General Biochemistry

BCH 201
((3+0
BCH 201
Dr. Arjumand Warsy

Dr.Amina ElGezeery
(Continuous Assessment Tests (CAT
• Two Tests --------------------------50 Marks
• Final----------------------------------50 Marks
• Dates for CAT:
– 1st CAT: Saturday 18 Rabi II 1431
– 2nd CAT: Saturday 1 Jumad II 1431

Time: 12-1.00
Lecture Room: To be announced
Books
• Biochemistry by Stryer
• Lehninger: Pronciples of Biochemistry by DL.
Nelson and MI. Cox
Outline of lectures 1 and 2
• General Introduction to Biochemistry
- Distinctive Properties of Living Systems
- Biomolecules: Molecules of Life
- Biomolecular Hierarchy (packing order)
- Properties of Biomolecules
- Organization and Structure of Cells
- Viruses as Cell Parasites
Biochemistry
• Chemistry is the study of the interactions of
matter .
• Biochemistry is the chemistry of living things.
• Biochemistry
– Provides fundamental understanding of the
molecular basis for the function (and malfunction) of
living things.
– Provides a broad understanding of the molecular
basis of life.
– Explains what goes wrong to produce a disease.
Biochemistry
• Biochemistry is a special branch of organic
chemistry that deals with matter inside
the living cell called protoplasm .

• Protoplasm is an enormously complex

mixture of organic compounds where
high levels of chemical activity occur.
?What is matter
• Anything that:
– Takes up space
– Has mass (weight)

• Matter includes living AND non-living things.

?What is matter made of
• Living and non-living matter:
– Both are made of elements.
• Elements cannot be broken down to
substances with different properties.
• So an element can’t be broken down
– Elements can be broken down to atoms, but each
of the atoms will have the same properties! (i.e.
the same number of protons)
• 92 natural elements (additional man-made
elements are on the periodic table).
Common Elements
Examples of elements include: The most common
• Oxygen
elements found in living
• Carbon
• Hydrogen
organisms:
• Gold • Carbon
• Silver • Oxygen
• Potassium
• Magnesium • Nitrogen
• Lead • Hydrogen
• Helium
• Lithium
• Phosphorus
• Sulfur
?What are elements made of
• An element consists of atoms of the same kind. (i.e.
The same number of protons, or atomic number.)

• For example, every atom that has 6 protons is the

element CARBON.
• Every atom that has 7 protons is NITROGEN.
• Every atom that has 8 protons is OXYGEN. Etc.
Atomic structure
• Atoms are made of sub-atomic particles:

Particle Charge Location in Atomic mass

the atom
Proton +1 Nucleus 1

Neutron 0 Nucleus 1

Electron -1 Electron 0
shells
Structure of an Atom
.Atoms combine to form compounds
• When atoms of 2 (or more) elements form bonds
together, the new combination is called a
COMPOUND, e.g. H2O, C6H12 O6
• Major types of Bonds: There are five major types of
bonds. These are:
1. Ionic bonds
2. Covalent bonds (polar & nonpolar)
3. Hydrogen bonds
4. Hydrophobic bonds
5. Van deer Waal’s forces
Living and Non-Living
• living organisms are complicated and highly
organized made up of cells containing many
kinds of complex molecules made up of specific
elements ( C, O, H, N,…..).in contrast , animate
matter ( non living things ) as soil ,rocks , water
………… consist of random mixtures of simple
chemical compounds made up of elements .
• Each part of living organism appears to have a
specific function .
• Living organisms have the capacity to extract
and transform energy from the environment
and use it for their own functions while
animate matter can not utilize external
energy to maintain its own structural
organization .
• Living organisms can grow and multiply while
non-living things cannot .
Distinctive Properties of Living
Systems
• Organisms are complicated and highly
organized
• Biological structures serve functional purposes
• Living systems are actively engaged in energy
transformations
• Living systems have a remarkable capacity for
self-replication
Properties of life
• Organization: Living things exhibit a very high order
of organization starting from elements …….. Cell
………………..organism .
• Regulation: The environment, total surroundings
around an organism, undergoes fluctuations like changes in
temperature. The organisms have self-regulatory
mechanisms to maintain internal conditions within limits.
This capability is called Homeostasis.
• Growth and Development: All organisms
grow from a smaller size to a bigger size by converting food
to living matter called protoplasm. This can happen at
single cell level - Amoeba, or from one cell to many cells -
humans.
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• Energy Utilization: All organisms must get
energy and transform it to other forms to do
activities like movements, Metabolism (sum of all
chemical changes occurring in body). All organisms
change the chemical energy of glucose to chemical
energy of ATP – the energy currency of cell.

• Reproduction: To produce again. All living

things produce individuals like them who can grow
to full size. Apple seeds grow into an apple tree. The
egg of a hen yields a chick that grows into hen/cock.
• Heredity: DNA: The transfer of information from
one generation to another is called Heredity. It is
passed through ladder like molecules called DNA.
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Six Characteristics of Living Things
1. Cells
2. Organization
3. Energy
4. Homeostasis
5. Growth
6. Reproduction
First Characteristic – Composed of
cells
• The first characteristic of living things is that
they are all composed of cells.
• Cells are the itsy bitsy puzzle pieces that
make up all living things.
Second Characteristic of Living Things-
Organization

• The second characteristic of living things is

Organization.
• All of the little cells that come together to
make living things do so in a specific order.
• For example a group of muscle cells come
together to form the muscles.
Third Characteristic of Living Things-
Need Energy
• The third characteristic of living things is all
living things use energy.

Animals and humans eat food Plants however use the

.to obtain their energy sunlight to obtain their
.energy
Fourth Characteristic of Living Things-
Homeostasis
• The fourth characteristic of living things is
homeostasis.
Fifth Characteristic of Living Things-
Growth
• The fifth characteristic of living things is that
all living things grow.
Sixth Characteristic of Living Things-
reproduce
• The sixth characteristic of living things is
reproduction. All living things need to
reproduce to survive.
Elements in living & non-living material
EARTH’S CRUST HUMAN TISSUES
RANK ELEMENT % ELEMENT %
1st Oxygen 62,5000 Hydrogen 60,300
2nd Silicon 21,2000 Oxygen 25,500
3rd Aluminium 6,4700 Carbon 10,500
4th Sodium 2,6400 Nitrogen 2,450
5th Calcium 1,9400 Sodium 0,730
6th Iron 1,9200 Calcium 0,266
7th Magnesium 1,8400 Phosphorus 0,134
8th Phosporus 1,4200 Sulphur 0,132
9th Carbon 0,0800 Potassium 0,036
10th Nitrogen 0,0001 Chlorine 0,032
Organization of Life
Organismal Level
• Tissues are made of cells of one kind and perform one
function. Muscular tissue, nervous tissue, epithelial
(surface forming) tissue.
• Organs: Different tissues join to form organs. Heart,
stomach, eye.
• Organ-Systems: Organs combine to form organ-
systems. Digestive system, respiratory system,
circulatory system.
• Organism: All levels together form a living body,
individual or organism. Each human, monkey, dog,
mushroom, plant, bacterium.
Organic substances are made of
carbon

• All living things are composed of organic

compounds.
Organic compounds are compounds
composed primarily of a Carbon skeleton
What makes Carbon Special? Why is Carbon so
different from all the other elements on the
periodic table?

• The answer derives from the ability of Carbon

atoms to bond together to form long chains
and rings
Carbon can covalently bond with up to
four other atoms.
Carbon can form immensely diverse
.compounds, from simple to complex

Methane with 1 Carbon DNA with tens of Billions of

atom Carbon atoms
Biomolecules: The Molecules of Life
• What property unites H, O, C and N and
renders these atoms so appropriate to the
chemistry of life?
• Answer: Their ability to form covalent bonds
by electron-pair sharing.
Properties of Biomolecules Reflect Their
Fitness to the Living Condition
• Macromolecules and Their Building Blocks
Have a “Sense” or Directionality
• Macromolecules are Informational
• Biomolecules Have Characteristic Three-
Dimensional Architecture
• Weak Forces Maintain Biological Structure
and Determine Biomolecular Interactions
A Biomolecular Hierarchy

Simple Molecules are the Units for Building

Complex Structures
• Metabolites and Macromolecules
• Organelles
• Membranes
• The Unit of Life is the Cell
Primary Organic Compounds

You are expected to 1. Carbohydrates

learn the structure
2. Lipids
and functions of
these organic 3. Proteins
:compounds 4. Nucleic Acids
Monomers
Macromolecule Monomer
Carbohydrates Monosaccharide

Lipids Not always polymers;

Hydrocarbon chains
Proteins Amino acids

Nucleic acids Nucleotides

?How do monomers form polymers
• In condensation reactions (also called
dehydration synthesis), a molecule of water
is removed from two monomers as they are
connected together.
Hydrolysis
• In a reaction opposite to condensation, a
water molecule can be added (along with the
use of an enzyme) to split a polymer in two.
Biomolecules: The Molecules of
Life
H, O, C and N make up 99+% of atoms in the human body

ELEMENT PERCENTAGE
Oxygen 63
Hydrogen 25.2
Carbon 9.5
Nitrogen 1.4

H, O, C and N make up 99+% of atoms in the human body

Carbohydrates
• Carbohydrates are made of carbon,
hydrogen, and oxygen atoms, always in a
ratio of 1:2:1.
• Carbohydrates are the key source of energy
used by living things.
• The building blocks of carbohydrates are
sugars, such as glucose and fructose.
Carbohydrates
• Main energy source for humans
• Formed by photosynthesis in plants
• Types of Carbohydrates
– Monosaccharide (1 sugar)
– Disaccharide (2 sugars linked in a chain)
– Oligosaccharides ( less than 10 sugars in a
chain .
– Polysaccharide (large No of sugars linked in
a chain)
Carbohydrate Biomolecules:
Carbon, Hydrogen & Oxygen

Figure 2-13-2: Carbohydrates

Carbohydrates
• What do the roots •
mono-, di-, oligo-, and
poly mean?
• Each of these roots can
be added to the word
saccharide to describe
the type of
carbohydrate you have.
Carbohydrate – Monosaccharides
• Two most common
– Glucose
• Primary storage form of
energy in human body
– Fructose Glucose
• Main sugar found in most
plants
• Others types consumed
– Galactose (from mammalian
milk)
Carbohydrate – Disaccharides

Sucrose
How do two monosaccharides combine to make
?a polysaccharide
•
Glucose C6H12 O6 Fructose C6H12 O6

H2O+
Disaccharide: Sucrose C12 H22 O11
Polysacchrides
Long chains of simple sugars bonded together.
Polysaccharides
Starch – a straight chain polysaccharide

• Starch is a polymer of the

monosaccharide glucose
• It’s a long straight chain
of glucose molecules joined
together ( 1,4 glucosidic )
• It is plants way to store
glucose
Glycogen – a branched polysaccharide
• Glycogen is a polymer of the monosaccharide
glucose
• It’s a branched chain of glucose molecules
joined together
• It is the human body’s way to store glucose in
liver and muscle
Cellulose – a cross-linked polysaccharide

• Made by plants
• Cross linking adds rigidity
• Hydrogen bonding occurs
between cellulose polymers
• Forms cell wall – used for
support in plants
Cellulose
• Animals can’t digest

linked glucose molecules 1500

Lipids: Mostly Carbon and Hydrogen;
little Oxygen

• Triglycerides: Glycerol,Fatty acid chains

• Steroids & Phospholipids
Lipids
• Lipids are molecules that consist of long
hydrocarbon chains. Attaching the three
chains together is usually a glycerol molecule.
Lipids are NONpolar.
Lipid Functions in the Human Body

• Storage form of energy for humans

• Insulation for heat retention
• Protection for delicate organs
• Key component of cell membranes
• Hormones that control certain body
functions
Lipids: Mostly Carbon and Hydrogen;
little Oxygen

Figure 2-14: Lipids and lipid-related molecules

Types of Lipid (Fat) Molecules
• Triglycerides
– Unsaturated fats are liquid at room temperature:
olive oil, canola oil
– Saturated fats are solids at room temperature:
lard, butter, animal fat
• Sterols
– Cholesterol
– Hormones: testosterone, estrogen,
• Phospholipids
– phosphoglycerides
Triglycerides
• Glycerol + 3 fatty acid chains
• Single and/or double bonds (C-H, C-C, C=C, C-O)
• Types of triglycerides
1
– unsaturated
– saturated
2

Glycerol Fatty acid chain

Triglycerides – saturated
• Animal fat: beef – chicken – fish
• Plant fat: coconut –palm – cocoa butter
• No more than 10% of daily calorie needs
• stearic acid, palmitic acid, and butyric acid

Stearic acid = octadecanoic acid

Butyric acid
Triglycerides– unsaturated
• Liquid at room temperature
• Vegetable oils: canola, olive, and peanut
• Cold water fish: salmon
• Recommendation: Up to 20% of daily calorie needs
• Unsaturated fats can be made by a process called
hydrogenation.

Olive oil
Triglycerides– essential
• important factor to healthy immune system.
• Critical for eye, brain, and neurological function
• help us in breaking down and in getting rid of saturated fatty acids.
• adjust cholesterol metabolism rate.
• Our bodies cannot make them. # Two most important groups of
EFAs (linolenic acid ) are:
– omega-6 (N6 EFA)
– omega-3 (N3 EFA)
• Sources of EFAs:
– in leafy green vegetables
– fish like Sardine, Salmons
– omega-3 eggs
– marine algae like sea weeds
Sterols

Cholesterol
Phospholipids
Basic building block of cell membranes •
Saturated vs. Unsaturated Fat
•
Proteins
• Proteins are building blocks of structures
called amino acids.
• A peptide bond forms between amino acids by
dehydration synthesis.
Proteins
made from chains of amino acids •

sequence is genetically determined •

The Biosynthesis of a Protein

• The amino acid sequence is encoded

in DNA
• Protein shape is determined by the
amino acid sequence
Levels of Protein Structure
•
Four Levels of Protein Structure

• Primary Structure –
the number, type and sequence (order) of the
amino acids in a polypeptide chain
• Secondary Structure –
hydrogen bonding effect – helices and sheets
• Tertiary Structure –
weaker electrostatic force effect – “globs”
• Quaternary Structure –
association of subunits
Protein Structure
Level Description
Primary The amino acid sequence
Secondary Helices and Sheets

Tertiary H-bond, electrostatic bonds,

hydrophobic bonds, Disulfide
bridges

Quaternary Multiple polypeptides connect

Protein Hybrids

• Lipoproteins – blood, membranes

and transportation of materials

• Glycoproteins – antibodies, cell surface proteins

• Nucleoproteins - ribosomes
Nucleic acids
• Two types
• - Deoxyribonucleic acid (DNA)
• - Ribonucleic acid (RNA)
• Made of nucleotides joined together by phospho
diester bond
• Transmit and store:
– Genetic Information (genetic code in DNA)
– Nucleotides involved as energy transfer molecules
• ATP
• Cyclic AMP
• NAD & FAD
Nucleotides
• Composition
– Base
– Sugar
– Phosphate
Nucleic Acids
• DNA – deoxyribonucleic acid
• built from deoxyribonucleotides
• adenine
• thymine
• guanine
• cytosine

• RNA – ribonucleic acid

• built from ribonucleotides
• adenine
• uracil
• guanine
• cytosine
DNA RNA
DNA RNA
DNA RNA
Sugar phosphate bonds (backbone of
(DNA
• Nucleotides are
connected to each
other via the
phosphate on one
nucleotide and the
sugar on the next
nucleotide
• A Polynucleotide

AS Biology. Gnetic control of protein

structure and function
DNA RNA
Polynucleotide Structure
Nucleic Acid Molecules
AS Biology. Gnetic control of protein
structure and function
:The Rule
• Adenine always base pairs with Thymine (or
Uracil if RNA)

• Cytosine always base pairs with Guanine.

• This is because there is exactly enough room

for one purine and one pyrimidine base
between the two polynucleotide strands of
DNA.

AS Biology. Gnetic control of protein

structure and function
Nucleotides, DNA, and RNA

Figure 2-18: RNA and DNA

Nucleic Acids - Roles

• DNA
• contains base sequences that code for proteins
• is passed on from generation to generation

• RNA
• Carries instructions from cell nucleus to
cytoplasm where proteins are made
• In viruses it can carry out DNA role
The levels of organisation in cells

THE CELL

Organelles CHLOROPLASTS, MITOCHONDRIA, NUCLEUS etc

Supramolecular ENZYME COMPLEXES, RIBOSOMES, CHROMOSOMES
assemblies

Macromolecules NUCLEIC ACID PROTEIN POLYSACCHARIDE LIPID

Building blocks NUCLEOTIDE AMINO SIMPLE SUGAR FATTY ACID

ACID &
GLYCEROL

Precursors from
the environment CO2, H2O, MINERALS

ODWS Paul Billiet 2007©

Combination Biomolecules
• Lipoproteins (blood transport molecules)
• Glycoproteins (membrane structure)
• Glycolipids (membrane receptors)
• Nucleoproteins

Figure 2-19: Chemistry summary

The hirerarchy in the molecular
organization of cells
• All organic biomolecules are derived from simple- low
Mol.Wt. precursors obtained from the environment
e.g. CO2 , water , nitrogen ..
• These precursors are converted by living matter via
sequence of metabolic reactions into metabolite
intermediates with larger Mol.Wt e.g. pyruvate ,
citrate , …………….
• The metabolites are converted into building – blocks
for biomolecules e.g amino acids , fatty acids ,
nucleotides , glycerol and monosaccharides .
• These building block molecules are then linked to
each other covalently to form the
macromolecules (biomolecules) of the cell e.g.
proteins , polysaccharides, nucleic acids and
lipids .
• Macromolecules non-covalently bonded to each
other to give supermolecular complexes e.g.
ribosomes, enzyme complex, lipoproteins..
• Various supramolecular complexes are
assembled into cell organelles e.g. nucleus,
mitochondria,………..
• The organelles are assembled into the cell .
• The various macromolecules and
supramolecular components are held together
by non-covalent interactions .
Cells
All living things are made up of one or many tiny units called cells. Algae,
mushrooms, yeasts, plants and animals, all are made of cells. Each has a
nucleus containing DNA, a living fluid called cytoplasm and covered by a
living membrane, cell membrane.

• Prokaryotic • Eukaryotic
• Nucleus absent • Nucleus present
• DNA lies in cytoplasm. • DNA lies in nucleus.
• All membrane bound organelles • All membrane bound organelles
like mitochondria are absent. like mitochondria are present.
• Hair like flagella are simple tubes. • Flagella are complex supported
• Ribosomes, the special organelles by 9+2 tubes.
for synthesizing proteins are • Ribosomes are larger in size =
smaller in size = 70 S 80 S

6/18/2007
Procaryotic Cell
Eucaryotic Cell
Virus infecting a Cell

Remember: Viruses are not

cells. They are
supramacromolecules made of
nucleic acids and protein coat.