BCH Exam 1 All Content

Alanine (3 letter code)

Ala

Alanine (1 letter code)

A

Valine (3 letter code)

Val

Leucine (3 letter code)

Leu

Isoleucine (3 letter code)

Ile

Methionine(3 letter code)

Met

Phenylalanine (3 letter code)

Phe

Tyrosine (3 letter code)

Tyr

Tryptophan (3 letter code)

Trp

Proline (3 letter code)

Pro

Glycine (3 letter code)

Gly

Serine (3 letter code)

Ser

Cysteine (3 letter code)

Cys

Threonine (3 letter code)

Thr

Aspartic Acid/Aspartate (3 letter code)

Asp

Glutamic Acid (Glutamate) (3 letter code)

Glu

Asparagine (3 letter code)

Asn

Glutamine (3 letter code)

Gln

Histidine (3 letter code)

His

Arginine (3 letter code)

Arg

Arginine (1 letter code)

R

Lysine (3 letter code)

Lys

Lysine (1 letter code)

K

Histidine (1 letter code)

H

Glutamine (1 letter code)

Q

Asparagine (1 letter code)

N

Glutamic Acid (Glutamate) (1 letter code)

E

Aspartic Acid/Aspartate (1 letter code)

D

Threonine (1 letter code)

T

Cysteine (1 letter code)

C

Serine (1 letter code)

S

Glycine (1 letter code)

G

Proline (1 letter code)

P

Tryptophan (1 letter code)

W

Tyrosine (1 letter code)

Y

Phenylalanine (1 letter code)

F

Methionine (1 letter code)

M

Isoleucine (1 letter code)

I

Leucine (1 letter code)

L

Valine (1 letter code)

V

Amino acids are joined by what type of bond

Covalent

Protein structures are stabilized by _________ interactions and forces

NONcovalent

Two kinds of secondary strucures

A helix, B conformation

3D folded conformation of a protein

Tertiary Structure

Multisubunit interactions (2+ proteins) make

Quaternary structures

3 ways to determine 3D strucuters

NMR, X Ray Crustallography, Cryo EM

Covalent bonds linking the amino acid sequence of a polypeptide chain

Primary Structure

Peptide bonds are stable because

(resonance)(partial double bond character)

N-Ca bond

Phi

Ca-C bond

psi

C-N bond

omega

Peptide (omega) bonds rotate Freely

False

Phi and Psi bonds rotate Freely

True

How many atoms in a peptide chain lie in a single plane

6 (six)

Secondary structure= arrangement of (main/side) chain

Main

Tertiary structure= arrangement of (main/side) chain

side

Secondary structures are stabilized by what kind of interactions

NON covalent

The uniformity of the secondary structure is produced by:

repetition of phi and psi angle

Simplest arrangement of a secondary strucure

Alpha helix

Secondary strucure with the MAXimum number of Hydrogen bonds

Alpha helix

What protrudes out of the alpha helix

R group (this means R groups affect protein function and interactions)

Each helical turn in an alpha helix is how many Å (distance)

5.4 Å

How many residues make up an alpha helical turn

4 (3.6)

Interactions between (R groups/main chains) can stabilize or destabilize the alpha helix

R groups

Alpha helix is formed by __________ (type of interaction) between the N-H of residue n and the carbonyl O of residue ___

hydrogen bonding; n+4

Alpha helix is made by hydrogen bonds between (side chains/main chains)

MAIN chains

Two amino acids that disrupt or prevent alpha helices

P, G

More common Alpha Helix handedness

Right handed

Less stable Alpha helix handedness

Left handed

The N+ to C- structure of a polypeptide produces a

net dipole

Alternative helix structure: 3₁₀ helix has how many residues per turn

3.0 (skinnier)

Alternative helix structure: π helix has how many residues per turn

4.4 (fatter)

Side groups are always oriented in cis/trans along a polypeptide chain

trans

Zigzagging polypeptide backbone

B conformation

Multiple Beta strands side by side make up a

B sheet

A single protein segment in B conformation

Beta strand

Two orientations of Beta sheets

Parallel,Antiparallel

More frequent and stable orientation of a B sheet

Antiparallel

Why is the antiparallel orientation of a Beta sheet more stable

in-line H bonding

Parallel strands have X H bonds, making them Y

angled, weaker

Secondary structures known as turns can be:

beta or gamma

Connects ends of two adjacent segments of an antiparallel Beta sheet

Beta turn

Beta turns involve how many residues

4

Type I Beta turns have a characteristic X residue at the #Y position

P2

Type II Beta turns have a characteristic X residue at the #Y position

G3

Beta turns span how many residues total

4

Beta turns are formed by hydrogen bonds between which resiudes

1 and 4

Gamma turns span how many residues

3

Both B and G turns are Xº

180

Gamma turns have a characteristic X amino acid at the #Y residue

P2

Plotting phi and psi angles make a _________ plot

Ramachandran

Label A

Antiparallel B sheet

Label B

Parallel B sheet

Label C

Collagen triple helix

Label D

Right twisted B sheet

Label E

Left handed alpha helix

Label F

Right handed alpha helix

Label G

Forbidden angle

The top right quadrant of a Ramachandran plot contains what secondary structure

Left-Handed Helix

The bottom left quadrant of a Ramachandran plot contains what secondary structure

Right handed alpha helix