UNIT I

• Introduction to Biochemistry
• Macromolecules
• Central Dogma of Molecular Biology
• Structure of nucleic acids
• Amino acids
• Protein: Architecture, conformational flexibility, folding
problem and validation
• Enzymes: Introduction, enzyme mechanisms
Levels of Organization in Nature
 Biochemistry:
Where Chemistry & Biology Meet
• Living things require millions of chemical
reactions just to survive.
• Metabolism = all the chemical reactions
occurring in the body.
• Organic molecules:
– usually associated with living things.
– always contain CARBON.
– are “large” molecules, with many atoms
– always have covalent bonds (share electrons)
 Biochemistry and Human Biology
• Biochemistry: Science concerned with the chemical
constituents of living cells and with the reaction and process
that they undergo.
– Complete understanding at the molecular level of all the chemical
processes associated with living cells
– Biochemistry of less complex form of life is often direct relevance to
human biochemistry

• Reciprocal relationship between biochemistry and medicine

has stimulated mutual advance
– Biochemistry studies have illuminated many aspects of health & disease
 Biochemistry

Nucleic
acid Protein Lipid Carbohydrates

Sickle cell Atherosclerosis Diabetes

Genetic
anemia mellitus
disease

Medicine
 Giant Molecules - Polymers

•Large molecules are called polymers

•Polymers are built from smaller

molecules called monomers

•Biologists call them macromolecules

Macromolecules in Organisms
• There are four categories of large molecules in cells:

Carbohydrates
Lipids
Proteins
Nucleic Acids
 Carbohydrates
•Carbohydrates
include:
–Small sugar
molecules in soft
drinks
–Long starch
molecules in rice,
wheat, pasta and
potatoes
 Linking Monomers

Cells link monomers by a process called

condensation or dehydration synthesis
(removing a molecule of water)

Remove
H

H2O Forms

Remove OH

This process joins two sugar monomers to

make a double sugar
 Breaking Down Polymers

• Cells break down

macromolecules by
a process called
hydrolysis (adding a
molecule of water)

Water added to split a double sugar

 Monosaccharides

• Called simple sugars

Include glucose, fructose,

& galactose

Have the same

chemical, but different
structural formulas

C6H12O6
 Disaccharides

•A disaccharide is a
double sugar.
They’re made by
joining two
monosaccharides
Involves removing a
water molecule
(condensation)

Bond called a GLYCOSIDIC bond

 Polysaccharides

•Complex
carbohydrates

Composed of many
sugar monomers linked
together
Glucose Monomer
Polymers of
Starch
monosaccharide
chains
Glycogen

Cellulose
 Lipids
• Lipids are hydrophobic –”water fearing”
• Do NOT mix with water
• Includes fats, waxes, steroids, & oils
•Fats store energy,
help to insulate
the body, and
cushion and
protect organs

FAT MOLECULE

13
 Types of Fatty Acids
Saturated fatty acids have the Single
Bonds in
maximum number of Carbon
hydrogens bonded to the chain
carbons (all single bonds
between carbons)

Unsaturated fatty acids have

less than the maximum number
of hydrogens bonded to the
carbons (a double bond
between carbons)
Double bond in carbon chain

14
 Triglyceride
• Monomer of lipids
• Composed of Glycerol & 3
fatty acid chains
• Glycerol forms the
“backbone” of the fat

Organic Alcohol
(-OL ending)

Glycerol Fatty Acid Chains

 Lipids & Cell Membranes
• Cell membranes are made of lipids
called phospholipids
• Phospholipids have a head that is
polar & attract water (hydrophilic)
• Phospholipids also have 2 tails that
are nonpolar and do not attract
water (hydrophobic)

Cell membrane with proteins &

phospholipids
 Proteins

• Proteins are polymers made of monomers called

amino acids

All proteins are made of 20 different amino acids

linked in different orders

Proteins are used to build cells, act as hormones

& enzymes, and do much of the work in a cell
 Nucleic Acids
•Store
hereditary
information
•Contain
information for
making all the
body’s proteins
•Two types exist ---
DNA & RNA
 DNA-Deoxyribonucleic acid
Backbone

Nucleotide
•Two strands of
DNA join
together to form
a double helix
Base
pair
•Nucleotides form long
chains called DNA Bases

•Nucleotides are joined by

sugars & phosphates on DNA strand
the side
Double helix
 Nucleic Acids
Nitrogenous base
(A,G,C, or T)

Nucleic acids
are polymers
of nucleotides Phosphate
group
Thymine (T)

Sugar
(deoxyribose)
Phosphate

Base
Sugar

Nucleotide
 Bases
•Each DNA
nucleotide has one of
the following bases:

Thymine (T) Cytosine (C)

–Adenine (A)

–Guanine (G)

–Thymine (T)

–Cytosine (C)
Adenine (A) Guanine (G)
 RNA – Ribonucleic Acid
Nitrogenous base
•Ribose sugar has (A,G,C, or U)

an extra –OH or
hydroxyl group

•It has the base

uracil (U) instead of Phosphate
Uracil

thymine (T) group

Sugar (ribose)
Macromolecules
Central Dogma of Molecular Biology

DNA RNA PROTEIN

Storage Transmission
medium medium
 Protein Synthesis DNA
 The production
Transcription
(synthesis) of Prokaryotic mRNA
polypeptide chains Cell
Translation
(proteins) Ribosome

 Two phases: Protein

Transcription & Nuclear membrane

Translation Eukaryotic DNA

Cell
 mRNA must be Transcription
Pre-mRNA
processed before it
RNA Processing
leaves the nucleus of mRNA
eukaryotic cells Ribosome

Translation
Protein
 Discovery of DNA structure
 Walter Sutton discovered chromosomes were
made of DNA and Protein
 However, scientists were NOT sure which one
(protein or DNA) was the actual genetic
material of the cell
 Frederick Griffith in 1928 showed the DNA was
the cell’s genetic material
• Rosalind Franklin took diffraction x-ray
photographs of DNA crystals
• Watson & Crick in the 1950’s built the 1st
model of DNA

Rosalind Franklin
 Discovery of DNA Structure
• Erwin Chargaff showed the amounts of the four
bases on DNA ( A,T,C,G)
• In a body or somatic cell:
A = 30.3%
T = 30.3%
G = 19.5%
C = 19.9%
• Chargaff’s rule:
– Adenine must pair with Thymine
– Guanine must pair with Cytosine
– The bases form weak hydrogen bonds

T A G C
 Structure of DNA
 DNA is made of subunits called nucleotides
 DNA nucleotides are composed of a phosphate,
deoxyribose sugar, and a nitrogen-containing base
 The 4 bases in DNA are: adenine (A), thymine (T),
guanine (G), and cytosine (C)
• Purines have single rings of carbon-nitrogen (G,
A)
• Pyrimidines have double carbon-nitrogen rings
(C, T)
• This is called complementary base pairing because
a purine is always paired with a pyrimidine
 5’ to 3’ Sugars
When the DNA double helix
. unwinds, it resembles a
ladder
Anti-Parallel Strands of
The sides of the ladder are DNA
the sugar-phosphate
backbones
The rungs of the ladder are
the complementary paired
bases
The two DNA strands are
anti-parallel (they run in
opposite directions)
 Steps in DNA Replication
Occurs when chromosomes
duplicate (make copies)
An exact copy of the DNA is
produced with the aid of the
enzyme DNA polymerase
Hydrogen bonds between bases
break and enzymes “unzip” the
molecule
Each old strand of nucleotides
serves as a template for each new
strand
New nucleotides move into
complementary positions are
Two New, Identical
joined by DNA polymerase DNA Strands Result
from Replication
Another View of Replication
 RNA Differs from DNA

1. RNA has a sugar ribose

DNA has a sugar deoxyribose
2. RNA contains the base uracil (U)
DNA has thymine (T)
3. RNA molecule is single-stranded
DNA is double-stranded
.
Three Types of RNA
• Messenger RNA (mRNA) carries genetic
information to the ribosomes
(blueprint for the construction of a protein)

• Ribosomal RNA (rRNA), along with protein,

makes up the ribosomes
(construction site where the protein is made)

• Transfer RNA (tRNA) transfers amino acids to

the ribosomes where proteins are synthesized
(truck delivering the proper amino acid to the site at
the right time)
 Genes & Proteins
 Proteins are made of amino acids linked together by peptide bonds
 20 different amino acids exist
 Amino acids chains are called polypeptides
 Segment of DNA that codes for the amino acid sequence in a protein are
called genes

Genetic Code:
 DNA contains a triplet code
 Every three bases on DNA stands for ONE amino acid
 Each three-letter unit on mRNA is called a codon
 Most amino acids have more than one codon!
 There are 20 amino acids with a possible 64 different triplets
 The code is nearly universal among living organisms
35
 Overview of Transcription
 During transcription in the
nucleus, a segment of DNA
unwinds and unzips, and the DNA
serves as a template for mRNA
formation
 RNA polymerase joins the RNA
nucleotides so that the codons in
mRNA are complementary to the
triplet code in DNA
 The transfer of information in the
nucleus from a DNA molecule to
an RNA molecule
 Only 1 DNA strand serves as the
template
 Starts at promoter DNA (TATA
box)
 Ends at terminator DNA (stop)
 When complete, pre-RNA
molecule is released
 RNA Polymerase
 Enzyme found in the nucleus
 Separates the two DNA strands by breaking the
hydrogen bonds between the bases
 Then moves along one of the DNA strands and links
RNA nucleotides together

DNA

RNA Polymerase

pre-mRNA
 Processing Pre-mRNA
• Also occurs in the nucleus
• Pre-mRNA made up of segments called introns & exons
• Exons code for proteins, while introns do NOT!
• Introns spliced out by splicesome-enzyme and exons re-join
• End product is a mature RNA molecule that leaves the nucleus to the
cytoplasm
pre-RNA molecule
exon intron exon intron exon

intron intron

exon exon exon

splicesome splicesome

exon exon exon

Mature RNA molecule

 Messenger RNA (mRNA)
• Carries the information for a specific protein
• Made up of 500 to 1000 nucleotides long
• Sequence of 3 bases called codon
• AUG – methionine or start codon
• UAA, UAG, or UGA – stop codons

start
codon

mRNA A U G G G C U C C A U C G G C G C A U A A

codon 1 codon 2 codon 3 codon 4 codon 5 codon 6 codon 7

protein methionine glycine serine isoleucine glycine alanine stop
codon
Primary structure of a protein
aa1 aa2 aa3 aa4 aa5 aa6

peptide bonds
 Transfer RNA (tRNA)
• Made up of 75 to 80 nucleotides amino acid
long attachment site

• Picks up the appropriate amino methionine

acid floating in the cytoplasm
• Transports amino acids to the
mRNA

• Have anticodons that are

complementary to mRNA codons

• Recognizes the appropriate codons

on the mRNA and bonds to them
with H-bonds

• Four ATP’s are required for each

amino acid added to the polypeptide
chain:Two to "charge" the tRNA ,
one to carry the charged tRNA to U A C
the ribosome and one to move the
ribosome to the next codon. anticodon
 Ribosomal RNA (rRNA)
• Made up of rRNA is 100 to 3000
nucleotides long
• Made inside the nucleus of a cell
• Associates with proteins to form
ribosomes

Ribosomes
• Made of a large and small subunit
• Composed of rRNA (40%) and proteins (60%)
• Have two sites for tRNA attachment --- P and A
 Ribosomes
P= Peptide site
A= Amino acid site

Large
subunit
P A
Site Site

mRNA
A U G C U A C U U C G
Small
subunit
 Translation
• Synthesis of proteins in the cytoplasm
• Involves the following:
1. mRNA (codons)
2. tRNA (anticodons)
3. ribosomes
4. amino acids

• Three steps:
1. initiation: start codon (AUG)
2. elongation: amino acids linked
3. termination: stop codon (UAG, UAA, or UGA).
 mRNA Codons Join the Ribosome

Large
subunit
P A
Site Site

mRNA
A U G C U A C U U C G
Small subunit
 Initiation

aa2
aa1

2-tRNA
1-tRNA
G A U
anticodon U A C
hydrogen A U G C U A C U U C G A
bonds codon mRNA
 Elongation
peptide bond
aa3
aa1 aa2

3-tRNA

1-tRNA 2-tRNA G A A
anticodon U A C G A U
hydrogen A U G C U A C U U C G A
bonds codon mRNA
 aa1 peptide bond
aa3
aa2

1-tRNA

U A C 3-tRNA
(leaves)
2-tRNA G A A

G A U
A U G C U A C U U C G A
mRNA

Ribosomes move over one codon

 peptide bonds
aa1 aa4

aa2 aa3

4-tRNA

2-tRNA 3-tRNA G C U

G A U G A A
A U G C U A C U U C G A A C U
mRNA
 peptide bonds
aa1 aa4
aa2

aa3

2-tRNA
4-tRNA
G A U
(leaves) 3-tRNA G C U

G A A
A U G C U A C U U C G A A C U
mRNA

Ribosomes move over one codon

 peptide bonds aa5
aa1
aa2
aa4
aa3

5-tRNA

U G A
3-tRNA 4-tRNA

G A A G C U
G C U A C U U C G A A C U
mRNA
 aa1 peptide bonds aa5
aa2
aa3
aa4

5-tRNA

3-tRNA U G A
G A A 4-tRNA

G C U
G C U A C U U C G A A C U
mRNA

Ribosomes move over one codon

 aa5
aa4 aa199 Termination
aa3 primary aa200
structure
aa2 of a protein

aa1
terminator
200-tRNA
or stop
codon
A C U C A U G U U U A G
mRNA
 End Product –The Protein!
• The end products of protein synthesis is a
primary structure of a protein
• A sequence of amino acid bonded together by
peptide bonds

aa5
aa3 aa4
aa2 aa199

aa1 aa200
53
Amino acids
 Amino acids
Each amino acid consists of
• A carbon atom
• Amino group
• Hydrogen atom
• Carboxyl group and Side chain (R group)
 Amino acids grouping

Amino acids can be classified into

• Polar (Hydrophilic)
• Non-polar (Hydrophobic)
• Acidic
• Basic
• Aromatic amino acids.

Properties of amino acids

• Size, shape, charge, polarity, hydrophobicity, aromaticity.
• Conformation (usually determined by side chain)
• Relative position in protein ( determine the properties of protein )
• Propensity to adopt particular conformation ( helix, sheets)
 Unique amino acids
• Glycine & Proline are the unique amino acids
• Glycine is a simplest amino acid which has hydrogen as a R-group
• It does not make chiral
Proline: It has imino group
Hydrophobic amino acids (Non polar)
• Hydrophobic amino acids comprised of carbon & hydrogen in their side
chains.
• They tend to away from solvent.
• Alanine, Valine, Leucine, Isoleucine, Methionine
Hydrophilic amino acids (Polar)
• Polar amino acids comprised of oxygen & nitrogen in their side chains and
participate in polar interaction .
• Polar amino acids participate in hydrogen bonding.
• Asparagine, Glutamine, Serine, Threonine, Cysteine, Histidine
 Acidic amino acids
• The two amino acids in this group are aspartic acid and glutamic acid
• Each has a carboxylic acid on its side chain that gives it acidic
(proton-donating) 
Basic amino acids
• The three amino acids in this group are arginine, lysine and Histidine.
• Each side chain is basic (accept a proton)

Aromatic amino acids

• Phenylalanine
• Tyrosine
• Tryptophan
 Grouping of amino acids

Polar amino acids Non-polar amino acids

Aspartic acid ( negative amino acid) Alanine
Glutamic acid ( negative amino acid) Glycine
Arginine ( positive amino acids) Valine
Lysine ( positive amino acids) Leucine
Histamine ( positive amino acids) Isoleucine
Asparagine (uncharged polar) Proline
Glutamine (uncharged polar ) Phenylalanine
Serine ( uncharged polar) Methionine
Threonine (uncharged polar) Tryptophan
Tyrosine (uncharged polar ) Cysteine
Protein Structure
 Protein Structure
• Peptide - a short chain of amino acids
• Polypeptide – a longer chain of amino acids
• Protein – a polypeptide that occurs in nature and folds into a defined three-
dimensional structure

• The beginning of the protein is known as the amino-terminus and the end of the
protein is known as the carboxyl-terminus.
 Proteins
• Proteins are polymers
(macromolecules) made of
monomers called amino
acids
• All proteins are made of 20
different amino acids linked
in different orders
• Proteins are used to build Arginine

cells, act as hormones &

enzymes, and do much of
the work in a cell
64
64
 Protein Functions in the Body
Storage
• There are many different proteins in
your body, and they perform
different functions. Proteins
functions include:
– Contributing to enzyme activity that
promotes chemical reactions in the
body
– Signaling cells what to do and when Structural
to do it
– Transporting substances around the
body
– Keeping fluids and pH balanced in
the body
– Serving as building blocks for
hormone production
– Helping blood clot
– Promoting antibody activity that Transport
controls immune and allergy
functions
– Serving as structural components
that give our body parts their shapes
65
 Polypeptides

• Amino acids are linked to each other by peptide bonds.

• Carboxyl group of one amino acid is joined to the amino group of other, with the
loss of a molecule of water.
Protein architecture
• Primary structure (sequence of amino acids)
• Secondary structure
• Tertiary structure
• Quaternary structure

Secondary structure
Two major types
• Alpha helical regions
• Beta sheets
Other classification
• Turns
• Transmembrane protein
• Internal region
• External region
• Antigenic region
 Primary Protein Structure

The primary
structure is the
specific sequence of
amino acids in a
protein
Called polypeptide

Amino Acid

68
Protein architecture
 Protein Structures
• Secondary protein structures occur when protein chains
coil or fold

• When protein chains called polypeptides join together,

the tertiary structure forms because R groups interact
with each other

• In the watery environment of a cell, proteins become

globular in their quaternary structure

70
• Physical properties of protein that influence stability therefore it
determines its fold
• Rigidity of backbone

• Amino acid interaction with water (Hydropathy index for side chains)

• Interactions among amino acids

1. Electrostatic interaction (Electrostatic interactions comprise the attractive

or repulsive interactions between charged molecules)

2. Hydrogen bonds (Hydrogen atom covalently bonded to a very

electronegative atom such as a N, O, or F)

3. S-S bonds (A disulfide bond is a covalent bond between two sulfur atoms)

4. Volume constraints
 Residue Globular protein Membrane protein

Non-polar In interior hydrophobic Surface-lipid anchor

VLIMFYW core

Polar-charged Surface catalytic sites. Hydrophilic core

RKDEH

Polar neutral H-bond network Inside surface part of

STNQYW channel

Globular protein Membrane protein

Conformation flexibility
• Backbone (main chain of atoms in peptide bond)
• Torsion or rotation angles around
• C-N bond (φ )
• C-C bond (ψ )
• Sterical hinderance

Most – Pro

Least - Gly

Geometry
• Distance (diatomic molecule)
• Angle (triatomic molecule)
• Dihedral angle ( four atoms)
Torsion angle

Phi (φ) torsion angles around N-Cα bond and Psi (ψ) angle around
Cα-C bond
Solving protein structures

Only two kinds of techniques allow one to get atomic resolution pictures of

macromolecules.
• X-ray crystallography ( first applied in 1961) Kendrew & Perutz
• NMR spectroscopy ( first applied in 1983 )
• Structure – function
• Structure – Mechanism
• Structure – origin/evolution
• Structure based drug design
• Solving the protein folding problem
 Classes of proteins
Based on structure and solubility, proteins can be grouped into three large classes

• Fibrous protein
• Globular protein
• Membrane protein

Fibrous Globular Membrane

Fibrous protein
• Fibrous proteins contain polypeptide chains organized parallel
along a single axis, producing long fibers or large sheets.
• They are mechanically strong, play structural role in nature.
• Difficult to dissolve in water.
• Example : α keratins & collagen
• α keratins found in hair, finger nails, bones.
• Sequence consists of long alpha helical rod segments capped
with non-helical N and C terminus.
• β keratins found in silk and consist of Gly-Ala repeat sequences.

• Ala is small & can be packed within the sheets.

Globular proteins
• Globular proteins are classified according to the type &
arrangement of secondary structure.
• Antiparallel alpha helix proteins

• Parallel or mixed beta sheet proteins

• Antiparallel beta sheet proteins.

Forces driving protein folding
• It is believed that hydrophobic collapse is a key driving force for protein
folding.
• Hydrophobic core

• Polar surface interacting with solvent

• Minimum volume

• Disulfide bond formation stabilizes

• Hydrogen bonds

• Polar and electrostatic interactions

Native state is typically only 5 to 10 kcal/mol more stable than the unfolded
form
Protein structure stabilizing interactions

Higher interactions energy than a simple van der waals interaction.

• Non covalent

• Van der waals forces (transient, weak electrical attraction of one atom for
another )
• Hydrophobic ( clustering of non polar groups)

• Hydrogen bonding

• Covalent

• Disulfide bonds ( bonds, angles, torsion angles )

E covalent + E non-covalent = Total energy (the total energy should be minimum

which results stable structure)
 Interaction Approx bond strength in kj/mol

Covalent bonds > 200 ( ranging up to 900)

Ionic bonds 20-40

Hydrogen bonds -5-10

Hydrophobic -8

Van der waals -4

Features of the native state
• Well defined 3D structure

• Isoelectric point

• Some characterized molecular function

• Many proteins fold spontaneously to their native structure

• Protein folding is relatively fast

• Chaperones speed up folding, but do not alter the structure

 What Are Enzymes?
• Most enzymes are Proteins (tertiary and
quaternary structures)

• Act as Catalyst to accelerates a reaction

• Not permanently changed in the process

• Are specific for what they will

catalyze

• Are Reusable

• End in –ase
-Sucrase
-Lactase
-Maltase

83
 Why Enzymes?

Natural catalysts

Speed: 1016 over un-catalyzed rates!

Specificity: only the desired reaction occurs

Permit reactions under mild conditions

 Enzyme Action: Lock and Key Model

Conventionally we say the enzyme (E) acts on the substrate (S)

to yield products (P)
E
S P
Since E is a catalyst it remains unchanged at the end of
the reaction
 Hexokinase, an enzyme (blue), binding its substrate,
The active site glucose (yellow).

Typically a pocket or groove on

the surface of the protein into
which the substrate fits.

The specificity of an enzyme

–fit between the active site and
that of the substrate.

Enzyme changes shape

–tighter induced fit, bringing
chemical groups in position to
catalyze the reaction.
 3. Enzyme Inhibitors
Two Types:
a. Competitive inhibitors: Substrate Enzyme
are chemicals that
resemble an enzyme’s
normal substrate and Competitive
compete with it for the
active site. inhibitor

b. Noncompetitive
inhibitors: Inhibitors that
do not enter the active
site, but bind to another
part of the enzyme
causing the enzyme to
change its shape, which
Substrate Noncompetitive
in turn alters the active Enzyme Inhibitor
site. active site
altered