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Biochemistry

Organic Chemistry

All biological molecules are built on a carbon skeleton


Functional groups give character to different classes of molecules

Characteristic features of Organic Compounds

All organic compounds contain carbon, and most contain hydrogen


bonds
Carbon always forms 4 covalent bonds and hydrogen one
Organic compounds can also contain other elements (F,Cl,Br.I) that is
called a Heteroatom

A C atom surrounded by 4 atoms = single bond


A C atom surrounded by 3 atoms = one double bond
A C atom surrounded by two atoms = a triple bond

Why carbon?

Forms 4 covalent bonds


Double and triple bonds are possible
Plays well with other atoms (H,N,O)
Can form long chains, ring structures
Shapes of Organic Molecules

An Atom surrounded by 2 groups is linear and has a bond angle of 180


degrees

An Atom surrounded by 3 groups is trigonal planar and has a bond angle


of 120

An atom surrounded by 4 groups is tetrahydral and has a bond angle of


109.5

Shortcuts
a. Condensed structures (omit most bonds and add parentheses)

b. Skeletal structures
each vertex = a C atom Add H atoms to get 4 bonds per C atom

Why are Hydrocarbons unreactive and water-insoluble?

It has no functional groups


no polarity

Functional Groups

Combinations of atoms that have characteristic chemical or physical


properties

They determine: how a molecule can react, what other molecules it


can interact with and how soluble it is in water

Look for heteroatoms: O,N,S,P (any carbon-containing group, or rest


of structure)
compound chemical structure example 3D structure
functional group

Thiol RSH SH
sulfhydryl group

Phosphate ROPO32 nucleotide

Phosphoryl Group
Functional groups make organic compounds polar
Polar or ionic compounds are more soluble in water
All polar functional groups can from hydrogen bonds
All charged functional groups can form ionic bonds with oppositely
charged groups
Different classes of biological molecules contain different types of
functional groups

Hydrocarbons

Alkanes only C-C single bonds, no functional group (CH3CH3


Ethane)
Alkenes have C-C double bond as functional group (CH2=CH2)
Alkynes have C-C triple bond as functional group

Compounds containing a C=O Group

Aldehyde has H atom bonded directly to Carbonyl carbon


Carboxylic acid OH group directly bonded to carbonyl carbon
Ester OR group directly bonded to carbonyl carbon

pH

a. Acid and Bases

An acid can donate a proton, a base can accept a proton


Water can act as acid or base:

Strong acids completely dissociate in aqueous solution

Weak acids reach equilibrium, so some molecules are HA, some are A-

In biological system, the strongest acid is H3O+, and the strongest base
-
is OH
Why?

b. Meaning of pH

H2O can dissociate into ions


pH affects the structures of acidic and basic functional groups in
biological molecules

c. effect of pH on amino and carboxyl groups

Carboxyl groups act as acids (we usually see them after they have
given up a proton)

Equilibrium point for most carboxylic acid groups is about 2-4


Carboxylate group is half dissociated at that pH (half is
protonated other half is unprotonated)

At cellular pH (neutral), most carboxylic groups are


unprotonated

If protons are added pH decreases, carboxylate ion can be


protonated (RCOO- RCOOH)
Amino groups act as bases (we usually see them after they have
accepted a proton)

Equilibrium point for most amino groups is about 9 pH


Amino group is half dissociated at that pH

If protons are removed pH increases, amino group can become


unprotonated (RNH3 + RNH2)

d. Buffering

Cells and biological fluids contain multiple weak acids/bases that react
with (or buffer) excess H+ or OH- to maintain constant pH

This keeps functional groups in biological molecules in the proper ionic


state

pH of blood is maintained at 7.4 in part through the bicarbonate buffering


system
Biological Molecules

Monosaccharides

1. Intro to Carbohydrates
2. Monosaccharide Structures
3. Cyclic Forms
4. Monosaccharide reactions

A. Carbohydrates (sugars, saccharides)

General Formula (CH2O)n


Multiple hydroxyl groups
Mono-,di-, polysaccharides
Metabolic fuel, structure, cell markers

Are polyhydroxy aldehydes and ketones

Reducing group

Monosaccharides are simple sugars (Glucose, fructose)


Dissacharides are two monosaccharides joined together
(Lactose)
Polysaccharides have three or more monosaccharides joined
(Starch)

Monosaccharides

have 3-6 carbons with a carbonyl group at either the terminal carbon
Monosaccharides with a carbonyl group at C1 are aldehydes called aldoses
Monosaccharides with a carbonyl group at C2 are ketones called ketoses

Structure of Monosaccharides

aldose or ketose
tri-,tetr-,pent,-hexose
lots of constitutional isomers (same formula, different arrangements of
atoms)

Chirality

When C is bonded to 4 different groups, it has handedness (D and L)


The 2 isomers are enantiomers, nonsuperimposable mirror images
Fischer projection

Horizontal bonds (wedges) point out


Vertical bonds (dashes) point back

Most naturally occurring monosaccharides have the D configuration


A D monosaccharide has the OH group on the chirality center farthest
from the carbonyl on the right
An L monosacchride has the OH group on the left

Biological polymers

Assembly: directly or indirectly due to condensation (dehydration) rxn


Dissasembly: usually hydrolysis
Condensation reaction involves 2 functional groups H2O is a reaction
product (H2O comes out)
Two molecules (monomers) condense to form a covalent bond
(polymer)

What is left of the monomer is called a residue


The bond is broken in a hydrolysis reaction H2O is a reactant (H2O
goes in)

Condensation:

2 monosaccharides condense to form a dissacharide. The bond linking the


monosaccharide residues is a glycosidic bond.

2 amino acids condense to form a peptide bond. The bond linking the
amino acid residues is a peptide bond.

Hydrolysis:

3. Cyclic Forms of Monosaccharides

Reaction of carbonyl group and hydroxyl group forms a hemiacetal


Carbon bonds to OH and OR group
The carbon atom that is part of the hemiacetal is a new chirality center,
called anomeric carbon

The alpha anomer has the OH group drawn down, below the fint
The beta anomer has the OH group drans up, above the ring

Cyclization is reversible, yields two possible products alpha and beta


anomer freely interconvert (unless another group condenses with the
OH)

Cyclic drawing is a Haworth projection

Ketoses also cyclize:


5. Monosaccharide Reactions

Functional groups can undergo chemical reactions

convert carbonyl to hydroxyl


Convert carbonyl to carboxyl
attach amino or amide group

All aldoses are reducing sugars

2. Dissacharides

Composed of two monosaccharides


Hemiacetal of 1st sugar reacts with hemiacetal of 2nd sugar or hydroxyl
group
Glycosidic bond can have alpha or beta configuration, no
interconversion
Compound is called a glycoside
Disaccharides are often encountered as the products of polysaccharide
digestion

Lactose: source of metabolic fuel for young mammals


Sucrose: transportable form of sugar in plants

6. Polysaccharides

Are homopolymers (same 1 or 2 residues, same glycosidic bond)

Fuel storage: starch, glycogen


Structural support: cellulose (&chitin), peptidoglycan
Linkage matters!
Shapes and properties of polymers differ
Different enzymes catalyze hydrolysis of alpha and beta glycosidic
bonds

Peptidoglycan

Cross-linked polysaccharide and polypeptide chains


Forms a capsule around bacteria cell membrane, protects and
shapes cell

Oligosaccharides

Oligo = few
shorter chains of different monosaccharides residues
Function as markers on cell surface
7. Glycosaminoglycans

Polysaccharides of repeating disaccharides


Can be enormous, highly hydrophilic
Function as lubricants (mucus), space-fillers, and shock absorbers

Biofilm

Extracellular material (mostly polysaccharide) produced by


populations of bacteria
Protects cell from being washed away, allows some metabolic
cooperation
Can be a problem when it forms on catheters, tubes, etc.

Amino Acids

1. Structures

Amino group (NH2)


Carboxyl group (COOH)
side chain (R group): 20 different kinds
bonded to alpha carbon

Amino acids with an additional COOH group are called acidic amino
acids
Those with an additional basic N atom in the side chain are called
basic amino acids
All others are neutral amino acids

Amino acids never exist in nature as neutral molecules


Since they contain a base and an acid (COOH), proton transfer from the
acid to the base forms a salt (zwitterion, that contains both negative and
positive charge)
Zwitterions are water soluble and have high melting points
2. Biological Roles of Amino Acids

Building blocks for polypeptide chains


Source of C and N atoms to build nucleotide bases
Metabolic fuel
Precursors of some hormones and neurotransmitter

MSG (monosodium glutamate)

binds to umami taste receptors

3. Amino Acid Derivatives

Neurotransmitter: a chemical signal from one neuron to another (Is


packaged in vesicles inside a presynaptic cell, is released, and diffuses to
receptor on postsynaptic cell)

Hormone: a substance produced by one tissue that affects other tissues.


Most hormones travel throughout body in the bloodstream
Dopamine:

In brain, controls movement and emotions


Parkinson disease: loss of neurons that make dopamine. Treat by giving
L-dopa

Epinephrine (adrenalin)

Hormone released by adrenal glands


Triggers fight-or-flight response
Hypertension treatment: block the epinephrine receptor to prevent a
stressed heart from working even harder

Serotonin:

Neurotransmitter that helps regulate mood, sleep and activity levels


Some drug prolong its effects by preventing re-uptake by presynaptic
cell

Histamine:

Local signal released by mast cells (type of WBC in skin, resp. tract,
GI tract)
Triggers bronchoconstriction, mucus production, vasodilation and
increased vascular permeability
Part of immune response to bacteria and parasites (and allergens)
4. Peptide Bonds

Condensation reaction involving carboxyl group and amino group


Chain of amino acid residues has a backbone, with R groups (side
chains) sticking out
Peptide = short chain, polypeptide = long chain
A protein molecule may contain more than one polypeptide chain
Conformation of peptide is limited due to partial double-bond
character of peptide bond

Amino Acid with free H3N+ group on alpha carbon is called N-


terminal amino acid
Amino acid with free COO- group on alpha carbon is called C-
terminal amino acid
Partial double-bond character of peptide bond limits rotation. This
constrains the conformational freedom of the polypeptide chain, so it tends
to fold in certain ways

Proteins
Configuration = depends on covalent bonding (cannot be changed unless
bonds are broken)

Conformation = depends on bond rotation (changes as chain flexes; involves


ionic interactions, H bonds etc)

1. Structure

Each protein chain has a unique shape, described by four structural


levels: primary, secondary, tertiary, quaternary

Primary Structure

Unique sequence of amino acids


Primary structure determines all higher-level structure

Secondary Structure

Results from hydrogen bonding between carboxyl oxygen of one amino


acid residue and the amino hydrogen of another in a regular, repeating
fashion

Two patterns are seen: alpha helix, beta helix

Alpha helix:

right-handed, 3.6 residues per turn


H bond between 1st and 4th residues
R group point outward
Backbone represented by twisted ribbon
Example: keratin in Hair, myosin in muscle
Beta helix:

more or less planar, but pleated


H bonds between strands
R groups point up and down
backbone represented by flat arrow

Most protein structures include alpha helices, beta strands, and


irregular structure
Often only the backbone conformation is shown

Tertiary Structure

Amino acid R groups (side chains) are largely responsible for a


polypeptides three-dimensional shape

Every atom has a designated place

Polar/ionic groups are usually on surface; hydrophobic groups


interior
polar functional groups hydrogen bond with each other, and amino
acids with charged side chains can stabilize the structure by
electrostatic interactions

Disulfide bonds

Covalent linkage forms between sulfhydryl groups of two cysteine


residues
Common in extracellular proteins, where additional stability is needed
Are the only covalent bonds that stabilize tertiary structure

Quaternary Structure

Contain several polypeptide subunits


The protein subunits may be identical or different
identical = symmetrical
Example: hemoglobin
2. Fibrous Proteins

Made of extended chains or globular proteins that form extended


structures
Almost always have a structural role
often insoluble

Collagen

3 extended chains wrap around each other in a 3-stranded structure


Moslty Gly and Pro
Bundles of these form strong cables: bone, cartilage, extracellular
matrix

Keratin

2 alpha helices wrap around each other in a 2-stranded structure


fibers in nails, hair, outer layers of skin

3. Globular Proteins

Protein folds into a compact, irregular shape

4. Protein Stability and Denaturation

Folded shape of protein = native conformation


Stabilizing forces are weak (H bonds, ionic interactions, London dispersion)
and can be disrupted by changing conditions

Denaturation: loss of native structure and function


amide bonds stay, shape of protein alters

(Covalent bonds do not break when a protein is denatured)

High temperature, acid, base, salt, increase pH = can disrupt noncovalent


interactions

Heat breaks up weak London dispersion forces


Heat, acid and base disrupt hydrogen bonding interactions between polar
amino acids

makes protein less soluble in water, as hydrophobic regions get exposed

Nucleotides and Nucleic Acids

1. Nucleosides and Nucleotides

Nucleic acids are unbranched polymers composed of repeating monomers


called nucleotides

Nucleoside = base + sugar


Nucleotide = base + sugar + phosphate(s)
nitrogenous bases

(not important as proton acceptors)


single rings: pyrimidines (cytosine, uracil, thymine)
double rings: purines (adenine, guanine)

DNA contains the bases A,G,C,T


RNA contains the bases A,G,C,U

5 carbon sugar
ribose in RNA
2-deoxyribose in DNA

In RNA, the monosaccharide is the aldopentose D-ribose


In DNA, the monosaccharide is D-2deoxyribose, an aldopentose
that lacks a OH at C2

N-glycosidic bond links base and sugar


Primes () indicate sugar atoms

anomeric carbon joins with a nitrogen atom of the base

Naming Nucleosides:

derived from a pyrimidine base: -idine


derived from a purine base: -osine

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