Chemistry 3

Biochemistry
Introduction to Biochemistry
Part 1

Maria Cyril Del Villar-Dalusong, RMT

What is Biochemistry?

Bio-

means life

The term Biochemistry was introduced by Carl

Neuberg in 1903 scientist that describes the
structure and function of living organism in the
language of chemistry

Deals with the chemistry of life and living

process

A synthesis of biology and chemistry

Most comprehensive of all branches of

chemistry

What is Biochemistry?
The

study of the molecules that constitute

our bodies and those of other living
organisms, and the chemical reactions that
occur within cells
Deal with the study of the chemistry of life
Relatively new branch of science
Study of what is occurring inside living
things taking into consideration the
chemical point of view

Researches in Biochemistry
Researches about photosynthesis, respiration, nucleic acids, metabolism
and others can be considered as the beginning of Biochemistry
Louis

Pasteur (1860)- fermentation and pasteurization and the

importance of enzymes
Emil Fisher(1890) substrate must have a lock and key
systems with enzymes
(1891) configured D-glucose; process of separation of
amino acids from hydrosylate of protein; primary structure of
protein
Hans Krebs & Kurt Heneleit (1932) proposed Urea Cycle 1 st
metabolic pathway to be discovered
(1937) Krebs discovered the famous citric acid
cycle
(Krebs cycle)

Researches in Biochemistry
Gustav

Embolen, Otto Meyerhof, Carl

Nueberg, Jacob Parmas (1940)
complete glycolic pathway (EmbolenMeyerholf pathway)
James Watson & Francis Crick (1953)
proposed the 3D model of DNA;
mechanism of DNA replication
undertanding gene function in molecular
term ( one of the most significant
discovery in history of biology)
Reference: http://chemistry.tutorvista.com/biochemistry.html

Researches in Biochemistry
H.

Govind Khorana (1964) synthesized

polyribonucleicide with a defined repeating
sequence
(1966) completed the genetic code and
function of individual codons coding for amino
acids in protein synthesis
Anthony Lavoister (1743-1794) Known as the
father of modern biochemistry; investigated the
burning in the body oxygen is consumed in
oxidation reaction, carbon dioxide is eliminated
and heat is involved
Reference: http://chemistry.tutorvista.com/biochemistry.html

What is the importance of

Biochemistry?
To

study:
Structure and properties of substance that constitute
the framework of cells and tissues; as source of
energy/ leaving the cells as waste products
Helps in the diagnosis of diseases ( arthritis, diabetes,
etc)
Discovery of new drugs
Application in laboratory
Improvement of agriculture
Nutrition
Beauty and wellness

 Living

matter is composed of mainly

six elements
Carbon (C)
constitute about
Hydrogen (H)
90% of the dry
weight
Oxygen (O)
of the human body.
Several
Nitrogen (N)
phosphorus (P)
sulfur (S)

The Carbon (C)

Carbon (C)

most
most predominant
predominant and
and versatile
versatile element
element of
of life
life
possesses
possesses unique
unique property
property to
to form
form infinite
infinite number
number of
of
compounds
compounds
ability
ability of
of carbon
carbon to
to form
form stable
stable covalent
covalent bonds
bonds and
and C-C
C-C
chains
chains of
of unlimited
unlimited length
length
estimated
estimated that
that about
about 90%
90% of
of compounds
compounds found
found in
in living
living
system
system invariably
invariably contain
contain carbon
carbon

Chemical Composition
of Man

Water
Water is
is
the
the solvent
solvent of
of life
life and
and
contributes
contributes to
to more
more
than
than
60%
60% of
of the
the weight
weight
protein
protein
(mostly
(mostly in
in muscle)
muscle)
lipid
lipid (mostly
(mostly in
in
adipose
adipose
Tissue
Tissue
carbohydrate
carbohydrate
content
content is
is rather
rather
low
low
which
which is
is in
in the
the form
form of
of
glycogen.
glycogen.

The Biomolecules of
Cells

The Cell

A single
adult body consists of
an unbelievably large
number of cells...
between 60 and
100 trillion.
The cell is the smallest
unit inside our bodies
that can be
classified as living.

Cell
Cell is
is the
the
structural
structural and
and
functional
functional unit
unit
of
of life.
life.
It
may
It may be
be also
also
regarded
regarded as
as the
the
basic
basic unit
unit
of
of biological
biological
activity
activity

Concept
Concept of
of cell
cell
originated
originated from
from
the
contributions
the contributions
of
of Schleiden
Schleiden and
and
Schwann
Schwann (1838)
(1838)
It
It was
was only
only
after
after 1940,
1940, the
the
complexities
complexities of
of
cell
cell structure
structure
were
were exposed
exposed

Cells of Living Kingdom

Prokaryotes

Greek: pro - before; karyon nucleus

lack a well defined nucleus and possess relatively
simple structure
These include the various bacteria

Eukaryotes

Greek: eu-true; karyon - nucleus

Possess a well defined nucleus and are more
complex in their structure and function
The higher organisms (animals and plants) are

composed of eukaryotic cells

Comparison

Animal Cell

Plant Cell

Nucleus
Largest cellular organelle
surrounded by double membrane
nuclear envelope
Contains DNA
repository of
genetic info
Associated with basic protein called histone (1:1
ratio)
Form
nucleosomes
an
assembly
constitutes
chromatin fibres of
chromosomes( Greek chroma colour; soma
body)
A single human chromosome is composed of about a
million nucleosomes
Number of chromosomes is a characteristic feature of the
species
Humans have 46 chromosomesc, compactly
packed in the nucleus

Nucleus
Contains nucleolus
rich in RNA (ribosomal RNA)
enters the cytosol through nuclear pore
ground material of the nucleus is often referred to as
nucleoplasm
rich in enzymes such as DNA
polymerases and RNA polymerase
visible in the nucleus, frequently near the nuclear
membrane, is chromatin, an aggregate of DNA and
protein.

Mitochondria
(Greek'. mitos - thread; chondros granule)
center for the cellular
respiration and energy
metabolism
like the nucleus, has a double
membrane
outer membrane has a fairly smooth
surface, but the inner membrane
exhibits many folds called cristae
(Latin crests)
space within the inner membrane is called the matrix
or mitosol ( contains a circular double stranded DNA
(mtDNA), RNA and ribosome)

Mitochondria

contain ribosomes similar to those found in bacteria

approximately the size of many bacteria, typically about
1 m in diameter and 2 to 8 m in length
Regarded as the power houses of the cell
principal producers of ATP in the aerobic cells ( ATP
energy currency, exported to all parts of the cell to
provide energy for the cellular work

Endoplasmic
Reticulum (ER)
attached to the cell membrane and
to the nuclear membrane
two forms, rough and smooth
o rough endoplasmic
reticulum is studded with
ribosomes bound to the
membrane
sites of protein synthesis in all organisms
o smooth endoplasmic reticulum does not have
ribosomes bound to it
is involved in the
synthesis of lipids (triaglycerols, phospholipids,
sterols)and metabolism of drugs, besides supplying
Ca for the cellular functions

Golgi Apparatus

frequently found close to the

smooth endoplasmic
reticulum
contain a unique cluster of
membrane vesicles known as
dictyosomes which, in turn,
constitute Golgi apparatus
(or Golgi complex sacs)
involved in secretion of
proteins from the cell, but
it also appears in cells in
which the primary function is
not protein secretion

Golgi Apparatus

site in the cell in which sugars are linked to

other cellular components, such as proteins
involved in the membrane synthesis,
particularly for the formation of intracellular
organelles (e.g. peroxisomes, lysosomes)

Lysosomes

regarded as the digestive tract of

the cell, since they are actively
involved in digestion of cellular
substances-namely proteins, lipids,
carbohydrates and nucleic acids
Lysosomal enzymes are
categorized as hydrolases:
o a-Glucosidase( glycogen)
o Cathepsins( proteins)
o Lipases( lipids)
o Ribonucleases (RNA)
pH of the lysosomal matrix is more acidic (pH <
5) than the cytosol (pH-7) and this facilitates the
degradation of different compound

Lysosomes

responsible for maintaining

the cellular compounds in
a dynamic state, by their
degradation and recycling
occurrence of several diseases (e.g. arthritis,
muscle diseases, allergic disorders) has been
partly attributed to the powerful lysosomal
enzymes accidental release ( can kill their host
cell)
certain residual products, rich in lipids and
proteins, collectively known as Iipofuscin
accumulate in the cell. (age pigment or wear
and tear pigment which has been implicated in
ageing process

Peroxisomes

known as microbodies, are

single membrane cellular
organelles
are spherical or oval in shape
and contain the enzyme
catalase
similar to lysosomes; their
principal characteristic is that
they contain enzymes
involved in the metabolism
of hydrogen peroxide
(H2O2), which is toxic to the
cell.
also involved in the oxidation of long chain
fatty acids and synthesis of plasmalogens
and glycolipids

Peroxisomes

Glyoxysomes (only in plants) , a specialized type

of peroxisomes, involved in the glyoxylate
pathway (pathway that converts some lipids to
carbohydrate with glyoxylic acid as an
intermediate)
Peroxisome biogenesis disorders (PBDs), are a
group of rare diseases involving the enzyme
activities of peroxisomes
most severe form of PBDs is Zellweger
syndrome, a condition characterized by the
absence of functional peroxisomes

Cytosol &
Cytoskeleton

Known as cellular matrix

compartment containing several
enzymes/ metabolites and salts
in an aqueous gel like medium
dynamic three-dimensional structure
that fills the cytoplasm
acts as both muscle and skeleton, for
movement and stability
the long fibers of the cytoskeleton are
polymers of subunits
the primary types of fibers comprising
the cytoskeleton are microfilaments,
microtubules, and intermediate
filaments

In summary..

What Happens Inside

a Cell?

Inside Cells

Cells create proteins and generate the

energy required for an organism to live.
They are building blocks that act in
conjunction with other cells to construct the
bodies of living creaturesfour main
processes:
1. Protein synthesis
2. Metabolism
3. Energy production
4. Photosynthesis (occurs in plants, algae,
and some bacteria)

Protein synthesis

Proteins are vital substances that are largely

responsible for keeping our bodies functioning..
Maintenance

of cellular structure

Digestion
Muscle

creation
Protection from viral, fungal, and parasitic
infections
Proteins are continuously manufactured by
every cell in our body.

Protein Synthesis

Metabolism
Once proteins are created, they do important
jobs:
catalyzing the breakdown of foods or
medicines that enter the body into something
useful

breaking down unnecessary or harmful

substances into something that can be
expelled more easily

metabolism
Play the central role in driving metabolism

Metabolism

Metabolism

Things you eat or

drink are generally
metabolized like this..

Energy Production

o To maintain essential
cellular and
metabolic processes,
cells must produce a
constant supply of
ATP
o To do this, they
require sugar content
(that is, saccharides
or carbohydrates)
and oxygen
o ATP is created by
mitochondria and
proteins found in the
cytosol
Remember:
ATP is the common currency
of
energy thats used by proteins
to keep us alive.

Photosynthesis
Photosynthesis is a reaction that uses sunlight and carbon
dioxide to synthesize carbohydrates (saccharides)..
Carbohydrates were required to create ATP, and oxygen is
created as a by-product of photosynthesis..
Carbohydrates and oxygen are required to create ATP, which is
essential for our bodies... and both of those things are produced
by photosynthesis!

Photosynthesis
Photosynthesis occurs
occurs
in
in chloroplasts,
chloroplasts, which
which
are
are special
special organelles
organelles
found
found in
in plant
plant cells
cells

Biochemistry of Protein Synthesis

Protein synthesis is
carried out by
ribosomes,
which float in the
cytoplasm
or are stuck to the
endoplasmic
reticulum.

Biochemistry of Protein Synthesis

How does the
ribosome make
proteins?

Amino acids
are combined by
chemical
reactions
to form
proteins...
Protein
So protein
synthesis is in
fact...
biochemistry!

Biochemistry of Metabolism
For example,
gluconeogenesis,
which is performed by liver or
kidney cells, is a chemical
reaction that changes pyruvic
acid into a saccharide called
glucose.

changing one substance

into another is called
metabolism

Lipogenesis is a chemical
reaction that changes
saccharides into fat when too
many saccharides are absorbed
into your body.

Biochemistry of Energy
Production
To produce energy, glucose
is first broken down into
pyruvic
acid in cytosol.

Energy production
is also a kind of
metabolism.

The
reverse version of
gluconeogenesis,
called glycolysis

is all about
breaking down
carbohydrates!

Biochemistry of Energy
Production

Mitochondria use pyruvic

acid and oxygen to
create energy (ATP).
This energy production
is a complex process
that consists of many
chemical reactions
occurring simultaneously
in different places.

Biochemistry of
Photosynthesis
A
A complex
complex
chemical
chemical
reaction
reaction occurs
occurs
when
when light
light strikes
strikes
chloroplasts
chloroplasts in
in a
a
plant's
plant's cells.
cells.

Summary

The processes
that occur in
our
cells are
chemical
reactions!

Tight regulation of
these processes
ensures that
everything occurs
in the proper order,
which is essential
to cell life.

ical
m
he
c
ing
s
k
s
a
tle are t u,
n
u
Co
ns de yo !
o
i
t
i
k
c
rea ce ins spea
pla as we
n
e ve

They are happening

unbelievably fastin
the blink of an eye!

Ecosystems and the

Biogeochemical Cycle

Closely

related to our environment is the

idea of an ecosystem.
This term collectively refers to all the plants,
animals, and organisms that inhabit a
particular area, along with the nonliving
elements of the surrounding environment...
It indicates that they're all part of a single
whole, or system.
The food chain is importantthat indicates
which organisms eat which other organisms
Everything is linked through the
biogeochemical cycle.

 The

elements of the global ecosystem,

including the food chain, respiration, and
photosynthesis, are all part of a worldwide
cycle known as the biogeochemical cycle.
When one organism, like a bear, eats
another organism, such as a fish, the
material that made up the fish becomes
part of the bear.
A very important substance in this transfer
is carbon (C).

 When

you breathe, the carbon that was

inside your body becomes carbon dioxide
(CO2) and is expelled from your body.
Then the carbon that left your body is
captured by plants through photosynthesis
and is transformed into the carbon that
makes up starch
Then is eaten by you(or a cow or some other
hungry creature),and the carbon is returned
once more to the body of an animal.

Ecosystems and the

Biogeochemical Cycle

Ecosystems and the

Biogeochemical Cycle
So the rice,
potatoes, and
apples that I eat
were originally
related to
carbon dixiode
that somebody
else exhaled.

When this cycle

works smoothly,
the ecosystem
and the global
environment are
healthy.

Hydrogen (H), oxygen (O), nitrogen (N), and sulfur (S)

cycle around the Earth as well, going from organism to
organism, getting emitted into the atmosphere, dissolved into
the ocean, or buried deep underground.

Carbon Cycle
Carbon is one of the most
important chemical elements
to living creatures Carbon is at the center of amino
acids, which are the building
blocks of proteins.
Its also the element that
creates the framework of
carbohydrates and lipids, and
its a vital part of DNA.

Carbon Cycle
When carbon leaves an
organisms body, it can bond with
two oxygen atoms to become
carbon dioxide (CO2) or bond
with four hydrogen atoms to
become methane (CH4).
it can accumulate deep underground and, over
long periods of time, it will become crude oil,
coal, and, in some cases, even diamonds.

How plants produce oxygen

and carbohydrates from the
sunlight?

Photophosphorylation
The
The two
two most
most
important
important reactions
reactions
in
in photosynthesis
photosynthesis are
are
photophosphorylatio
photophosphorylatio
n
n
and
and carbon
carbon dioxide
dioxide
fixation
fixation

Photophosphorylation
Different shapes is a complex
These are the part of the
consisting of several proteins
electron transport chain.
gathered together.

When sunlight
strikes
chlorophyll,
the molecule is
"excited" by the
light energy

Electrons fly off only from

the central reaction
center chlorophyll. The
other chlorophyll
molecules act as
amplifiers to feed energy
into the reaction center,
which enables the
electrons to detach

The free electron

is then delivered to
another protein
complex near the
chlorophyll

Photophosphorylation
Since the electrons are passed along to another complex, it's
called an "electron transport chain.

Photophosphorylation

Photophosphorylation

Photophosphorylation

So ATP is synthesized
by
the flow of electrons
triggered by sunlight...
Light energy turns into
Chemical energy!

References
Biochemistry,

3rd Edition; 2006; Dn U.

Satyanarayana, M.Sc, .P h.D. ,F . l .C. ,F
A.C.B/India

Mary K. Campbell, Shawn O. Farrell,

Biochemistry, 7th Edition;2012; /USA

Masaharu

Takemura and Office Sawa, Guide

to Biochemistry, English version; 2011/Japan

H,Stephen

Stoker, Biochemistry, 7 th Edition,

Cenage Learning/Phil