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AS MODULE 1: Biochemistry
Water
Polar term used to describe a molecule with an uneven distribution of charge in molecules
In water the hydrogen has a slight positive charge and the oxygen has a slight negative charge so water is polar
The polar nature of water results in the formation of hydrogen bonds between adjacent water molecules
...
These
hydrogen bonds are not strong and are easily broken
...
Water is
capable of dissolving inorganic and organic substances, molecules with charged groups
...


•

Its ability to act as a transport medium in living organisms
...


Biological importance of water:
Water has many important functions in biological reactions some of which are
Metabolic functions: water is used directly as a reagent (reactant) in photosynthesis and is also the medium
in which all biochemical reactions take place
...

Lubricant properties: water’s cohesive and adhesive properties mean that it is viscous, making it a useful
lubricant in biological systems
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1

Inorganic Ions

Inorganic ion Biological compound

+

Role

Potassium

k ions

Maintaining electrical potentials across neurones

Calcium

Calcium pectate

Component of the middle lamella between plant
cells walls
Used in muscle contraction and blood clotting

Calcium

2+

Ca

Constituent of bone, enamel and shells
(Calcium Phosphate)

Chlorophyll
Magnesium

2+

Gives chlorophyll its light absorbing abilities

Mg

Iron

Haemoglobin

Nitrate

NO3

-

Phospholipid
Phosphate

3-

PO4

Hydrogen
Carbonate

HCO3

Constituent of haemoglobin and the electron
carries in respiration

Component of nucleic acids , amino acids and
chlorophyll

Phospholipids are a component of cell membranes,
ATP and nucleic acids

Acts as a natural buffer




2

Carbohydrates
Carbohydrates contain only carbon hydrogen and oxygen
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•

Disaccharides: are double sugars formed from two monosaccharide’s monomers

•

Polysaccharides: are complex molecules usually consisting of many monosaccharide monomers
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Glucose is a hexose monosaccharide with the
formula C6H12O6
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Three carbons is trios and five carbons is a
pentose sugar




Alpha glucose and beta glucose are very similar, but have a slight change in the arrangement of the atoms the
beta glucose’s hydrogen and hydroxyl (-OH) groups at carbon 1 are reversed
...
These hexose
sugars are also very important as energy sources in living organisms m


Isomers are substances which have the same molecular formula, but different structural formula





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Disaccharides
Disaccharides are formed when two monosaccharide’s, react together in a condensation reaction
...
As this bond forms between the 1 and 4 carbon is called 1, 4 glycosidic bond
Important Disaccharides
All disaccharides have the general formula C12 H22 O11 and they dissolve in water to produce sweet tasting
solutions
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Sucrose formed by an alpha glucose and a fructose molecule
o

Sucrose is the form in which carbohydrates are transported through the phloem in plants
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4

Polysaccharides
They are complex carbohydrates which often form very long chains of monomers joined through condensation
reactions
§

The general formula of a polysaccharide is (C6 H10 05)N where N is a large number that can vary
...


Starch
Starch is a polymer of alpha glucose that consists of a mixture of two types of chains:
Amylose: in amylose alpha glucose molecules are linked by alpha 1, 4 glycosidic bonds
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Amylopectin: amylopectin also links its constituent alpha glucose monomers together by alpha 1, 4 glycosidic
bonds
...






Starch as a Storage Molecule
Starch is an excellent storage carbohydrate and is the storage compound of many plants
...
Its benefits include:
•

Amylose and amylopectin are very compact aided by the coiled configuration, and therefore they
contain a rich store of glucose in a small space
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•

Being a large molecule it will not easily pass through the cell membrane


•

The branching nature of amylopectin creates many terminal ends that are easily hydrolysed
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Glycogen
This is the storage carbohydrate found in animal and fungal cells:
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It is stored as small granules
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Glycogen is stored in liver and muscle cells in mammals
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It has no unbranched chains and shorter chains than in amylopectin
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Cellulose
Cellulose is not a storage polysaccharide
...

Consequently, it has a very different structure to the relatively similar starch and glycogen
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This rotation is a necessary consequence due to the different structure of beta
glucose compared to alpha glucose






The ‘flipping’ of adjacent glucose monomers has two effects
•

The unbranched chains are straighter, as the bulky CH2OH side groups alternate between being above
and below the chain
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Although lipids form large molecules called macromolecules they are not polymers
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The main types of lipids are triglycerides, phospholipids, waxes and steroids
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Fatty acids are organic
acids that form long hydrocarbon tails linked to a carboxyl group (-COOH) at one end of the chain
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In each triglyceride, one glycerol molecule is joined with three fatty acid molecules by 3 condensation
reactions forming an ester bond is formed







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Saturated fatty acids and all the carbons are linked by a single carbon, carbon bond
Unsaturated fatty acids do not contain the maximum number of hydrogen atoms and have at least one
Carbon=Carbon double bond in the chain
...
Fats are solid at room temperature and oils are
liquid at room temperature
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Fats tend to be formed from saturated fatty acids, whereas oils are usually formed from triglycerides
with unsaturated hydrocarbon chains
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The fatty acid molecules are insoluble in water forming hydrophobic tails, whereas the phosphate gives the
glycerol part of the molecule hydrophilic properties making it soluble in water


Phospholipids form the basis of the structure of cell membranes
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Phospholipids with short fatty acids or unsaturated fatty acids are more fluid
than others
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It is found in cell
membranes and as it is hydrophobic it is found amongst the hydrocarbon chains of the phospholipid bilayer
...




8

Proteins
Proteins contain the elements carbon, hydrogen, oxygen, nitrogen and usually sulphur
...

The function of most proteins is very closely related to their shape; in turn the shape of the protein is
determined by the sequence of the amino acids in the protein
...
These involve condensation reactions with the loss of
water
...





Amino acids differ from each other through different R-groups
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There joined by a condensation reaction that can be undone with a hydrolysis reaction by the
addition of water
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These
groups have a positive and negatively charge respectively that enables the formation of hydrogen bonds
causing generalised structures to be formed
The two most common types of secondary structures are:
•

Alpha helix: in the alpha helix the hydrogen bonds are formed between amino acids occurring at
regular intervals in the sequence
...
They
are formed by sections of the polypeptide chain, orientated in opposite directions lying adjacent to
each other
...
This additional folding gives each
protein its unique 3-D shape and is due to the range of bonds formed between the R-groups of amino acids in
the chain
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Ionic bonds: are formed between amino and carboxyl groups in some of the amino acids R-groups
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•

Disulphide bonds ((bridges): are covalent bonds formed between R-groups of sulphur-containing
amino acids
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Hydrophobic and hydrophilic interactions: some amino acids may be hydrophobic while others
are hydrophilic
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These conjugated proteins include glycoproteins, which is important in membrane structure
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Each chain is attached to and iron-rich haem
group, which is an essential part of the molecule in the transport of oxygen
...
The chains are linked by cross-bridges form very strong and stable molecule
•

They are insoluble in water

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They are not easily denatured

One example of a fibrous protein is collagen:
Collagen is a fibrous protein consisting of three polypeptide chains around each other
...
Hydrogen bonds form between these coils, which are around 1000 amino acids in length, which
gives the structure strength
...
This strength is
increased by the fact that collagen molecules form further chains with other collagen molecule and form
covalent cross links with each other, which are staggered along the molecules to further increase stability
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Globular proteins
Globular proteins tend to form ball-like structure where hydrophilic parts are towards the centre and
hydrophobic parts are towards the centre and hydrophilic parts are towards the edges
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Its function is to carry oxygen around of the haem group which contains a
2+

Fe ion, onto which the oxygen molecules can bind




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Prions
Prions are a particular type of protein found in mammals and some other animals groups
...

c

sc

The normal form of prion protein, designated (PrP or PrP ) can convert to a disease-causing form (PrP )
...

sc

(PrP ) The disease-causing form has a higher proportion of beta sheets compared to alpha helices
...
The diseases associated with PrP proteins can arise in
a number of ways including:


sc

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The normal prion protein present PrP can ‘spontaneously’ adopt the PrP form
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Therefore the disease-causing from can be
passed from parent to offspring
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Prion diseases include:
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Scrapie that affects sheep
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Nucleic acids
The sub-unit of nucleic acids is the nucleotide
...



The three components are combined as a consequence of condensation reactions to form the nucleotide
...
The phosphodiester
bond joins adjacent nucleotides together
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The nucleic acid is a chain of nucleotides (polynucleotide) which
has a free 5’ end (with a ‘free’ phosphate) and a free 3’ end (with a
‘free’ sugar) Nucleic acids can also be broken down through
hydrolysis reactions to nucleotides
...
(Anti parallel means the two strands are running in opposite
directions)
The nature of base pairing always ensures that:
•

Adenine always pair with thymine (by two hydrogen bonds)

•

Guanine always pairs with cytosine (by three hydrogen bonds)


The DNA molecule is organised as a double helix
...
The organisation of DNA is
very regular, with there being ten base pairs for each complete turn of the helix
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DNA /RNA
RNA has the sugar ribose it is single stranded and much shorter than DNA
...
It regulates the development of living
organisms through the control of protein synthesis, in particular, the regulation of enzymes, the key catalysts
in metabolism
...

Genes can be described as a sequence of DNA that codes for a polypeptide
...
In effect, the code in read as
the sequence along the length of the coding strand of the DNA
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Functions of RNA
The different types of RNA also have crucial roles in protein synthesis:
•

Messenger RNA- Carries the code from the DNA in the nucleus to a ribosome in the cytoplasm where
protein synthesis takes place
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/ribosome where protein synthesis takes place
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•

Ribosomal RNA- is made in the nucleolus and forms over half the mass of each ribosome
...
it can also pass through the generations from parent to offspring
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Process of DNA Replication
•

The enzyme DNA helicase ‘unzips’ the two strands of the DNA by breaking the hydrogen bonds
between the bases
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•

Free nucleotides are linked to the template strands in the correct sequence as a consequence of base
pairing rules with the bases on the template strands
...


Each of the new DNA molecules contains one original strand and one new DNA strand
...








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The Meselson and Stahl (1958) experiment
There are two methods of replication:
•

The conservative model- this model proposed that the parental DNA remained intact but copied the
new DNA molecule
...

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Meselson and Stahl cultured the bacterium Escherichia coli using the ‘heavy’ isotope of nitrogen N
...

The bacteria were then transferred to a medium containing the lighter nitrogen-14
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•

Bacteria growing in nitrogen-14 (before transfer to nitrogen-15)

•

Bacteria growing in nitrogen-15(many generations after transfer from nitrogen -14)

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One generation after transfer to nitrogen-14

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Two generations after transfer to nitrogen-14


Density-gradient centrifugation was used to separate the bacterial DNA following sampling at the stages
...





Explanation of Meselson and Stahl’s results
•

After one generation – the intermediate position of the DNA can be explained but all the DNA
15

14

consisting of one strand that has bases containing N and one strand have bases containing N
•

15

14

After two generations – About half the DNA consisted of mixed DNA containing both N and N but
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the other half contained only N
Note: In the third generation the pattern would be the same as with the second generation
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Electron microscopes can resolve
points to 0
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2µm because electrons have a shorter
LIGHT MICROSCOPE

ELECTRON MICROSCOPE

Cheap to operate
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Small and portable
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Vacuum is not required
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Natural colour of sample maintained
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Artefacts due to preparation techniques



The Transmission Electron Microscope (TEM)
The electron has electrons passing through very thing specimen
...

Resolution and magnification are not as high but it is useful for giving a 3-D image of surface features
...
They have a membrane-bound nucleus,
chromosomes and a range of complex organelles that have specific roles within the cell r4


Feature

Prokaryotic cell

Eukaryotic cell

Size

Usually , 5µm

10-200 µm

Site of DNA

DNA free in cytoplasm

DNA inside membrane-bound nucleus

DNA

Circular(arranged as a loop) and

DNA linear and in chromosomes
...


peptidoglycan(glycoprotein)
Chitin cell wall in fungi
...

Plasmids

Usually present

Not present

Microtubules

Not present

Spindle fibres and other microtubules



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Animal cell
All animal cells are multicellular
...
Animal cells are surrounded by plasma membrane
and it contains the nucleus and organelles that are membrane bound
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The chromosomes are visible but are organised in chromatin which when densely packed appears
dark on electron microscopes
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The nucleolus contains the DNA that codes for ribosomal RNA (rRna) and makes ribosomes which are essential
in protein synthesis
...
It does this by isolating the
chromosomes from the rest of the cytoplasm and the reactions that take place there so the DNA is protected
from damage
...
This
is achieved by the presence of nuclear pores in the nuclear envelope
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The outer
membrane of the nuclear envelope is encrusted with ribosomes and it the origin of rough endoplasmic
reticulum
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Endoplasmic Reticulum(ER)
The ER is a membrane system that extends throughout the cytoplasm
...
Some of the ER has ribosome organelles dotted along the outside
(cytoplasmic side) of the membranes
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Other parts of the ER do not
have ribosomes attached
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The RER provides the ‘scaffolding’ for the ribosomes to make protein and the ER then operates as a
distribution network for the proteins
...
Once the primary structure of
the protein is synthesised on the RER, the secondary and tertiary structures develop within the cisternae
...


Ribosomes:
These very small organelles are visible as small black dots in electron micrographs
...

Each ribosome is formed of a large and a small sub-unit, and is made of protein and ribosomal RNA
...


Golgi Apparatus:
The Golgi apparatus can be described as a series of curved flattened sacs (cisternae) they have a number of
small vesicles both entering and leaving the system
...
(usually the edge closest to the
nucleus) Within the main body of the Golgi, the proteins are modified, for example;
•

They may have carbohydrates added to form glycoproteins

•

They may have lipids added to form lipoproteins

•

They may have prosthetic groups or cofactors added

•

Different polypeptides can be joined together to form proteins with a quaternary structure

•

They can be labelled, packaged or sorted for export

Once the protein is modified, vesicles containing the ‘finished’ proteins is pinched off from the
maturing(concave) face (usually the side furthest away from the nucleus)
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Lysosomes:
Lysosomes are tiny vesicles usually about 0
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They are formed by the Golgi apparatus and they
contain hydrolytic enzymes for internal use
...
They have an important role in phagocytes, where they digest engulfed
bacteria enclosed in a phagosome
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Note: Vesicles are not restricted to the Golgi apparatus they can be used for storage and transport
throughout the cell
Note: There has been a lot of debate as to lysosome action in plant cells some scientists believe others don’t

Mitochondria
Mitochondria are present in almost all types of animal cells
...
They are
typically ‘bean’ shaped but can vary in shape
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The inner membrane is folded to form cristae that extend into the matrix of the
mitochondrion
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The mitochondrion is the ‘powerhouse’ of the cell
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Mitochondria are particularly common in cells that have high energy requirements, such as muscle cells
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They form the cytoskeleton, the network
of fibres that maintains cell shape and keeps organelles anchored in place
...

The spindle fibres, important in the movement of chromosomes during mitosis and meiosis, are formed of
microtubules
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Note: Cytoplasm is a general term that means the all parts of the cell including organelles between the
surface membrane and the nucleus
...


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Plant Cell:
Plant cells are eukaryotic cells or cells with membrane bound nucleus
...
Plant cells are similar to animal
cells in being eukaryotic and they have similar cell organelles
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The cellulose is
laid down as microfibrils
...

During plant development the cell wall has two stages
Primary Cell Wall is made up of many microfibrils orientated in different and random directions
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Secondary Cell Wall: the secondary cell wall has additional layers of cellulose can be deposited to form the
secondary wall
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This
lattice type arrangement gives the great strength necessary in cell wall function
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The middle lamella is largely
made of polysaccharides called pectin
...

Plasmodesmata provide ‘gaps’ in the cell walls of adjacent cells that enable different kinds of molecules to pass
through
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Chloroplasts:
Chloroplasts are large organelles and are usually intermediate in size between the nucleus and mitochondrion
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Within the stroma is a system of membranes called thylakoids that are arranged in stacks called grana
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The thylakoids contain chlorophyll, which is most densely concentrated in the grana
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Chloroplasts are the sites of photosynthesis and are located in photosynthesising cells, in particular cells in the
palisade layer of leaves
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Large Vacuole
Plant cells have a large vacuole within the cytoplasm
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The tonoplast is also the name
of the membrane that bound the vacuole

Fungal cells:
Fungi are eukaryotic organisms and therefore they have eukaryotic cells
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They have other plant-like
features such as the presence of a vacuole
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They are more similar to animal cells in having glycogen as the carbohydrate store and also
though the presence of lysosomes
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Prokaryotes
Prokaryotic cells are simpler
...
Bacteria is an
example of a prokaryotic cell





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The Fluid Mosaic Model Membrane
The cell surface membrane is a critical component of cells
...

The cell surface membrane consists of two basic components, a phospholipid bilayer and protein
...

The phospholipids consist of hydrophilic ‘heads’ that can mix with water but the two hydrophobic ‘tails’ that
will not mix water,


Membrane Components
The Phospholipid Bilayer:
Due to hydrophobic and hydrophilic properties the molecules in the bilayer will arrange themselves in a
certain way
...



•

As well as being the backbone of the cell surface membrane it gives the membrane much of its
selectively permeable properties
...

•

At low temperatures the cholesterol helps to maintain membrane fluidity by acting as a wedge
between adjacent phospholipid molecules and stopping adjacent molecules sticking together
...









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Proteins:
Proteins are very important molecules in the membrane
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•

They may also act as enzymes
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•

Some membrane proteins act as adhesion sites, areas where adjacent cells are held together
...
Proteins are particularly
important in transporting substances across the bilayer
...
These channels may be
permanently open or have their opening controlled(gated)


•

Carriers: These proteins carry specific ions and molecules across the membrane
...
The carrier protein can change shape to carry the substance
from one side of the membrane to the other
...
Glycoproteins and
glycolipids are involved in cell-to-cell recognition allowing cells of similar type to recognise each other and
group together to form tissues
...
They can also act as receptor sites
...




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Viruses
Viruses are very small and unlike cells they are measured in nm not µm, varying in size between 10nm and
300nm
...
Depending on the virus concerned, the
nucleic acid can be DNA or RNA
Viruses are not true cells; they do not have cytoplasm and the organelles associated with it

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