Tingkat Organisasi Tubuh

Manusia (Kimiawi, Sel, Jaringan,

Organ dan Sistem Organ}

Dr. Marhaen Hardjo, M.Biomed, PhD

Bagian Biokimia Fakultas Kedokteran
Universitas Hasanuddin Makassar
1
 Biochemistry

• Chemistry of living organisms.

• The study of biology at the molecular level.
 What is Biochemistry ?
• Biochemistry is the application of chemistry to the
study of biological processes at the cellular and
molecular level.
• It emerged as a distinct discipline around the
beginning of the 20th century when scientists
combined chemistry, physiology and biology to
investigate the chemistry of living systems by:
A. Studying the structure and behavior of the complex
molecules found in biological material and

B. the ways these molecules interact to form cells, tissues and

whole organism

3
 Principles of Biochemistry
• Cells (basic structural units of living organisms) are highly
organized and constant source of energy is required to maintain
the ordered state.
• Living processes contain thousands of chemical pathways.
Precise regulation and integration of these pathways are
required to maintain life
• Certain important pathways e.g. Glycolysis is found in almost all
organisms.
• All organisms use the same type of molecules: carbohydrates,
proteins, lipids & nucleic acids.
• Instructions for growth, reproduction and developments for
each organism is encoded in their DNA

4
Organism, Organ, Cell
Organism

n
Orga

5
 The Cell Nucleus only in
eukaryotic cells.
The ER modifies proteins, makes macromolecules, Contains most of the
and transfers substances throughout the cell. cell's genetic material.

Ribosome translates
mRNA into a polypeptide
chain (e.g., a protein).

Mitochondrion
manufactures adenosine
triphosphate (ATP), which
is used as a source of • circa 100 trillion (1014) cells in a human organism
energy. • 200 different forms of cells
6
 Cells
• Basic building blocks of life
• Smallest living unit of an organism
• Grow, reproduce, use energy, adapt, respond to their
environment
• Many cannot be seen with the naked eye
• A cell may be an entire organism or it may be one of billions of
cells that make up the organism

• Basis Types of Cells

7
Nucleoid region contains the DNA Contain 3 basic cell structures:
•Cell membrane & cell wall • Nucleus
• Contain ribosomes (no membrane) • Cell Membrane
to make proteins in • Cytoplasm with organelles
their cytoplasm

8
Two Main Types of Eukaryotic Cells

9
Characteristic Bio-membranes and Organelles

Plasma Membrane
A lipid/protein/carbohydrate complex, providing a barrier and
containing transport and signaling systems.

Nucleus
Double membrane surrounding the chromosomes and the nucleolus.
Pores allow specific communication with the cytoplasm. The
nucleolus is a site for synthesis of RNA making up the ribosome

Mitochondrion
Surrounded by a double membrane with a series of folds
called cristae. Functions in energy production through metabolism.
Contains its own DNA, and is believed to have originated as a
captured bacterium.

Chloroplasts (plastids)
Surrounded by a double membrane, containing stacked thylakoid
membranes. Responsible for photosynthesis, the trapping of light
energy for the synthesis of sugars. Contains DNA, and like
mitochondria is believed to have originated as a captured
bacterium.
10
.

Rough endoplasmic reticulum (RER)

 
A network of interconnected membranes forming channels within the
cell. 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 network of interconnected membranes forming channels within the
cell. A site for synthesis and metabolism of lipids. Also contains
                 enzymes for detoxifying chemicals including drugs and pesticides.

     Golgi apparatus

A series of stacked membranes. Vesicles (small membrane

 
surrounded bags) carry materials from the RER to the Golgi
apparatus. Vesicles move between the stacks while the proteins are
"processed" to a mature form. Vesicles then carry newly formed
                  membrane and secreted proteins to their final destinations including
secretion or membrane localization.
     Lysosymes
A membrane bound organelle that is responsible for degrading
proteins and membranes in the cell, and also helps degrade materials
ingested by the cell. 11
 Vacuoles
Membrane surrounded "bags" that contain water and storage
materials in plants.

Peroxisomes or Microbodies
Produce and degrade hydrogen peroxide, a toxic
compound that can be produced during metabolism.

Cell wall
Plants have a rigid cell wall in addition to their cell membranes

Cytoplasm
enclosed by the plasma membrane, liquid portion called cytosol
and it houses the membranous organelles.

Cytoskeleton
Arrays of protein filaments in the cytosol. Gives the cell its
shape and provides basis for movement.
E.g. microtubules and microfilaments.

http://www.biology.arizona.edu copyright © 1997 - 2004.. 12

13
 Biolog. Nanostructures

Biochemistry 14
How did organic complex molecules evolved from
more simple molecules?

CH4, H2O, NH3, HCN

Biochemical Evolution

15
 How did organic complex molecules evolved
from more simple molecules?

• Urea was synthesized by heating the inorganic

compound ammonium cyanate (1828)
• This showed that compounds found exclusively in living
organisms could be synthesized from common inorganic
substances

16
The Urey-Miller experiment (1950)

Some amino acids could be produced:

17
 Many Important Biomolecules
are Polymers

• Biopolymers - macromolecules created by joining many

smaller organic molecules (monomers)

• Condensation reactions join monomers

(H2O is removed in the process)

• Residue - each monomer in a chain

18
19
Molecular Organisation of a cell

20
 Bio-molecules
• Just like cells are building blocks of tissues likewise molecules are
building blocks of cells.
• Animal and plant cells contain approximately 10, 000 kinds of
molecules (bio-molecules)
• Water constitutes 50-95% of cells content by weight.

• Ions like Na+, K+ and Ca+ may account for another 1%

• Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)

• Infinite variety of molecules contain C.

• Most bio-molecules considered to be derived from hydrocarbons.
• The chemical properties of organic bio-molecules are determined by
their functional groups. Most bio-molecules have more than one.

21
 Biomolecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic acid
 Biomolecules – Structure
Anabolic

• Building block • Macromolecule

• Simple sugar • Polysaccharide
• Amino acid • Protein (peptide)
• Nucleotide • RNA or DNA
• Fatty acid • Lipid

Catabolic

23
 Linking Monomers
Cells link monomers by a process
called dehydration synthesis
(removing a molecule of water)

Remove
H

H2O Forms

Remove OH

This process joins two sugar monomers

to make a double sugar
24
 Breaking Down Polymers
• Cells break down
macromolecules by
a process called
hydrolysis (adding
a molecule of
water)

Water added to split a double sugar

25
Macromolecules

26
Macromolecules

27
 Carbohydrates

• Composed of carbon, hydrogen, and oxygen.

• Sugars
• Monosaccharides
– Ex. Glucose
• Disaccharides
– Ex. Sucrose
• Polysaccharides
– Ex. Glycogen, Peptidoglycan
Carbohydrate - Glucose

www.palaeos.com
Carbohydrate - Sucrose

www.chm.bris.ac.uk
Carbohydrate - Peptidoglycan

www.biologie.uni-hamburg.de
Carbohydrate - Glycogen

www.elmhurst.edu
 Lipids
• Fatty Acids
– The building
blocks of
lipids.

biology.clc.uc.edu

courses.cm.utexas.edu
 Lipids
• Examples are:
– Waxes
– Fats and oils
– Phospholipids
– Steroids

Phospholipid Cell Membrane.

www.williamsclass.com
 Proteins

• Made up of
polymers of amino
acids.
• “beads on a
string.”
• 20 primary amino
acids exist.
• A polymer of 3 or
more amino acids
forms a
polypeptide.
 Proteins

• Primary Structure
– Linear sequence of amino acids.
• Secondary Structure
– Form helices or sheets due to their structure.
• Tertiary Structure
– A folded protein.
• Quaternary Structure
– 2 or more polypeptide chains bonded
together.
Protein Structure

www.denizyuret.com
 Enzymes
• Are proteins.
• Are considered
biological
catalysts.
– Speed up a chemical
reaction without
being altered.
• Names often end in
“-ase.”
– Ex. Lipase,
carbohydrase.
• Act on a substrate.
• Proteins, including
enzymes, can be
denatured.
 Nucleic Acids

• DNA and RNA.

– (DNA - deoxyribonucleic acid,
RNA - ribonucleic acid).
• Is the “hereditary molecule.”
• Contains genes that code for a certain
product.
• DNA is translated into RNA which is used
to produce a protein or other product.
 Nucleic Acid Structure

• DNA nucleotides
– Building blocks of DNA.
• RNA nucleotides
– Building blocks of RNA.
 Nucleic Acid Structure
• DNA
– Nitrogenous base www.microbelibrary.org

– Deoxyribose
– Phosphate group
• RNA
– Nitrogenous base
– Ribose
– Phosphate group
 Nitrogenous Bases

• Adenine (A)
• Guanine (G)
• Cytosine (C) DNA and RNA
• Thymine (T) – only DNA
• Uracil (U) – only RNA
 Nitrogenous Bases

• A and G
– Purines
(double-ring
structures)
• C, T, and U
– Pyrimidines
(single-ring
structures)
hyperphysics.phy-astr.gsu.edu
 DNA Structure
• Nucleotides bond
between sugar and
phosphate groups to
form long polymers.
• Double-stranded DNA
• - The two nucleotide
polymers bind at
the nitrogenous bases.
www.genome.gov
– Bonding forces cause
the double-stranded
polymer to form a
double helix.
 DNA Structure
• James Watson (left) and Francis Crick
(right) discovered the double-helix
structure of DNA and its process of
replication in the 1950s.

www.achievement.org
 Concepts of Life
Life is characterized by
• Biological diversity: lichen, microbes, jellyfish,
sequoias, hummingbirds, manta rays, gila
monsters, & you

• Chemical unity: living systems (on earth) obey

the rules of physical and organic chemistry –
there are no new principles

46
 Life needs 3 things:

(1) ENERGY, which it must

know how to:

• Extract
• Transform
• Utilize

47
 The Energetics of Life

• Photosynthetic
organisms capture
sunlight energy and use
it to synthesize organic
compounds
• Organic compounds
provide energy for all
organisms

48
Using toxic O2 to generate energy

2 H2O  O2 + 4e- + 4H+ (photosynthesis)

Glucose + 6O2  6CO2 + 6H2O + Energy

49
Glycolysis: the preferred way for the
formation of ATP

50
Life needs (2) SIMPLE MOLECULES,
which it must know how to:

• Convert
• Polymerize
• Degrade

51
 Life needs (3) CHEMICAL
MECHANISMS, to:

• Harness energy
• Drive sequential chemical reactions
• Synthesize & degrade macromolecules
• Maintain a dynamic steady state
• Self-assemble complex structures
• Replicate accurately & efficiently
• Maintain biochemical “order” vs outside

52
Trick #1: Life uses chemical coupling to
drive otherwise unfavorable reactions

53
Trick #2: Life uses enzymes to speed up
otherwise slow reactions

54
How does an enzyme do it,
thermodynamically?

55
How does an enzyme do it,
mechanistically?

56
 Chemical reaction types encountered in
biochemical processes
1. Nucleophilic Substitution
• One atom of group substituted for another

2. Elimination Reactions
• Double bond is formed when atoms in a molecule is removed

3. Addition Reactions:
• Two molecules combine to form a single product.
• A. Hydration Reactions
• Water added to alkene > alcohol (common addition pathway)

57
4. Isomerization Reactions.
• Involve intramolecular shift of atoms or groups

5. Oxidation-Reduction (redox) Reactions

• Occur when there is a transfer of e- from a donor to
an electron acceptor

6. Hydrolysis reactions
• Cleavage of double bond by water.

58
Summary of Key Concepts
 Biochemical Reactions
• Metabolism: total sum of the chemical reaction happening in a
living organism (highly coordinated and purposeful activity)
a. Anabolism- energy requiring biosynthetic pathways
b. Catabolism- degradation of fuel molecules and the production of
energy for cellular function

• All reactions are catalyzed by enzymes

• The primary functions of metabolism are:

a. acquisition & utilization of energy
b. Synthesis of molecules needed for cell structure and
functioning (i.e. proteins, nucleic acids, lipids, & CHO
c. Removal of waste products

60
Even though thousands of pathways sound very
large and complex in a tiny cell:

• The types of pathways are small

• Mechanisms of biochemical pathways are simple
• Reactions of central importance (for energy
production & synthesis and degradation of major cell
components) are relatively few in number

61
 Energy for Cells

• Living cells are inherently unstable.

• Constant flow of energy prevents them from
becoming disorganized.
• Cells obtains energy mainly by the oxidation of bio-
molecules (e- transferred from 1 molecule to another
and in doing so they lose energy)
• This energy captured by cells & used to maintain
highly organized cellular structure and functions

62
63