Lecture 2 Flashcards by Robert Enders

Dimer

Made of two polypeptides

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How many beta strands to make a beta sheet?

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Primary structure of a protein

The primary sequence of amino acids

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Homodimer

two dimers that are the same polypeptide (quaternary protein structure)

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4 main agents of protein function

Catalysis, Transport, Structure, and Motion

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4 properties of Amino acids that make them a good building block

Capacity to polymerize, useful acid-base properties, varied physical properties, and varied chemical functionality

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Chiral carbon

carbon with 4 different constituents

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Naming of amino acids starts and ends where

starts the N terminus (amino) and ends at the C terminus (carboxyl)

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Nonpolar, aliphatic amino acids

Gly, Ala, Pro, Val, Leu, Ile, Met

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Aromatic amino acids

Phe, Tyr, Trp

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Polar, uncharged amino acids

Ser, Thr, Asn, Gln, Cys

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Positively charged amino acids

His, Lys, Arg

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Negatively charged amino acids

Asp, Glu

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Zwitterions

when the net charge of an amino acid is zero. When the carboxyl group is deprotonated and the amino group is protonated.

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Isoelectric point

when it is net neutral

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Peptide formation of amino acids is through

condensation. Forming an amide.

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Cofactor

functional non-amino acid component.

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Coenzyme

organic cofactors.

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Prosthetic groups

covalently attached cofactors.

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Lipoproteins

Lipids as the prosthetic group. Likely will go to the membrane

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Glycoproteins

Carbohydrates as the prosthetic group. Provide protection and important for cell to cell signaling

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Phosphoproteins

phosphate group as the prosthetic group

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Hemoproteins

Heme (iron porphyrin) as the prosthetic group.

4 favorable interactions in protein folding

Hydrophobic effect, hydrogen bonding (dipole dipole interactions), Van der Waals interactions, electrostatic interactions

Hydrophobic effect

release of water molecules from the structured salvation layer around the molecule as protein folds (increases the entropy)

Hydrogen bonding

Interaction of N-H and C=O of the peptide bonds leads to local regular structures such as alpha helices and beta strands

Van der Waals

London dispersion and steric repulsion. Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein

Electrostatic interactions

Long-range strong interactions between permanently charged groups. Salt-bridge stabilize the protein

Phi angle

angle around the alpha carbon and amide nitrogen bond

psi angle

around the alpha carbon and the carbonyl carbon bond

Alpha helix

stabilized by hydrogen bonds between nearby residues. Side chains point out perpendicular to the helical axis. Peptide 1 is directly above peptide 8.

Beta sheet

stabilized by hydrogen bonds between adjacent segments that may not be nearby in the primary sequence. Side chain protrude from the sheet in an alternating up/down direction. Thus can be amphipathic.

How many residues in a turn for an alpha helix

3.6 residues

Good alpha helix residue makers

alanine and leucine

Helix breakers

Proline and glycine

Parallel and antiparallel orientation

Parallel - strands run in same direction. | Antiparallel - strands run in opposite directions.

How many residues does it take to complete a beta turn?

Proline position for a beta turn

2 (I have 2 pee)

Glycine position for a beta turn

Common secondary motifs

B-A-B loop, Beta barrel

Fibrous proteins

typically insoluble, made from a single secondary structure

Globular protein

water-soluble and lipid-soluble proteins

Tough fibrous protein structure

cross-linked alpha helixes. Rigid linker (S-S). Such as keratin

Non-stretching fibrous protein structure

cross-linked triple-helixes. flexible linker (Lys-HyLys). Such as collagen

Soft, flexible fibrous protein structure

Non-covalently held B sheets and Van der Waals interactions. Such as silk fibroin

Collagen structure and 3 important residues

left-handed helix. Gly, Pro, and hydroxyPro. Then 3 chains form a right-handed superhelical triple helix

Ways proteins can be denatured

heat or cold, pH extremes, organic solvents (extract hydrophobic parts), and chaotropic agents such as urea and guanidine hydrochloride (bind up water)

Chaperones

help to prevent misfolding. Can refold a partly denatured protein

The monomers of proteins...

Amino Acids

Amino Acid Nomenclature (Biochemist method)

Start from alpha-carbon and go down the R group | --N-terminus to C-terminus

Which is the only amino acid without an amino group attached to the alpha carbon?

Proline

Cofactor (protein)

Functional non-amino acid component (ex. metal ions or organic molecules)

Coenzyme

Organic cofactors (ex. NAD+)

Prosthetic Group

Covalently attached cofactors (ex. heme in myoglobin)

What are the jobs of DnaJ and DnaK?

To help fold other proteins

GroEL and Gro ES

Garbage can looking structure - -Denatured Proteins go inside --> come out correctly folded - -Has polar and nonpolar side chains