PRINCIPLE OF CELLULAR LIFE

BIOLOGI UMUM –
BIOLOGI 2016
OUTLINE
 Cell Theory.
 Cell Structure and Function.
 Organelles and Their Function.
(See also PPT SEL-Produksi Energi;
PPT SEL-Kasus & Manfaat)
 Energy and Nutrient Acquisition.
 Metabolism.
 Photosynthesis.
 Virus.
(See also PPT SEL-Virus)
 Prion.
 CELL THEORY
The Cell Theory is one of the foundations of modern biology.
Its major tenets are:
• All living things are composed of one or more cells.
• The chemical reactions of living cells take place within cells.
• All cells originate from pre-existing cells.
• Cells carry hereditary information, which is passed from one
generation to another.

Cells are every organism’s basic units of structure and function.

 TWO MAIN TYPES OF CELLS
Prokaryote and Eukaryote Cell
The two main types of cells are prokaryotic cells (in Bacteria and
Archaea) and eukaryotic cells (in Fungi, Protists, Plants and Animals).

Yeast (khamir)
Cell Size: why aren’t cells larger?

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Surface-to-volume ratio

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Comparison of Prokaryotic and Eukaryotic Cells
 CELL STRUCTURE

Basic features of all cells:

Cell (plasma) membrane.
Cytoplasm (contains semifluid substance called cytosol).
Cytosol  water with solutes (proteins, sugars, salts, etc.).
DNA-containing region (carry genes).
Ribosomes (make proteins).
 Cell (Plasma) Membrane
 The LIPID BILAYER model (also referred to as the
FLUID-MOSAIC MODEL).

The molecule in the model

is the PHOSPHOLIPID.
It has a polar (hydrophilic)
head and two nonpolar
(hydrophobic) tails.

• Separates the inner parts of the cell from the outer

environment.
• Acts as a selectively permeable barrier to allow certain
chemicals, namely water, to pass and others to not pass.
 Cytoplasm

- Most of the cell space is Cytoplasm.

- The cytoplasm is everything in the
cell interior except the DNA.
- The cytoplasm contains sugars,
amino acids, proteins, enzymes,
fatty acids.

 Cytosol: Gel-like fluid where most of the cells chemical

reactions take place.
 Organelles: Mini organs that carry out specific job
functions for the cell.
 Inclusions: Small substances in cytoplasm called
vesicles, vacuoles. Acts as deposits, storage.
DNA-containing Region (Nuclear Region)

Hereditary material (both DNA and RNA) is needed for a cell to be

able to replicate and/or reproduce.
Prokaryotic DNA is organized as a circular chromosome contained
in an area known as a nucleoid.
Eukaryotic DNA is organized in linear structures, the eukaryotic
chromosomes, contained in an area known as the nucleus.
 Eukaryotic chromosomes are associations of DNA and histones.
ORGANELLES AND THEIR FUNCTION
Three Groups of Organelles
Organelles possess specialized cellular function.
GROUP 1 GROUP 2 GROUP 3
Organelles in Bacteria-like Organelles
Endomembrane organelles involved in involved in gene
System energy production expression

Endoplasmic Mitochondria Nucleus

Reticulum
Chloroplast Ribosome
Golgi Bodies
Lysosome
 Group 1: Endomembrane System
The Endomembrane System:
 Endoplasmic reticulum
 Golgi Apparatus/Bodies
 Vesicle
 Lysosome
Lysosomes
 Contain digestive enzymes.
 Lyse (break open) and
release enzymes to break
down and recycle cell
parts.
 Break down food, bacteria,
and worn out cell parts.
 Programmed for cell death
(autolysis).
DIGESTING DIGESTING DIGESTING
FOOD ORGANELLES CELLS
Group 2: Organelles Involved in Energy Production

Endosymbiosis Theory
 Chloroplast
 Ancestor: ancient Cyanobacteria.
 Possess their own DNA  the
extra-chromosomal DNA (cpDNA).
 Possess two membranes: grana
(thylakoid membranes) and stroma.
 Produce ATP.
 Carry out photosynthesis.
Mitochondria
 Ancestor: ancient Proteobacteria.
 Possess their own DNA the extra-
chromosomal DNA (mtDNA).
 Possess two membranes: cristae and
outer membrane.
 Produce ATP.
 Carry out aerobic respiration.
Group 2: Organelles Involved in Gene Expression

Nucleus Nucleolus

 Control center of the cell.  Site of transcription.

 Contain chromosomal DNA (nuDNA).  Transcribe ribosomal RNA.
 Possess two membranes.  Site of assemble/make ribosomes.
 Usually one per cell.  It is made up of proteins and RNA.
 Contain nucleolus.
 Ribosome

 Translate (read) instructions from mRNA to build proteins.

 Site of making protein.
 Consist of two subunits; small and large subunits.
 Eukaryotes have 80S, prokaryotes 70S.
 Some are attached to ER; some are free in cytoplasm.
 Prokaryotes and Eukaryotes Possess Chromosomal
and Extra-chromosomal DNA
Prokaryote Eukaryote
Cells contain: Cells contain:
 Chromosomal DNA.  Chromosomal DNA.
 Plasmid DNA.  Plasmid DNA in yeasts.
 Chloroplast-DNA in
plants.
 Mitochondrial DNA in
yeasts, plants and
animals.
 Comparing Plant Cell and Animal Cell

• No Chloroplast • No Centriole
• No Cell wall • No Lysosome
 ENERGY ACQUISITION
Methods of Energy Acquisition
ORGANISMS

AUTOTROPHS
 Use inorganic C compounds as
carbon source.
 Form complex molecules by
reducing CO2 (or other C).
HETEROTROPHS
 Use organic C compounds as
carbon source.
 Form complex molecules by
reducing organic molecules.

PHOTO- CHEMO-AUTOTROPHS PHOTO- CHEMO-HETEROTROPHS

AUTOTROPHS  Use inorganic C HETEROTROPHS  Use organic C
 Use inorganic C compounds.  Use organic C compounds.
compounds.  Use chemical compounds.  Use chemical
 Use light as compounds as energy  Use light as compounds as energy
energy source. source. energy source. source.

The main types of energy-capturing metabolism

 Photo-autotroph Photo-heterotroph

Plantae Cyanobacteria: Cyanobacteria: Cyanobacteria:

Chlorobium Rhodopseudomonas Rhodospirillium

Chemo-autotroph Chemo-heterotroph

Archaea Bacteria: Fungi Animalia

Azotobacter
 Mode of Obtaining Food, or Nutrient
Saprophyte/Saprotroph
 Obtain food, or nutrient, from dead
organisms or decaying matter. Fungi

Parasite
 Obtain food, or nutrient, from living
organisms.
 Obtain food by living on or in the body of
Mealy bugs
the host.

Pathogen
 Organism that cause disease in other
organisms. Plant pathogen
 METABOLISM
METABOLISM
The total chemical reactions in an organism

CATABOLISM ANABOLISM
Catabolic pathways release energy Anabolic pathways consume
by breaking down complex energy to build complex
molecules into simpler compounds molecules from simpler ones

Enzyme 1 Enzyme 2 Enzyme 3

A B C D
Reaction 1 Reaction 2 Reaction 3
Starting Product
molecule A metabolic pathway begins with a
specific molecule and ends with a product
Nucleic Acid, Carbohydrate, Protein, and Lipid Are Energy
Sources for Metabolism

METABOLISM

CATABOLISM ANABOLISM
Energy-yielding metabolism Biosynthetic metabolism

Intracellular precursor pools

Energy sources
i.e. pyruvate, acetyl Co-A
(electron donors)
i.e. external nutrients
Biosynthetic intermediates
i.e. nucleotides, glucose, amino acids,
fatty acids
ATP
Heat Utilizable Biopolymers (i.e. nucleic acids)
energy ADP + Pi
Biopolymers (i.e. carbohydrates)

Ultimate metabolic Biopolymers (i.e. proteins)

products
i.e. CO2, H2O, NH3 Biopolymers (i.e. lipids)
 All catabolic reactions involve electron transfer

Energy is high-energy bonds in ATP

ATP is an excellent
energy carrier in cells
Energy is released from ATP when the phosphate bond is broken
Cellular Metabolism
The first Law of
Thermodynamics:
Energy can be
Nucleic transferred and
acids
Nucleotide
transformed, but it
s
cannot be created
or destroyed.

Beetle feeding on a leaf

Leaf as chemical energy

 Cellular Respiration
 Cellular respiration includes both Aerobic and
Anaerobic respiration.

 Cellular respiration has three stages:

 Glycolysis (breaks down glucose into two molecules
of pyruvate)  substrate-level phosphorylation.
 Citric acid cycle (completes the breakdown of
glucose).
 Oxidative phosphorylation (accounts for most of the
ATP synthesis)  electron transport chain system
and chemiosmosis.
Anaerobic and Aerobic Respiration
 The GLYCOLYSIS breaks down glucose into two molecules of pyruvate. It occurs in
the cytoplasm.
 In the presence of O2, pyruvate enters the mitochondrion.
 Pyruvate must be converted to Acetyl CoA, which links the cycle to glycolysis.
 The CITRIC ACID CYCLE, also called the KREBS CYCLE, takes place within the
mitochondrial matrix. The cycle oxidizes one pyruvate, generating 1 ATP, 3 NADH,
and 1 FADH2 per turn.
 The citric acid cycle has eight steps, each catalyzed by a specific enzyme.
 Electrons are transferred from NADH or FADH2 to the ELECTRON TRANSPORT
CHAIN. The electron transport chain is in the cristae of the mitochondrion.
 CHEMIOSMOSIS use the energy in a H+ gradient to produce ATP.

Enzyme Enzyme

ADP
P +
Substrate Product ATP
 Tahapan Respirasi Seluler
(integrated science: bio-chemist-physic)
Electrons Electrons carried
via NADH and
carried
FADH2
via NADH
Tahap 2
Tahap 3
Tahap 1
KREBS Electron transport
Glycolysis CYCLE
chain and oxidative
phosphorylation
Glucose ---pyruvate

Cytosol Mitochondria

ATP ATP ATP

Substrate-level Substrate-level Oxidative
phosphorylation
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 SUBSTRATE-LEVEL PHOSPHORYLATION
Energy released through the oxidation of a substrate is used to phosphorylate ADP
and to generate an ATP molecule.
OXIDATIVE PHOSPHORYLATION
Electrons are transferred from organic compounds to one group of electron carriers
(i.e. to NAD+ and FAD).
Electrons are passed through a series of different electron carriers (electron
transport chain system) to molecules of oxygen.
ELECTRON TRANSPORT CHAIN SYSTEM
Electrons are transferred from NADH or FADH2 to the electron transport chain.
Electrons are passed through a number of proteins including cytochromes to O2.
CHEMIOSMOSIS MECHANISM
The energy from a proton (H+) gradient formed across the cell membrane is used to
drive a membrane bound ATPase to produce ATP.

 NADH and FADH2 account for CHEMIOSMOSIS

most of the energy extracted
from food.
 These two electron carriers
donate electrons to the electron
transport chain.
Electron transfer in the electron transport chain causes proteins
to pump H+ from the mitochondrial matrix to the
intermembrane space.
H+ then moves back across the membrane, passing through
channels in ATP synthase. ATP synthase uses the exergonic flow
of H+ to drive phosphorylation of ATP.
An Example of Anaerobic Respiration: Fermentation

Yeast Saccharomyces cerevisiae

produces ethanol.

Burning feeling of Lactic acid bacteria

muscles during a (LAB) produce
workout. lactic acid.
 PHOTOSYNTHESIS

Overview of Photosynthesis
• The process that organisms use to
trap the sun’s energy and build
carbohydrates (glucose) that store
energy.
• It happens in two phases:
1) The Light (light-dependent)
Reaction creates ATP, releases
oxygen.
2) The Light-independent Reaction
uses ATP to make glucose.
 Energi Cahaya

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 Overall reaction of Photosynthesis

In Light-dependent Reaction:
Water is split in the process
(Photolysis), releasing oxygen as a
by-product of the reaction.
In a series of reactions the energy
is converted (along an electron
transport chain) into ATP and
NADPH.
In Light Independent Reaction:
The ATP and NADPH are used to
carry out carbon-fixing reaction
(Fixation of CO2) to make glucose.
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 VIRUS

 It has a core of genetic material (DNA or RNA, not both).

 A protein coat (capsid) enclosed the nucleic acid.
 The protein coat is covered by a membraneous
envelope (made of lipid bilayer from the host), in some
cases.
 Some Characteristics of A Virus

 Viruses are considered to be non-

living:
- Cannot replicate on their own.
- Only replicate inside living cells.
- Obligate intracellular parasite.
- No organelles to use energy.
- No cytoplasm.
 Each virus can only infect a
specific range of cell types.
 The study of viruses is called
Virology.
 Virus Diversity

Bacteriophage on Tobacco mosaic Ebola virus on

a bacterium cell virus on a leaf a human cell
 Virus Life Cycle
All viruses follow the same basic steps, the Lytic Cycle.

1. A virus particle attaches to a

host cell.
2. The particle releases its
genetic material into the host
cell.
3. The injected genetic material
recruits/hijacks the host cell’s
enzymes.
4. Enzymes make parts for more
new virus particles.
5. New particles assemble the
parts into new viruses.
6. New viruses break free from
the host cell resulting in cell
death.
7. New viruses able to infect new
host cell.
 PRION
 Prion means proteinaceous infectious particle (Prusiner,
1982).
 It’s usually pronounced PREE-on in the U.S. and PRY-on
in the U.K.
 Prions are bits of misfolded protein that have the
ability to spread by making other proteins misfold.

PRNP gene in your Cellular Prion protein  Scrapie prion (PrPsc) is an infectious particle
DNA (at (PrPc) is located on made up of misfolded prion proteins.
chromosome 20) the brain cells.  PrPc and PrPsc do not differ in sequences, but
encodes for normal differ in three-dimensional protein
prion protein. conformation.
 Prion disease or Transmissible
Spongiform Encephalopathy (TSE) is a
Brain cells group of neuro-degenerative disorder
 characterised by accumulation of
the prion protein (PrPsc) in central and
peripheral nervous system.
 Human Prion Disease
Sporadic
 Cause by spontaneous
conformational change of PrPc
(but at extremely low rate).
Examples:
- Sporadic Creutzfeldt-Jacob
disease (sCJD).
- Sporadic Fatal Insomnia (sFI).

Familial (Genetic) Examples:

- Fatal Familial Insomnia (FFI).
 Cause by a mutation of PrPc to PrPsc. - Familial CJD.
 Rare autosomal dominant-inherited - Gertsman-Straussler-Scheinker
disease  found in only 40 families. Syndrome (GSS).

Acquired by Transmission Examples:

- Kuru.
 Infection from neurosurgical instruments. - Variant CJD (vCJD).
 Dura mater grafts. - Mad cow disease (BSE: Bovine
 Prion-contaminated human growth- Spongiloform Encephalopathy).
hormone.
 Fisika Optik
Dari mikroskop cahaya Ke mikroskop elektron
 Mikroskop optik dan mikroskop elektron
berperan penting pada perkembangan ilmu
tentang sel (cell biology)
 Prinsip-prinsip yang digunakan pada
teknologi mikroskop adalah fisika optik,
antara lain mengenai cahaya, sifat-sifat
cahaya (pemantulan atau pembiasan), dan
lensa.
 Pelajari lebih lanjut pada Kuliah Fisika Dasar
 Terkait pula dengan pewarnaan sel.
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 SCANNING ELECTRON MICROSCOPE (SEM)

SEM 4000x

SEM 5400x

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TRANSMISSION ELECTRON MICROSCOPE (TEM)

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Next Week: Principle of Genetics