Biochemistry Introduction

What is Biochemistry?
• Biochemistry = chemistry of life.

• The Biochemist uses physical and

chemical principles to explain
biology at the molecular level.

• Basic principles of biochemistry are

common to all living organism
 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 contains thousands of chemical rxns. Precise

regulation and integration of these rxns are required to
maintain life

• Certain important rxns E.g. Glycolysis is found in almost all

organisms.

• All organisms use the same type of molecules: CHO, proteins,

lipids & nucleic acids.

• Instructions for growth, reproduction and developments for

each organism is encoded in their DNA
 How does biochemistry
impact you?
• Medicine

• Agriculture

• Industrial applications

• Environmental applications
 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
 Transgenic
Gene engineering animal

Clone Green Fluorescence protein

HGP from 1990, completed in 2003
 Principle Areas of
Biochemistry

• Structure and function of biological

macromolecules

• Metabolism – anabolic and catabolic

processes.

• Molecular Genetics – How life is

replicated
 Organization of Life
• elements
• simple organic compounds (monomers)
• macromolecules (polymers)
• supramolecular structures
• organelles
• cells
• tissues
• organisms
 Range of the
sizes of objects
studies by
Biochemist and
Biologist

1 angstrom = 0.1 nm
 Elements of Life

Most abundant, essential for all organisms: C, N, O, P, S, H

Less abundant, essential for all organisms : Na, Mg, K, Ca, Cl
Trace levels, essential for all organism: Mn, Fe, Co, Cu, Zn
Trace levels, essential for some organisms: V, Cr, Mo, B, Al, Ga, Sn, Si,
As, Se, I,
Important compounds, functional groups
 Many Important Biomolecules are Polymers

lipids proteins carbo nucleic acids

monomer fatty acid amino acid glucose nucleotide

polymer phospholipid protein subunit cellulose DNA

supramolecular
membrane protein complex cell wall chromosome
structure
 Lipids

monomer fatty acid

polymer phospholipid

supramolecular
membrane
structure
 Proteins

monomer amino acid

polymer protein subunit

supramolecular
structure Enzyme complex
 Carbohydrates

monomer glucose

polymer cellulose

supramolecular
structure cell wall
 Nucleic Acids

monomer nucleotide

polymer DNA

supramolecular
chromatin
structure
Common theme:

Monomers form
polymers through
condensations

Polymers are broken

down through
hydrolysis.
Prokaryote Cell
Cellular Organization
of an E. coli Cell

200 – 300 mg protein / mL cytoplasm

Eukaryote Cell
Nucleoid region contains the DNA
•Cell membrane & cell wall
• Contain ribosomes (no membrane)
to make proteins in
their cytoplasm
Contain 3 basic cell structures:
• Nucleus
• Cell Membrane
• Cytoplasm with organelles
Two Main Types of Eukaryotic Cells
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.
.

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.
 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..

 REFERENCES
1. David. L. Nelson & M.M. Cox, Lehninger Principles of
Biochemistry, 5th Edition, W.H. Freeman & Company,
New York, 2008.
2. Mc Kee, T. & J.R. McKee , Biochemistry: An
Introduction, 2nd Edition, Mc Graw Hill, New York,
1999.
3. Murray RK, Harper’s Illustrated Principles
Biochemistry, 26th Ed.
4. Sinaga, E., Biokimia Dasar, PT. ISFI, 2012
 I. SEL
 Sel : unit struktural dan fungsional dari
organisme hidup
 Organisme terkecil hanya terdiri dari satu sel
(uniseluler, mis. Bakteria)
 Organisme tingkat tinggi terdiri dari banyak sel
(multiseluler, mis. tubuh manusia terdiri atas 1014
sel)
 Organisme multiseluler mengandung bermacam sel
yang bervariasi dalam bentuk, ukuran, dan fungsi
khusus
 Bagaimanapun besar dan kompleksnya organisme, tiap
selnya tetap mempertahankan sifat individu dan
kebebasan
Ukuran sel
- Kebanyakan sel mempunyai volume antara 1-1000μm3
- Sel terkecil (Mycoplasma) mempunyai diameter 0,1μm
- Sel E. coli mempunyai panjang 2μm
- Sel neuron mempunyai panjang beberapa meter,
walaupun volumenya masih tetap dalam ukuran sel
Struktur sel eukariotik
- Dibandingkan dengan sel prokariot, sel eukariot penuh
dengan struktur bermembran
- Sel eukariot mempunyai satu nukleus dan sejumlah
organel sel
 Organel sel
- Organel sel adalah struktur subseluler dengan fungsi khusus
- Umumnya organel sel mempunyai membran, kecuali ribosom

Inti sel (nukleus)

- Merupakan pusat informasi genetik pada sel eukariot
- Dibungkus oleh selaput inti yang bermembran ganda
- Nukleus diisi oleh cairan nukleoplasma, tempat nukleoli dan
kromosom tersuspensi

Pori nukleus
- Merupakan saluran protein yang tersebar pada seluruh
selaput inti sel.
-Tip pori terdiri atas lebih dari 100 protein dan mempunyai
lubang berukuran sekitar 9 nm.
- Protein kecil dapat berdifusi secara pasif melalui lubang,
sedangkan protein yang lebih besar memerrlukan proses
transpor aktif yang dapat memperlebar lubang hingga 25 nm.
Kromosom
- Mengandung hampir semua material herediter dari suatu sel
- Kromosom tunggal mengandung sejumlah besar gen, yang
masing- masing mempunyai tempat (locus) pada kromosom
- Kromosom terdiri atas molekul DNA yang besar dan sejumlah
protein
- Kromosom berubah strukturnya secara dramatik selama siklus
sel
Nukleolus
- Berbentuk bulat, terdapat di dalam nuleus sel eukariot
- Tempat terjadinya transkripsi pada rRNA
- Mengandung rRNA dan gen yang mengkode rRNA
- Jumlah nukleus spesifik untuk tiap spesies, tapi umumnya hanya
satu buah

Sitoplasma
- Merupakan seluruh isi dari sel, kecuali nukleus
- Sitoplasma sel eukariot mengandung organel yang mempunyai
membran ganda
- Cairan dari sitoplasma dinamakan sitosol
Ribosoma
- Merupakan organel sel kecil dan terdiri atas rRNA dan protein,
tidak mempunyai membran
- Merupakan pabrik untuk sintesis protein, yang memperoleh
informasi genetik dari mRNA
- Terdiri atas 2 subunit, yaitu subunit 50S dan 30S; kedua
ini hanya bersatu dengan adanya tRNA yang bermuatan anti-
kodon yang cocok

Mitokondria
- Merupakan organel sel yang besar, tempat terjadinya respirasi
sel
- Mengandung enzim-enzim untuk siklus asam sitrat, rantai
pernafasan dan fosforilasi oksidatif
- Diselaputi oleh membran ganda; membran bagian dalam
membentuk lipatan-lipatan (cristae)
- Merupakan tempat menghasilkan ATP pada sel eukariot
Klororoplas
- Organel sel pada organisme fotosintetik dan algae
- Tempat terjadinya fotosintesis
- Selain mempunyai membran luardan membran dalam, juga
mempunyai membran tilakoid
- Siklus Calvin, yaitu pembentukan glukosa dari CO2 dan H2O
terjadi pada stroma
Endoplasmik Retikulum (ER)
- Merupakan kantong bermembran yang berbentuk pipih (flattened
sac)
- Terlibat dalam sintesis protein membran dan protein lain untuk
ekspor dari sel
- Protein permukaan menempel pada membran ER, sedangkan
protein yang larut ditranspor ke dalam cairan (lumen) ER
Badan golgi (Golgi bodies)
- Merupakan kantong pipih bermembran
- Tempat memilih dan modifikasi protein yang dihasilkan pada ER
- Muka cis --> menerima vesikel dari ER; muka trans --> mengeluar-
kan protein ke membran lain dan permukaan sel
Vesikel
- Organel kecil berbentuk bundar
- Terlibat dalam berbagai fungsi transpor
Lisosom
- Kantong berisi enzim-enzim hidrolitik untuk memecah makro-
molekul dalam sel
- Hasil pemecahan dikeluarkan melalui membran ke dalam sitosol
- Mempertahankan pH 5, dimana enzim dapat bekerja
Vacuola
- Suatu ruang berisi cairan
- Berfungsi sebagai tempat pencernaan atau tempat pembuangan
limbah metabolik
Dinding sel
- Membungkus sel tanaman, protista, jamur dan bakteri
- Mempertahankan bentuk sel; bersifat kaku