Biochem Lecture 1 (Amino Acids, Protein Folding)

Biochemistry

the study that deals with the molecules and molecular events by which cells carry out essential processes

Proteins

linear heteropolymers of amino acids, that have a primary, secondary, tertiary, and quaternary structure

Functions of amino acids (besides building proteins)

Fuel for ATP synthesis, neurotransmitters, precursors of hormones and bioactive agents (ex. histidine- histamine)

Amino acids

building blocks of proteins (among other things)

L-amino acids

in proteins, amino acids are in the structure of an _-_________ ______

alpha

in an amino acid, the _-carbon always has four substituents

tetrahedral

the molecular geometry of an amino acid

proline, acidic, basic, hydrogen, alpha

All amino acids (except _________, have an _______ carboxyl group, a _______ amino group, and an __________-hydrogen connected to the alpha-carbon

unique

the R group is ____________ to each amino acid

alpha carbon

when naming the carbons of the amino acid, you start at the _______-______________ and go down the R group

glycine, gly, G, nonpolar/aliphatic

name, 3 letter abbreviation, 1 letter code, category

alanine, ala, A, nonpolar/aliphatic

name, 3 letter abbreviation, 1 letter code, category

valine, Val, V, nonpolar/aliphatic

name, 3 letter abbreviation, 1 letter code, category

methionine, Met, M, nonpolar/aliphatic

name, 3 letter abbreviation, 1 letter code, category

proline, pro, P, nonpolar/aliphatic

name, 3 letter abbreviation, 1 letter code, category

leucine, leu, L, nonpolar/aliphatic

name, 3 letter abbreviation, 1 letter code, category

isoleucine, Ile, I, nonpolar/aliphatic

name, 3 letter abbreviation, 1 letter code, category

phenylalanine, Phe, F, aromatic

name, 3 letter abbreviation, 1 letter code, category

Tyrosine, Tyr, Y, aromatic

name, 3 letter abbreviation, 1 letter code, category

tryptophan, Trp, W, aromatic

name, 3 letter abbreviation, 1 letter code, category

asparagine, Asn, N, polar/uncharged

name, 3 letter abbreviation, 1 letter code, category

cysteine, Cys, C, polar/uncharged

name, 3 letter abbreviation, 1 letter code, category

serine, Ser, S, polar/uncharged

name, 3 letter abbreviation, 1 letter code, category

Threonine, Thr, T, polar/uncharged

name, 3 letter abbreviation, 1 letter code, category

Glutamine, Gln, Q, polar/uncharged

name, 3 letter abbreviation, 1 letter code, category

Arginine, Arg, R, positively charged

name, 3 letter abbreviation, 1 letter code, category

Histidine, His, H, positively charged

name, 3 letter abbreviation, 1 letter code, category

Lysine, Lys, K, positively charged

name, 3 letter abbreviation, 1 letter code, category

Aspartate, Asp, D, Negatively charged

name, 3 letter abbreviation, 1 letter code, category

Glutamate, Glu, E, Negatively charged

name, 3 letter abbreviation, 1 letter code, category

Half

For a weak acid or base, the pKa is the pH at which the group is _______ protonated

Amine, carboxylic acid

two functional groups in every amino acid

Acidic, neutral, basic (alkaline)

for amino acids, at ___________ pH both groups are protonated, at a ___________ the carboxyl group is deprotonated, amino group is protonated, at a ____________ pH both groups are protonate

Zwitterion

at a neutral pH the carboxyl group is negative, and the amino group is positive causing a net neutral charge, also known as

protonated, deprotonated

if pH

3D

most protein molecules adopt a specific ____ conformation

native fold

the specific 3D conformation of a polypeptide

hydrophobic effect

the release of water molecules from around hydrophobic amino acids increases net entropy, happens due to this effect and allows protein to fold

hydrogen bonds

the type of interaction that allows alpha helices and beta sheets due to the interaction of N-H and C=O bonds

van Der walls interactions (LDFs)

medium range weak attraction between all atoms that stabilizes the interior of the protein

Electrostatic interactions

the long range strong interactions between permanently charged groups that stabilize a protein (can also be from salt bridges)

Partial double bond, rotate

the peptide bond has some resonance, meaning that it is a _____ _______ __________, and this restricts that amount that the bond can ________

ramachandran plot

Shows favorable phi-psi angle combinations. 3 main "wells" for α-helices, ß-sheets, and left-handed α-helices.

Phi angle

angle around the alpha carbon-amide nitrogen bond

Psi angle

angle around the alpha carbon-carboxyl carbon bond

alpha helix

type of secondary structure that is stabilized by hydrogen bonds between the NEARBY residues

beta sheet

type of secondary structure that is stabilized by hydrogen bonds between ADJACENT SEGMENTS that may not be nearby

random coil

an irregular arrangement of the polypetide chain that is also a type of secondary structure

N, N+4

the helical backbone of an alpha helix is held together by hydrogen bonds between the backbone of N-H and C=O, of the _ amino acid and the _+_ amino acid

3.6 residues per turn

a right handed alpha helix has ____ residues per turn

out, perpendicular

on an alpha helix, side chains point _____ and are roughly ____________ with the helical axis

4-5 angstroms

the inner diameter of an alpha helix is this measurement

10-12 angstroms

the outer diameter of the helix (with side chains) is this measurement, which lets it fit well into the major groove of dsDNA

1, 8

residues _ and _ lie on top of each other in an alpha helix

antiparallel beta sheet

this type of beta sheet has one row start at N terminus and end at C terminus from left to right, and then the next row will start with the C terminus, and end with the N terminus from left to right (alternating)

parallel beta sheet

this type of beta sheet has each row start at the N terminus and then end at the C terminus (all the same)

antiparallel

this type of beta sheet is stronger than the other because of the strong LINEAR Hydrogen bonding, because the other has weak H bonding due to the bending nature of the H bonds

glycine, proline

these two amino acids are usually in beta turns to connect the antiparallel beta strands

side chains

the tertiary structure of a protein folds due to interactions from the _____ _________ of the amino acids

quaternary structure

the structure of a protein that is multiple different subunits to form one protein complex

fibrous

type of protein that is shaped like a long strand/sheet, usually provides structural support as its function

globular

the type of protein that has a spherical shape, usually is an enzyme or regulatory protein

membrane proteins

this type of protein has a hydrophobic surface, and a hydrophilic interior in order to properly cross hydrophobic membranes

True

ture or false, a protein can have a mix of shapes of proteins