protein modeling cram

Arginine

R

Asparagine

N

Aspartate (aspartic acid)

D

Glutamine

Q

Glutamate (glutamic acid)

E

Lysine

K

Phenylalanine

F

Tryptophan

W

Tyrosine

Y

Selenocysteine

U

Pyrrolysine

O

Asx (Asp or Asn)

B

Glx (Glu or Gln)

Z

Unknown amino acid (Xaa)

X

Leu or Ile (Xle)

J

Only amino acid with NO L/D isomers

Glycine — achiral, side chain is just H

Amino acid that forms disulfide bonds

Cysteine — two SH groups oxidize into an S–S bridge

How a peptide bond forms

Dehydration synthesis — carboxyl C of one AA to amino N of the next, releasing H2O

FASTA sequence reads

N-terminus → C-terminus, left to right

Alpha helix hydrogen bond

C=O of residue i to N–H of residue i+4 (3.6 residues per turn)

Hydrophilic one out of Leu / Val / Pro / Thr

Threonine (the other three are nonpolar)

Inside of a globular protein (core)

Hydrophobic amino acids

Carbons in each backbone unit

2 (the alpha carbon + the carbonyl carbon)

Four levels of protein structure

Primary, secondary, tertiary, quaternary

Secondary structure is held together by

Hydrogen bonds

Beta sheets belong to which level

Secondary structure

Isoelectric point

The pH where the amino acid has zero net electrical charge

Interactions that hold a folded protein together

Hydrogen bonds, ionic/salt bridges, hydrophobic effect, disulfide bridges, van der Waals (London dispersion), pi-pi, cation-pi

Parts of a nucleotide

Nitrogenous base + phosphate + five-carbon sugar

The four DNA bases

A = adenine, T = thymine, G = guanine, C = cytosine

The purines

Adenine and Guanine ("Pure As Gold")

Cytosine always pairs with

Guanine

CRISPR stands for

Clustered Regularly Interspaced Short Palindromic Repeats

CRISPR-Cas9's guide strand is made of

RNA (not DNA)

PAM stands for

Protospacer Adjacent Motif

CRISPR-Cas systems are found in

Bacteria and archaea

Cas9's class and type

Class 2, Type II

Type I-E CRISPR's class

Class 1

The three CRISPR steps in order

1. Adaptation (viral DNA saved as spacers), 2. crRNA production (transcribe + cut into guides), 3. Targeting (guide finds the match, Cas9 cuts)

Michaelis-Menten equation

V₀ = Vmax[S] / (Km + [S])

Vmax depends on

Enzyme concentration (Vmax = kcat·[E]) — NOT substrate concentration

Km when V₀ = Vmax/4

3[S]

Why the MM derivation ignores the reverse reaction

At t ≈ 0, [product] ≈ 0, so its rate ≈ 0

Lineweaver-Burk: competitive inhibition

Y-intercept (1/Vmax) stays the SAME

Lineweaver-Burk: y-intercept changes

Mixed or uncompetitive inhibition

Why allosteric enzymes break Michaelis-Menten

Substrate can bind outside the active site too — the ES complex isn't the only complex

Allosteric velocity curve shape

Sigmoidal (S-shaped), not hyperbolic

Positive cooperativity means

Binding affinity INCREASES as more substrate binds

The two allosteric models

Sequential and concerted

Cytidine deaminase converts

Cytidine → uridine (C → U)

After base editing, a GC pair becomes

An AT pair

BE1 stands for

Base Editor 1

Cytidine deaminase prefers

RNA over DNA

CDA gene mutation is linked to

Decreased sensitivity to cytosine arabinoside (a childhood leukemia drug)

A lane with no cleavage bands means

That sgRNA didn't cut — no indels detected

Estimating indel frequency from a gel

Compare the cleavage product sizes to the original band size

How accidental indels happen with CRISPR

The sgRNA matches another site in the genome (off-target)