A Tour of the Cell

The three main parts of the Cell theory are: (Schleiden and Schwann)

All organisms are made up of one or more cells.

The cell is the fundamental unit of structure and function in living things.
All cells are essentially the same in chemical composition.

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Mikroskop, 2 kelimeden olumaktadr. "micro",kk "scope" ise nesnelere bakmaya yarayan aygt anlamna gelmektedir.

Robert Hooke, 16351703,ngiliz Matematiki,Fiziki

Micrographia (1665) kitabnda

;gelitirdii bileik mikroskopla, ince kesilmi ie mantarnda boluklar gzlemlemi ve onlar Hcre olarak isimlendirmitir.
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1674 Leeuwenhoek protozoalar incelemitir. Dokuz yl sonra ilk kez bakteri grmtr.

Antonie Leeuwenhoek (16321723), arap gurmesi,vergi mfettii, kuma tccar 1677 Eritrositler ve sperm kefi 1683 Bakterileri tanmlam Kan dolam teorisine katkda bulunmu. Tek mercekli mikroskobun kefi x200
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 Light microscopes (LMs)

Pass visible light through a specimen Magnify cellular structures with lenses

10 m 1m
Human height Length of some nerve and muscle cells

0.1 m
Chicken egg

1 cm
Frog egg

1 mm Electron microscope

100 m
Most plant and Animal cells

10 m
Nucleus Most bacteria Mitochondrion

Light microscope

1m

100 nm 10 nm

Smallest bacteria Viruses

Ribosomes Proteins

1 nm

Lipids
Small molecules

0.1 nm

Atoms

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Electron microscope

 Use different methods for enhancing visualization of cellular structures

TECHNIQUE

RESULT

(a) Brightfield (unstained specimen).

Passes light directly through specimen. Unless cell is naturally pigmented or artificially stained, image has little contrast. [Parts (a)(d) show a human cheek epithelial cell.]
50 m

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

(c) Phase-contrast. Enhances contrast in unstained cells by amplifying variations in density within specimen; especially useful for examining living, unpigmented cells.

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(d) Differential-interference-contrast (Nomarski). Like phase-contrast microscopy, it uses optical modifications to exaggerate differences in density, making the image appear almost 3D. (e) Fluorescence. Shows the locations of specific molecules in the cell 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.
50 m

(f) Confocal. Uses lasers and special optics for optical sectioning of fluorescently-stained specimens. Only a single plane of focus is illuminated; out-of-focus fluorescence 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
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Electron microscopes (EMs)

Focus a beam of electrons through a specimen (TEM) or onto its surface (SEM)
SEM provides for detailed study of the surface of a specimen
TECHNIQUE
(a) 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.

RESULTS
Cilia

1 m

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 The transmission electron microscope (TEM)

Provides for detailed study of the internal ultrastructure of cells
Longitudinal section of cilium (b) 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. Cross section of cilium
1 m

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Isolating Organelles by Cell Fractionation Cell fractionation

Takes cells apart and separates the major organelles from one another
Tissue cells Homogenization

1000 g Homogenate (1000 times the force of gravity) Differential centrifugation 10 min
Supernatant poured into next tube 20,000 g 20 min

The centrifuge Is used to fractionate cells into their component parts

Pellet rich in nuclei and cellular debris

80,000 g 60 min 150,000 g 3 hr

Pellet rich in mitochondria (and chloroplasts if cells are from a Pellet rich in plant) microsomes (pieces of plasma membranes and Pellet rich in cells internal ribosomes membranes)

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Comparing Prokaryotic and Eukaryotic Cells All cells have several basic features in common
They are bounded by a plasma membrane

They contain a semifluid substance called the cytosol They contain chromosomes They all have ribosomes

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 Prokaryotic cells
Do not contain a nucleus

Have their DNA located in a region called the nucleoid

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Pili: attachment structures on the surface of some prokaryotes Nucleoid: region where the cells DNA is located (not enclosed by a membrane) Ribosomes: organelles that synthesize proteins Plasma membrane: membrane enclosing the cytoplasm Cell wall: rigid structure outside the plasma membrane Capsule: jelly-like outer coating of many prokaryotes 0.5 m Flagella: locomotion organelles of some bacteria (b) A thin section through the bacterium Bacillus coagulans (TEM)

Bacterial chromosome (a) A typical rod-shaped bacterium

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 Eukaryotic cells
Contain a true nucleus, bounded by a membranous nuclear envelope Are generally quite a bit bigger than prokaryotic cells

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 A animal cell
ENDOPLASMIC RETICULUM (ER)

Nuclear envelope Nucleolus Chromatin NUCLEUS

Rough ER

Smooth ER

Flagelium
Centrosome Plasma membrane

CYTOSKELETON Microfilaments Intermediate filaments Microtubules Ribosomes

Microvilli
Golgi apparatus

Peroxisome Mitochondrion
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Lysosome

In animal cells but not plant cells: Lysosomes Centrioles Flagella (in some plant sperm)

 A plant cell
NUCLEUS

Nuclear envelope Nucleolus Chromatin Rough endoplasmic reticulum Smooth endoplasmic reticulum

Centrosome

Ribosomes (small brwon dots)

Central vacuole Tonoplast Golgi apparatus Microfilaments Intermediate filaments Microtubules

CYTOSKELETON

Mitochondrion Peroxisome Plasma membrane Chloroplast Cell wall Plasmodesmata Wall of adjacent cell
In plant cells but not animal cells: Chloroplasts Central vacuole and tonoplast Cell wall Plasmodesmata

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Relative Volumes Occupied by the Major Intracellular Compartments

INTRACELLULAR COMPARTMENT PERCENTAGE OF TOTAL CELL VOLUME
54

Cytosol

Mitochondria
Rough ER cisternae Smooth ER cisternae plus Golgi cisternae Nucleus Peroxisomes Lysosomes Endosomes
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9 6 6 1 1 1

DNA

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Cell Nucleus

Structure of the Nucleus Nucleus:

largest organelle

Stores genetic information as DNA

Contains genetic information for making proteins

Controls all cellular activities and protein synthesis

Nuclear envelope: double membrane around the nucleus, connected to ER Nuclear pores with regulator proteins: Control exchange of materials between cytoplasm and nucleus
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nuclear lamina an attachment site for

b) c)

The continuity of the outer nuclear membrane with ER. So the space between the inner and outer nuclear membranes is directly connected with the lumen fo the ER. The inner nuclear membrane is lined by the nuclear lamina, which serves as an attachment site for chromatin (nuclear Copyright 2005 Pearson Education,lamina) Inc. publishing as Benjamin Cummings

Nuclear Lamina
Meshwork of intermediate filaments
Consists of "intermediate filaments", 30100 nm thick.

These intermediate filaments are polymers of lamin, ranging from 60-75 kD.
A-type lamins are inside, next to nucleoplasm; B-type lamins are near the nuclear membrane (inner). They may bind to integral proteins inside that membrane. Maintenance of nuclear shape Spatial organization of nuclear pores Regulation of transcription Anchoring of interphase chromatin DNA replication

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Within the Nucleus

Nucleoplasm:
fluid containing ions, proteins (enzymes), DNA, RNA, and nucleoli

Nucleolus: Dark areas

site of rRNA synthesis and packaging into ribosomal subunits Contains rRNA (ribosomal ribonucleic acid), proteins (85%) and ribosomal DNA

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The Nucleolus and rRNA Processing Nucleolus: Site for rRNA transcription, processing,

some aspects of ribosome assembly. Actively growing mammalian cells have 5 to 10 x 106 ribosomes, must be synthesized each time cell divides. Nucleolus is not surrounded by a membrane All cells contain multiple copies of rRNA genes (ex.oocytes) If removed, the cell can not divide Chro 13,14,15, 21 & 22 in charge

Nucleolar organizing regions (NORs): The areas for ribosome RNA are located and They can synthesize the 28S, 18S, and 5.8S rRNA for ribosome, 5S from nucleus
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Structure of nucleolus
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 Heterochromatin is highly condensed, transcriptionally inactive Euchromatin is decondensed, distributed throughout Heterochromatin

Heterochromatin (dark staining) and euchromatin (bright staining) Basic dyes (hematoxylin)

Euchromatin
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DNA replication:
Mammalian cells: clustered sites from labeling newly synthesized DNA with bromodeoxyuridine (BrdU in place of T) newly replicated DNA in discrete clusters

A: early replication B, late replication

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Organization of DNA
Chromatin is composed of DNA, histone, nonhistone protein, and some RNA DNA in chromatin is organized into Nucleosomes (DNA coiled around histones) During Nuclear Division, Chromatin is tightly coiled into visible chromosomes (23 pairs in humans)

Chromosome
Chromosomes are rod-like, coiled structures Chromosomes remain condensed and visible in the nucleus just prior to cell division. Humans have 46 chromosomes except in gamete cells.

Function: Contains all the genetic information in

triplet codes. e.g. CAT GAG TCA.

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 Histone:
Histone is positively charged and contains arginine and lycine. Histone protein is synthesized during the S phase only. Histones can be sorted as two types: 1. Highly conserved core histone including H2A, H2B, H3, and H4. 2. Non conserved linker histone including H1 only. The core histone is highly conserved, especially the H4 is.

NonHistone Protein: Negatively charged and acidic nonhistone protein binds to the specific DNA sequence of chromosome. Nonhistone protein can be synthesized during the whole cell cycle
The functions of nonhistone are as the follows: Help DNA molecules to form different structure domains that are beneficial to DNA replication and gene transcription. Help to start DNA replication reactio (topoisomerase II) Regulate transcription and gene expression.

Basic histone protein makes an easy binding to negative DNA 27

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From DNA to chromosome: If you open and extend the DNA molecule in each chromosome; It will be 5cm long. If you link all DNA molecules in a nucleus together, it will be 1.7 2.0 m long.

But, the diameter of nucleus is shorter than 10m.

Nucleosome (110A0 in dia.): Nucleosome is a beaded structure composed of core particles and linker DNA. Nucleosome can be described : Each nucleosome includes about 200bp DNA, one histone core, and an H1. The octameric histone core is composed of 8 molecules from H2A, H2B, H3, and H4 by two molecules from each. DNA molecule winds the core particle with a left hand helix and 80bp for each circle. 1.75 circles for each structure Adjacent core particles are linked by a 60bp linker DNA
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Structures of nucleosome

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Ribosomes
Are particles made of ribosomal RNA and protein the site of protein synthesis in the cell found within the cytosol of the cytoplasm and attached to internal membranes
Ribosomes Cytosol

Free ribosomes

Bound ribosomes Large subunit Small subunit

Diagram of a ribosome

0.5 m
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ER and ribosomes

Ribosomes
Made of 2 sub-units, rRNA (ribosomal RNA) & proteins, therefore they are not membrane-bound. rRNA sub-unit is produced by the nucleolus. They may be free, i.e. suspended in the cytoplasm or attached to the rough endoplasmic reticulum. 65% RNA, 35% protein Mito &Chloroplast have their own ribosomes Function: Site of protein synthesis
1) RER ribosomes are for ER, Golgi, Secretion & integral membrane proteins,
2) Free ribosomes are for cytoplasmal & peripheral proteins

Ribosome assembly
Formation of ribosomes requires assembly of pre-rRNA
with ribosomal proteins, then export of subunit
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mRNA Synthesized protein 1 = large sub-unit (+49 protein) 2 = small sub-unit (+33 protein)

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Polysomes A linear collection of several ribosomes attached to one mRNA.

Function: produces many copies of polypeptides when attached to the mRNA, e.g. the protein pigment Hb (hemoglobin)

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Endomembrane System

Surrounds cytoplasm

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How it works.
*The following membrane-bound structures, nucleus/nuclear envelope, ER (rough and smooth), Golgi bodies, vesicles, vacuoles and lysosomes, have a functional interrelationship. They function together in the synthesis and transport of molecules within the cell or for export out of the cell.

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Endomembrane System (Golgi Ap, ER &Lysosomes) The endoplasmic reticulum (ER) (5-6nm in dia.)
Accounts for more than half the total membrane in many eukaryotic cells
Is continuous with the nuclear envelope Rough ER
Smooth ER Nuclear envelope

There are two distinct regions of ER: SER (no riosome) & RER (bound ribosome)
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ER lumen Cisternae Ribosomes Transport vesicle Smooth ER

Transitional ER

Rough ER

200 m

Functions of Smooth ER
Synthesizes fosfolipids, ceramide & steroids (enzymes in the membrane) Glycogen metabolism Stores calcium (muscle) Detoxification (poisons/drugs/cholesterol using cytochrome p450) Establishing resistance to medicine (new born baby) NOTE: We see, in common, in liver, testis, ovary, kidney, stomach, striated muscle cells, eye (excess give shape)
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Functions of Rough ER
Ribosomes attached (also to nuclear outer membrane)

Produce proteins (soluble, integral & secreted) which are then transported throughout the cell in tubules/canals to be exported out
Attachment of carbohydrate especially for secreted proteins (Glycolysation) Membrane assembly Folding (ex.:lysosome proteins), quality control & degradation

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The Golgi Apparatus: Shipping & Receiving Center

Receives many of the transport vesicles produced in the rough ER

Consists of flattened membranous sacs called cisternae

Functions of the Golgi apparatus include: Modification of the products of the rough ER -( N-linked glycosylation (N-acetyl glucoseamine, fucose, galactose, N-acetyl neuraminic acid), - adding phosphates to mannose residues, - adding sulphate) Maturation of proteins O-linked glycosylation Manufacture of certain macromolecules
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 Functions of the Golgi apparatus

Golgi apparatus cis face (receiving side of Golgi apparatus)

1 Vesicles move 2 Vesicles coalesce to 6 Vesicles also form new cis Golgi cisternae from ER to Golgi transport certain Cisternae proteins back to ER 3 Cisternal maturation: Golgi cisternae move in a cisto-trans direction 4 Vesicles form and leave Golgi, carrying specific proteins to other locations or to the plasma membrane for secretion

0.1 0 m

5 Vesicles transport specific proteins backward to newer Golgi cisternae

trans face (shipping side of Golgi apparatus)

TEM of Golgi apparatus

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Protein Secretion
Interior of Golgi apparatus 1. In the endomembrane system, proteins bound for different destinations are given different carbohydrate "tags."

2. Proteins are sorted in the Golgi apparatus.

3. Transport vesicles bud from the Golgi apparatus and travel to their destinations. Return to the ER

To plasma membrane for secretion 4. Proteins on vesicle surface interact with receptors at destination.
5. Vesicle delivers contents.

Lysome

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Vesicles
Cellular processes which make use of vesicles includes (example):
autolysis, Secretion (enzyme, hormone & proteins, etc.) intracellular digestion,

Pinocytosis & phagocytosis,

packaging of neurotransmitters & viruses, storage of Ca 2+ in muscle cells or macromolecules in liver & muscle cells & plant cells, detoxification of alcohol & drugs into H2O-soluble products,

breaking down H2O2 (hydrogen peroxide: a toxic byproduct made by many enzymes) into H2O + O2 via the enzyme catalase (i.e. in peroxisomes) located in the liver

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Lysosomes (0,2-06mm)
Large, irregular structures surrounded by single membrane, form by breaking off from the Golgi apparatus Glycoprotein rich interior membrane The interior of these structures, is more acidic than the rest of the cytoplasm, is filled with large numbers of small granules, which are protein aggregates of as many as 40 different hydrolase (digestive) enzymes Most abundantly found in lung, spleen and WBC The lysosomes provide an intracellular digestive system that allows the cell to digest; damaged cellular structures, food particle & unwanted matter such as bacteria. Lysosomal storage diseases (I- cell Disease, Tay Sach (hexominidase)

FORMATION OF LYSOSOMES AND LYSOSOMAL ENZYMES

Lysosomal enzymes produced on membrane- bound ribosome. They are channel into matrix of endoplasmic reticulum. Goes to golgi appratus Package in the form of secretory granules or primary lysosomes Then fuse to vacuole (food, microorganism by endocytosis, pinocytosis & phagocytosis) to become secondary lysosome
Note: not found in plant & not found in erytrocyte

 Lysosomes carry out intracellular digestion by Phagocytosis

Nucleus

1 m

Lysosome

Lysosome contains active hydrolytic enzymes

Food vacuole fuses with lysosome

Hydrolytic enzymes digest food particles

Digestive enzymes

Lysosome Plasma membrane

Digestion Food vacuole

(a) Phagocytosis: lysosome digesting food

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These are all part of endomembrane system

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Lysosome: Autophagy

Vacoule
Vacuoles are formed by phagocytosis A larger membrane-enclosed sac.

Pigment Vacuole (pigment) and Contractile Vacuole (expel water)

Function Storage of macromolecules such as a food vacuole formed by phagocytosis.
Central vacuole Cytosol
Tonoplast

Central vacuoles

Are found in plant cells

Hold reserves of important
Nucleus Cell wall Chloroplast

Central vacuole

organic compounds and water

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5 m

Relationships among organelles of the endomembrane system

1
Nuclear envelope is connected to rough ER, which is also continuous with smooth ER
Nucleus

Rough ER

Membranes and proteins produced by the ER flow in the form of transport vesicles to the Golgi

Smooth ER Nuclear envelop

cis Golgi

Golgi pinches off transport Vesicles and other vesicles that give rise to lysosomes and Vacuoles
trans Golgi

Plasma membrane

Lysosome available for fusion with another vesicle for digestion

5 Transport vesicle carries

proteins to plasma membrane for secretion

Plasma membrane expands by fusion of vesicles; proteins are secreted from cell

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 Mitochondria and Chloroplasts change energy from one form to another

Mitochondria
Are the sites of cellular respiration Are found in nearly all eukaryotic cells

Chloroplasts
Found only in plants, are the sites of photosynthesis

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Mitochondria (except erytrocytes), 0,5mm

Traditionally not considered to be part of endomembrane system

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Mitochondria -1
The powerhouse of the cell Membrane-bound organelle with its own DNA (deoxyribonucleic acid, i.e. mDNA (mitochondrial DNA) Contains 2 membranes: an inner folded (70% protein) /convoluted membrane called cristae & a smooth outer membrane (Porin, 5kDa, enzymes for lipid synthesis). Cristae; increases surface area for cellular respiration and the production of ATP with the aid of several proteins and complexes (e.g. ATP complexes, transport proteins/electron transport chains).

The matrix is the inner fluid-filled space containing DNA, RNA, ribosomes, proteins, enzymes, H+/protons etc. (Note: membranes are also composed of phospholipids and proteins)

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Mitochondria -2
The inner membane proteins:
Cytochorome Permease (transport in & out metabolites) ATP synthase (FoF1ATP synthase) Phosphate Translocase (H2PO4- & H+) Electron exchanger (such as malate aspartate exchanger for NADH)

Matrix:
Enzymes for Crebs Cycle(TCA), pruvate & fat acid oxidation Excess Ca+2 storage Note: urea synthesis in liver cells, partial steroid synthesis & heme synthesis for Hemoglobin

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Mitochondria -2

MtDNA
2-10 circular double helix DNA (light & heavy) About 17Kb Self replication (any time) & transcription 13 protein, 22 tRNA & 2 rRNA (cytochrome oxidase, NADH dehydrogenase No packing with histone as chromosomal DNA Almost completely coding Codon show difference in comparison to nuclear codon. Ex: UGA for trytophan, instead of stop codon Maternal inheritance (not much from paternal) No quality control for DNA replicaion error (10 times higher mutation rate in comparison to nuclear) Mutation can be homoplasmic or heteroplasmic

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Peroxisome (Microbodies, 0,1-1mm)

All animal cells (except erythrocytes) contain peroxisomes
Roughly spherical & single membrane-enclosed organelles Contains 50 different enzymes

Do not contain DNA or ribosomes

Peroxisome protein synthesized on free ribozymes

Not part of the endomembrane system

Contain Oxidative enzymes such as catalase, glucoseurate & d-amino acid oxidase

Peroxisome is the source of H2O2

* glyoxysomes in plants contain enzymes for converting fats to carbohydrates
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58

FUNCTIONS OF PEROXISOME
Detoxification (breakdown the excess fatty acids (the very long

one), uric acid, amino acid, methanol)

Accelerate gluconeogensis from fats (by enzymes) Degrade purine to uric acid (bile acid), The site of oxygen utilization in the cell Cholesterol, bile acid & ether lipid (plasmalogen) biosynthesis

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Centrosomes and Centrioles

Centrosome is considered to be a microtubule-organizing center
Contains a pair of centrioles
Centrosome

Microtubule Centrioles 0.25 m

Longitudinal section of one centriole

Microtubules

Cross section of the other centriole

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Centrosomes
Also called the centrosphere or cell center, which refers to a specialized zone of cytoplasm containing the centrioles and a variable number of small dense bodies called centriolar satellites. Considered to be a center of activities associated with cell division, usually adjacent to the nucleus. The Golgi apparatus often partially surrounds the centrosome on the side away from the nucleus. Plant and fungal cells have a structure equivalent to a

centrosome, although they do not contain centrioles .

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 Centrioles are self-duplicating organelles that exhibit

continuity from one cell generation to the next. They double in number immediately before cell division Paired centrioles are called diplosome.

Microtubule organizing centers (MTOCs) become nucleation sites around each centriole to form the fibers of the aster and the mitotic spindle. MTOCs determine cell polarity including the organization of cell organelles, direction of membrane trafficking, and orientation of microtubules. Because microtubule assembly is nucleated from MTOCs, the (-) end of most microtubules is adjacent to the MTOC & the (+) end is distal.
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 The matrix of the centrosome is organized by a pair of centrioles. The ring of modified microtubules of the centriole is visible, surrounded by the fibrous centrosome matrix. In EM, each centriole is found to be a hollow cylinder, closed at one end & open at the other In transverse section, its wall is composed of 9 evenly spaced triplet microtubules (9x3

A centrosome with attached microtubules. The minus end of each microtubule is embedded in the centrosome, having grown from a tubulin ring complex, whereas the plus end of each microtubule is free in the cytoplasm.

 The centrioles and other components of the centrosome are duplicated in interphase cells, But they remain together on one side of the nucleus until the beginning of mitosis. The two centrosomes then separate and move to opposite sides of the nucleus, forming the two poles of the mitotic spindle. As mitosis proceeds, the two chromatids of each chromosome are then pulled to opposite poles of the spindle. This chromosome movement is mediated by motor proteins

associated with the spindle microtubules.

After cell division, each cell acquires 2 centrioles, one from the parent cell, and one which arose as a procentriole. If mitotic cells are exposed to drugs like colchicine (binds to monomeric tubulin and prevent polymerization), vinblastine and taxol (disrupt microtubule dynamics), microtubules disappear and mitosis is arrested because of inadequate formation of the mitotic spindle.

These drugs are useful in the treatment of certain cancers.

 Cells rely on the integration of structures and organelles in order to function

5 m

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