Wk 2 Biochem

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CHNG 3804 CHNG 3804 Biological SystemsBiological Systems

Introductory Biochemistry

Fariba Dehghani

Why do you need to know this?Why do you need to know this?

• Biochemistry explains how living organisms operateBioprocess engineering seeks to exploit biological

processes

““Mother Nature does it betterMother Nature does it better””

The molecular logic of life The molecular logic of life

Living organismsLiving organisms• are structurally very complex• have highly organised structures • use energy to maintain themselves• have the capacity for self-replication

DNA information

Protein synthesis

BiomacromoleculesBiomacromolecules

• Built from a few simple organic compounds of molecular weight < 500

• All built from the same building blocks

• There are underlying patterns in their structures

• The identity of each organism is preserved through its having distinctive sets of biomacromolecules

Chemicals of LifeChemicals of LifePercentage of Dry Weight E.coliElement

50Carbon

20Oxygen

14Nitrogen

8Hydrogen

3Phosphorus

1Sulfur

1Potassium

1Sodium

0.5Calcium

0.5Magnesium

0.5Chlorine

0.2Iron

~0.3All others

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Chemicals of LifeChemicals of Life

• Water• Lipids• Sugars and Polysaccharides• DNA and RNA• Amino Acids and Proteins• Enzymes

LipidsLipids

• Biological Compounds which are soluble in non-polar solvents and practically insoluble in water.

• Glycerides and waxes form a sub-group of compounds which have an ester as the major functional group and include: waxes, fats, triglycerides, and phospholipids

• Another diverse group of compounds which do not have any ester functional groups are also classified as lipids.

– steroids, fatty acids, soaps, sphingolipids, and prostaglandins.• Lipid Functions:

– Fats and lipids are important because they serve as energy source, as well as a storage for energy in the form of fat cells.

– Lipids have a major cellular function as structural components in cell membranes. These membranes in association with carbohydrates and proteins regulate the flow of water, ions, and other molecules into and out of the cells.

– Hormone steroids and prostaglandins are chemical messengers between body tissues.

– Vitamins A, D, E, and K are lipid soluble and regulate critical biological processes. Other lipids add in vitamin absorption and transportation.

– Lipids act as a shock absorber to protect vital organs and insulate the body from temperature extremes.

http://www.elmhurst.edu/~chm/vchembook/555lipidsII.html

Lipid ClassificationFatty Acids

Saturated Fatty Acids

Unsaturated Fatty Acids

Soap (salt of fatty acid)

Prostaglandins

Glycerides

Triglycerides

Phosphoglycerides

Non glyceride Lipids

Waxes

Steroids

Sphingolipids

Lipoproteins

Fatty AcidsFatty Acids

• Fatty Acids have the general formulaCH3-(CH2)n-COOH

• The value of n is an even number typically between 12-20

• Can be unsaturated– Linoleic acid (omega3):CH3(CH2)4CH=CH(CH2)CH(CH2)7COOH– Linolenic acid(omega6): CH3(CH2-CH=CH)3(CH2)7COOH

• Hydrocarbon chain nearly insoluble in water.• Carboxyl group is hydrophilic• Form orientated mono-layers with water at low

concentrations and micelles at higher concentrations.

MonolayerMonolayer

Water

Air

Fats

• Fats are Glycerol tri-esters of Fatty Acids.

CH2OH HO-OC(CH2)n1-CH3 CH2OOC(CH2)n1-CH3

I ICHOH + HO-OC(CH2)n2-CH3 = CHOOC(CH2)n2-CH3

I ICH2OH HO-OC(CH2)n3-CH3 CH2OOC(CH2)n3-CH3 +3H2O

• Hydrolyzed to Glycerol and soap by heating in alkaline solution.

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PhosphoglyceridesPhosphoglycerides• Similar to Fats in structure, phosphoric acid replaces

the carboxylic acid in the fatty acid.• Will form micelles at high concentrations.• Also form flat bilayers. • Biological plasma membranes typically contain

appreciable quantities of phospholipids and other polar lipids.

• Phospholipid bilayers can serve as study systems for cell membranes.

http://www.elmhurst.edu/~chm/vchembook/555lipidsII.html

BilayersBilayers

• Impermeable to highly charged species.

• Allows cell to contain charged nutrients and metabolic intermediates.

• Can be modified to change transport properties.

Lipid Lipid BilayersBilayers Lipids (Continued)Lipids (Continued)

• Waxes– Composed of long chain of carboxylic acid and long chain

alcohols– Serve as protective coating for both plants and animals.

• Steroid (sex hormones & cholesterol)– A fused rings system consisting of 3 six-member rings and

one five member ring. – highly hydrophobic having only single hydroxyl group – It is widely spread in biological but not in prokaryotic cell

membranes.– harmful effects on health. It will develop athersclerosis a

condition in which lipid deposits block the blood vessels and lead to heart diseases.

Lipid Soluble Vitamins Lipid Soluble Vitamins

• Vitamin A: The unsaturated hydrocarbon β-carotene is the precursor for vitamin A (retinol). When an organism require vitamin A, β-carotene is converted to the vitamin A with enzymatic reaction in liver. A derivative of vitamin A paly a crucial role in vision when it is bound to a protein called opsin.

• Vitamin D: such as cholescalciferol (D3) is formed from cholesterol by the action of UV from the sun, and further processed in the body to form hydroxylated derivatives. The presence of vitamin D3, increased synthesis of a Ca-binding protein, which increases in absorption of dietary calcium. This process results in calcium uptake by the bone.

• A deficiency in vitamin D lead to rickets, a conditions that the bones of growing children become soft.

• Vitamin E: The most active form of vitamin E is α-tocopherol. That is an anti-oxidant (a good reducing agent). Therefore it reacts oxidising agents before they can attack other biomolecules. The interaction of vitamin E with membranes enhances its effectiveness as anti-oxidant. Another function of Vitamin E is to react with, and thus remove, the very reactive and highly dangerous substances known as free radicals. A free radical has at least one unpaired electron, which accounts for its high degree of reactivity. Free radicals may paly a part in the development of cancer and in the aging process.

• Vitamin K: This vitamin is an important factor in the blood clotting process. It is a bicyclic ring system contains two carbonyl groups, the only polar groups on the molecule. There is a long unsaturated hydrocarbon side chain that consists of repeating isoprene units, the number of which determines the exact form of vitamin K.

Sugars and PolysaccharidesSugars and Polysaccharides

• Monosaccharides (simple sugars) are the smallest carbohydrates containing 3 to 9 carbons (CH2O)n.

• D-glucose is by far the most common simple sugar, other sugars are found in microorganisms.

• D-glucose is normally present as a ring structure

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GlucoseGlucose Five Five MemberedMembered SugarsSugars

D-Ribose

O

OH

OH OH

CH2OH O

OH

OH

CH2OH

Deoxyribose

Major components of the nucleic acid monomers of DNA and RNA and other biochemicals

DisaccharidesDisaccharides

• Sucrose: Glucose and Fructose• Maltose: Glucose and Glucose• Lactose: Glucose and Galactose

O

OH

OH

CH2OH

CH2OH

FructoseOH

O

CH2OH

OH OHOH

Glucose

O

CH2OH

OH

OHOH

OHGalactose

Polysaccharides Formation from Monosaccharides

Madigan, M. T.; Martinko, J. M., Brock Biology of Microorganisms, 2006

StarchesStarches

• Starch is a polymer of glucose.• Strait chain polymers Amylose• Branched chained polymers Amylopectin• Highly branched chain polymers Glycogen.

AmyloseAmylose

• Water Insoluble• Molecular weight: several thousand to 1

million.

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AmylopectinAmylopectin

• Branched – average amylose segment between branches is 25 glucose monomers.

• Molecular weights 1 to 2 million.• Form Gels with water.

AmylopectinAmylopectin

CelluloseCellulose

• Glucose polymer.• Structural material in plants, e.g. Cotton and

Wood.• Differs from starch by the bonding.

Polysaccharides Formation from Monosaccharides

Madigan, M. T.; Martinko, J. M., Brock Biology of Microorganisms, 2006

CelluloseCellulose

• Estimated 1011tons per year of cellulose formed in the biosphere.

• More difficult to breakdown than starches.• Active area of research for ethanol

production.• Cellulose is often encased in Lignin.

DNA and RNADNA and RNA

• Deoxyribonucleic acid (DNA)• Ribonucleic acid (RNA)• Genes are long stretches of double helical

DNA.• In a process mediated by RNA, DNA

specifies the amino acid sequence of a protein which in turn specifies its structure.

• Both DNA and RNA consist of nucleotides joined by phosphodiester bonds to form a sugar-phosphate backbone.

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Madigan, M. T.; Martinko, J. M., Brock Biology of Microorganisms, 2006 Madigan, M. T.; Martinko, J. M., Brock Biology of Microorganisms, 2006

Nucleic acids

• http://www.blc.arizona.edu/Molecular_Graphics/DNA_Structure/DNA_Tutorial.HTML

• http://web.indstate.edu/thcme/mwking/nucleic-acids.html#nomenclature• http://www.people.virginia.edu/~rjh9u/dnareq2.html• http://learn.genetics.utah.edu/units/basics/

<>

http://www.hcs.ohio-state.edu/hcs300/biochem2.htm

AdenineAdenine--ThymineThymineGuanineGuanine--cytosinecytosineUracil replace T in RNA.Uracil replace T in RNA.

Nitrogenous base in DNA & RNA moleculesNitrogenous base in DNA & RNA molecules

DNADNA

• Informational Biopolymer.• Consists of two anti parallel

helical strands.• Bases

– Cytosine (C)– Thymine (T)– Adenine (A)– Guanine (G)

• G is always paired with C• A is always paired with T

http://en.wikipedia.org/wiki/Dna

DNA StructureDNA Structure

“We wish to put forward a radically different structure for the salt of deoxyribose nucleic acid. This structure has two helical chains each coiled around the same axis. We have made the usual chemical assumptions, namely, that each chain consists of phosphate diester groups joining β-D-deoxyribofuranose residues with 3',5' linkages. The two chains (but not their bases) are related by a dyad perpendicular to the fiber axis. Both chains follow right-handed helices, but owing to the dyad the sequences of the atoms in the two chains run in opposite directions.”

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DNA and GeneticsDNA and Genetics

“It has been found experimentally that the ratio of the amounts of adenine to thymine, and the ratio of guanine to cytosine, are always very close to unity for deoxyribose nucleic acid.”

“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”

DNA ReplicationDNA Replication

• The sequence of the four different nitrogenous bases along the chain carries genetic information.

• The two strands of DNA run in opposite directions.

• Each helix can serve as a template for the replication of another.

• Semi-conservative replication.

Structure of DNA

• DNA is a long chain of nucleotides which consist of :

• Deoxyribose (a pentose = sugar with 5 carbons)

• Phosphoric Acid • Organic (nitrogenous)

bases (Purines - Adenine and Guanine, or Pyrimidines -Cytosine and Thymine

• DNA consists of two associated polynucleotide strands that wind together in a helical fashion.

• Each polynucleotide is a linear polymer in which the monomers (deoxynucleotides), are linked together by means of phosphodiesterbridges , or bonds. These bonds link the 3' carbon in the ribose of one deoxynucleotide to the 5' carbon in the ribose of the adjacent deoxynucleotide.

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DNA Replication Growth of replication forks as DNA is replicated base by base

Semiconservative replication would produce two DNA molecules, each of which was composed of one-half of the parental DNA along with an entirely new complementary strand. In other words the new DNA would consist of one new and one old strand of DNA. The existing strands would serve as complementary templates for the new strand.

Crick’s ‘Central Dogma’

Central DogmaCentral Dogma

• The Central Dogma of biology is that information flow

• DNA=> RNA=>Protein• The first step is called transcription• The second is called translation• DNA is protected• Multiple RNA can be made• Better control of Gene Expression

RNARNA

• DNA stores instructions for the synthesis of RNA.

• A segment of DNA which codes for an RNA molecule is called a gene.

• RNA sequences are constructed using information from DNA.

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RNA BasesRNA Bases

• Bases – Cytosine (C)– Uracil (U)– Adenine (A)– Guanine (G)

DNA to RNADNA to RNA

CG

GC

UA

AT

RNA (Being Assembled)DNA (Template)

Types of RNATypes of RNA

• There are three types of RNA– Messenger RNA (mRNA)– Ribosomal RNA (rRNA)– Transfer RNA (tRNA)

http://learn.genetics.utah.edu/units/basics/

mRNAmRNA

• mRNA is complementary to a base sequence from a gene in DNA.

• mRNA directs amino acid sequence of proteins.

• Vary from 103-104 nucleotides in length.

rRNArRNA

• Ribosomes consist of proteins and rRNA.• Ribosomes are the site for protein synthesis.• rRNA is large and only a few types are found

in each cell.

tRNAtRNA

• tRNA transfers amino acids to Ribosomes.• At least one, and frequently several types of

tRNA for each amino acid.

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RNA polymerase opens the part of the DNA to be transcribed. Only one strand of DNA (the template strand) is transcribed. RNA nucleotides are available in the region of the chromatin (this process only occurs during Interphase) and are linked together similar to the DNA process

Generation of mRNA

• Ribosomes are the organelle where proteins are synthesized.

• They consist of two-thirds rRNA and one-third protein. Ribosomes consist of a small (in E. coli , 30S) and larger (50S) subunits

• The smaller subunit has a binding site for the mRNA.

• The larger subunit has two binding sites for tRNA.

• tRNA carries the proper amino acid to the ribosome when the codons call for them.

• At the top of the large loop are three bases, the anticodon, which is the complement of the codon.

• There are 61 different tRNAs, each having a different binding site for the amino acid and a different anticodon

Translation• Translation is the process of converting the

mRNA codon sequences into an amino acid sequence.

• The initiator codon (AUG) codes for the amino acid N-formylmethionine (f-Met). No transcription occurs without the AUG codon. f-Met is always the first amino acid in a polypeptide chain, although frequently it is removed after translation.

• The imitator tRNA/mRNA/small ribosomal unit is called the initiation complex. The larger subunit attaches to the initiation complex.

• After the initiation phase the message gets longer during the elongation phase

• New tRNAs bring their amino acids to the open binding site on the ribosome/mRNA complex, forming a peptide bond between the amino acids.

• The complex then shifts along the mRNA to the next triplet, opening the A site. The new tRNA enters at the A site. When the codon in the A site is a termination codon, a releasing factor binds to the site, stopping translation and releasing the ribosomal complex and mRNA.

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Often many ribosomes will read the same message, a structure known as a polysomeforms. In this way a cell may rapidly make many proteins (Hb)

ProteinsProteins

• Proteins are important biological molecules, typically making up 30 to 70 percent of cells on a dry weight basis

• Proteins are essentially non-repeating polymers of amino acids, however they may contain other molecules and atoms.

• Those that only contain amino acids are termed simple proteins, those, which contain other molecules or atoms, are termed conjugate proteins.

• Small polymers, those below 6,000-10,000 molecular weight (MW) are commonly termed polypeptides with the term protein being restricted to those that are larger than 10,000 MW.

The Peptide BondThe Peptide Bond

• Amino acids can be joined by a covalent bond between the αααα-carboxyl and the αααα-amino groups.

• Water is eliminated in the process.• Usually written as a single bind.• Some double bond character - limited

rotation.

Poly PeptidesPoly Peptides

• A number of small peptides are of biological and commercial importance.

• L-Aspartyl-L-phenyalanine is 200 times sweeter than sugar.

• The methyl ester is known as Aspartame an marketed as Nutra Sweet.

• Hormones:– Oxytocin induces labour.– Vasopressin controls blood pressure and

readsorption of water by the kidneys.– These hormones have very similar structures,

differing by only one amino acid.

Production of proteins in cellsProduction of proteins in cells

• Assembly of amino acids in correct sequence– in the ribosome

• Post-translational modification- In the Golgi body

• Folding of the peptide chain– Chaperone proteins

http://en.wikipedia.org/wiki/Golgi_Apparatus

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Ensuring the correct amino acid Ensuring the correct amino acid sequence sequence -- the genetic codethe genetic code

• Transcription– DNA to RNA

• Translation– RNA to protein

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Please see the website : http://learn.genetics.utah.edu/units/basics/

Proteins

• http://www.johnkyrk.com/aminoacid.html• http://web.indstate.edu/thcme/mwking/amino-

acids.html• http://www.sp.uconn.edu/~bi107vc/fa02/terry/pro

teins.html

• http://www.bbc.co.uk/education/asguru/biology/02biologicalmolecules/01proteins/13structures/index.shtml

Building blocks: amino acids

http://www.sp.uconn.edu/~bi107vc/fa02/terry/proteins.html

Amino acids – protein building blocks


Peptide bonds link amino acidsPeptide bonds link amino acids

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Amino AcidsAmino Acids

• Amino group and Carboxyl group bonded to αααα carbon.

• The αααα carbon is also bonded to H and Side group R

• Only 20 amino acids are usually found in nature

• Most are Chiral, only L form found in proteins.

• Exist as Zwitterions at neutral pH

VValValine

YTyrTyrosine

WTrpTryptophan

TThrThreonine

SSerSerine

PProProline

FPhePhenyalanine

MMetMethionine

KLysLysine

LLeuLeucine

IIleIsoleucine

HHisHistidine

GGlyGlycine

QGlnGlutamine

EGluGlutamic Acid

CCysCysteine

DAspAspartic Acid

NAsnAsparagine

RArgArginine

AAlaAlanine

One Letter AbbreviationThree Letter AbbreviationAmino Acid

ProteinsProteins

• The structure of proteins is of great importance to their function. The structure of a protein is described by up to 4 levels. These levels are termed the primary, secondary, tertiary and quaternary structure.

Primary StructurePrimary Structure

• The primary structure of a protein is the order of the amino acids in the polymer.

• Every protein has its own unique amino acid sequence


Secondary StructureSecondary Structure

• The secondary structure of the protein refers to the structural configuration of neighbouring amino acid residues.

• Due to the planar (partial double bond) nature of the peptide link, only limited rotation is possible.

• Helix and sheet structures are the most common structures.

Peptide chains fold to give more stable secondary Peptide chains fold to give more stable secondary structuresstructures

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Tertiary StructureTertiary Structure

• The tertiary structure is the overall 3-D structure. • Cross links, disulfide bonds between cysteine

amino acids are of great importance to the 3-D structure

• As are the interactions between bulky side groups, such as those found on phenyalanineand tryptophan.

Quaternary StructureQuaternary Structure

• The quaternary structure refers to how protein chains fit together

Protein subProtein sub--units are assembled to give units are assembled to give oligomericoligomeric structure structure -- ““quaternary structurequaternary structure””

Protein structure/functionProtein structure/function

• Each protein has function determined by – its amino acid structure– 3-d protein folding

• Folding is essential for function

• A prosthetic group may be included (eg., haem or Cu2+)

• Identity depends on– Amino acid sequence = primary structure– Folding = secondary and tertiary structure

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Functions of ProteinsFunctions of Proteinsall depend on molecular interactionsall depend on molecular interactions

• Enzymes (trypsin that hydrolyze some peptides)

• Regulatory (hormones, insulin that regulate the glucose metabolism)

• Transport (hemoglobin that transport O2 in blood)

• Motions (muscle, cilia)

• Communication – nerves

• Protective (antibodies form complexes with foreign molecules)

• Toxins (causes disease, clostridium botulinum toxin that causes bacterial food poisoning)

• Storage (casein in milk protein)

• Contractile (dynein in cilia & flagella)

• Contribute in structural of cell membrane (collagen and elastin for cartilage and ligaments)

MultimericMultimeric ProteinsProteins

• Use a few general motifs• Sub-units usually associate by non-covalent

bonding• Maybe homo-oligomeric or hetero-oligomeric• Must be assembled to function• May share an active site


Fibrous proteins are insoluble Fibrous proteins are insoluble egeg., fibroin in silk., fibroin in silk

Protein function Protein function –– transporttransport

[Trans-membrane transport]

Proteins are easily denatured Proteins are easily denatured �� loss of functionloss of function Protein FoldingProtein Folding

• The exact mechanism of in vivo protein folding is not fully understood. However, it is thought that folding is initiated by the unique amino acid sequence of the protein.

• This is still an ongoing area of research

• http://ocw.mit.edu/OcwWeb/Biology/7-88JProtein-Folding-ProblemFall2003/CourseHome/index.htm

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SummarySummary

• In this lecture we have a brief introduction to some important biochemicals– Lipids– Sugars and Polysaccharides– DNA and RNA– Amino Acids and Proteins

ReferencesReferences

• Bailey J. E., Ollis D. F., Biochemical Engineering Fundamentals, 2nd

Edition, 1986, McGrawHill Book Company• Campbell M. K., Biochemistry. Saunders College publishing

Harcourt Brace College Publisher,1999• http://learn.genetics.utah.edu/units/basics/ • http://en.wikipedia.org/wiki/Dna• http://www.bbc.co.uk/education/asguru/biology/02biologi

calmolecules/01proteins/13structures/index.shtml• Some part of this lecture was adapted from seminar presented by S.

G. Burton in School of Chemical and biomolecular Engineering in 2005.

Wk 2 Biochem

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