Do you know that

humans have an estimated 100

trillion or 1014 cells a typical cell size is 10 m a typical cell mass is 1 nanogram

STBP 1023 Cell Biology

Assoc. Prof. Dr. Hasidah Mohd. Sidek Mohd. hasidah@ukm.my
School of Biosciences & Biotechnology Faculty of Science & Technology (Level 1 Biological Science Building)

Course Objectives
At the end of the course, students will : understand the biochemical basis of the living system understand the concept of the cell as the basic unit of life and appreciate the structure & function of cell components

Course Objectives (continued)

understand the principles of bioenergetics in order to appreciate how intermediary metabolism though complex is very systematic and orderly understand the concept of energy utilisation and production of energy (ATP) in the cell

Course Structure
Lectures Tutorials

Evaluation
Mid(30 Mid-semester Examination (30-40%) Final Examination (60-70%) (60-

Course Facilitators

 Assoc. Prof. Dr. Hasidah Mohd. Sidek (HMS) Mohd. Dr. Izyanti Ibrahim (II) Dr. Sharom Md. Yusof (SMY) *

* Coordinator (sharom@ukm.my)

Lecture Schedule One Set

  

Monday Tuesday Thursday

11:00-12:00 11:0008:0008:00-09:00 08:0008:00-09:00

DKG129BB DKG129BB DKG130BB

Course Outline

1. Cell as the basic unit of life (2 h)

- Overview of cell structure & function - Techniques to study cell structure & function (microscopy, cell fractionation)

2. Structure & function of cells (3h)

- Organelles (mitochondria, chloroplasts, ribosomes, nucleus, Golgi complex, ribosomes, endoplasmic reticulum, bacterial & plant cell walls, cytoskeleton)

3. Cell buffering system (4 h)

- Characteristics of water, acids, bases & properties of buffers - Physiological buffers

4. Macromolecules in cells (5 h)
- Proteins - Polysaccharides - Lipids

5. Membrane Biology (4 h)
- Structure, composition & models of membranes - Transport across membranes

6. Enzymatic reactions in cells (5h)

- Types & functions of enzymes
- Catalytic characteristics - Factors influencing enzyme reactions - Isoenzymes & coenzymes

7. Bioenergetics (2 h)
- Principles of thermodynamics - Involvement of ATP in coupled reactions

8. Energy metabolism & ATP synthesis (7 h)

Glycolysis TCA cycle Respiratory chain & synthesis of ATP F-oxidation of fatty acids Shuttle systems

Recommended Text


Campbell N.A. & Reece J.B. 2005. Biology. 7th Edition. San Francisco: Pearson Benjamin Cummings. Campbell M.K. & Farrell S.O. 2006. Biochemistry. 5th Edition. Belmont: Thomson Brooks / Cole. Nelson, D.L. & Cox, M.M. 2008 or 2006. 2006. Lehninger Principles of Biochemistry. 5th or 4th Edition. New York: W.H. Freeman. Edition.

First 2 lectures


Cell as the basic unit of life (2 h) - Overview of cell structure & function - Techniques to study cell structure & function (microscopy, cell fractionation)

All Living Things are Composed of Cells



Cell
Mass of protoplasm Bound by membrane Smallest living unit

In other words, the cell is the basic unit of life Anything lower than the cell is considered non-living non-

 Cells comprise of : - molecules - atoms

(organised into macromolecules)

Individually, molecules and atoms are non-living noncomponents molecules and atoms are not able to carry out life processes

We will review later on what properties make the cell living as compared to its nonnon-living constituents (molecules and atoms)

http://www.sinauer.com/cooper/4e/chapter01.html July 5th 2009

All present-day cells (both prokaryotes & presenteukaryotes) are descended from a single ancestor The first cell arose at least 3.8 billion years ago as a result of enclosure of self-replicating RNA in selfa phospholipid membrane

PresentPresent-day prokaryotes are divided into two groups :

the archaebacteria the eubacteria

Eukaryotic cells:
are larger and more complex than prokaryotic cells contain a nucleus consist of cytoplasmic organelles and a cytoskeleton

The simplest eukaryotes are unicellular organisms (e.g. yeasts & amoebas) Multicellular organisms evolved from associations between such unicellular eukaryotes Division of labor led to the development of the many kinds of specialised cells that make up presentpresent-day plants & animals

In research, cells have been used as experimental models

Examples of cells as experimental models



The bacteria, E. coli is useful for investigating fundamental aspects of biochemistry & molecular biology (related to the genetic simplicity of the bacteria thus easily studied)

science.howstuffworks.com 12 Sept 2011

en.wikipedia.org 12 Sept 2011

some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls the harmless strains are part of the normal flora of the gut

 E. coli is the most widely studied prokaryotic model organism an important species in the fields of biotechnology and microbiology (it has served as the host organism for the majority of work with recombinant DNA)

More examples of cells (and organisms) as experimental models

senescence.info 12 Sept 2011

Yeasts, Yeasts, as the simplest eukaryotic cells, are important models for studying various aspects of eukaryotic cell biology

The nematode, Caenorhabditis elegans is a simple multicellular organism that serves as an important model in developmental biology

The fruitfly, Drosophila fruitfly, melanogaster has been extensively studied in terms of its genetics and contribute to major advances in understanding animal development

Also the small flowering plant, Arabidopsis thaliana is widely used as a model for studies of plant molecular biology & development

- Its small stature and short generation time facilitates rapid genetic studies - Arabidopsis was the first plant to have its genome sequenced
genotyping.wordpress.com Sept 12 2011

In addition, many kinds of vertebrate cells can be grown in culture where they can be studied under controlled laboratory conditions Specialised cell types, such as neurons & muscle cells, provide useful models for investigating particular aspects of cell biology

Epithelial cells in culture, stained for keratin (red) and DNA (green)

Growth of Animal Cells in Culture: The propagation of animal cells in culture has allowed studies of the mechanisms that control cell growth & differentiation Culture of Plant Cells: Cultured plant cells can differentiate to form specialised cell types &, in some cases, can regenerate entire plants Viruses: Viruses provide simple models for studies of cell function

At the level of organisms



The frog Xenopus laevis & zebrafish are important models for studies of early vertebrate development The mouse is a mammalian species suitable for genetic analysis and also for in vivo trials

The ease of manipulation in amphibian embryos has given them an important place in modern developmental biology.

- Fully-sequenced genome - Well understood, easily observable and testable - relatively easy to maintain and handle developmental - reproduce quickly behaviors - share a high degree of homology with humans (mouse genome already sequenced)

Tools which have facilitated studies in cell biology include

Light Microscopy allows for:

- visualisation of cells & subcellular
structures - determination of intracellular localisation of specific molecules

Electron Microscopy (with a resolution b 100 fold greater than fold light microscopy) allows:
- detailed analysis of cell structure

 Subcellular

Fractionation: allows organelle isolation from eukaryotic cells for further biochemical analysis

(via differential centrifugation)

Animation of subcellular fractionation

thin slices of cork as observed by Robert Hooke

internal ultrastructure of cells -transmission electron microscope

surface details of cilia - scanning electron microscope

Blood components
(surface details)

scanning
electron microscope

The early microscope!

SEM

Overview of cell structure & function

   

 

Objectives Introduction Cell theory General characteristics of a cell Classification Different cell shapes
Figure 1.8

EUKARYOTIC CELL

PROKARYOTIC CELL DNA (no nucleus) Membrane

Membrane Cytoplasm

Organelles Nucleus (contains DNA) 1 m

OBJECTIVES


To discuss the cell theory & its formulation To understand the general characteristics of a cell similarities in structure & biochemical reactions To distinguish between prokaryotic & eukaryotic cells

Development of microscopy contributed to the formulation of the cell theory

Cell theory historical timeline

Basic tenets of the Cell Theory

1. All organisms consist of one or more cells 2. The cell is the basic unit of structure for all organisms 3. All cells arise only from prepreexisting cells

The combined work of Schleiden, Schwann & Virchow led to the Cell Theory

This would not have been possible without the contribution of microscopists

Robert Hooke

Anton van Leeuwenhoek

Cells are the basic structural units of all living organisms Organisms may be made up of single or multiple cells

in other words, organisms are unicellular or multicellular

Therefore


The cell is the lowest level of organisation that can perform all activities required for life

25 m Figure 1.5 Any lower level of organisation is non-living

Cell structure is diverse but all cells share common characteristics

General characteristics of cells

The chemical composition of all cells are basically the same

Basic elements in cells C, H, N, O, P, S NonNon-living elements form cellular macromolecules - proteins, nucleic acids, carbohydrates & lipids Activities carried out by cells depend on properties & functions of macromolecules

All cells are bounded by a plasma membrane

The plasma membrane : separates activities occurring in neighboring cells gives each cell an independent entity
Lipid bilayer of the plasma membrane

Lateral movement (~107 times per second) (a) Movement of phospholipids

Hydrophillic head exposed toFlip-flop aqueous environment (~ once per month) Hydrophobic tail hidden from the environment

Cells are highly complexed & organised

Organisation of Life
Cell Tissue Organ Organ System Organism Population Community Ecosystem Biosphere

Smallest Level

Largest Level

Cells possess a genetic program & the means to use it

Genetic information is contained in genes Genes constitute blueprints for cell structure, activities & multiplication

The Cells Heritable Information



Cells contain chromosomes made partly of DNA (the substance of genes)

DNA programs the cellular production of proteins and transmit information from parents to offspring
Sperm cell Nuclei containing DNA Fertilized egg with DNA from both parents Embyros cells with copies of inherited DNA

Egg cell
Figure 1.6

Offspring with traits inherited from both parents

 Cells

are capable of producing more of themselves

Reproduce by division (mitosis)

 Cells

@ acquire and utilise energy

Developing and maintaining complexity requires energy from the sun Photosynthesis converts light energy into chemical energy sucrose and starch Animal cells contains prepackaged energy in the form of glucose


Glucose metabolism produces ATP

 Cells

perform a variety of chemical reactions

Cell processes based on biochemical reactions Require enzymes Biological catalysts increase reaction rate without increase in temperature

 Cells

engage in numerous mechanical activities

Transport, assembly and degradation These activities are based on dynamic changes in protein structure

Cells are able to respond to stimuli

Visible responses cilliate moves away from object or moves towards a source of nutrients Less obvious for multicellular organism  Receptors on cell surface interact with substances hormones, growth factors etc  Respond by altering metabolic activities, preparing for cell division, committing suicide(!)

Cells are capable of self-regulation selfTo maintain constant ordered state Failure to correct mistake during DNA replication may cause mutation leading to diseases e.g. cancer

Summary
The chemical composition of all cells are basically the same All cells are bounded by a plasma membrane Cells are highly complexed & organized Cells possess a genetic program & the means to use it Cells are capable of producing more of themselves Cells acquire and utilize energy Cells perform a variety of chemical reactions Cells engage in numerous mechanical activities Cells are able to respond to stimuli Cells are capable of selfregulation

Thus far, we have looked at common characteristics of cells There are differences too

Cells vary in size



smallest bacteria - 0.2 Qm in diameter longest in mammals (nerve cells, giraffe neck) largest volume (yolk of ostrich egg-also the largest eggsingle cell in the world)

Animal and plant cells large enough to be seen with a light microscope Smaller molecules only observed with an electron microscope

Cells vary in shape & function



Nerve cells are enormously extended to allow transmission of electrical signals Human red blood cells are flattened to allow transport of O2

Cell classification


Based on the presence or absence of a nucleus Two basic types of cells

Eukaryotes (from the Greek word eu meaning truly and karyon, a nucleus) karyon, Prokaryotes (from pro, meaning before) pro,

A Brief History of Life on Earth

4.5 billion years ago 3.5 billion years ago

Earth formed First life - prokaryotic bacteria dominate

Nucleated cells arise - eukaryotic Cambrian explosion multicellular eukaryotes arise

1.5 billion years ago 0.5 billion years ago

Prokaryotes evolved earlier than eukaryotes

Two basic types of cells http://cellbiologypowerpoints.googlepages.com/home July 5th. 2009

_____________________

_____________________

Prokaryote

Eukaryote
Diagrams: Prokaryotic & Eukaryotic Cell, Mariana Ruiz

Generally,


Prokaryotes are almost always singlesinglecelled

(except for prokaryote colonies)

Prokaryotes do not contain any cell nucleus or any other membrane-bound membraneorganelles
(@DNA travels openly around the cell)

Prokaryotes reproduce by binary fission

(generation of another copy by dividing)

Binary Fission

All bacteria (Kingdom=Monera) (Kingdom=Monera) are prokaryotes

Eukaryotic vs prokaryotic cells

Also to put things in perspective in terms of size

Thiomargarita (Sulfur Pearl of Namibia) Atypically-sized prokaryote >100 X bacterial size (typical size b1-5 Qm) large nitrate-storing vacuole contributes to the size

 When

compared to prokaryotic cells, eukaryotic cells are more complex

containing membrane-enclosed membraneorganelles absent in prokaryotes

Eukaryotes are 10-20 X larger 10than prokaryotes (~10-100 Qm) (~10Multicellular eukaryotes eukaryotes

(human, animal, plant, fungus, protist) protist)

 Unicellular

(yeast, Paramecium)

Yeast Paramecium

Candida albicans

Acetabularia (Mermaid's wineglass algae)

AtypicallyAtypically-sized eukaryotic cell  A single giant cell ~5-7 cm in length ~5

Eukaryotic cells are more complex in structure

Contain nucleus with membrane Are subdivided by internal membranes into various membranemembraneenclosed organelles

Red blood cell is a eukaryotic cell without nucleus



Unable to undergo mitosis

 Some

eukaryotic cells have more than one nuclei

Fungi - fused cells, multinucleate Human skeletal muscle cells multinucleate

Cross section of skeletal muscle : with peripheral nuclei and large amounts of cytoplasm / small extracelluar space

Multinucleated eukaryotic cells

Figure 4 - Skeletal muscle transverse section (Bright field illumination). Bar is 30 microns

www.bris.ac.uk/.../m1_index/histprac/page3.htm 7 July 2007

Techniques to study cell structure & function (microscopy, cell fractionation)

Different methods for enhancing visualisation of cellular structures in microscopy

(a)

Unstained versus stained human cheek epithelial cells

E

Brightfield microscopy : light passes directly through specimen Image has little contrast unless cell is naturally pigmented or artificially stained
(b)

50 m

Staining with various dyes enhances contrast Most staining procedures require that cells be fixed (preserved)

(b)

Brightfield (stained specimen). Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved).

In phase-contrast microscopy, phasecontrast of unstained cells may be enhanced by optical modification

For differential-interference-contrast differential-interference(Nomarski) microscopy, image appears 3 D through optical modification

In fluorescence microscopy, the locations of specific molecules in the cell are shown by tagging the molecules with fluorescent dyes or antibodies These fluorescent substances absorb ultraviolet radiation and emit visible light, as shown here in a cell from an artery
ocal. Uses lasers and special optics for cal sectioning of fluorescently-stained mens. Only a single plane of focus is
50 m

the cell by tagging the molecules cent dyes or antibodies. These substances absorb ultraviolet d emit visible light, as shown ll from an artery.

Confocal
50 m

Uses lasers and special optics for optical sectioning of fluorescently -stained specimens. Only a single plane of focus is illuminated; out-of-focus out-offluorescence above and below the plane is subtracted by a computer. A sharp image results, as seen in stained nervous tissue (top), where nerve cells are green, support cells are red, and regions of overlap are yellow. A standard fluorescence micrograph (bottom) of this relatively thick tissue is blurry
50 m

 In

electron microscopy,
a beam of electrons is focused through a specimen (TEM) or onto its surface (SEM)

Transmission electron micrograph

allows for detailed study of the internal ultrastructure of cells

Transmission electron microscopy (TEM). A transmission electron microscope profiles a thin section of a specimen. Here we see a section through a tracheal cell, revealing its ultrastructure. In preparing the TEM, some cilia were cut along their lengths, creating longitudinal sections, while other cilia were cut straight across, creating cross sections.

Figure 6.4 (b)

In contrast, scanning electron micrograph.

allows for detailed study of the surface of a specimen RESULTS
Scanning electron microscopy (SEM). Micrographs taken with a scanning electron microscope show a 3D image of the surface of a specimen. This SEM shows the surface of a cell from a rabbit trachea (windpipe) covered with motile organelles called cilia. Beating of the cilia helps move inhaled debris upward toward the throat.

TECHNIQUE

Figure 6.4 (a)

Importance of cellular fractionation for the study of cell structure & function

Cell Fractionation
A combination of various methods used to separate cell organelles & components Consists of two phases :
homogenisation centrifugation
http://www.freewebs.com/ltaing/ july 9 2008

Homogenisation
The process of breaking open cells Accomplished with the use of : chemicals
enzymes sound waves

Forcing cells through small spaces at high pressure may also break cells apart

Centrifugation
Isolation of cell organelles Results in the isolation of mitochondria, nucleus, chloroplast etc.

Generally
Applications for centrifugation are many including :
sedimentation of cells & viruses isolation of macromolecules (e.g. DNA, RNA, proteins, or lipids) separation of sub-cellular suborganelles

 increases knowledge on organelle functions

In cell biology, rich Because this cell fraction iscellin mitochondria, this is evidence that the fractionation mitochondria is the site for cellular respiration
isolate organelles into pure groups i.e. specific cell components

e.g. by centrifugation, a specific cell fraction was determined to have enzymes that function in cellular respiration

Microscopy is used to identify the organelles in each pellet Biochemical methods are then used to determine the metabolic functions associated with each type of organelle Cell fractionation is now widely used to isolate particular organelles in order to study further details of their function

Subcellular Fraction

Marker Enzyme

http://www.wpi.edu/Academics/Depts/Chemistry/Courses/General/fractionation.html 9 July 2007

Mitochondria Lysosomes Microsomes Cytosol

Succinate Dehydrogenase Acid Phosphatase GlucoseGlucose-6Phosphatase Lactate Dehydrogenase

Uses of centrifugation
separation of blood components plasma mostly H2O content erythrocytes (red blood cells) buffy coat (white blood cells & platelets)

Uses of differential centrifugation

sperm separation (fertility clinic)
sperm with an X chromosome (for girls) weigh a little more than sperm with a Y chromosome (for boys) sperms can be sorted out & prepared for insemination

Course Outline (revisited)



1. Cell as the basic unit of life (2h) - Overview of cell structure & function - Techniques to study cell structure & function (microscopy, cell fractionation) 2. Structure and function of cells (2h) - Organelles (mitochondria, chloroplasts, ribosomes, nucleus, Golgi complex, endoplasmic reticulum, bacterial & plant cell walls, cytoskeleton)

Course Outline (continued)



3. Cell buffering system (4 h) - Characteristics of water, acids, bases & properties of buffers - Physiological buffers 4. Macromolecules in cells (6 h) - Proteins - Polysaccharides - Lipids