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Topic A: Cell Structure

Bi ology AS Level 2014-15 1Notes by Adeel Ahmad Khokhar KSA

Notes

CELL STRUCTURE

Content

• The microscope in cell studies

• Cells as the basic units of living organisms

• Detailed structure of typical animal and plant cells, as seen using the electron

microscope

• Outline functions of organelles in plant and animal cells

• Characteristics of prokaryotic and eukaryotic cells

Learning Outcomes

Candidates should be able to:

(a) [PA] use an eyepiece graticule and stage micrometer scale to measure cells and be

familiar with units (millimetre, micrometre, nanometre) used in cell studies;

(b) explain and distinguish between resolution and magnification (see section 5), with

reference to light microscopy and electron microscopy;

(c) describe and interpret drawings and photographs of typical animal and plant cells,

as seen using the electron microscope, recognising the following: rough endoplasmic

reticulum and smooth endoplasmic reticulum, Golgi body (Golgi apparatus or Golgi

complex), mitochondria, ribosomes, lysosomes, chloroplasts, cell surface membrane,nuclear envelope, centrioles, nucleus, nucleolus, microvilli, cell wall, the large

permanent vacuole and tonoplast (of plant cells) and plasmodesmata. (knowledge that

ribosomes occurring in the mitochondria and chloroplasts are 70S (smaller) than those

in the rest of the cell (80S) should be included. The existence of small circular DNA in

the mitochondrion and chloroplast should be noted);

(d) outline the functions of the structures listed in (c);

(e) [PA] compare the structure of typical animal and plant cells;

(f) [PA] draw and label low power plan diagrams of tissues and organs (including a

transverse section of stems, roots and leaves);

(g) [PA] calculate linear magnification of drawings and photographs;

(h) [PA] calculate actual sizes of specimens from drawings and photographs;

(i) outline key structural features of typical prokaryotic cells (including: unicellular, 1-

5 μ m diameter, peptidoglycan cell walls, lack of membrane-bound organelles, naked

circular DNA, 70S ribosomes) and compare and contrast the structure of prokaryotic

cells with eukaryotic cells (reference to mesosomes should not be included);

(j) use the knowledge gained in this section in new situations or to solve related

problems.





Magnification

Magnification is the size of an image of an object compared to the actual size. It is

calculated using the formula M = I/A (M is magnification, I is the size of the image and

A is the actual size of the object, using the same units for both sizes). This formula can

be rearranged to give the actual size of an object where the size of the image andmagnification are known: A = I/M.

e.g., if a cell is 10m in diameter, and a microscope produces an image of it which is

1mm (1000m) in diameter, than the microscope has magnified the image 100 times.

(x100)

Magnification Calculations

Microscope drawings and photographs (micrographs) are usually magnified. There are

two ways of doing this:

1. Using a Magnification Factor

Sometimes the image has a magnification factor on it. The formula for the

magnification is:

For example if this drawing of an object is 40 mm long and

the magnification is x 1000, then the object's actual length is:

Answer has to be converted into appropriate units, usually μm for cells and organelles.

Sometimes you have to calculate the magnification. For

example if this drawing of an object is 40 mm long and its

actual length is 25 μm, the magnification of the drawing is:

Remember, the image and actual length must be in the same units. Magnifications can

also be less than one (e.g. x 0.1), which means that the drawing is smaller than the

actual object.

2. Using a Scale Bar

Sometimes the picture has a scale bar on it. The formula for calculating the actual

length is:





The image size and bar length must be measured in the same units (usually mm), and

the actual size will come out in the same units as the bar scale.

For example if this drawing of an object is 40 mm long and

the 5 μm scale bar is 10 mm long, then the object's actual

size is:

It's good to have a rough idea of the size of objects, to avoid silly mistakes. A

mitochondrion is not 30 mm long! Scale bars make this much easier than

magnification factors.

The magnification produced by a light microscope depends on the strengths of the

objective lens and the eyepiece lens. If you are using a ×40 objective lens and a ×10

eyepiece lens, then the image is being magnified 400 times.

Resolution

Resolution is the ability of a microscope to distinguish two objects as separate from

one another. The smaller and closer together the objects that can be distinguished, the

higher the resolution. Resolution is determined by the wavelength of the radiation

used to view the specimen. If the parts of the specimen are smaller than the

wavelength of the radiation, then the waves are not stopped by them and they are not

seen. Light microscopes have limited resolution compared to electron microscopes

because light has a much longer wavelength than the beam of electrons in an electron

microscope.





The limit of resolution depends upon the wavelength of light. The resolution limit is

about 0.45 times the wavelength. Shorter wavelengths give the best (smallest)

resolution. The shortest wavelength light which we can see is blue light, which has a

wavelength of about 450 nm. This gives a resolution of about 0.45 x 450 nm, which is

close to 200 nm. Any objects smaller than this or any points less than 200 nm apart

will either be invisible or appear as blurs.

Electron beams, however, have a much shorter wavelength than light; so much better

resolutions can be achieved. Electron microscopes have a maximum resolution around

400 times better than that of light microscopes, being able to separate objects as little

as 0.5 nm apart.

Microscopy

Microscopy is the use of microscopes to study the structural details of organisms and

the organelles within the cell by magnifying the image.

Different kinds of Microscope.

1.

Light Microscope.

This is the oldest, simplest and most widely-used form of

microscope.

Specimens are illuminated with light, which is focused using glass lenses and viewedusing the eye or photographic film. Specimens can be living or dead, but often need to

60 m 30 m 15 m

3.7 m7.5 m 1.6 m





be coloured with a coloured stain to make them visible. Many different stains are

available that stain specific parts of the cell such as DNA, lipids, cytoskeleton, etc. All

light microscopes today are compound microscopes, which mean they use several

lenses to obtain high magnification.

Light microscopy has a resolution of about 200 nm, which is good enough to see

tissues and cells, but not the details of cell organelles. There has been a recent

resurgence in the use of light microscopy, partly due to technical improvements,

which have dramatically improved the resolution far beyond the theoretical limit. For

example fluorescence microscopy has a resolution of about 10 nm, while interference

microscopy has a resolution of about 1 nm.

2. Electron Microscope. This uses a beam of electrons, rather than

electromagnetic radiation, to "illuminate" the specimen. This may seem strange,

but electrons behave like waves and can easily be produced (using a hot wire),

focused (using electromagnets) and detected (using a phosphor screen or

photographic film).





A beam of electrons has an effective wavelength of less than 1 nm, so can be used to

resolve small sub-cellular ultrastructure. The development of the electron microscope

in the 1930s revolutionised biology, allowing organelles such as mitochondria, ER and

membranes to be seen in detail for the first time.

There are several problems with the electron microscopy: the electron beam is scattered by air molecules, so to avoid this there is a

vacuum inside an electron microscope, so it can't be used for living organisms.

specimens must be very thin, so are embedded in plastic for support, so can't be

manipulated under the microscope.

specimens can be damaged by the electron beam, so delicate structures and

molecules can be destroyed.

specimens are usually transparent to electrons, so must be stained with an

electron-dense chemical (usually heavy metals like osmium, lead or gold).

Initially there was a problem of artefacts (i.e. observed structures that were dueto the preparation process and were not real), but improvements in technique

have eliminated most of these.

There are two kinds of electron microscope. The transmission electron microscope

(TEM) works much like a light microscope, transmitting a beam of electrons through a

thin specimen and then focusing the electrons to form an image on a screen or on

film. This is the most common form of electron microscope and has the best

resolution. The scanning electron microscope (SEM) scans a fine beam of electron

onto a specimen and collects the electrons scattered by the surface. This has poorer

resolution, but gives excellent 3-dimentional images of surfaces.

Measurements used in Microscopy

1 centimeter (cm) = 1/100 meter = 0.4 inch = 10-2 m

1 millimeter (mm) = 1/1,000 meter = 1/10 cm = 10-3 m

1 micrometer (m) = 1/1,000,000 meter = 1/10,000 cm = 10-6 m

1 nanometer (nm) = 1/1,000,000,000 meter = 1/10,000,000 cm = 10-9 m

1 angstrom (A) = 1/10,000,000,000 meter = 1/100,000,000 cm = 10-10 m

1 meter = 102 cm = 103 mm = 106 m = 109 nm = 1010 A

3 a) Convert the following. All the answers are to be written in standard form.

0.00254 micrometer into millimeter

1.0665x10-5 nanometer into centimeter

6.211 x10-5 millimeter into nanometer

2449.88 micrometer into nanometer

b)

Calculate the magnification of a drawing 22 mm long of an object having an

actual length of 0.06 micrometer.

c)

What is the actual length of an organelle 4mm long shown in a drawing with amagnification of x4000.





Comparison between the Light microscope Electron Microscope

Light Microscope Electron Microscope

1. Source of radiation Uses light rays of

wavelength between 400to 700 nm

Uses electron beams of

wavelength 0.005 nm

2. Lenses Eyepiece and objective

lenses made of glass

Electromagnets

3. Stains used Dyes with suitable colours Heavy metals such as lead

4. Maximum

magnification

5. Maximum resolution

6. Depth of field

Disadvantages

It only magnifies objects to

an extent of 1500 times.

200 nm

The depth of field is

restricted.

Advantages

It is able to magnify objects

over 250,000 times (for

TEM) and over 100,000

times (SEM)

0.5 nm

The depth of field possible

is greater.

1.

Price and operation

2.

Portability

3.

Type of specimen

4.

Magnetic fields

5. Preparation of

specimen

6.

Image produced

Advantages

Inexpensive to purchase

and easier to operate.

Easy and small.

Living or non-living

organisms.

Magnetic fields have no

effect on it.

Preparation of specimen is

simple and fast

Coloured, with the naturalcolour of specimen or dye

Disadvantages

Expensive to purchase and

operation requires

expertise.

Bulky and less portable.

Only non-living organisms.

Magnetic fields have an

effect on it.

Preparation of specimen is

complex and needs

considerable time and

experience.

Black and white only





The Cell

All living things are made of cells, and cells are the smallest units that can be alive.

There are thousands of different kinds of cell, but the biggest division is between the

cells of the prokaryote kingdom (the bacteria) and those of the other four kingdoms

(animals, plants, fungi and protoctista), which are all eukaryotic cells. Prokaryotic

cells are smaller and simpler than eukaryotic cells, and do not have a nucleus.

Prokaryote = without a nucleus

Eukaryote = with a nucleus

These two kinds of cell are being examined in detail, based on structures seen in

electron micrographs.

These show the individual organelles inside a cell.

Euakryotic Cells

Cytoplasm (or Cytosol).

This is the solution within the cell membrane. It contains enzymes for

glycolysis (part of respiration) and other metabolic reactions together with sugars,

salts, amino acids, nucleotides and everything else needed for the cell to function.





Membrane Systems and Organelles:

Endoplasmic Reticulum (ER)

This is a series of membrane channels involved in synthesising and transporting

materials. Rough Endoplasmic Reticulum (RER) is studded with numerous ribosomes,

which give it its rough appearance. The ribosomes synthesise proteins, which are

processed in the RER (e.g. by enzymatically modifying the polypeptide chain, or

adding carbohydrates), before being exported from the cell via the Golgi Body.

Smooth Endoplasmic Reticulum (SER) does not have ribosomes and is used to process

materials, mainly lipids, needed by the cell.

Golgi Apparatus

Another series of flattened

membrane vesicles, formed from

the endoplasmic reticulum. Its

job is to transport proteins from

the RER to the cell membrane

for export.

Parts of the RER containing

proteins fuse with one side of

the Golgi body membranes,

while at the other side small

vesicles bud off and movetowards the cell membrane, where they fuse, releasing their contents by exocytosis.





Mitochondrion (pl. Mitochondria)

This is a sausage shaped organelle (8μm

long), and is where aerobic respiration takes

place in all eukaryotic cells. Mitochondria

are surrounded by a double membrane: the

outer membrane is simple and quite

permeable, while the inner membrane is

highly folded into cristae, which give it a

large surface area for enzyme reactions. The

space enclosed by the inner membrane is

called the mitochondrial matrix, and contains small circular strands of DNA. The

inner membrane is studded with stalked particles, which are the site of ATP synthesis

during respiration.

Role of Golgi apparatus





Ribosomes

These are the smallest and

most numerous of the cell

organelles, and are the sites of

protein synthesis. They arecomposed of protein and

RNA, and are manufactured

in the nucleolus of the

nucleus.

Ribosomes are either found

free in the cytoplasm, where

they make proteins for the cell's own use, or they are found attached to the rough

endoplasmic reticulum, where they make proteins for export from the cell. All

eukaryotic ribosomes are of the larger, "80S", type.

Lysosomes

These are small membrane-bound vesicles formed from the RER containing a cocktail

of digestive enzymes. They are used to break down unwanted chemicals, toxins,

organelles or even whole cells, so that the materials may be recycled. They can also

fuse with a feeding vacuole to digest its contents.

Role of Lysosome in a cell





It is very important that the enzymes contained within Lysosomes are isolated from

the rest of the cell inside the Lysosomes membrane, otherwise their release would

result in self-digestion of the cell. In fact, this sometimes happens in certain tissues,

such as the tadpole’s tail when it is changing into a frog; this process is called apoptosis

or programmed cell death

Centrioles

This is a special pair of short cytoskeleton

fibres involved in cell division. They initiate

the spindle that organises and separates the

chromosomes.

Cell Surface Membrane

The cell surface membrane is the boundary

between the cell and its environment. It has

little mechanical strength but plays a vital

role in controlling which materials pass in and out of the cell.

Although basically a double layer of phospholipids molecules, arranged tail to tail, cellsurface membrane is a complex structure, studded with proteins. These can be

embedded in the membrane or they can penetrate the bilayer forming pores through

which molecules can pass.

Centrioles





Chloroplasts

Bigger and fatter than mitochondria, chloroplasts are where photosynthesis takes

place, so are only found in photosynthetic organisms (plants and algae).

Like mitochondria they are enclosed by a double membrane, but chloroplasts also

have a third membrane called the thylakoid membrane. The thylakoid membrane is

folded into thylakoid disks, which are then stacked into piles called grana. The space

between the inner membrane and the thylakoid is called the stroma. The thylakoid

membrane contains chlorophyll and chloroplasts also contain starch grains, ribosomes

and circular DNA.

Large Permanent Vacuole and Tonoplast (of Plant Cells):

Vacuoles are membrane-bound sacs within the cytoplasm of a cell that function in

several different ways. In mature plant cells, vacuoles tend to be very large and are

extremely important in providing structural support, as well as serving functions such

as storage, waste disposal, protection, and growth. Many plant cells have a large, single

central vacuole that typically takes up most

of the room in the cell (80 percent or more).

Vacuoles in animal cells, however, tend to be

much smaller, and are more commonly used

to temporarily store materials or to transport

substances.

The central vacuole in plant cells is enclosed

by a membrane termed the tonoplast, an

important and highly integrated componentof the plant internal membrane network





(endomembrane) system. This large vacuole slowly develops as the cell matures by

fusion of smaller vacuoles derived from the endoplasmic reticulum and Golgi

apparatus. Because the central vacuole is highly selective in transporting materials

through its membrane, the chemical palette of the vacuole solution (termed the cell

sap) differs markedly from that of the surrounding cytoplasm.

Plasmodesmata:

Plasmodesmata (singular, plasmodesma) are small channels that directly connect the

cytoplasm of neighboring plant cells to each other, establishing living bridges between

cells. Similar to the gap junctions found in animal cells, the plasmodesmata, which

penetrate both the primary and secondary cell walls, allow certain molecules to pass

directly from one cell to another and are important in cellular communication.

Nucleus:

This is the largest

organelle. It is

surrounded by a

nuclear envelope,

which is a doublemembrane with

nuclear pores–large

holes containing

proteins that

control the exit of

substances such as

RNA and ribosomes

from the nucleus. The interior is called the nucleoplasm, which is full of chromatin –

the DNA/protein complex.





During cell division the chromatin becomes condensed into discrete observable

chromosomes.

The nucleolus is a dark region of chromatin, involved in making ribosomes.

Euchromatin and Heterochromatin

The DNA in the nucleus exists in two forms that reflect the level of activity of the cell.

Heterochromatin appears as small, darkly staining, irregular particles scattered

throughout the nucleus or accumulated adjacent to the nuclear envelope.

Euchromatin is dispersed and not readily stainable. Euchromatin is prevalent in cells

that are active in the transcription of many of their genes while heterochromatin is

most abundant in cells that are less active or not active.

Functions of Nucleus

To control all cellular activities.

To produce RNA.

To control the synthesis of proteins, including enzymes, in the cell, and so

control the cell’s activities.

To undergo nuclear division in the start of cell division, ensuring that the

daughter cells have exact copies of the cell’s genetic material in their

chromosomes.

To assemble ribosomes (function of the nucleolus).





Comparison of Animal and Plant Cells





Double membranous

organelles

Single membranous

organelles

Non-membranous

organelles

Nucleus Endoplasmic reticula ribosome

Chloroplast Golgi apparatus

Mitochondria Lysosome

Organelle Location and

occurrence in cell

Size Function

Nucleus Usually one per cell in

cytoplasm

10 - 20m Contains the hereditary material

(DNA) which codes for synthesis of

proteins in the cytoplasmNucleolus One to several in

nucleus

1 - 2m Synthesizes ribosomal RNA and

manufactures ribosomes

Rough

endoplasmic

reticulum

Throughout cytoplasm Membranes

about 4nm

thick,

enclosing

Transport of proteins synthesized

on ribosomes

Smooth

endoplasmic

reticulum

In cytoplasm. Extent

depends on types of

cell

Cisternae of

varying

diameter

Synthesis of lipids

Ribosomes Attached to rough

endoplasmic reticulum

or free in cytoplasm

20 – 25 nm Site of protein synthesis

Golgi

apparatus

In cytoplasm Variable Synthesis of glycoproteins,

packaging of proteins.

Lysosomes In cytoplasm 100nm Digestion of unwanted materials

and worn-out organelles

Mitochondria In cytoplasm. Severalto thousands per cell.

1 m wideand up to 10

m in

length

Production of energy by aerobicrespiration

Centrioles Pair, in cytoplasm,

usually near nucleus

0.5 m X 0.2

m

Form the spindle fibres during cell

division of animal and fungal cells

Chloroplasts In cytoplasm of some

plant cells

2 – 10 m in

diameter

Site of photosynthesis

Summary of Cell Organelles





Prokaryotic Cells

1. The word prokaryotes means ‘before nucleus’. This describes the main

difference between eukaryotic and prokaryotic cells: prokaryotes have no

nucleus or nuclear membrane. Their DNA is therefore not separated from the

cytoplasm, but forms a single circular loop, sometimes called a bacterialchromosome.

2. Their DNA is not associated with proteins, unlike eukaryotic chromosomes.

Bacteria also have smaller loops of DNA in the cytoplasm, called plasmids.

3. Prokaryotic cells are much smaller than eukaryotic ones, and much simpler in

their structure.

4. They lack endoplasmic reticulum and membrane-bound organelles like

mitochondria and chloroplasts and any complex structures such as Golgi bodies,

cytoskeleton or lyososmes.

Structure of Bacterium (A Prokaryotic Cell)

Prokaryotic cells are smaller than

eukaryotic cells and do not have a

nucleus or indeed any membrane-

bound organelles. All prokaryotes are

bacteria. Prokaryotic cells are much

older than eukaryotic cells and they

are far more abundant (there are tentimes as many bacteria cells in a

human than there are human cells).

The main features of prokaryotic

cells are:

Cytoplasm. Contains all the

enzymes needed for all metabolic

reactions, since there are no

organelles

Ribosomes. The smaller (70S) type,

all free in the cytoplasm and never attached to membranes. Used for protein synthesis.

Nuclear Zone (or Nucleoid). The region of the cytoplasm that contains DNA. It is

not surrounded by a nuclear membrane.

DNA. Always circular (i.e. a closed loop), and not associated with any proteins to

form chromatin. Sometimes confusingly referred to as the bacterial chromosome.





Plasmid. Small circles of DNA, separate from the main DNA loop. Used to exchange

DNA between bacterial cells, and also very useful for genetic engineering.

Cell membrane. Made of phospholipids and proteins, like eukaryotic membranes.

Mesosome. A tightly-folded region of the cell membrane containing all themembrane-bound proteins required for respiration and photosynthesis. Can also be

associated with the nucleoid.

This is now thought to be an artefact of the electron microscope and not real

structure.

Cell Wall. Made of murein (not cellulose), which is a glycoprotein (i.e. a

protein/carbohydrate complex, also called peptidoglycan).

Capsule. A thick polysaccharide layer outside of the cell wall. Used for sticking cells

together, as a food reserve, as protection against desiccation and chemicals, and as

protection against phagocytosis. In some species the capsules of many cells fuse

together forming a mass of sticky cells called a biofilm. Dental plaque is an example of

a biofilm.

Flagellum. A rigid rotating helical-shaped tail used for propulsion. The motor is

embedded in the cell membrane and is driven by a H+ gradient across the membrane.

Anticlockwise rotation drives the cell forwards, while clockwise rotation causes a

chaotic spin.





Differences between eukaryotic and prokaryotic cells

Eukaryotic Cells Prokaryotic Cells

1. True nucleus surrounded by a nuclear

envelop.

No true nucleus

2. Linear DNA associated with histone

proteins forming true chromosomes.

Circular DNA not associated with

proteins. Separate loops of DNA called

plasmids.3. Cell wall, if present, made of cellulose

(plants and algae) or chitin (fungi).

Cell wall containing peptidoglycan

4. Endoplasmic reticulum present. No endoplasmic reticulum or associated

organelles such as Golgi apparatus.

5. Membrane–bound organelles such as

mitochondria and chloroplast (in plants

and algae).

No membrane-bound organelles.

Mesosomes and thylakoids present in

some bacteria.

6. Large (80S) ribosomes attached to

endoplasmic reticulum.

Small (70S) ribosomes scattered in the

cytoplasm.

7. If present, flagella have (9+2)

arrangement of microtubules.

If present, flagella are made of a single

microtubule.

8. Cells are large, typically 10-100m in

diameter, some cells can be up to 400m.

Cells are small, typically 0.5-3m in

diameter, Volume may be as little as

1/10,000th of eukaryotic cell.

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