Transcript Biochemistry

Dr. Amina R ELGezeery
Biochemistry Dept
King Saud University
Continuous Assessment Tests (CAT)
• Two Tests --------------------------40 Marks
• Two Quiz --------------------------10 Marks
• Final----------------------------------50 Marks
• Dates for CAT:
– 1st CAT: … Saturday 22 Dhu-Al-Qadah 1431
– 2nd CAT: Saturday ……… 5 Muharram 1432
Time: 12-1.00
Lecture Room: To be announced
Ref.Books
• Biochemistry by
• Lehninger: Pronciples of Biochemistry
by DL. Nelson and MI. Cox
-Biochemistry : Lippincott illustrated
reviews . By : Champe P.C & Harvey R.A
Biochemistry
Biochemistry can be defined as the science
concerned with the chemical basis of life
The cell is the structural unit of living systems.
Thus, biochemistry can also be described as the
science concerned with the chemical constituents
of living cells and with the reactions and
processes they undergo.
The Aim of Biochemistry Is to
Describe &Explain, in Molecular
Terms, All Chemical Processes of
Living Cells
Biochemistry describes in molecular terms the
structures,mechanisms, and chemical processes
shared by all organisms and provides organizing
principles that underlie life in all its diverse forms,
principles we refer to collectively as the molecular
logic of life .
Biochemistry provides important insights and
practical applications in medicine, agriculture,
nutrition, and Industry .
Outline of lectures 1-6
What is matter ?
What is matter made of?
Common Elements
What are elements made of?
Atomic Structure
Structure of an Atom
Elements in Living and NonLiving Materials
Living and Non-living
Distinctive Properties of
Living Systems
Systems
Properties of Life
The hirerarchy in the molecular
organization of cells
Organization
Organismal level
The Levels of organization
in cells
Structural hierarchy in the molecular organization of cells
In this plant cell, the nucleus is an organelle containing several types of
supramolecular complexes, including chromosomes. Chromosomes
consist of macromolecules of DNA and many different proteins.
Each type of macromolecule is made up of simple subunits—DNA of
nucleotides (deoxyribonucleotides), for example.
Biomolecules
Four major classes :
Polymers ands Monomers
 Each of these types of
biomolecules are polymers
that are assembled from single
units called monomers.
Biomolecule
Carbohydrates
Monomer
Monosaccharide
Lipids
Proteins
Not always polymers;
Hydrocarbon chains
Amino acids
Nucleic acids
Nucleotides
How do monomers form polymers??
• In condensation reactions (also called
dehydration reaction), a molecule 
water is removed from two monomers and
they are connected together .
Synthesis of Polymer
Dehydration
Hydrolysis
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25.5
60.3
10.5
2.4
The four most abundant elements in living organisms,
in terms of percentage of total number of atoms, are
hydrogen, oxygen, nitrogen, and carbon, which
together make up more than 99% of the mass of
most cells.
They are the lightest elements capable of forming
one, two, three, and four coavelent bonds,
respectively; . Thus they can react with each other to
form a large number of different coavelent
compounds .
Strengths of Bonds Common in Biomolecules
Organic substances are
made of Carbon
Examples of ring & long
chain carbon compounds
Biomolecules Are Compounds of Carbon
with a Variety of Functional Groups
-The chemistry of living organisms is organized
around carbon, which accounts for more than
half the dry weight of cells.
Why carbon is special?
-Carbon can form single bonds with hydrogen atoms, and both
nitrogen atoms.single and double bonds with oxygen and
-the ability of carbon atoms to form very stable carbon–carbon
single bonds. Each carbon atom can form single bonds with up to
four other carbon atoms. Two carbon atoms also can share two (or
three) electron pairs, thus forming double (or triple) bonds.
Versatility of carbon bonding. Carbon can form covalent
single, double, and triple bonds (in red), particularly with other carbon atoms. Triple
bonds are rare in biomolecules.
 Carbon atom posses a significant property;
capacity to bond with each other . ( since a
carbon atom may either accept or donate
four electrons to complete an outer octet , it
can form covalent bonds with other four
carbon atoms )
 In this way covalently linked carbon atoms
can form linear or branched or cyclic
backbones of different organic molecules .
- The four single bonds that can be formed by a carbon
atom are arranged tetrahedrally, with an angle of
about 109.5 between any two bonds (Fig.) and an
average length of 0.154 nm.
- There is free rotation around each single bond, unless
very large or highly charged groups are attached to both
carbon atoms, in which case rotation may be restricted.
-A double bond is shorter (about 0.134 nm) and rigid and
allows little rotation about its axis .
- Thus organic molecules with many single bonds can
assume a number of different shapes , called
conformation , depending on the degree to which each
single bond is rotated .
Geometry of carbon bonding.
(a) Carbon atoms have a characteristic tetrahedral arrangement of their four single
bonds.
(b) Carbon–carbon single bonds have freedom of rotation, as shown for the compound
ethane (CH3OCH3).
(c) Double bonds are shorter and do not allow free rotation. The two doubly bonded
carbons and the atoms designated A, B, X, and Y all lie in the same rigid plane.
 As a result , organic biomolecules have
characteristic size and three dimensional




conformation .
The three dimensional conformation of
biomolecules is important in many aspects of
biochemistry , eg. :
- In the reaction between the catalytic site of an
enzyme and its substrate , the two molecules
must fit each other .
- Also hormone and receptor .
- Replication of DNA .
.
To these carbon skeletons are added groups of
other atoms, called functional groups, which confer
specific chemical properties on the molecule. It seems
likely that the bonding versatility of carbon was a major
factor in the selection of carbon compounds for the
molecular machinery of cells during the origin and evolution
of living organisms.
No other chemical element can form molecules of such
widely different sizes and shapes or with such a variety of
functional groups.