Biochemistry notes.

1. Lecture 1
Introduction to Biochemistry
M.Phil
Ist semester

2. History of Life

3. Introduction
 What is the Biochemistry?
 History and development
 How to study Biochemistry?

4. Elements
• Make up all matter.
• 92 occur in nature.
• Identified by names or chemical symbols
(abbreviations of modern or Latin names).
• Identified by number (based on structure of
subunits or atoms).
• Described and organized in periodic table.

5. Periodic Table

6. Atoms
• Subunits of elements.
• Smallest complete units of matter.
• Cannot be broken down or changed by
ordinary chemical and physical means.

7. Atomic Structure
 Nucleus
 Positively charged protons.
 Neutrally charged neutrons.
 Surrounded by negatively charged
electrons.

8. Molecules and compounds
Molecules
• Formed when two or more atoms unite on the
basis of their electron structures
• Can be made of like atoms or atoms of different
elements
Compounds
• Composed of two or more elements

9. Biomolecules
 Carbohydrates
 Lipids
 Proteins
 Nucleic acid

10. 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.

11. Biochemistry
 Aim: to describe and explain, in
molecular terms, all chemical
processes of living cells
 Structure-function
 Metabolism and Regulation
 How life began？

12. 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

13. 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

14. 2. History and development of
Biochemistry
1903, Neuberg (German):
“Biochemistry”
“Chemistry of Life”

15. 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

16.  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
Some historic events

17.  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

18. Gene engineering
Clone
Transgenic
animal
Green Fluorescence protein

19. HGP from 1990, completed in 2003

20. 3.What dose 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

21. 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.

22. Macromolecule
Carbohydrates
Lipids
Proteins
Nucleic acids
Monomer
Monosaccharide
Not always polymers;
Hydrocarbon chains
Amino acids
Nucleotides

23. 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.

25.  Building block
 Simple sugar
 Amino acid
 Nucleotide
 Fatty acid
 Macromolecule
 Polysaccharide
 Protein (peptide)
 RNA or DNA
 Lipid
Anabolic
Catabolic

26. 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.)

27. 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

28. •Cell membrane & cell wall
•Nucleoid region contains the DNA
•Contain ribosomes (no membrane)
• Cell Membrane
• Nucleus
• Cytoplasm with organelles

30. Characteristic Bio-membranes and Organelles
• 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.
•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

31. •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.
Endoplasmic reticulum (ER) – The transport network for molecules

32. •Cytoplasm
enclosed by the plasma membrane, liquid
portion called cytosol and it houses the
membranous organelles.
•Lysosomes-contain digestive enzyme
A membrane bound organelle that is
responsible for degrading proteins and
membranes in the cell.
•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.

33. 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.

34. 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.

35. Carbon can form immensely diverse
compounds, from simple to complex.
Methane with 1
Carbon atom
DNA with tens of Billions
of Carbon atoms

36. Biomolecules
are
compounds
of carbon
with a variety
of functional
groups

37. 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)

38. 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

39. Structural hierarchy in the molecular organization of cells

40. 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

41.  Carbohydrates
 Lipids
 Proteins
 Nucleic Acids
1. You are
expected to learn
the structure and
functions of these
organic compounds:
How much biochemistry do you need to
know for this course?
2. You will be expected to learn the basic
biochemical processes of major cell
functions, such as respiration, protein
synthesis and so on.

42. Topics
1 Introduction , amino acid and protein (8h)
2 Nucleic acid: Structure and properties (4h)
3 Carbohydrates: Structure and properties (2h)
4 Vitamins and coenzymes (4h)
5 Enzymes (6h)
6 Metabolism of carbohydrates (8h)
7 Assessment
8 Bioenergetics (4h)
9 Metabolism of lipids (8h)
10 Metabolism of amino acids (6h)
11 Integration of metabolism and review(2h)

43. • U Satyanarayana, Biochemistry
• Murray RK, Harper’s Illustrated
Biochemistry, 26th ed.
• Nelson DL and Cox MM. Lehninger
Principles of Biochemistry, 5th ed.
2008.
6. Text book and references

44. • Inspiring interest, confidence
• Previewing and reviewing freshly
• Taking studying notes
• Discussing in groups
• Practice, crosstalk with other subjects
• Making use of internet
7. Some tips for study of biochemistry

45. 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”

46. Final theory grade
 Final theory grade=
 First Assessment: 30~35%
 Final exam: 45~50%
 Daily performance: 20%
 Notice: 1/3 absent, can not take part
in the final exam.