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78 Cards in this Set

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What does the "Native Structure" of proteins refer to?
The unique 3-dimensional structure that has the lowest free energy of all possible FUNCTIONAL folding patterns.
What force drives protein folding?
Hydrophobic force -> sequesters nonpolar AA's in the protein's core.
What is the central carbon in each amino acid?
The alpha carbon - it's chiral except for glycine.
What configuration are all amino acids in the body?
L-form
Why are amino acids classified based on hydration characteristics?
-HydroPHOBIC prefer to be on the protein's INTERIOR.
-HydroPHILIC prefer to be on the protein's SURFACE.
What are the 2 subcategories of HydroPHOBIC amino acids?
1. Aliphatic
2. Aromatic
List the aliphatic AA's:
(7)
GAVLIMP
Glycine
Alanine
Valine
Leucine
Isoleucine
Methionine
Proline
List the aromatic AA's:
(3)
PTT
Phenylalanine
Tyrosine
Tryptophan
What makes proline unique?
It posseses an IMINO group which facilitates turns in B-sheets.
What's the difference btwn an IMINO and AMINO side group?
Imino = NH2+ in 5-memb ring
Amino = independent NH3+
What is common to all the hydrophobic aliphatic AA's?
-Methyl group spacer to prevent steric repulsion
-Ring structure
What is the ring structure in:
-Phe
-Tyr
-Trp
Phe = benzene
Tyr = benzene + OH
Trp = indole
What are the letters for the aromatics?
F = Phe
Y = Tyr
W = Trp
What does aromaticity of F/Y/W allow?
The ability to measure unique UV Spectra at 280 nm
Which aromatic AA has the highest absorbance? Lowest?
Which 2 are more similar/Why?
Highest = Trp/W
Lowest = Phe/F
Phe/Tyr are similar b/c both have the benzene ring. The indole makes Trp the oddball.
What about the aliphatics do we measure based on absorbance?
Protein concentration
What are the 2 subcategories of hydrophilic amino acids?
Uncharged
Charged
What are the 5 uncharged polar amino acids?
STAGC
Serine
Threonine
Asparagine
Glutamine
Cysteine
What are the 5 charged polar amino acids?
LAAGH
Lys
Argine
Aspartate
Glutamate
Histidine
Which uncharged polar AA contains sulfar?
Cysteine
What other amino acid contains sulfar?
Methionine
What are the basic polar amino acids?
Lys, Arg, His
What are the acidic polar amino acids?
Glu and Asp
What 2 AA's not classified as polar have dissociable protons?
Tyr (OH) and Cys (SH)
Relative pKA of
-Amino group
-Carboxyl group
NH3 = 8.0

COOH = 3.1
Relative pKA of:
-Asp/Glu
4.4
Relative pKA of:
Histidine
6.5
(NH in the imino group)
Relative pKA of:
Cysteine
8.5
(SH sulfhydryl)
Relative pKA of:
Tyrosine
10.0
(phenol)
Relative pKA of:
Lysine
10.0 (NH3+)
Relative pKA of:
Arginine
12.0
(NH2+ --- NH2+)
What is the isolectric point?
The unique pH at which an amino acid has 0 net charge.
What is the pKa?
The pH where 50% of the ionizable R groups in solution are ionized and 50% are not.
What is the unique characteristic of Met?
Always the first amino acid in nascent protein
What clinical correlation can be made with Met?
The amino group is oxidizable b/c it's the end terminal.
What proteolytic enzyme that has Met in its active site protects alveoli from degradn?
alpha-Antitrypsin
What happens when the Met in alpha-AT gets oxidized?
It no longer works and the alveoli get chewed up.
What oxidizes alpha-AT and what is the result?
Cigarette smoke; Emphysema.
What else can cause alpha-AT to be unavailable?
Transport failure from genetic mutation
What type of bonds constitute primary protein structure?
Covalent peptide bonds
What type of bonds constitute Secondary protein structure?
Only Hydrogen Bonds btwn carbonyl Oxygens and Amino Nitrogens in peptide backbone.
What is super secondary structure?
Folding motifs composed of different combos of secondary structures.
Why do super-secondary structures exist?
To solve the packing and folding requirements of proteins by minimizing energy.
What type of bonds constitute super-secondary structure?
Interactions between R groups.
What is a domain?
The smallest thermodynamically stable unit of protein structure - result of 2ndary/Super-2ndary structure associations.
What is tertiary structure?
The smallest COMPLETE unit of a protein; the final 3-D structure of 1 polypep chain.
What is quaternary structure?
Tertiary combined into a globular protein.
How do polypeptide bonds form?
A carboxyl combines with amino group with loss of one water.
What is the nature of a peptide bond?
Resonance:
-Double bond C=O 60% of time;
-Double bond C=N 40% of time.
What results from the delocalized resonance of peptide bonds?
The bond is unable to rotate.
What orientation of R groups at the peptide bond is favored by ribosomes?
TRANS - R's pointed away from each other.
Which bond CAN rotate in pp chains?
The bonds between:
-Amino -> alpha-Carbon (Phi)
-Alpha-carbon -> Carboxyl (Psi)
What are the bond angles in:
-RH alpha helices?
-LH alpha helices?
-Beta sheets?
RH alpha: -60/-60
LH alpha: 60/60
Beta: 120/-120
What's a characteristic of Cysteine to take note of?
Its ability to spontaneously oxidize and form a disulfide bond within a protein.
What proteins from disulfide bridges more often?
Extracellular - for more stability.
What molecule were Disulfide bonds first seen in?
Insulin
What are the important features of Right-hand alpha helix?
-3.6 res/turn
-H-bonds between C=O of i and NH3+ of (i+4)
What does amphipathic mean?
Hydrophilic face points out;
Hydrophobic face points in;
-Refers to R groups in alpha helices.
So the outside of an alpha helix is:
And the inside of it is:
Outside = hydrophilic

Inside core = hydrophobic
The difference between H bonds in B-sheets and a-helices is:
-Helices have H bonds perpendicular to the aa chain.
-Sheets have H bonds parallel to the sheet.
What are 3 types of b-sheets?
1. Parallel
2. Antiparallel
3. Mixed beta
What distinguishes an Antiparallel sheet?
Peptides alternate in direction.
What distinguishes Parallel sheets?
Peptides are lined up.
What distinguishes a mixed beta sheet?
It contains both parallel and antiparallel sheets.
Where are beta sheets typically found?
In the interior of proteins.
What are "reverse turns"?
Aka beta turns or hairpin loops;
-A 2dry structure that connects runs of antiparallel B-sheets.
What is the structure of a Reverse Turn?
-4 residues
-H bond connects AA1 to AA4
What is the difference btwn Type I and Type II reverse turns?
Orientation of peptide bond between AA2 and AA3
What is unique about Type II reverse turns?
The close proximity of AA3's R group to the C=O of peptide between AA2 and AA3 only accomadates Gly at AA3.
What is the least common type of reverse turn?
3 ten helix
What characterizes supersecondary structure?
Stability achieved by intramolecular interactions of R groups.
What is the most common type of supersecondary element observed?
Why are they needed?
Cross-over elements for parallel beta sheets.
What 2 categories of crossover elements exist, which is preferred?
RH or LH; RH is preferred.
What are the 3 main types of beta-sheet crossover elements?
-Beta-coil-beta
-Betabetabeta
-Beta-alpha-beta
What is the most common beta crsossover element?
Beta-alpha-beta
What stabilizes the B-a-B motif?
Intercalation of R groups projecting up from B-sheets, and R groups radiating out from amphipathic a-helices.
What is a Rossmann fold?
A series of BaB motif repeats that make a donut-shaped a-B barrel.
Where are rossmann folds commonly found?
In enzymes of the glycolytic metabolic pathway.