Biochem Comp 1

Hydrogen Bonding

occurs between an electron rich atom that has a lone pair of e- (N / O) and an e- deficient hydrogen

What is unique to H bonds?

An interaction of orbitals takes place

H Bond Donor

The group in which (x-h) are bound covalently. X has a high attraction for e- (aka it donates an Hydrogen)

H Bond Acceptor

group that provides an e- rich atom (accepts H)

OH and NH2 function as both

H bond donors and acceptors

What increases solubility?

• ability to form H bonds

• ionized (polar) functional groups

Hydrophobic effect

separation of hydrophobic molecules and water

Covalent Bonding

• strongest INTRAmolecular force

• formed when 2 atoms with half filled orbitals overlap and e- align with opposite spins

Ionic Bonding

when 2 ions with opposite charges are attracted to form a bond

Van Der Waals Interactions

very weak interactions that occur between hydrophobic regions of different molecules

How do VDW occur?

Atoms have small dipoles which influence dipoles in other molecules. The strength of these interactions depends on distance.

Thermodynamics

studies the spontaneity of a chemical reaction

Kinetics

study of the speed of a rxn

A favorable reaction…

heat is given off —> products have less energy and less complex (more random)

G < 0

proceeds to right (products) —> exergonic and spontaneous

G > 0

proceed to left (reactants) —> Endergonic

Alkanes and Alkenes

• Only intermolecular bonding in VDW interactions

• Can’t bond with water, but dissolves in lipids

An alkane with a 1-4 carbon backbone is in

gaseos state

An alkane with a 5-20 carbon backbone is

liquid

Alkanes are more stable than alkenes due to alkenes haveing a double bond

true

Aromatic Rings

• hydrophobic structures that mainly form VDW interactions

• have a cloud of e- above and below

• this cloud allows them to form strong VDW

Cation - PI

[in aromatics] bond between an e- rich pi system and cation

Pi-PI interactions

only between rings in close proximity

Alcohols

OH that is attached to an aliphatic (chain) carbon

Phenols

OH attached directly to aromatic

Alcohols and Phenols

• have an OH group that participates in H Bonds

• Water soluble

Alcohols are generally stable, unless in the presence of

oxidizing agents

Ketones and aldehydes

Both contain a carbon atom that is attached to an oxygen atom through a double bond (carbonyl)

In Ketones, the carbonyl can create 2

H bonds while being a H bond acceptor

Ether

R - O - R

• low boiling point and chemically inactive

• Electrons are shielded, leading to low water solubility and low HBA

Carboxylic Acids

• carbonyl + hydroxy; —> HDB + HBA

• can form ionic interactions while in carboxylate ion state, which is a good binding ligand for metal ions

Amines

• most common funct. group in medicine due to balance hydrophilicity (passes membranes)

Primary and secondary amines have N-H groups that can

partake in H bonding

The ionization of an amine group leds to the inability to HBA. It can still function as a HBD, which is

stronger

Quaternary Ammonium Salts

• N is bound to 4 carbons through covalent bonds

• stable compounds

• common in drugs because it is water soluble (polar)

Esters

carboxylic acid derv. where the H is replaces with an alkyl.

• can only HBA at carbonyl O

In vivo, esters are suspectable to

esterase enzymes (hydrolysis)

Intramolecular cyclization of OH + carboxylic acid lead to

lactone formation

Amides

• result from combining polar carboxylic acid with weakly polar primary and secondary amine or ammonia

• Peptide bond does not rotate

• stable

Amides can from

2 H bonds where the carbonyl acts as a HBA

Intramolecular cyclization of amides form

lactams

Electrolytes

strong electrolytes are completely charged when dissolved in water (NaCl —> Na+ Cl - )

Acid

proton donor (H donor)

Base

Proton acceptor

A strong acid

dissociates completely in a solution

Strong bases

dissociates completely in a solution

Ka is the measure of

the strength of an acid

The stronger the acid,

the higher the Ka value

The lower the pKa value

the stronger the acid

Weak acids are described with pKa, which is equal to

-log Ka

Ka =

[H3O+] [A-] / [HA]

The stronger the base,

the higher the KB

The weaker the base, the

higher the pkb

pkw =

pka + pkb; 14

What is pH

was to quantify acidity or basicity of solution [pH = -log [H3O+]

A-

conjugate base

HA

conjugate acid

Henderson-Hasselbalch equation

pH = pKa + log (A/HA)

Buffer

combination of substances that when added to an aqueous solution, allows this solution to maintain a desired pH at a relatively constant level

Components of a buffer system

• weak acid and conjugate base (acetic acid and sodium acetate)

• weak base and conjugate acid (ammonia and ammonium chloride)

How do buffers work?

When additional base is added to a buffer system, the weak acid reacts to neutralize it (and vice versa)

Effective buffering range is

pKa ± 1 ph unit

Major Functions of Carbohydrates

• component of nucleic acids

• cell recognition

• structural support

Monosaccharides

single sugar units

Oligosaccarides

composed of 3-10 monos linked together

D sugars have the OH on the

right

L sugars have the OH group on the

left

Most monosaccharides are D sugars

true

Anomeric carbon

the carbonyl carbon that becomes a new chiral center after ring formation

Alpha anomeric carbon

OH below the ring

Beta anomeric carbon

OH above the ring

The anomeric carbon on glucose, mannose, and galactose is

carbon 1

The anomeric carbon on fructose is

carbon 2

Disaccharides have a glycosidic bond which is a

covalent linkage between 2 monos (can be alpha or beta)

Glycogen

polysacc —> animal storage for excess glucose

Glycogen unit

alpha 1,4 linked glucose units

Starch

amylose and amylopectin

amylose units

alpha 1,4 linked glucose units

amylopectin

alpha 1,6 linked

Cellulose

• not water soluble

• can’t be digested

Cellulose unit

beta 1,4 linked glucose

Reducing sugars

possess a free anomeric carbon that can reduce mild oxidizing agents

Monos are considered

reducing sugars because they contain an aldehyde group

Fructose can act as a reducing sugar by

isomerization to an aldehyde (formed under alkaline conditions)8

Polysacc are non reducing sugars because

their anomeric carbons are involved in glycosidic bonds (unavailable to open)

Glycoproteins

monosacc combined with amino acids

N linkage

reducing sugar linked to asparagine side chain

O linkage

reducing sugar linked to serine or threonine side chains

Glycoaminoglycans

• polymers of repeating disacc

• increases water retention

• used in ECM scaffolding

Proteoglycans

specialized molecules made of a core protein attached to long sugar chains called glycosaminoglycans

Glycerol Backbones

• 3 carbon chain

• ester bonds

• energy storage

Spingosine Backbones

• 18 carbon

• amide backbone

• cell recognition, signalling

Saturated

no double bonds

Monosaturated

one double bond

Polyunsaturated

two + double bonds

In animals, double bonds are

cis and not conjugated

How are carbons numbered?

ex: C16:0 (16 carbons, no double bonds)

How are double bonds numbered?

ex. 18:2 —> 2 double bonds

How are position of double bonds numbered?

ex: 18:2 delta 9, 12 (18 carbons, 2 doubles at carbons 9 and 12 counting from COOH end

Omega Notation

counts from CH3 end —> omega 3 = first double bond is 3 carbons from methyl end