Introduction to Biochemistry

Introduction
What is the Biochemistry?

History and development

How to study Biochemistry?

1. Biochemistry
Definition: The chemistry of life
The science concerned with the chemical
basis of life.
The science concerned with the various
molecules that occur in living cells and
organisms and with their chemical reaction.
Anything more than a superficial
comprehension of life in all its diverse
manifestation - demands a knowledge of
biochemistry.
What is Biochemistry?
Biochemistry = chemistry of life.
Biochemists use physical and chemical
principles to explain biology at the
molecular level.
Basic principles of biochemistry are
common to all living organism
Biochemistry
Aim: to describe and explain, in
molecular terms, all chemical
processes of living cells
Structure-function
Metabolism and Regulation
How life began
Biochemistry
Significance: be essential to all life
sciences as the common knowledge
Genetics; Cell biology; Molecular biology
Physiology and Immunology
Pharmacology and Pharmacy
Toxicology; Pathology; Microbiology
Zoology and Botany
Biochemistry
Student Nurses who acquire a sound
knowledge of biochemistry will be in a strong
position to deal with two central concerns of
the health sciences:
(1) the understanding and maintenance of
health
(2) the understanding and effective
treatment of disease
Causes of cancers
Molecular lesions causing various genetic diseases
Rational design of new drugs
Origins of Biochemistry:
A challenge to Vitalism.
Vitalism: idea that substances and processes
associated with living organisms did not
behave according to the known laws of physics
and chemistry
Evidence:
1) Only living things have a high degree of complexity
2) Only living things extract, transform and utilize
energy from their environment
3) Only living things are capable of self assembly and
self replication
1926 James B. Sumner

UREASE an enzyme, a protein

 History and development of
Biochemistry

1903
Carl Alexander
Neuberg
(German):
Biochemistry

Chemistry of Life
Two notable breakthroughs

(1) Discovery of the role of enzymes

as catalysts
(2) Identification of nucleic acids as
information molecules

Flow of information: from nucleic acids to proteins

DNA RNA Protein
 More Historic Events

In
1937 Krebs for the discovery of the
Citric Acid Cycle-won the Nobel Prize in
Physiology or Medicine in 1953
1944 Avery, MacLeod and McCarty
identified DNA as information molecules
1953 Watson (still alive) and Crick
proposed the structure of DNA
1958 Crick proposed the central dogma
of Biology
 In 1953Watson & Crick for the discovery
of the DNA Double Helix -won the Nobel
Prize in Physiology or Medicine in 1962
 More Historic Events

In 1955Sanger for the determination of

insulin sequence- won the Nobel Prize in
Physiology or Medicine in 1956
In 1980 Sanger & Gilbert for Sequencing
of DNA-won the Nobel Prize in Chemistry in
1980
In 1993, Kary B. Mullis for invention of PCR
method -won the Nobel Prize in Chemistry in
1993
 Transgenic
Gene engineering animal

Clone Green Fluorescence protein

HGP from 1990, completed in 2003
What to expect in Biochemistry class?
structure and function of cellular
components
proteins, carbohydrates, lipids, nucleic
acids and other biomolecules

Metabolism and Regulation

Gene expression and modulation

DNA RNA Protein

Biochemistry = the chemistry of life

Elements - These are single substances which cannot be

broken down any more. there are 110 different
elements that are known to man.

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Polymers and Monomers
Each of these types of molecules are
polymers that are assembled from
single units called monomers.

Each type of macromolecule is an

assemblage of a different type of
monomer.
Macromolecule Monomer

Carbohydrates Monosaccharide

Lipids Not always polymers;

Hydrocarbon chains

Proteins Amino acids

Nucleic acids Nucleotides

How do monomers form polymers?
In condensation
reactions (also
called dehydration
synthesis), a
molecule of water
is removed from
two monomers as
they are connected
together.
 Metabolic Processes

Anabolic

Building block Macromolecule

Simple sugar Polysaccharide
Amino acid Protein (peptide)
Nucleotide RNA or DNA
Fatty acid Lipid
Catabolic
Cells: a review
Basic building blocks of life
Smallest living unit of an organism
A cell may be an entire organism (unicellular)
or it may be one of billions of cells that
make up the organism (multicellular).
Grow, reproduce, use energy, adapt, respond
to their environment

Many cannot be seen with the naked eye

a typical cell size is 10m; a typical cell mass is
1 nanogram.)
Cells May be Prokaryotic or Eukaryotic

Prokaryotes (Greek: pro-before;

karyon-nucleus) include various
bacteria
lack a nucleus or membrane-bound
structures called organelles

Eukaryotes (Greek: eu-true; karyon-

nucleus) include most other cells
(plants, fungi, & animals)
have a nucleus and membrane-bound
organelles
Cell membrane & cell wall Cell Membrane
Nucleoid region contains the DNA Nucleus
Contain ribosomes (no membrane) Cytoplasm with organelles
Characteristic Bio-membranes and Organelles

Plasma Membrane-Cells defining boundary

Providing a barrier and containing
transport and signaling systems.

Nucleus Cells information center

Double membrane surrounding the chromosomes and
the nucleolus. The place where almost all DNA
replication and RNA synthesis occur. The nucleolus is
a site for synthesis of RNA making up the ribosome

Mitochondria- the power generators

Mitochondria (Greek: mitos-thread; chondros-granule):
Surrounded by a double membrane with a series of
folds called cristae. Functions in energy production
through metabolism. Contains its own DNA.
Endoplasmic reticulum (ER) The transport network for molecules

Rough endoplasmic reticulum (RER)

Covered with ribosomes (causing the "rough"
appearance) which are in the process of
synthesizing proteins for secretion or
localization in membranes.

Ribosomes
Protein and RNA complex responsible for
protein synthesis

Smooth endoplasmic reticulum (SER)

A site for synthesis and metabolism of lipids.
 Golgi apparatus -process and package the
macromolecules.
A series of stacked membranes. Vesicles
carry materials from the RER to the Golgi
apparatus. Vesicles move between the stacks
while the proteins are "processed" to a
mature form.

Lysosomes-contain digestive enzyme

A membrane bound organelle that is
responsible for degrading proteins and
membranes in the cell.

Cytoplasm
enclosed by the plasma membrane, liquid
portion called cytosol and it houses the
membranous organelles.
Biomolecules
Just like cells are building blocks of tissues,
biomolecules are building blocks of cells.
Animal and plant cells contain approximately
10,000 kinds of biomolecules.
Water constitutes 50-95% of cells content
by weight.
Ions like Na+, K+ and Ca2+ may account for
another 1%.
Almost all other kinds of biomolecules are
organic (C, H, N, O, P, S).
Organic compounds are compounds composed
primarily of a Carbon skeleton.
Carbon
Carbon is more abundant in living
organisms than it is in the rest of the
universe.
What makes Carbon Special? Why is
Carbon so different from all the other
elements on the periodic table?
The answer derives from the ability of
Carbon atoms to bond together to form
long chains and rings.
Carbon can form immensely diverse
compounds, from simple to complex.

Methane with 1 DNA with tens of Billions

Carbon atom of Carbon atoms
Biomolecules
are
compounds
of carbon
with a variety
of functional
groups
Types of biomolecules: (another look)
Small molecules:
Lipid, phospholipid, glycolipid, sterol,
Vitamin
Hormone, neurotransmitter
Carbohydrate, sugar
Monomers:
Amino acids
Nucleotides
Monosaccharides
Polymers:
Peptides, oligopeptides, polypeptides, proteins
Nucleic acids, i.e. DNA, RNA
Oligosaccharides, polysaccharides (including
cellulose)
Structural hierarchy in the molecular organization of cells
Similarities among cells
All cells use nucleic acids (DNA) to store
information
Except RNA viruses, but not true cells
(incapable of autonomous replication)
All cells use nucleic acids (RNA) to access
stored information
All cells use proteins as catalysts (enzymes) for
chemical reactions
A few examples of RNA based enzymes, which may
reflect primordial use of RNA
All cells use lipids for membrane components
Different types of lipids in different types of cells
All cells use carbohydrates for cell walls (if
present), recognition, and energy generation
Water
About 60-90 percent
of an organism is
water

Water is used in
most reactions in
the body
Water is called
the universal
solvent
Copyright Cmassengale 55
Chemical composition of a normal man
(weight 65 kg)

Constituent Percent (%) Weight (kg)

Water 61.6 40

Protein 17.0 11

Lipid 13.8 9

Carbohydrate 1.5 1

Minerals 6.1 4
 pH. pH is measured on a scale of 0-14. The low end is acidic. The
high end is basic. 7 is neutral (middle)

0-1 234 56 (7) 89 10 11 12 13 14

strongly moder- slightly neutral slightly moderately strongly
acidic ately acidic basic basic basic
acidic

How to remember if a pH is acidic or basic:

go from left to right when you read - low numbers on left,
high numbers on right

Alphabet: "A" is left of "B" - low numbers are acidic, high

numbers are basic

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pH and Buffers
Water is Weakly Ionizable
2 H2O <===> OH+ H3O+
Weakly means this doesnt happen
often
[OH] = [H3O+] = 1 10-7M,
[OH] [H3O+] = 1 10-14, the
basis of the pH scale
Equilibrium Constants Mathematically
Represent Degree of Dissociation

Keq is used in biochemistry to denote

modified standard state.
Keq = [Products] / [Reactants]
aA + bB cC + dD
Keq= [C]c [D]d / [A]a [B] b
Equilibrium Constants Mathematically
Represent Degree of Dissociation
 pKa Values are Used to Describe
Ionization of Acids

CH3COOH + H2O <===> CH3COO +

H3O+
Keq = Ka = 1.74 x 10-5
pKa= 4.76

The pKa is the pH at the point where

buffering occurs
Buffers
Buffer-a compound that does not allow
the pH to change even if acid or base
is added to the system.
Amphiprotic compounds are also good
buffers.
Amphiprotic compound-a compound that
can act as a proton donor or as a
proton acceptor.
The Henderson-HasselbalchEquation is Used to
Determine the pH of Buffered Solutions

pH = pKa+ log [salt]

[acid]

When pH = pKa, There is Equal Amounts of A and HA

How much biochemistry do you need to
know for this course?

1. You are Carbohydrates

expected to learn Lipids
the structure and
functions of these
Proteins
organic compounds: Nucleic Acids

2. You will be expected to learn the basic

biochemical processes of major HUMAN cell
functions, such as respiration, protein
synthesis and so on.