Chud ass class

Loop E motif

Reverse Hoogsteen AU pair, bulge important for recognition

K-turn

both types of BPing, Unpaired residues stick out(important for recognition)

Strong acid(pkA)

large Ka small pKA

pKA

-log(Ka)

Buffer region

around were pH=pKa

peptide bond

Condensation reaction forms a H bond donor(NH) and acceptor( O=C)

Peptide bond is

planar due to double bond character(trans favored)

Φ

N-A, Phi

Ψ

C-C=O, psi

at psi 165

Phi can be between -70 to -170

alpha-helix

3.6 per turn, right handed, R groups out

Helix location

often on the outside, but can be anywhere

Amphipathic helix

hydrophobic/philic sides

Helix destabilizing residues

Proline(ring), glycine(spacing)

310 helix

smaller, least favored

pi-helix

largest, 15% of proteins

b-sheets

slight right hand twist. side chain alternate above and below. long range interactions

Loops

usually polar, substrate binding and catalysis. Disordered until they bind to substrate

Helix turn helix

structural motif common in DNA binding proteins

calmodulin

Helix loop helix protein which bind Ca2+(loops binds Ca2+)

Helix loop helix

Loop is longer than a turn(helix turn helix)

Greek-Key

4 anti-parallels beta-strands connected by short turns(loop connects 3 and 4)

Beta-alpha-beta

two parralel beta-strands connected by an alpha-helix. More rigid

Coiled-Coils

2 amphipathic a-helices. homo and heterodimers(a-helices for 2 proteins coil). Left handed superstructure.(7.2)

Heptad-repeats

if i and i+7 are hydrophobic, likely coiled coils.

Coiled-coil “ ‘ “

prime indicates anti-parallels(a-d’)

Alanine

A, Ala, 2, 10

Coiled-coil specificity

Additional interactions(H-bond, charge-charge) gives coiled-coils specificity.

Four helix bundle

Almost parallels a-helices(pairs). Hydrophobic core

a-b barrels

beta-alpha-beta repeats forming a beta strand tube(helices outside)

b-barrels

barrels formed by anti-parallel beta-strands

Glycine

Gly, G. 2, 10

Valine

Val, v. 2, 10.

Leucine

Leu, L. 2, 10

Isoleucine

ile, I. 2, 10

Methionine

Met, M. 2, 9

Proline

Pro/P, P. 2, 10

Phenylalanine

Phe, F. 2, 9.

Tryptophan

Trp, W. 2, 9.

Serine

Ser, S. 2, 9.

Threonine

Thr, T. 2, 9.

Asparagine

Asn, N. 2, 9.

Glutamine

Gln, Q. 2, 9.

Tyrosine

Tyr, Y. 2, 9, 10.

Cysteine

Cys, C. 2, 10, 8.

Lysine

Lys, K. 2, 9, 10.

Arginine

Arg, R. 2, 9, 12.

Histidine

His, H. 2, 9, 6.

Aspartic acid

Asp, D. 2, 10, 4.

Glutamic acid

Glu, E. 2, 9, 4,

membrane helcies

around 20 AA long and mostly hydrophobic residues, held together by Vander walls

Exo vs Endo conformation

Closer(endo) or farther(exo) from C5

C2 vs C3

Which is sticking up(same as base)

B form

A form

DNA can pucker

at both C2 and C3

A from RNA can only pucker at

C3(due to hydroxyl)

RNA C3 endo(less stretch)

DNA C2 endo(more stretch)

B-Form DNA

Typical DNA form

Major groove

intercalation

Flat aromatic molecules are insert between bases and disrupt transcription

GU wobble base pair

Most common non-conical BPing. Stability is close to canonical AU base pair. Twists and forms a bulge(room for ion)

pseudoknot

Family A

Family B

Family c

Coaxial stacking

terminal loops allow helices to stack allowing for 3d structure

Kissing loops

Long range WC interactions between hairpins

Self-cleaving RNA

Hammerhead/Hairpin, 2’ hydroxyl cleaves backbone.

Group 1 introns

2 tetra loop receptors(L2, L9). Pseudoknot belt pulls everything together

Programmed frameshift

Pseudoknot/hairpin and slippery sequence(repeats). Ribosome stopping can cause frameshifting

internal ribosomal entry sites(IRES)

Viral RNA element which mimics eukaryotic 5’ caps

Group 1 IRES

3 pseudoknots and 2 stem loops. Domain 3 mimics AUG start codon in the p-site

Aptamer

Riboswitch binding sites(highly conserved)

Expression platform

active site, intrinsic termination site, or hides shine-Dalgarno ribosome binding site(translation).(poorly conserved)

Guanine/adenine riboswitch

Three way junction. Conserved pyrimidine can BP or base stack with G/A.(regulates G/A concentrations)

TPP riboswitch

Highly conserved and widespread. TPP bridges parallel elements.

SAM 1

4 way junction. cation pi interaction. Intrinsic termination.

SAM 2

H-type, pseudoknot. Sam stretched in the pseudoknot region

SAM 3

Same as SAM, but positive charge is stabilized by sugar and base