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CHNG 3804
Biological Systems
Introductory Biochemistry
Fariba Dehghani
Mother Nature does it better
better
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
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.
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
Phosphoglycerides
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
Phosphoglycerides
Bilayers
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.
Glucose
CH2OH
CH2OH
OH
OH
OH
OH
OH
Deoxyribose
D-Ribose
Major components of the nucleic acid monomers of DNA and RNA and other
biochemicals
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
Amylose
Water Insoluble
Molecular weight: several thousand to 1
million.
Amylopectin
Amylopectin
Cellulose
Glucose polymer.
Structural material in plants, e.g. Cotton and
Wood.
Differs from starch by the bonding.
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.
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)
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 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 Replication
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
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)
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
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
10
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.
http://en.wikipedia.org/wiki/Golgi_Apparatus
11
Translation
RNA to protein
Proteins
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
http://www.sp.uconn.edu/~bi107vc/fa02/terry/proteins.html
12
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.
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
13
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 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
Communication nerves
[Trans-membrane transport]
http://www.sp.uconn.edu/~bi107vc/fa02/terry/proteins.html
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
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
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