Kul 1& 2 Biohemistry I

8/12/2019 Kul 1& 2 Biohemistry I

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Biochemistry

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

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What is Biochemistry ? Biochemistry is the application of chemistry to the

study of biological processes at the cellular andmolecular level.

It emerged as a distinct discipline around thebeginning of the 20th century when scientistscombined chemistry, physiology and biology toinvestigate 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 andwhole 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 maintainthe 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 foreach 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 DNACell 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 acaptured bacterium.

Plasma Membrane A lipid/protein/carbohydrate complex, providing a barrier andcontaining transport and signaling systems.

Nucleus Double membrane surrounding the chromosomes and the nucleolus.Pores allow specific communication with the cytoplasm. Thenucleolus is a site for synthesis of RNA making up the ribosome

Chloroplasts (plastids) Surrounded by a double membrane, containing stacked thylakoidmembranes. Responsible for photosynthesis, the trapping of lightenergy for the synthesis of sugars. Contains DNA, and likemitochondria is believed to have originated as a capturedbacterium.

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Rough endoplasmic reticulum (RER) A network of interconnected membranes forming channels within thecell. Covered with ribosomes (causing the "rough" appearance) whichare in the process of synthesizing proteins for secretion or

localization in membranes.Ribosomes Protein 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 containsenzymes for detoxifying chemicals including drugs and pesticides .

Golgi apparatus A series of stacked membranes. Vesicles (small membranesurrounded bags) carry materials from the RER to the Golgiapparatus. Vesicles move between the stacks while the proteins are"processed" to a mature form. Vesicles then carry newly formedmembrane and secreted proteins to their final destinations includingsecretion or membrane localization.

Lysosymes A membrane bound organelle that is responsible for degradingproteins and membranes in the cell, and also helps degrade materialsingested by the cell. 8


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Vacuoles Membrane surrounded "bags" that contain water and storagematerials in plants .

Peroxisomes or Microbodies Produce and degrade hydrogen peroxide, a toxiccompound that can be produced during metabolism .

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

Cytoplasm enclosed by the plasma membrane, liquid portion called cytosoland it houses the membranous organelles.

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

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


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10Biochemistry

Biolog. Nanostructures


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Biochemical Evolution

?

CH 4, H 2O, NH 3, HCN

How did organic complex molecules evolved frommore simple molecules?

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How did organic complex molecules evolvedfrom more simple molecules?

Urea was synthesized by heating the inorganiccompound ammonium cyanate (1828)

This showed that compounds found exclusively in livingorganisms could be synthesized from common inorganicsubstances


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The Urey-Miller experiment (1950)

Some amino acids could be produced:

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Many Important Biomoleculesare Polymers

Biopolymers - macromolecules created by joining manysmaller organic molecules ( monomers)

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

Residue - each monomer in a chain


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Water

About 60-90 percentof an organism is water

Water is used inmost reactions inthe body

Water is calledthe universalsolvent


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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

Anabolic

Catabolic


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Linking Monomers

Cells link monomers by a process called dehydration synthesis(removing a molecule of water)

This process joins two sugar monomersto make a double sugar

Remove

H

Remove OH

H2O Forms


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Breaking Down Polymers Cells break down

macromolecules bya process calledhydrolysis (addinga molecule ofwater)

Water added to split a double sugar


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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


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Monosaccharides -Polysaccharides

Glycosidic bonds connectingglucose residues are in red

Glucose - Cellulose


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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, sexhormones), 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

Glycerol Fatty Acid Chains


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Structure of a biological membrane

A lipid bilayer with associated proteins


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Steroids

The carbon skeleton ofsteroids is bent to form4 fused rings

Cholesterol is the

base steroid fromwhich your bodyproduces othersteroids

Estrogen &testosterone are alsosteroids

Cholesterol

TestosteroneEstrogen

Synthetic Anabolic Steroids are variants of testosterone


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Nucleic Acids

Store hereditary informationContain information for making all thebodys proteins

Two types exist --- DNA & RNA


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Proteins as Enzymes

Many proteins act as biological catalysts or enzymes

Thousands of different enzymes exist in the body

Enzymes control the rate of chemical reactions byweakening bonds, thus lowering the amount ofactivation energy needed for the reaction ->Catalysator

-> No not interfere with the equilibrium of reaction-> Enzymes are reusable !!!!


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Macromolecules


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Macromolecules


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Concepts of LifeLife is characterized by

Biological diversity: lichen, microbes, jellyfish, sequoias, hummingbirds, mantarays, gila monsters, & you

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


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Life needs 3 things :

(1) ENERGY , which it mustknow how to:

Extract Transform Utilize


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The Energetics of Life

Photosyntheticorganisms capturesunlight energy and useit to synthesize organiccompounds

Organic compoundsprovide energy for allorganisms


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Glycolysis: the preferred way for theformation 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) CHEMICALMECHANISMS , 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 todrive otherwise unfavorable reactions


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Trick #2: Life uses enzymes to speed upotherwise 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 inbiochemical 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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Summary of Key Concepts


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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 pathwaysb. 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 energyb. Synthesis of molecules needed for cell structure and

functioning (i.e. proteins, nucleic acids, lipids, & CHOc. Removal of waste products

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

The types of pathways are small

Mechanisms of biochemical pathways are simple

Reactions of central importance (for energyproduction & synthesis and degradation of major cellcomponents) 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 anotherand in doing so they lose energy)

This energy captured by cells & used to maintain

highly organized cellular structure and functions

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Kul 1& 2 Biohemistry I

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