Biochemistry

Preparing for chemistry student

UNIVERSITAS NEGERI SEMARANG

 Topics
1 Introduction , amino acid and protein
2 Nucleic acid: Structure and properties
3 Carbohydrates: Structure and properties
4 Vitamins and coenzymes
5 Enzymes
6 Metabolism of carbohydrates
7 Mid Test
8 Bioenergetics
9 Metabolism of lipids
10 Metabolism of amino acids
11 Integration of metabolism and review
Text book and references

• U Satyanarayana, Biochemistry
• Murray RK, Harper’s Illustrated Biochemistry,
26th ed.
• Nelson DL and Cox MM. Lehninger Principles
of Biochemistry, 5th ed. 2008.
 FINAL THEORY GRADE
 Final theory grade=
 First Assessment (Mid Test): Max 40%  Max 2 portion
 Final exam: Min 40%  Min 2 portion
 Daily performance: 20%  1 portion

 Notice: >25% absent, can not take part in the final

exam.
Just do as some proverbs say:
“I hear, and I forget,
I see, and I remember,
I do, and I understand.”

“Practice makes perfect”

“No pains, no gains”

 Lecture #1

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.
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
 Medical students 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
 Chemistry student ?
2. History and development of Biochemistry

1903, 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
Some historic events
 In 1937，Krebs for the discovery of the Citric Acid
Cycle-won the Nobel Prize in Physiology or Medicine in
1953
 In 1953，Watson & Crick for the discovery of the
“DNA Double Helix” -won the Nobel Prize in
Physiology or Medicine in 1962
 In 1955，Sanger 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
3.What does the Biochemistry discuss?
 structure and function of cellular components
 proteins, carbohydrates, lipids, nucleic acids and
other biomolecules

 Metabolism and Regulation

 Gene expression and modulation

DNA RNA Protein

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.
 Anabolic

 Building block  Macromolecule

 Simple sugar  Polysaccharide
 Amino acid  Protein (peptide)
 Nucleotide  RNA or DNA
 Fatty acid  Lipid
Catabolic
 4. Cells
 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 10µm; 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-Cell’s defining boundary

Providing a barrier and containing transport and
signaling systems.

•Nucleus – Cell’s 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.
5. 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
 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)
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
Structural hierarchy in the molecular organization of cells
 Similarities among all types of 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
 How much biochemistry do you need
to know for this course?

1. You are expected to  Carbohydrates

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

2. You will be expected to learn the basic biochemical

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