STORY

of
BIOCHEMISTRY
for
BIOTECHNOLOGY
Biochem. for Biotech. 1
CHEMISTRY OF LIFE

Elements: simplest form of a substance -

cannot be broken down any further without
changing what it is.
Atom: the actual basic unit - composed of
protons, neutrons, and electrons.

Biochem. for Biotech. 2

ATOM
Just like cells are the basic unit of life, the
ATOM is the basic unit of matter.
They are very small. If placed side by side
one million would stretch a distance of 1cm.
The atom is made up of 3 particles.
Particle Charge
PROTON +
NEUTRON NEUTRAL
ELECTRON -

Biochem. for Biotech. 3

 Electrons are not present within the atom, instead
THEY REVOLVE AROUND THE NUCELUS OF THE
ATOM & FORM THE ELECTRON CLOUD.
Draw a helium atom. Indicate where the protons,
neutrons and electrons are

NEUTRONS
PROTONS
-
+ +
ELECTRONS -
ATOMIC No. = 2 (PROTONS)
ATOMIC MASS = 4
(PROTONS & NEUTRONS)
Biochem. for Biotech. 4
 ISOTOPES
Atoms of the same element that HAVE A
DIFFERENT NUMBER OF NEUTRONS
Some isotopes are radioactive. This means that their
nuclei is unstable and will break down at a
CONSTANT RATE over time.
There are several practical uses for radioactive
isotopes:
1. CARBON DATING
2. TRACERS
3. KILL BACTERIA / CANCER CELLS
Biochem. for Biotech. 5
Biochem. for Biotech. 6
COMPOUNDS
a substance formed by the chemical combination of
2 or more elements in definite proportions
Ex: water, salt, glucose, carbon dioxide

Biochem. for Biotech. 7

Biochem. for Biotech. 8
 The cell is a COMPLEX CHEMICAL FACTORY
containing some of the same elements found in
the nonliving environment.

carbon (C), hydrogen (H), oxygen (O), and

nitrogen (N) are present in the greatest
percentages.

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TWO TYPES OF COMPOUNDS

Organic - Contain C, H, and O in some ratio

(usually referred to as chemicals of life)
Carbohydrates, Proteins, Lipids, Nucleic Acids

Inorganic - usually "support" life - no specific

ratio of C, H, and O
Water (H2O), Carbon dioxide (CO2)

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CHEMICAL BONDS

Chemical bonds hold the atoms in a molecule

together.

There are 2 types of chemical bonds IONIC and

COVALENT.

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IONIC BONDS
Occur when 1 or more electrons are TRANSFERRED
from one atom to another.
When an atom loses an electron it is a POSITIVE
charge.
When an atom gains an electron it is a NEGATIVE
charge.
These newly charged atoms are now called IONS
Example: NaCl (SALT) = Na+ Cl-

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Biochem. for Biotech. 13
COVALENT BONDS

Occur when electrons are SHARED by atoms.

These new structures that result from covalent bonds
are called MOLECULES.
In general, the more chemical bonds a molecule has
the more energy it contains.
SHARING IS CARING!

Biochem. for Biotech. 14

MIXTURES
Water is not always pure. It is often found as part of a
mixture.
A mixture is a material composed of TWO OR MORE
ELEMENTS OR COMPOUNDS THAT ARE
PHYSICALLY MIXED.
Ex: salt & pepper mixed, sugar and sand can be easily
separated

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SOLUTION
Two parts:
SOLUTE SUBSTANCE THAT IS BEING
DISSOLVED (SUGAR / SALT).
SOLVENT - the substance in which the solute
dissolves.
Materials that do not dissolve are known as
SUSPENSIONS.
Blood is the most common example of a suspension.
Cells & other particles remain in suspension.

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FORMULA
The chemical symbols and numbers that compose a
compound ("recipe").
Structural Formula Line drawings of the
compound that shows the elements in proportion
and how they are bonded.

Molecular Formula the ACTUAL formula for a

compound
C2H6O = C2H5OH
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ACIDS & BASES
Acids: always (almost) begin with "H" because of the
excess of H+ ions (hydrogen)
Ex: lemon juice (3), stomach acid (1.5), acid rain (4.5),
normal rain (6)
Facts about Acids
Acids turn litmus paper BLUE and usually taste
SOUR.
You eat acids daily (coffee, vinegar, soda, spicy
foods, etc)
Biochem. for Biotech. 18
ACIDS & BASES
Bases: always (almost) end with -OH because of the
excess of hydroxide ions (Oxygen & Hydrogen)
EX: oven cleaner, bleach, ammonia, sea water, blood,
pure water
Facts about Bases
Bases turn litmus BLUE.
Bases usually feel SLIPPERY to touch and taste
BITTER.

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Neutralization Reactions

When an acid reacts with a base to produce a

salt and water.

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pH SCALE
measures degree of substance
alkalinity or acidity

Ranges from 0 to 14

0 5 strong acid
6-7 neutral
8-14 strong base

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 The goal of the body is to maintain HOMEOSTASIS
(neutrality) to do this when pH is concerned, we
add weak acids & bases to prevent sharp changes in
pH.
These are called BUFFERS

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And now for the Biochemistry
portion of things.

Biochem. for Biotech. 23

Biochem. for Biotech. 24
CARBOHYDRATES

Living things use carbohydrates as a key source of

ENERGY.
Plants use carbohydrates for structure (CELLULOSE)
include sugars and complex carbohydrates (starches)
contain the elements carbon, hydrogen, and oxygen (the
hydrogen is in a 2:1 ratio to oxygen)

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Monosaccharides (simple sugars)
all have the formula C6 H12 O6
all have a single ring structure
(glucose is an example)

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Glucose and fructose have the same molecular formula
C6 H12O6, but they have different structural formulas

27
Disaccharides (double sugars)
all have the formula C12 H22 O11
sucrose (table sugar) is an example

Biochem. for Biotech. 28

Polysaccharides

Formed of three or more simple sugar units.

Glycogen - animal starch stored in liver & muscles.
Cellulose - indigestible in humans - forms cell walls
Starches - used as energy storage.

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 How are complex
carbohydrates formed and
broken down?

Biochem. for Biotech. 30

Dehydration Synthesis
Combining simple molecules to form a more complex
one with the removal of water
ex. monosaccharide + monosaccharide ---->
disaccharide + water
C6H12O6 + C6H12O6 ----> C12H22O11 + H2O

Polysaccharides are formed from repeated

dehydration syntheses of water.
They are the stored extra sugars known as starch.

Biochem. for Biotech. 31

Hydrolysis
Addition of WATER to a compound to split it into
smaller subunits :
also called chemical digestion
ex. disaccharide + H2O ---> monosaccharide
+ monosaccharide

C12 H22 O11 + H2 O ---> C6 H12 O6 + C6 H12 O6

Biochem. for Biotech. 32

 glucosidase

Biochem. for Biotech. 33

Lipids (Fats)
Fats, oils, waxes, steroids
Chiefly function in energy storage, protection, and insulation.
Contain carbon, hydrogen, and oxygen but the H:O is not in a
2:1 ratio.
Tend to be large molecules -- an example of a neutral lipid is
below.

Biochem. for Biotech. 34

 Neutral lipids are formed from the union of one glycerol
molecule and 3 fatty acids.
3 fatty acids + glycerol ----> neutral fat (lipid)
Fats -- found chiefly in animals
Oils and waxes -- found chiefly in plants
Oils are liquid at room temperature, waxes are solids
Lipids along with proteins are key components of cell
membranes.
Steroids are special lipids used to build many
reproductive hormones and cholesterol.
Biochem. for Biotech. 35
Membrane
Formation

Biochem. for Biotech. 36

Biochem. for Biotech. 37
The Urey-Miller experiment (1950)

Some amino acids could be produced.

38
CO2 CO + [O] (atomic oxygen)
CH4 + 2[O] CH2O + H2O
CO + NH3 HCN + H2O
CH4 + NH3 HCN + 3H2

The formaldehyde, ammonia and HCN then react to form amino acids and
other biomolecules:

CH2O + HCN + NH3 NH2-CH2-CN + H 2O

formaldehyde cyanide ammonia aminoacetonitrile water

NH2-CH2-CN + 2H2O NH3 + NH2-CH2-COOH

aminoacetonitrile water ammonia glycine

Furthermore, water and formaldehyde can react, via Butlerov's reaction to

produce various sugars like ribose.
PROTEINS
contain the elements carbon, hydrogen, oxygen, and
nitrogen.
Composed of many amino acid subunits.
It is the arrangement of the amino acid that forms the
primary structure of proteins.
The basic amino acid form has a carboxyl group on
one end, a methyl group that only has one
hydrogen in the middle, and a amino group on the
other end.
Attached to the methyl group is a R group.
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R GROUP IS ANY GROUP OF
ATOMS THIS CHANGES THE
PROPERTIES OF THE
PROTEIN.

Biochem. for Biotech. 41

Biochem. for Biotech. 42
FUNCTIONAL GROUPS
There are certain groups of atoms that are frequently
attached to the organic molecules we will be studying, and
these are called functional groups.
These are things like hydroxyl groups which form alcohols,
carbonyl groups which form aldehydes or ketones,
carboxyl groups which form carboxylic acids, and amino
groups which form amines.

carbonyl group
Biochem. for Biotech. 43
Major Protein Functions

Growth and repair

Energy
Buffer -- helps keep body pH constant

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Dipeptide
formed from two amino acid subunits
Formed by the process of Dehydration Synthesis
amino acid + amino acid ----- dipeptide + water

Biochem. for Biotech. 45

Hydrolysis of a dipeptide
Breaking down of a dipeptide into amino acids
dipeptide + H2O ---> amino acid + amino acid

Biochem. for Biotech. 46

Polypeptide (protein)
Polypeptide composed of three or more amino acids
linked by synthesis reactions.
Examples of proteins include insulin, hemoglobin,
and enzymes.
There are an extremely large number of different
proteins.
The bases for variability include differences in the
number, kinds and sequences of amino acids in the
proteins.
Biochem. for Biotech. 47
Structure of Proteins
Primary Structure

48
Biochem. for Biotech. 49
 Secondary Structure
Alpha Helix
A helix can turn right or
left from N to C terminus
only right-handed are
observed in nature as this
produces less clashes
All hydrogen bonds are
satisfied except at the
ends = stable

50
Alpha Helix

There are 3.6 residues

per turn
A helical wheel will
outline the surface
properties of the helix

51
Beta Sheets

52
 Other Secondary
Structures Loop or Coil
Often functionally significant
Different types
Hairpin loops (aka reverse turns) often
between anti-parallel beta strands
Omega loops beginning and end close
(6-16 residues)
Extended loops more than 16 residues

53
 Tertiary Structure

Proteins exist in an aqueous environment where hydrophilic residues tend to

group at the surface and hydrophobic residues form the core
Polar residues
Ion pairs interactions
Disulphide linkages between cysteines form the strongest

Fold
Domain
Motif

myoglobin
dihydrofolate reductase
54
Quaternary Structure

Immunoglobulin
55
Quaternary Structure

Heme

Hemoglobin

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Quaternary Structure
complex structure

Biochem. for Biotech. 57

NUCLEIC ACIDS
in all cells
composed of NUCLEOTIDES
store & transmit heredity/genetic information
Nucleotides consist of 3 parts:
1. 5-Carbon Sugar
2. Phosphate Group
3. Nitrogenous Base

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 Watson And Crick

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Rosalind Franklin
Copyright Cmassengale 60
Nucleic Acids

Copyright Cmassengale 61
Nitrogen Base
(A) (G)

(C) (T)

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DNA (deoxyribonucleic acid)
contains the genetic code of instructions that direct a
cell's behavior through the synthesis of proteins.
found in the chromosomes of the nucleus (and a few
other organelles).

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RNA (ribonucleic acid)
directs cellular protein synthesis
found in ribosomes & nucleoli

Biochem. for Biotech. 64

 DNA Organization
E. Coli genome ~ 4 million bp 1.2 mm Human genome ~ 6 billion bp 2000 mm
E. Coli dimensions ~ 2 m3 Nucleus dimensions ~ 750 m3
 DNA
organization
in
Eukaryotes
Human Chromosome
Complex of DNA and protein is called chromatin
44 homologous chromosomes and 2 sex chromosomes
Complementary DNA with different Dyes
The arrangement of the full chromosome set is called karyotype
Banding Pattern of
human chromosomes
Giemsa Staining
Green line regions:
centromeres
The organization of genes of a human chromosome
The size of bacterial chromosomes ranges from 0.6 -10 Mbp, and
the size of Archael range from 0.5 - 5.8 Mbp, whereas Eukaryotic
chromosomes range from 2.9 - 4,000 Mbp.
CHEMICAL REACTIONS
a process that changes one set of chemicals into
another set of chemicals.
REACTANTS elements or compounds that enter into
a chemical reaction.
PRODUCTS elements or compounds that are
produced in a chemical reaction.
Chemical reactions always involve the breaking of
bonds in reactants and the formation of new bonds in
products.
Biochem. for Biotech. 71
 In a reaction, energy is either TAKEN IN
(ENDOTHERMIC) or GIVEN OFF
(EXOTHERMIC)

Can you think of an everyday example of each

type of reaction?

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Enzymes and Enzyme Action
catalyst: inorganic or organic substance which speeds
up the rate of a chemical reaction without entering the
reaction itself.
enzymes: organic catalysts made of protein.
most enzyme names end in ase.
enzymes lower the energy needed to start a chemical
reaction. (activation energy).
begin to be destroyed above 45C. (above this
temperature all proteins begin to be destroyed).
Biochem. for Biotech. 73
It is thought that, in order for an enzyme to affect the rate of
a reaction, the following events must take place.
1. The enzyme must form a temporary association with the
substance or substances whose reaction rate it affects.
These substances are known as substrates.
2. The association between enzyme and substrate is thought to
form a close physical association between the molecules and
is called the enzyme-substrate complex.
3. While the enzyme-substrate complex is formed, enzyme
action takes place.
4. Upon completion of the reaction, the enzyme and product(s)
separate. The enzyme molecule is now available to form
additional complexes.
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How do enzymes work?
substrate: molecules upon which an enzyme acts

The enzyme is shaped so that it can only lock up with

a specific substrate molecule.

enzyme
substrate -------------> product

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"Lock and Key Theory"
each enzyme is specific for one and ONLY one
substrate (one lock - one key).
this theory has many weaknesses, but it explains
some basic things about enzyme function.

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Induced Fit Theory"

Restriction enzyme Mva1 (grey) is shown

wrapped around DNA (multicolored) (Kaus-
Drobek et al. 2007). Protein database ID: 2OAA.

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Biochem. for Biotech. 78
Factors Influencing Rate of Enzyme Action

1. pH - the optimum (best) in most living things is close

to 7 (neutral).
high or low pH levels usually slow enzyme activity.
A few enzymes (such as gastric protease) work best
at a pH of about 2.0

Biochem. for Biotech. 79

2. Temperature - strongly influences enzyme activity
optimum temperature for maximum enzyme function is
usually about 35-40 oC.
reactions proceed slowly below optimal temperatures
above 45 oC most enzymes are denatured (change in
their shape so the enzyme active site no longer fits
with the substrate and the enzyme can't function)

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Biochem. for Biotech. 81
3. Concentrations of Enzyme and Substrate
When there is a fixed amount of enzyme and an
excess of substrate molecules -- the rate of reaction
will increase to a point and then level off.

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Cofactors

Cofactors are nonprotein enzyme helpers.

Coenzymes are organic cofactors.
Enzyme kinetics
MichaelisMenten LineweaverBurk
model plot

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Enzyme Inhibitors

Competitive inhibitors bind to the active site of an enzyme,

competing with the substrate.
Noncompetitive inhibitors bind to another part of an enzyme,
causing the enzyme to change shape and making the active
site less effective.
 A substrate can Substrate
bind normally to the
active site of an Active site
enzyme.

Enzyme

Normal binding

A competitive
inhibitor mimics the
substrate, competing Competitive
for the active site. inhibitor

Competitive inhibition

A noncompetitive
inhibitor binds to the
enzyme away from the
active site, altering the
conformation of the
enzyme so that its
active site no longer
Noncompetitive inhibitor
functions.
Noncompetitive inhibition
Enzyme Inhibitors

MichaelisMenten model LineweaverBurk plot

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Enzyme Inhibitors

Competitive inhibition

Biochem. for Biotech. 88

Feedback Inhibition

In feedback inhibition, the end product of a metabolic pathway

shuts down the pathway.
Feedback inhibition prevents a cell from wasting chemical
resources by synthesizing more product than is needed.
 Initial substrate
(threonine)
Active site
available Threonine
in active site

Enzyme 1
(threonine
Isoleucine deaminase)
used up by
cell
Intermediate A
Feedback
inhibition Enzyme 2
Active site of
enzyme 1 cant
bind Intermediate B
theonine
pathway off
Enzyme 3

Intermediate C
Isoleucine
binds to Enzyme 4
allosteric
site
Intermediate D

Enzyme 5

End product
(isoleucine)
 Summary Biomolecules Structure
Anabolic

Building block Macromolecule

Simple sugar Polysaccharide
Amino acid Protein (peptide)
Nucleotide RNA or DNA
Fatty acid Lipid
Catabolic

91