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CHNG 3804
Biological Systems

Biochemistry explains how living organisms operate

Bioprocess engineering seeks to exploit biological
processes

Introductory Biochemistry
Fariba Dehghani
Mother Nature does it better
better

The molecular logic of life

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

Biomacromolecules
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

DNA
information

Protein
synthesis

Chemicals of Life
Element

Percentage of Dry Weight E.coli

Carbon

50

Oxygen

20

Nitrogen

14

Hydrogen

Phosphorus

Sulfur

Potassium

Sodium

Calcium

0.5

Magnesium

0.5

Chlorine

0.5

Iron

0.2

All others

~0.3

Chemicals of Life

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

Lipids

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.

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.

Lipid Functions:

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

Lipid Classification

Fatty Acids

Fatty Acids

Fatty Acids have the general formula

CH3-(CH2)n-COOH
The value of n is an even number typically between
12-20
Can be unsaturated

Saturated Fatty Acids

Unsaturated Fatty Acids
Soap (salt of fatty acid)
Prostaglandins
Glycerides
Triglycerides

Linoleic acid (omega3):CH3(CH2)4CH=CH(CH2)CH(CH2)7COOH

Linolenic acid(omega6): CH3(CH2-CH=CH)3(CH2)7COOH

Phosphoglycerides

Hydrocarbon chain nearly insoluble in water.

Carboxyl group is hydrophilic
Form orientated mono-layers with water at low
concentrations and micelles at higher
concentrations.

Non glyceride Lipids

Waxes
Steroids
Sphingolipids
Lipoproteins

Monolayer

Fats
Fats are Glycerol tri-esters of Fatty Acids.

Air

Water

CH2OH
I
CHOH +
I
CH2OH

HO-OC(CH2)n1-CH3

CH2OOC(CH2)n1-CH3
I
HO-OC(CH2)n2-CH3 = CHOOC(CH2)n2-CH3
I
HO-OC(CH2)n3-CH3
CH2OOC(CH2)n3-CH3 +3H2O

Hydrolyzed to Glycerol and soap by heating in

alkaline solution.

Phosphoglycerides

Bilayers

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.

Impermeable to highly
charged species.
Allows cell to contain
charged nutrients and
metabolic intermediates.
Can be modified to change
transport properties.

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

Lipid Bilayers

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

Vitamin A: The unsaturated hydrocarbon -carotene is the precursor for vitamin A

(retinol). When an organism require vitamin A, -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 -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 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

Glucose

Five Membered Sugars

O

CH2OH

CH2OH

OH
OH

OH

OH
OH

Deoxyribose

D-Ribose

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

Polysaccharides Formation from Monosaccharides

Disaccharides
Sucrose: Glucose and Fructose
Maltose: Glucose and Glucose
Lactose: Glucose and Galactose
CH2OH

CH2OH

O
CH2OH

OH

OH

OH

OH
OH

CH2OH

OH

Fructose

Glucose

O
OH
OH
OH

Galactose

Starches

OH

Starch is a polymer of glucose.

Strait chain polymers Amylose
Branched chained polymers Amylopectin
Highly branched chain polymers Glycogen.

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

Amylose
Water Insoluble
Molecular weight: several thousand to 1
million.

Amylopectin

Amylopectin

Branched average amylose segment

between branches is 25 glucose monomers.
Molecular weights 1 to 2 million.
Form Gels with water.

Cellulose

Polysaccharides Formation from Monosaccharides

Glucose polymer.
Structural material in plants, e.g. Cotton and
Wood.
Differs from starch by the bonding.

Madigan, M. T.; Martinko, J.

M., Brock Biology of
Microorganisms, 2006

Cellulose
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 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.

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.HTM
L
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/

DNA
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

Nitrogenous base in DNA & RNA molecules

AdenineAdenine-Thymine
GuanineGuanine-cytosine
Uracil replace T in RNA.

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

DNA 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 -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.

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

DNA 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 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 phosphodiester
bridges , 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.

DNA Replication

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.

Central 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

Growth of replication forks as DNA is

replicated base by base

Cricks Central Dogma

RNA
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.

RNA Bases
Bases
Cytosine (C)
Uracil (U)
Adenine (A)
Guanine (G)

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

DNA to RNA
DNA (Template)

RNA (Being Assembled)

mRNA
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.

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

rRNA
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.

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

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

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.

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

Generation of mRNA

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

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 polysome
forms. In this way a cell may rapidly make
many proteins (Hb)

Proteins
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.

Poly 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.

The Peptide Bond

Amino acids can be joined by a covalent
bond between the -carboxyl and the amino groups.
Water is eliminated in the process.
Usually written as a single bind.
Some double bond character - limited
rotation.

Production 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

11

Ensuring the correct amino acid

sequence - the genetic code
Transcription
DNA to RNA

Translation
RNA to protein

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

Proteins

Amino acids protein building blocks

Building blocks: amino acids

http://www.johnkyrk.com/aminoacid.html
http://web.indstate.edu/thcme/mwking/aminoacids.html
http://www.sp.uconn.edu/~bi107vc/fa02/terry/pro
teins.html

http://www.bbc.co.uk/education/asguru/bio
logy/02biologicalmolecules/01proteins/13s
tructures/index.shtml
http://www.sp.uconn.edu/~bi107vc/fa02/terry/proteins.html

Peptide bonds link amino acids

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

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Amino Acid

Amino Acids
Amino group and Carboxyl group bonded to
carbon.
The 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

Proteins
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.

Three Letter Abbreviation

One Letter Abbreviation

Alanine

Ala

Arginine

Arg

Asparagine

Asn

Aspartic Acid

Asp

Cysteine

Cys

Glutamic Acid

Glu

Glutamine

Gln

Glycine

Gly

G
H

Histidine

His

Isoleucine

Ile

Leucine

Leu

Lys

Methionine

Met

Phenyalanine

Lysine

Phe

Proline

Pro

P
S

Serine

Ser

Threonine

Thr

Tryptophan

Trp

Tyrosine

Tyr

Valine

Val

Primary 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

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

Secondary Structure

Peptide chains fold to give more stable secondary

structures

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.

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Tertiary 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 phenyalanine
and tryptophan.

Quaternary Structure

Protein subsub-units are assembled to give

oligomeric structure - quaternary structure
structure

The quaternary structure refers to how protein

chains fit together

Protein 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

14

Functions of Proteins

Multimeric Proteins

all 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)

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 eg.,

eg., fibroin in silk

Protein function transport

[Trans-membrane transport]
http://www.sp.uconn.edu/~bi107vc/fa02/terry/proteins.html

Proteins are easily denatured

loss of function

Protein 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

15

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

References

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

Some part of this lecture was adapted from seminar presented by S.

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

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

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