Introduction to Biochemistry

What is Biochemistry&
why study Biochemistry
Dr. Maryam al-ghamdi
2014
What is Biochemistry?
Simplest definition: Chemistry of the living cell
Uses basic laws of chemistry and biology to
explain processes of living cells.
Biochemistry: Biochemistry is the science
concerned with studying the various molecules
that occur in living cells and organisms and
with their chemical reactions.
Biochemistry brides the gap between
Biology
The study of the structures and
interactions of cells and organisms.
Chemistry
The study of the structure and interactions
of atoms and molecules

Why study biochemistry?

Lead us to fundamental understanding of life.
Understand important issues in medicine, health,
and Nutrition
Molecular understanding of diseases such as
diabetes, sickle cell anemia, AIDS, cancer and
Alzheimers Disease.
Goals:
To describe lifes processes using the language of
molecules applying the principles and methods
of chemistry to determine molecular structure
from which it is often possible to explain
biological function

Three areas to study:
1. Structural and
Functional Biochemistry:
Chemical structures and
3D arrangements of
molecules.
2. Informational
Biochemistry:
Language for storing
biological data and for
transmitting that data in
cells and organisms.
3. Bioenergetics:
The flow of energy in
living organisms and how
it is transferred from one
process to another
Tools to study biochemistry:

Know chemical structures and reactivates
of molecules that participate in cellular
reactions
Know biological function of cellular
molecules
Know how all of the pieces and different
pathways fit together
Use knowledge from general chemistry,
organic chemistry, and biology and apply it
to biological systems.
Biochemistry and the Organization of
Cells
Complex living organism originate from
simple elements. Carbon, hydrogen, oxygen,
sulfur, and nitrogen combine to make up
many different kind of biomolecules such as
carbohydrates, fatty acids, amino acids which
combine to make proteins.
In turn phosphorus is the most ingredients for
making DNA &RNA. A collection of
interacting molecules, becomes a cell the basic
unit of life.

Most abundant, essential for all organisms: C, N, O, P, S, H
Less abundant, essential for all organisms : Na, Mg, K, Ca, Cl
Trace levels, essential for all organism: Mn, Fe, Co, Cu, Zn
Trace levels, essential for some organisms: V, Cr, Mo, B, Al, Ga,
Sn, Si, As, Se, I,

Elements of Life

Major Classes of Biomolecules Serve As Building
Blocks For Larger Macromolecules:
1. Carbohydrates e.g. glucose, fructose, sucrose
Mainly used as sources of cellular energy
2. Lipids: commonly known as fats
Organic compounds that are not very water soluble
Used as sources of cellular energy
Components of cell membranes
3. Amino Acids:
20 natural amino acids in total
Used as building blocks for proteins
4. Nucleotides:
5 in total
Used as building blocks for DNA and RNA precursors
5. OTHER:
Vitamins: organic compounds necessary for proper growth and
development
Heme: Organometallic compound containing iron; important
for transporting oxygen in your blood stream.
Building blocks are used to create macromolecules: polymer of
several, hundreds, to sometimes millions of building blocks.
Starch and Cellulose:
polymers of glucose molecules that
differ only by how the glucose
monomers are linked.
Proteins/polypeptid:es amino
acid monomers linked together
DNA:deoxyribonucleic acid Heteropolymer of monomeric
Nucleotides o Storage of genetic information
RNA: ribonucleic acid heteropolymer of monomeric nucleotides
involved in the transfer of the genetic informationencoded by DNA
Biomacromolecules:
- self-assemble into cellular structures and complexes.
- recognize and interact with one another in specific ways to
perform essential cellular functions (e.g. membranes are
complexes of lipids and proteins)
- Interactions are weak and reversible
- Molecules have three dimensions and shapes! Much of
biochemistry relies on this fact.





Starch and Cellulose:
polymers of glucose molecules
that
differ only by how the glucose
monomers are linked.
Proteins/polypeptid: amino
acid monomers linked together
DNA:deoxyribonucleic acid
o Heteropolymer of monomeric
Nucleotides o Storage of genetic
information
RNA: ribonucleic acid
Heteropolymer of monomeric
nucleotides
Involved in the TRANSFER
of the genetic information
encoded by DNA
Building blocks are used to create macromolecules: polymer of several,
hundreds, to sometimes millions of building blocks.

ORGANISMS:
Two basic classes of organisms:
Prokaryote: Greek derivation meaning before the
nucleus
single-celled organisms include bacteria and
cyanobacteria (blue green algae)
Eukaryote: Greek derivation meaning true nucleus
contain a well-defined nucleus surrounded by a
nuclear membrane
can be single celled, such as yeasts and Paramecium,
or multicellular, such as animals and plants
We will focus on eukaryotic cells and the biochemistry that
occurs in these cells.
Similar processes occur in ALL cells, including prokaryotes.

In fact, much of the biochemistry that we understand was
first uncovered in prokaryotic systems.
Comparison of Prokaryotes and
Eukaryotes.
Definition & Classification of matter :
Matter: is anything that has mass and takes up
space. Matter also undergoes other kinds of
chemical changes &physical changes. Matter can
exist in three statesgas, liquid, and solid.
Chemistry: is the science that deals with matter
Classification:
Element: simplest form of a substance - cannot be
broken down any further without changing what it
is.
Compounds : a substance formed by the chemical
combination of 2 or more elements in definite
proportions for example : water, salt, glucose,
carbon dioxide.
Mixtures: a combination of two or more pure
substance for example :blood, soap,

SOLUTIONS
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 where
Cells & other particles remain in
suspension.

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

CHEMICAL BONDS


Chemical bonds hold the atoms in a
molecule together.
There are Two Major Types of Chemical
Bonds of chemical bonds:
IONIC and COVALENT


IONIC BONDS:
The attraction between a positive ion and
negative ion

In ionic bonding, electrons are completely
transferred from one atom to another.
Ionic bond usually formed between a metal
and non metal. Example: The reaction of
sodium with chlorine
Ionic compounds dissolve easily in water
and other polar solvents.
In solution, ionic compounds easily conduct
electricity.
Ionic compounds tend to form crystalline
solids with high melting temperatures.


COVALENT BONDS:

Attraction between two atoms that share
one or more pairs of electrons.
This most commonly occurs when two
nonmetals bond together .
Example: The bond between two hydrogen
atoms, Cl
2
-

H
2
O -CH
4



SHARING IS CARING!
all covalent bonds involve the sharing of electrons, they
differ widely in the degree of sharing.
Covalent bonds are classified in tow categoriesdepending on
the difference in electronegativity between the bonded
atoms.
Polar bonding results when two different atoms
unequally share electrons between them.
1.If the difference in the electronegativity between the
two bonded atoms is between 0.5 and 2.1, then the bond
formed is considered to be polar covalent.
Non-polar bonding results when two atoms equally share
electrons between them.
1.If the difference in the electronegativity between the
two bonded atoms is less than 0.5 then the bond formed is
considered to be non-polar covalent.

Covalent bonds between different atoms are
generally dipolar:
Because one of the atoms is usually
more electronegative than the other.
When a dipolar bond breaks:
The bonding electrons often stay with
the more electronegative atom, which
then becomes a negatively charged ion,
or an anion
The other part of the molecule
becomes a positively charged ion, or a
cation.
Hydrogen bond
A noncovalent force of attraction between the
partial positive charge on hydrogen bonded
to an atom of high electronegativity, most
commonly O or N, and the partial negative
charge on a nearby O or N.

The hydrogen bond
in water is a
classic example:
A hydrogen atom
in one molecule is
attracted to a
pair of electrons
in the outer shell
of an oxygen
atom in an
adjacent water
molecule.

ACIDS & BASES
Acids: always (almost) begin with "H"
because of the excess of H+ ions
(hydrogen).
Bases or alkaline: always (almost) end
with -OH because of the excess of
hydroxide ions (Oxygen & Hydrogen)

When an acid reacts with a base they
produce a salt and water.
This process known as Neutralization



Acid and Base Strength
Strong Acid: An acid that ionizes
completely in aqueous solution.
Weak Acid: An acid that is only partially
ionized in aqueous solution.
Strong Base: A base that ionizes
completely in aqueous solution.
Weak Base: A base that is only partially
ionized in aqueous solution.

Examples
Structure and properties of water
Water covers about
75% of the arths
surface in the form
of oceans, ice caps,
lakes and rivers.

Structure of the Water Molecule
Many of the
physical and
chemical
properties of water
are due to its
structure.
The atoms in the
water molecule are
arranged with the
two H-O bonds
Water in the body
55% to 78% human body is
water depending on body
size. A rule of thumb, 2/3 of
body is consists of water,
and it is the main
component of human body.
Muscle consists of 75%
water
Brain consists of 90% of
water
Bone consists of 22% of
water
Blood consists of 83%
water
Compounds that dissolve easily in water are
hydrophilic.
Compounds that do not dissolve in water are
hydrophobic such as waxes and lipids. Thats
why they need organic solvents to dissolve
them.
Other compounds contain regions that are
polar (charged) and regions that are nonpolar.
These molecules are known as amphipathic
compounds which is term describing a chemical
compound possessing both hydrophilic and
hydrophobic properties)
Water is a polar solvent. It can dissolve most
biomolecules, which are charged (polar).