New Notes and Stuff

Kf vs Kr vs Kb

Kf = Equilibrium constant for formation (Products multiplied)
Kr = Equilibrium constant in reverse direction, dissociation (Reactants multiplied)
Kb = Boltzmann’s Constant

0th vs. first vs. second order

0th: Rate = Kf, M/s or Moles per sec
1st: Rate = Kf*[A], 1/s or s^-1
2nd: Rate = Kf*[A]*[B] or Kf*[A]², M^-1 s^-1 units

Enzyme names

Often called “Substrate” + -Ase

Enzyme Commission

EC, numbering system for enzymes (Ex: EC 3.1.1.1)

Leftmost number is responsible for cleaving bonds for rightmost number

Standard Conditions

25 C, 1 atm, 7.0 pH

Michaelis-Menton Equation

V(i) = (Vmax*[S])/(Km*[S])

[S] = Substrate concentration
V(i)/max = reaction velocity
Km = Michaelis constant

Relates reaction velocity to substrate concentration

Kcat meaning

Molecules/sec converted to product at V(max) (maximum reaction rate)
K(cat) = V(max) / initial Enzyme Concentration, or [E](0)

Michaelis Constant

K(m), K(m) = (K(2) + K(-1))/K(1)

If either K2 or K(-1) is much bigger than the other, it is the Rate Determining Step, and K(m) = K(d)

K(m)

Substrate concentration when V = 0.5*V(max)
Higher means lower affinity for substrate, and vice versa

Allosteric Enzymes

Allosteric enzymes can bind to non-substrates

Allosterism

When enzymes/proteins undergo conformational changes upon binding to ligand

Allosteric Effector

ligand that introduces conformational change

Also called “binding modulator”

Psuedo-Catalysts

Speeds up reaction, and is consumed
Known as “activator” if used in enzymes

K(i)

Inhibitor dissociation constant
K(i) = ([E]*[I])/[EI]

Class 1 Enzyme

Oxoreductases, Catalyze Electron Transfer

Class 2 Enzyme

Transferases, catalyze group transfer

Class 3 Enzyme

Hydrolases, catalyze wa

Class 4 Enzyme

Lysases, cleave C-C, C-O, C-N bonds, leaving double bonds

Class 5 Enzyme

Isomerases, transfer groups to create isomers

Class 6 Enzyme

Lygases, Form C-C, C-S, C-O, C-N bonds via condensation

Class 7 Enzyme

Translocases, Move Molecules/Ions across membranes

Holo Vs. Apoenzyme

Holoenzyme has cofactors, Apoenzyme does not

∆G vs. ∆G’

∆G is free energy at standard conditions (298 K)
∆G’ is free energy at standard conditions and 7.0 pH (Biochemical standard)

Optimal Enzyme Temp (typically)

36-37 C

Degree of Inhibition

E(i) = 1 - (V/V(0))
V = rate of inhibited reaction

V(0) = rate of uninhibited reaction

Carbohydrates

Chains of “polyhydroxyl” aldehydes/ketones in chain structure
Used as energy storage, structure, cell-cell recognition

Isomer types

Enantiomer: Isomers which are “left/right hand” of one another (L/D)

Epimer: Differ at one carbon

Carbyhydrate Building Blocks

Pectin
Amylose
Amylopectin
Glycogen

Sugar vs. Carb

Sugars are simple carbohydrates

Aldoase

Sugar with C=O at end, making Aldehyde
Ex: Glucose

Ketose

Sugar with C=O in middle of carbon chain
Ex: Fructose

D vs. L Isomers

OH on right = D isomer
OH on left = L Isomer
Must look from last chiral center (highest number)

Modulators

Ligands which change protein conformations, inhibiting or activating them

Homotropic

Multiple molecules of same ligand bind to multi-subunit protein, changing binding affinity

Heterotropic

When modulator is molecule other than normal ligand

Globulins

Soluble proteins with immune defense, transport, blood clotting functions
Roughly spherical
Soluble in dilute salts

Kd

K(off)/K(on) for ligands, dissociation equilibrium constant

Antibody regions

Variable Heavy in front of Variable Light (Immunoglobin G)
Fab region: Responsible for antigen recognition
Fc region: Responsible for activation, receptor binding

Glucose, Alpha Anomer

Glucose, Beta Anomer

Fructose, Alpha Anomer

Fructose, Beta Anomer

Pyranose

6-membered carbon ring with oxygen (Glucose)

Furanose

5-membered ring with oxygen (Fructose)

Ribose

Galactose

Fructose Fischer

Remember left = Up, right = Down

Glucose Fischer

Remember left = Up, right = Down

Epimer calculation

2^n chiral centers

Alpha-Pyranose conformation

Alpha is trans, other groups are equatorial
Alpha < Beta stability

Beta-Pyranose conformation

C1 is Equatorial or Axial Up
Beta > Alpha stability

Sugar Acids

Detoxify Liver via “Glucuronidation”
Inactivate hormones

Structural components in carbs

Sugar alcohols

(both sides)

Deoxy sugars

Sugars with -OH replaced with -H, including DNA

Amino Sugars

Have Amino/Amide Group
Found in structural components

Reducing Sugars

Sugars which become acidic as reducing agents (oxidized)

Glycotransferase

Enzyme which polymerizes monoshaccarides
Has no stop mechanism

Homopolysaccharides

Contain only 1 sugar unit,
ex: Glycogen and Starch, energy storage

Starch Structure

A1-4 “Glycosidic” bond
Hydrogen bonding between Glucoses

Heteropolysaccarides

Contain multiple sugar units
Often branched, Protein/Lipid Associated
Found in Extracellular Matrices, Connective Tissue, Mucus

Cellulose/Chitin Structure

Varies at R group (Carbon 2)

Glycoproteins

N-linked (Asn) or O-linked (Ser/Thr)
Protein with carbohydrates attached
Protein heavier than carbs
Many roles, ex: membrane proteins

Proteoglycan

Protein attached to “Glycoaminoglycan” (GAG)

Carb heavier than protein
Structural/Lubricant

Mucin/Mucoprotein

Hydrophobic protein attached to carb by “N-Acetylgalactoamine”
Often lubricants

Glyolipids

Play critical role in:
-Cell signalling
-Immunity
-Nervous System function
Usually has few sugars in carb

Lectins

Bind to sugars, are proteins

Cell-Cell recognition
Non-Enzymatic
Highly Specific
Multivalent (Binds to multiple sugar/glycoproteins at once)

Selectins

Transmembrane Glycoprotein with Sugar head
L- Leucytes (White Blood Cells)

E- Endothelial Cells
P- Platlets (blood clotting)

Fucosylation

Done by Fucosyltransferase, adds fucose to glycans, detected by Selectins

Sialylation

Done by Siayltransferases, adds sialic acid to glycans, detected by Selectins

Furanose puckering

C2 puckers for DNA
C3 puckers for RNA

Adenine

Connects to sugar at NH

Guanine

Connects to sugar at NH

Thymine/Uracil

Connects to sugar at NH

Cytosine

Connects to sugar at NH

Nucleoside

Nucleotide without Phsophate

RNA Hydrolysis

Oxygen on C2 attacks Phosphate

GAGs

GlycoAminoGlycans

Act as Lubricants

Chondritan Sulfate

Connective and Heart Tissue, flexibility

Riboses

5-carbon sugars with Aldehyde group

Nucleotide Conformation

Beta, D isomer (-OH on right)
(B1-4)

T-A vs. C-G

T-A has 2 hydro bonds
C-G has 3 hydro bonds

Hairpin

“Palindrome” can also form hairpin

Palindrome, Mirror Repeats

Cruciform

DNA only

Wattson-Crick vs. Hoogstein

Triplex DNA

Forms at low pH, lots of C/G

Tetraplex

Forms from Guanine
Forms around Potassium
Stack on one another

Long RNAs

Ribosomal RNA (rRNA)
Enhancer RNA (eRNA)
Long Intergenic RNA (lincRNA)

DNA variants

A-form: anti-anti, dehydrated
B-form: anti-anti, most common
Z-form: anti-syn, high G-C content, left handed

t-RNA

D-loop: Aminoacyl-tRNA recognition site
Anticodon Loop: Binds only to corresponding anticodon

T-loop: Allows tRNA to dock

Hyper/Hypochromic Effect

Hypo - Close base packing in DNA decreases UV absorption
Hyper - Close base packing in DNA increases UV absorption

t(m)

Temperature at which half of DNA is double stranded, half is single

Deanimation

Loss of amino group becomes O= bond on Amino Acid, ex: Cytosine to Urocil

Depurination

N glycocidic bond lost with sugar

Thymine dimers

Two thymines merge together at 5 and 6 carbons

DNA Methylation

Usually happens to Adenine/Cytosine, controls expression

NAD+

Glycolysis (Oxidative Phosphorylation), Citric Acid Cycle

Coenzyme A

Used in:
Kreb’s Cycle
Fatty Acid Oxidation/Synthesis
Amino Acid Metabolism
Thiol (-SH) is active group

cGMP

Relaxes muscles/blood cells
Maintains ion balance

cAMP

Stimulates glucose/fat breakdown
Regulates kidney water balance