the primary structure of a peptide or protein
3
Q
Hydroxyproline
A
- Post-translationally modified in collagen structures
4
Q
Gamma Carboxyglutamate
A
- Post-translationally modified in clotting factors and protein C
5
Q
Prosthetic groups
A
- Covalently bound accessory components
6
Q
Weak Acids
A
- Allows side chain functional group of amino acids to donate or accept (act as a base) protons as environmental pH fluctuates
7
Q
Covalent peptide bonds (amide bonds)
A
- Formed between α-amino acids
- Bonds formed by condensation reactions and use energy
- Trans bonds that are stable
- Unionized at physiological pH
- Coplanar, exist in linear orientation
8
Q
Primary structure
A
- Linear sequence of amino acids
- Connected by peptide bonds
- Determines functional 3D shape
9
Q
Insulin
A
- Synthesized in the pancreatic ß-cells
10
Q
Proteolytic cleavage
A
- Releases C-peptide and biologically active hormone
11
Q
Hemoglobin
A
- Transport protein
- Bind with oxygen to transport it through the blood
12
Q
Edman Degradation
A
- Historically used to determine the primary structure of a protein
- Amino terminal residue is labeled with a phenylisothionate at pH 9.0
- Forms a phenylthiocarbamoyle derivative
- Derivative cyclized under mild acidic conditions
- Released from peptide, leaving remaining bonds intact
13
Q
Secondary enzyme
A
- Partially digests the parent peptide to generate overlapping peptides
14
Q
Denaturation
A
- Achieved by diothreitol and alkylation with iodoacetate
- Prevents bonds from reforming
- Also may be achieved by treatment with 2-mercaptoethanol
15
Q
Secondary structure
A
- Local spontaneous repeated folding of a protein/polypeptide
- Stabilized predominantly by H-bonds
16
Q
Alpha helix
A
- Stabilized by H-bonds between NH and CO groups of amino acids 4 residues
- Can extend up to 650 residues in length
- Distinct polar and non-polar sides of the chain
- Spiral molecule
17
Q
Beta pleated sheet
A
- Fully extended polypeptide chains
- Linked together by interchain H-bonds between CP and NH groups
- Composed of up to 10 polypeptide strands lying adjacent to each other
- Can run parallel in the N > C direction or antiparallel in the opposite N > C direction
18
Q
Tertiary structure
A
- Energetically favored conformation
- Folding of protein/peptide into a 3D conformation that remains flexible and dynamic
- Contains multiple domains or sections
- Stabilized by variety of bonds
19
Q
Tertiary structure bond types
A
- Ionic linkages
- Hydrogen bonds
- Hydrophobic interactions
- Van de Waa’ls forces
20
Q
Quaternary structure
A
- Spatial organization of of monomeric subunits
- Stabilized predominantly by hydrophobic interactions, hydrogen bonds, and Van der Waal’s forces
21
Q
Oligomeric proteins
A
- Multi subunit proteins
- Possess multiple interacting polypeptide chains
- Only types of proteins that possess a quaternary structure
22
Q
Hemoglobin
A
- Alpha 2 Beta 2 tetramer
- Quaternary structure stabilized by non-covalent interactions
23
Q
Thalassemias
A
- Insufficient amounts of subunits are produced
- Occurs as a consequence of gene deletion or defects during transcription/translation
24
Q
Protein denaturation
A
- Occurs with the disruption or dismantling of the active three dimensional protein configuration
- Most often happens with extreme heat
- pH and ionic strength that may dismantle the non-covalent interactions that stabilize the protein structure
25
Primary structure review
- Linear sequence of amino acids connected by the peptide bonds
- Determines its functional three dimensional shape
26
Edman degradation procedure review
- Can be used to determine the primary structure of a protein
- Specific cleavage of peptides into shorter fragments improves the reliability and usability of the technique
27
Secondary structure review
- Local recurring arrangement of a protein
- Wide variety of structures has been identified
- Alpha helix and beta pleated sheet most familiar and important confirmations
28
Tertiary structure review
- Spatial organization of amino acids that are far apart in the protein's primary structure
- Stabilized by non-covalent interactions between the amino acid side chains
29
Quaternary structure review
- Proteins that are composed of multiple subunits
| - Interaction between side chains in separate polypeptide chains
30
Denaturation review
- Reversible
| - Occurs by extremes of pH, temperature, heavy metals, detergents, and organic solvents
