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Biochemistry has become the foundation for understanding all biological

processes.

It has provided explanations for the causes of many diseases in humans,

animals and plants

What is Biochemistry ? Biochemistry is the application of chemistry to

the study of biological processes at the cellular and molecular level.

It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology and biology to investigate the chemistry of living systems by:

A. Studying the structure and behavior of the complex molecules found in biological material and

B. the ways these molecules interact to form cells, tissues and whole organism

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Principles of Biochemistry

Cells (basic structural units of living organisms) are highly organized and constant source of energy is required to maintain the ordered state.

Living processes contain thousands of chemical pathways. Precise regulation and integration of these pathways are required to maintain life

Certain important pathways e.g. Glycolysis is found in almost all organisms.

All organisms use the same type of molecules: carbohydrates, proteins, lipids & nucleic acids.

Instructions for growth, reproduction and developments for each organism is encoded in their DNA

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Cells

Basic building blocks of life

Smallest living unit of an organism

Grow, reproduce, use energy, adapt, respond to their environment

Many cannot be seen with the naked eye

A cell may be an entire organism or it may be one of billions of cells that make up the organism

Basis Types of Cells

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Nucleoid region contains the DNA•Cell membrane & cell wall• Contain ribosomes (no membrane) to make proteins intheir cytoplasm

Contain 3 basic cell structures:• Nucleus• Cell Membrane• Cytoplasm with organelles

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Two Main Types of Eukaryotic Cells

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Characteristic Bio-membranes and Organelles

MitochondrionSurrounded by a double membrane with a series of foldscalled cristae. Functions in energy production through metabolism. Contains its own DNA, and is believed to have originated as a captured bacterium.

Plasma MembraneA lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems. NucleusDouble membrane surrounding the chromosomes and the nucleolus. Pores allow specific communication with the cytoplasm. The nucleolus is a site for synthesis of RNA making up the ribosome

Chloroplasts (plastids)Surrounded by a double membrane, containing stacked thylakoid membranes. Responsible for photosynthesis, the trapping of light energy for the synthesis of sugars. Contains DNA, and like mitochondria is believed to have originated as a captured bacterium.

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Rough endoplasmic reticulum (RER)A network of interconnected membranes forming channels within the cell. Covered with ribosomes (causing the "rough" appearance) which are in the process of synthesizing proteins for secretion or localization in membranes.RibosomesProtein and RNA complex responsible for protein synthesis

Smooth endoplasmic reticulum (SER)A network of interconnected membranes forming channels within the cell. A site for synthesis and metabolism of lipids. Also contains enzymes for detoxifying chemicals including drugs and pesticides.

Golgi apparatusA series of stacked membranes. Vesicles (small membrane surrounded bags) carry materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are "processed" to a mature form. Vesicles then carry newly formed membrane and secreted proteins to their final destinations including secretion or membrane localization. Lysosymes

A membrane bound organelle that is responsible for degrading proteins and membranes in the cell, and also helps degrade materials ingested by the cell.

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VacuolesMembrane surrounded "bags" that contain water and storage materials in plants.

Peroxisomes or MicrobodiesProduce and degrade hydrogen peroxide, a toxic compound that can be produced during metabolism.

Cell wallPlants have a rigid cell wall in addition to their cell membranes

Cytoplasmenclosed by the plasma membrane, liquid portion called cytosol and it houses the membranous organelles.

CytoskeletonArrays of protein filaments in the cytosol. Gives the cell its shape and provides basis for movement. E.g. microtubules and microfilaments.

http://www.biology.arizona.edu copyright © 1997 - 2004.. 9

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Biochemistry

Biolog. Nanostructures

How did organic complex molecules evolved from more simple molecules?

Biochemical Evolution

CH4, H2O, NH3, HCN

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How did organic complex molecules evolved from more simple molecules?

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• Urea was synthesized by heating the inorganic compound ammonium cyanate (1828)

• This showed that compounds found exclusively in living organisms could be synthesized from common inorganic substances

The Urey-Miller experiment (1950)

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Some amino acids could be produced:

Many Important Biomolecules are Polymers

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• Biopolymers - macromolecules created by joining many smaller organic molecules (monomers)

• Condensation reactions join monomers (H2O is removed in the process)

• Residue - each monomer in a chain

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Molecular Organisation of a cell

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WaterAbout 60-90 percent of an organism is water

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Water is used in most reactions in the bodyWater is called the universal solvent

Bio-molecules Just like cells are building blocks of tissues likewise molecules are

building blocks of cells.

Animal and plant cells contain approximately 10, 000 kinds of molecules (bio-molecules)

Water constitutes 50-95% of cells content by weight.

Ions like Na+, K+ and Ca+ may account for another 1%

Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)

Infinite variety of molecules contain C. Most bio-molecules considered to be derived from hydrocarbons.

The chemical properties of organic bio-molecules are determined by their functional groups. Most bio-molecules have more than one.

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Biomolecules – Structure

Building block Simple sugar Amino acid Nucleotide Fatty acid

Macromolecule Polysaccharide Protein (peptide) RNA or DNA Lipid

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Anabolic

Catabolic

Linking Monomers

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Cells link monomers by a process called dehydration

synthesis (removing a molecule of water)

This process joins two sugar monomers to make a double

sugar

Remove H

Remove OH

H2O Forms

Breaking Down Polymers Cells break down

macromolecules by a process called hydrolysis (adding a molecule of water)

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Water added to split a double sugar

Sugars

Carbohydrates most abundant organic molecule found in nature.

Initially synthesized in plants from a complex series of reactions involving photosynthesis.

Basic unit is monosaccharides.

Monosaccharides can form larger molecules e.g. glycogen, plant starch or cellulose.

Functions Store energy in the form of starch (photosynthesis in

plants) or glycogen (in animals and humans).

Provide energy through metabolism pathways and cycles.

Supply carbon for synthesis of other compounds.

Form structural components in cells and tissues.

Intercellular communications 22

Monosaccharides -Polysaccharides

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Glycosidic bonds connecting glucose residues are in red

Glucose - Cellulose

Fatty acids - Lipids

Are monocarboxylic acid contains even number C atoms

Two types: saturated (C-C sb) and unsaturated (C-C db)

Fatty acids are components of several lipid molecules.

E,g. of lipids are triacylglycerol, steriods (cholestrol, sex hormones), fat soluble vitamins.

Functions Storage of energy in the form of fat Membrane structures Insulation (thermal blanket) Synthesis of hormones

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Triglyceride

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Glycerol Fatty Acid Chains

Structure of a biological membrane

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• A lipid bilayer with associated proteins

Steroids

The carbon skeleton of steroids is bent to form 4 fused rings

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Cholesterol is the “base steroid” from which your body produces other steroids

Estrogen & testosterone are also steroids

Cholesterol

TestosteroneEstrogen

Synthetic Anabolic Steroids are variants of testosterone

Nucleic Acids

Store hereditary information

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Contain information for making all the body’s proteins

Two types exist --- DNA & RNA

Amino acids - Proteins:

Amino acids:

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• Building blocks of proteins.

• R Group (side chains) determines the chemical properties of each amino acids.

• Also determines how the protein folds and its biological function.

• Functions as transport proteins, structural proteins, enzymes, antibodies, cell receptors.

Proteins as Enzymes

Many proteins act as biological catalysts or enzymes

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Thousands of different enzymes exist in the bodyEnzymes control the rate of chemical reactions by weakening bonds, thus lowering the amount of activation energy needed for the reaction -> Catalysator

-> No not interfere with the equilibrium of reaction

-> Enzymes are reusable !!!!

Enzymes:

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• Active site - a cleft or groove in an enzyme that binds the substrates of a reaction

Egg white lysozyme

The nature and arrangement of amino acids in the active site make it specific for only one type of substrate. (accepts just one enaniomer)

Macromolecules

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Macromolecules

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Concepts of Life

Life is characterized by

Biological diversity: lichen, microbes, jellyfish, sequoias, hummingbirds, manta

rays, gila monsters, & you

Chemical unity: living systems (on earth) obey the rules of physical and organic chemistry – there are no new principles

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Life needs 3 things:

(1) ENERGY, which it must know how to: Extract

Transform Utilize

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The Energetics of Life

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•Photosynthetic organisms capture sunlight energy and use it to synthesize organic compounds

•Organic compounds provide energy for all organisms

Using toxic O2 to generate energy

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2 H2O O2 + 4e- + 4H+ (photosynthesis)

Glucose + 6O2 6CO2 + 6H2O + Energy

Glycolysis: the preferred way for the formation of ATP

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Life needs (2) SIMPLE MOLECULES, which it must know how to:

Convert Polymerize Degrade

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Life needs (3) CHEMICAL MECHANISMS, to:

Harness energy Drive sequential chemical reactions Synthesize & degrade macromolecules Maintain a dynamic steady state Self-assemble complex structures Replicate accurately & efficiently Maintain biochemical “order” vs outside

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Trick #1: Life uses chemical coupling to drive otherwise unfavorable reactions

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Trick #2: Life uses enzymes to speed up otherwise slow reactions

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How does an enzyme do it, thermodynamically?

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How does an enzyme do it, mechanistically?

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Chemical reaction types encountered in biochemical processes

1. Nucleophilic Substitution One atom of group substituted for another

2. Elimination Reactions Double bond is formed when atoms in a molecule is

removed

3. Addition Reactions: Two molecules combine to form a single product. A. Hydration Reactions Water added to alkene > alcohol (common addition

pathway)

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4. Isomerization Reactions. Involve intramolecular shift of atoms or groups

5. Oxidation-Reduction (redox) Reactions Occur when there is a transfer of e- from a donor

to an electron acceptor

6. Hydrolysis reactions Cleavage of double bond by water.

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Biochemical Reactions Metabolism: total sum of the chemical reaction

happening in a living organism (highly coordinated and purposeful activity)

a. Anabolism- energy requiring biosynthetic pathways b. Catabolism- degradation of fuel molecules and the

production of energy for cellular function

All reactions are catalyzed by enzymes

The primary functions of metabolism are: a. acquisition & utilization of energy b. Synthesis of molecules needed for cell structure and functioning (i.e. proteins, nucleic acids, lipids, & CHO c. Removal of waste products

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Even though thousands of pathways sound very large and complex in a tiny cell:

The types of pathways are small

Mechanisms of biochemical pathways are simple

Reactions of central importance (for energy production & synthesis and degradation of major cell components) are relatively few in number

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Energy for Cells

Living cells are inherently unstable.

Constant flow of energy prevents them from becoming disorganized.

Cells obtains energy mainly by the oxidation of bio-molecules (e- transferred from 1 molecule to another and in doing so they lose energy)

This energy captured by cells & used to maintain highly organized cellular structure and functions

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