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 1432Time: 12-1.00Lecture 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 can be defined as the science concerned with the chemical basis of lifeThe 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.

Biochemistry

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 Non- Living Materials

Living and Non-living

Distinctive Properties of Living SystemsSystems

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. Chromosomesconsist of macromolecules of DNA and many different proteins.Each type of macromolecule is made up of simple subunits—DNA of nucleotides (deoxyribonucleotides), for example.

BiomoleculesFour major classes:

Polymers ands Monomers

Each of these types of biomolecules are polymers that are assembled from single units called monomers.

BiomoleculeCarbohydrates

Lipids

Proteins

Nucleic acids

Monomer Monosaccharide

Not always polymers; Hydrocarbon chains

Amino 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

5

60.325.5

10.52.4

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 single and double bonds with oxygen and .nitrogen atoms

-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 covalentsingle, 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 carbonatom are arranged tetrahedrally, with an angle ofabout 109.5 between any two bonds (Fig.) and anaverage 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 ) 3 3(. for the compound ethane CH OCH

) ( c D ouble 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 ofother atoms, called functional groups, which conferspecific chemical properties on the molecule. It seemslikely that the bonding versatility of carbon was a majorfactor in the selection of carbon compounds for themolecular machinery of cells during the origin and evolutionof living organisms. No other chemical element can form molecules of such widely different sizes and shapes or with such a variety of functional groups.