introduction & biomolecules

8/18/2019 Introduction & Biomolecules

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CHAPTER 1

INTRODU TION &

BIOMOLE ULES

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Introduction and Biomolecules

Subtopic:

Definition of biochemical engineering

Carbohydrates

Amino acids and protein

The central Dogma of molecular biology Buffer solution


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What is Biochemical Engineering?

The application of engineering principles to

conceive, design, develop, operate, or use processes

and products based on biological and biochemical

phenomena.

It is a subset of chemical engineering that mainly

deals with the design and construction of unit

processes that involve biological organisms or

molecules.

It enhances the quality of our lives by defining ways

in which new biological discoveries can be

sensitively translated into practical realities.

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What do Biochemical Engineer do?

Typical employers come

from all sectors of the

biotechnology industries,

including those with

interests in

pharmaceuticals,

food,environment, wastetreatment, and

consulting

.


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arbohydrates

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What are carbohydrates?

Play key roles as structural and storage

compounds in cells.

Polyhydroxy compounds (poly-alcohols) that

contain a carbonyl (C=O) group.

The formula for a carbohydrate is (CH2O)n, where

n≥ 3.

D form is biologically more abundant than L form.

The usual chemical test for the simpler

carbohydrates is heating with Benedict's solution.


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arbohydrates - The Functions

Most important source of energy for living organisms. Linked to proteins or lipids.

Form structural tissues in plants and in

microorganisms (cellulose, lignin, murein).

Participates in biological transport, cell- cell

recognition, activation of growth factors, modulation

of the immune system.

DNA and RNA framework.

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lassifying carbohydrates

Simple carbohydrates

1) Monosaccharides

Glucose, fructose, galactose

2) Disaccharides

Lactose, sucrose, maltose

Complex carbohydrates

1) Oligosaccharides

Raffinose, stachyose

2) PolysaccharidesStarch, glycogen, cellulose

* chaining relise on 'bridging' of oxygen atoms - glycoside bonds


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lassifying carbohydrates

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Monosaccharides

Smallest carbohydrates, also known as simple sugars.

Monosaccharides are categorized by:

1) number of carbons (typically 3-9)

2) whether an aldehyde or ketone

Sugar containing an aldehydes is known as an aldose.

Sugar containing a ketones is known as a ketose.


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Aldose sugars

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Aldose sugars


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Ketose sugars

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Ketose sugars


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D and L notation

D, L tells which of the two chiral isomers we arereferring to.

If the –OH group on the next to the bottom

carbon atom points to the right , the isomer is a

D-isomer; if it points left, the isomer is L.

The D form is usually the isomer found in nature.

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D and L notation


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D and L notation

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D notation

C

C

CH2OH

OHH

OHH

CO

H

Right = D


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Structural of representation of sugars

Fisher projection: straight chain representation.

Haworth projection: simple ring in perspective.

Conformational representation: chair and boat

configurations.

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Rules of drawing Haworth projections

Draw either a six or 5-membered ring including

oxygen as one atom.

Most aldohexoses are six-membered.

Aldotetroses, aldopentoses, ketohexoses are 5-

membered.


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Next number the ring clockwise starting next tothe oxygen

If the substituent is to the right in the Fisher

projection, it will be drawn down in the Haworthprojection (Down-Right Rule)

O O

1

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23

4

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For D-sugars the highest numbered carbon

(furthest from the carbonyl) is drawn up. For L-

sugars, it is drawn down.

For D-sugars, the OH group at the anomeric

position is drawn down for α and up for β. For L-

sugars α is up and β is down.


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Haworth Structure for D-Glucose

Write –OH groups on the right (C2, C4) down.

Write –OH groups on the left (C3) up.

The new –OH on C1 has two possibilites: down

for anomer, up for anomer.

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Haworth Structure for D-Galactose


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Haworth Structure for D-Fructose

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Isomers

Isomers are molecules that have the same chemical formula but

different structures.

Stereoisomer differs in the 3-D orientation of atoms.

Diastereomers are isomers with > 1 chiral center.

– Pairs of isomers that have opposite configurations at one

or more of the chiral centers but that are not mirror

images of each other

Epimers are a special type of diastereomer.

– Stereoisomers with more than one chiral center which

differ in chirality at only one chiral center– A chemical reaction which causes a change in chirality at

one of many chiral center is called an epimerisation


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Enantiomers

Isomerism in which two isomers are mirror

images of each other (D vs L).

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Disaccharides

Consist of 2 monosaccharides bonded

together.


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Glycosidic Bond

This is when two monosaccharides join to form aDisaccharide.

The reaction is similar to condensation.

The reaction involves the water been given off.

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Oligosaccharides

3-10 monosaccharides.

Components of cell membranes and part of milk,

particularly human milk.


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Polysaccharides

>10 monosaccharides.Most are made up of hundreds of monosaccharides

bonded together.

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ellulose


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Amino Acids &

Protein

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Types of Protein

Type Examples

• Structural tendons, cartilage, hair, nails

• Contractile muscles

• Transport hemoglobin

• Storage milk

• Hormonal insulin, growth hormone

• Enzyme catalyzes reactions in cells

• Protection immune response


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Protein play key roles in a living system

Almost all chemical reactions in a living cell arecatalyzed by protein enzymes.

Storage and transport of biochemical molecules,

such as oxygen, ions, and so on.

Physical cell support and shape (collagen).

Regulatory and information transfer (hormones).

Mechanical movement (flagella, mitosis, muscles).

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Amino acid: Basic unit of protein


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Examples of Amino acid

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Zwitterionic form of Amino Acids

Zwitterion (dipolar ions) has both + and – charge

Zwitterion is neutral overall

Under normal cellular conditions amino acids are

zwitterions:

Amino group = -NH3+

Carboxyl group = - OO-


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pH and Ionization

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The peptide bond ( O - NH linkage)


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Bacteria cell wall

Provide strength and rigidity for the organism.

Consists of a polypeptide-polysaccharide known as

petidoglycan or murein.

Determines the Gram staining characteristic of the

bacteria.

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Primary Structure of Proteins

Primary structure of a proteins is the particular

sequence of amino acids connected by peptide bonds.

Proteins are linear polymers of amino acids


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Secondary Structure

Secondary structure of a protein is the arrangement

of polypeptide backbone of the protein in space.

The secondary structure includes two kinds of

repeating pattern known as helixes (α-helix, triple

helix) and sheet (β-sheet).

Hydrogen bonding between backbone atoms are

responsible for both of these secondary structures.

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Basic structural units of proteins:

Secondary structure


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Tertiary Structure

The overall three dimensional shape that results

from the folding of a protein chain. Tertiary structure depends mainly on interactions

of amino acid R groups that are far apart along the

same backbone.

Cross links between R groups of amino acids in

chain:

disulfide –S–S– +ionic –COO– H3N–

H bonds C=O HO–

hydrophobic –CH3 H3C–

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Tertiary Structure


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Quaternary Structure

• The way in which two or more polypeptidechains associate to form a single three-

dimensional protein unit. Non-covalent

forces are responsible for quaternary

structure essential to the function of proteins.

• Example is hemoglobin that carries oxygen

in blood.

-Four polypeptide chains

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Protein Hydrolysis

• Break down of peptide bonds

• Requires acid or base, water and heat

• Gives smaller peptides and amino acids

• Similar to digestion of proteins usingenzymes

• Occurs in cells to provide amino acids tosynthesize other proteins and tissues


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Hydrolysis of Dipeptide

H3N CH

CH3

C

O

N

H

CH C

OCH2

OH

OH

+

H3N CH

CH3

COH

O

+ CH C

OCH2

OH

OHH3N

H2O, H+

+

+

heat

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Denaturation

Disruption of secondary, tertiary and quaternaryprotein structure by

heat/organics

Break apart H bonds and disrupt hydrophobicattractions

acids/ bases

Break H bonds between polar R groups and

ionic bonds

heavy metal ionsReact with S-S bonds to form solids

agitation

Stretches chains until bonds break


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Application of Denaturation

• Hard boiling an egg• Wiping the skin with alcohol swab for

injection

• Cooking food to destroy E. coli.

• Heat used to cauterize blood vessels

• Autoclave sterilizes instruments

• Milk is heated to make yogurt

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The entral Dogma of

Molecular Biology


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What is DNA and RNA?

• DNA – Deoxyribonucleic acid

• RNA – Ribonucleic acid

• DNA stores and preserves genetic

information

• RNA plays a central role in protein synthesis

• Both DNA and RNA are large polymersmade of their corresponding nucleotides

(condensation)


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Nucleotide

• Building block of DNA and RNA

• Consists of 3 major components:

1) phosphoric acid

2) pentose (5-carbon sugar)

-ribose or deoxyribose

3) base (purine or pyrimidine)

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Nucleotide - Adenosine Mono Phosphate (AMP)


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Base Pairing - Guanine & ytosine


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Base Pairing - Adenine & Thymine

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Think About it!!!!

– DNA is the genetic material of cells. The

sequence of nucleotide bases in the

strands of DNA carries some sort of code.

In order for that code to work, the cell

must be able to understand it.

– What, exactly, do those bases code for?

Where is the cell’s decoding system?


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entral Dogma

RNA

Protein

DNA

Proposed by Francis Crick in 1958 to

describe the flow of information in a cell.

Information stored in DNA is transferred

residue-by-residue to RNA which in turn

transfers the information residue-by-

residue to protein.

The Central Dogma was proposed by Crick

to help scientists think about molecular

biology. It has undergone numerous

revisions in the past 45 years.

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entral Dogma

RNA

Protein

DNA

DNA


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DNA

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Terminology of DNA


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DNA Structure

1. DNA is double stranded

2. DNA strands are

antiparallel

3. G-C pairs have 3 hydrogen

bonds

4. A-T pairs have 2 hydrogen

bonds

5. One strand is the

complement of the other

6. Major and minor grooves

present different

surfaces

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RNA

RNA

Protein

DNA

entral Dogma


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Terminology of RNA

Base Nucleoside (RNA)Deoxynucleoside (DNA)

Adenine Adenosine Deoxyadenosine

Guanine Guanosine Deoxyguanosine

Cytosine Cytidine Deoxycytidine

UracilUridine (not usually found)

Thymine (not usually found) (Deoxy)thymidinea

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Terminology of RNA


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– How does RNA differ from DNA?

– There are three important differences

between RNA and DNA: (1) the sugar in RNA

is ribose instead of deoxyribose, (2) RNA is

generally single-stranded and not double-

stranded, and (3) RNA contains uracil in

place of thymine.

RNA

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– There are three important differencesbetween RNA and DNA:

– (1) The sugar in RNA is ribose instead ofdeoxyribose.

– (2) RNA is generally single-stranded andnot double-stranded.

– (3) RNA contains uracil in place of thymine.

– These chemical differences make it easyfor the enzymes in the cell to tell DNA andRNA apart.

ompairing RNA and DNA


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RNA

Protein

DNA

Protein

entral Dogma

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Protein

Structure

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– We first examine the simplest way of

looking at protein synthesis as expressed in

the so called Central Dogma of Biology,

namely that the direction of information

flow in the cell is from DNA to mRNA to

proteins.

The central of Dogma

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– How does the cell make RNA?

– In transcription, segments of DNA serve as

templates to produce complementary RNA

molecules.

RNA Synthesis


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– Most of the work of making RNA takes

place during transcription. During

transcription, segments of DNA serve as

templates to produce complementary

RNA molecules.

– The base sequences of the transcribed

RNA complement the base sequences of

the template DNA.

Transcription

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– Genes contain coded DNA instructions that

tell cells how to build proteins.

– The first step in decoding these genetic

instructions is to copy part of the base

sequence from DNA into RNA.

– RNA, like DNA, is a nucleic acid that

consists of a long chain of nucleotides. – RNA then uses the base sequence copied

from DNA to direct the production of

proteins.

The role of RNA (Translation)


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– The roles played by DNA and RNA are

similar to the master plans and blueprints

used by builders.

The role of RNA (Translation) - cont

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– A master plan has all the information

needed to construct a building. Builders

never bring a valuable master plan to the

building site, where it might be damaged

or lost. Instead, they prepare inexpensive,

disposable copies of the master plan

called blueprints.



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– Similarly, the cell uses DNA “master plan”

to prepare RNA “blueprints.”

– The DNA molecule stays safely in the

cell’s nucleus, while RNA molecules go to

the protein-building sites in the

cytoplasm—the ribosomes.

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– You can think of an RNA molecule, as a

disposable copy of a segment of DNA, a

working copy of a single gene.

– RNA has many functions, but most RNA

molecules are involved in protein

synthesis only.

– RNA controls the assembly of amino acids

into proteins. Each type of RNA molecule

specializes in a different aspect of this job.


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Function of RNA

– The three main types of RNA are

messenger RNA, ribosomal RNA, and

transfer RNA.

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– Most genes containinstructions forassembling amino acidsinto proteins.

– The RNA molecules thatcarry copies of theseinstructions are known

as messenger RNA(mRNA): They carryinformation from DNAto other parts of the cell.

Messenger of RNA


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• A critical feature of mRNA and how it is

translated is the fact that each three

nucleotides in the mRNA is called a codon

and it is the codon that is translated.

• Thus the sequence of codons corresponds to

the sequence of amino acids in the

polypeptide.

Messenger of RNA

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– Proteins are assembled

on ribosomes, small

organelles composed of

two subunits.

– These ribosome subunits

are made up of severalribosomal RNA (rRNA)

molecules and as many

as 80 different proteins.

Ribosomal of RNA


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– You will see that the tRNA molecules

have a set of three nucleotide bases

at one end that are complementary to

a corresponding codon. The bases on

the tRNA are called the anti codon.

– This is critical because the anti

codons make the connection between

the codons and the correct aminoacids that go with each codon.

Transfer of RNA

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– When a protein is

built, a transfer RNA

(tRNA) molecule

transfers each amino

acid to the ribosome

as it is specified by

the coded messages in

mRNA.

Transfer of RNA


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Compartmentalization of processes

(thus, transport is important)

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Buffer Solution


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Buffer Solutions

• A buffer is a solution characterised by the

ability to resist changes in pH when limited

amounts of acid or base are added to it.

• Buffers contain either a weak acid and its

conjugate base or a weak base and its

conjugate acid.

• Thus, a buffer solution contains both an acid

species and a base species in equilibrium.

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• In a solution there is an equilibrium between aweak acid, HA, and its conjugate base, A-.

• When hydrogen ions are added to the solutionthe equilibrium moves to the left, inaccordance with Le Chatelier's principle, asthere are hydrogen ions on the right-hand sideof the equilibrium expression. When hydroxideions are added the equilibrium moves to theright as hydrogen ions are removed in thereaction H+ + OH- → H2O.

Buffer Solutions


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• The acid dissociation constant for a weakacid, HA, is defined as

• Simple manipulation with logarithms givesthe Henderson-Hasselbalch equation, whichdescribes pH in terms of pKa

Buffer Solutions

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Buffer Solutions

• In this equation [A−] is the concentration of theconjugate base and [HA] is the concentration of theacid. It follows that when the concentrations ofacid and conjugate base are equal, often describedas half-neutralization, pH = pKa.

• Maximum buffering capacity is found when pH =pKa, and buffer range is considered to be at pH =pKa±1.

• In general a buffer solution may be made up ofmore than one weak acid and its conjugate base; ifthe individual buffer regions overlap a widerbuffer region is created by mixing the twobuffering agents.


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Buffer Solutions

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Buffer Solutions


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Application of Buffer

• Their resistance to changes in pH makes buffersolutions very useful for chemical manufacturing

and essential for many biochemical processes. The

ideal buffer for a particular pH has a pKa equal to

that pH, since such a solution has maximum buffer

capacity.

• Buffer solutions are necessary to keep the correct

pH for enzymes in many organisms to work. Many

enzymes work only under very precise conditions; if

the pH strays too far out of the margin, the enzymesslow or stop working and can denature, thus

permanently disabling its catalytic activity.

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• A buffer of carbonic acid (H2CO3) and bicarbonate

(HCO3−) is present in blood plasma, to maintain a

pH between 7.35 and 7.45.

• Industrially, buffer solutions are used in

fermentation processes and in setting the correct

conditions for dyes used in colouring fabrics. They

are also used in chemical analysis and calibration

of pH meters.• Majority of biological samples that are used in

research are made in buffers specially PBS

(phosphate buffer saline) at pH 7.4.

Application of Buffer


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Summary

• Biological systems are composed of carbon,

oxygen, hydrogen, and nitrogen.(Note: somecellular molecules contain metals and sulfuris frequently present in disulfide bonds.)

• These molecules are used to build lipids,proteins, carbohydrates, and nucleic acids,the building blocks for cell structure andchemical reagents for cell function.

• Proteins conduct the business of the cell by

regulating cell function.• Carbohydrates serve primarily as energy

sources.

• The receptors on the surface of the cell are

primarily carbohydrates. They are highly

specific and receive molecules destined to

enter the cell.

• The information structure of the cell is

found in nucleotides.

Summary

introduction & biomolecules

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