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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
...




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
...


•

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

•

Polysaccharides: are complex molecules usually consisting of many monosaccharide monomers
...
Glucose is a hexose monosaccharide with the
formula C6H12O6
...
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





3

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
...



•

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
...







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
...


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
...



•

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
...





5

Glycogen
This is the storage carbohydrate found in animal and fungal cells:
•

It is stored as small granules
...


•

Glycogen is stored in liver and muscle cells in mammals
...


•

It has no unbranched chains and shorter chains than in amylopectin
...


Cellulose
Cellulose is not a storage polysaccharide
...

Consequently, it has a very different structure to the relatively similar starch and glycogen
...
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
...

Although lipids form large molecules called macromolecules they are not polymers
...

The main types of lipids are triglycerides, phospholipids, waxes and steroids
...
Fatty acids are organic
acids that form long hydrocarbon tails linked to a carboxyl group (-COOH) at one end of the chain
...






In each triglyceride, one glycerol molecule is joined with three fatty acid molecules by 3 condensation
reactions forming an ester bond is formed







...

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
...
Fats tend to be formed from saturated fatty acids, whereas oils are usually formed from triglycerides
with unsaturated hydrocarbon chains
...

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
...
Phospholipids with short fatty acids or unsaturated fatty acids are more fluid
than others
...
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
...
There joined by a condensation reaction that can be undone with a hydrolysis reaction by the
addition of water
...
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
...


•

Ionic bonds: are formed between amino and carboxyl groups in some of the amino acids R-groups
...


10


•

Disulphide bonds ((bridges): are covalent bonds formed between R-groups of sulphur-containing
amino acids
...


•

Hydrophobic and hydrophilic interactions: some amino acids may be hydrophobic while others
are hydrophilic
...

These conjugated proteins include glycoproteins, which is important in membrane structure
...
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

•

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
...

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
...
Its function is to carry oxygen around of the haem group which contains a
2+

Fe ion, onto which the oxygen molecules can bind




12


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

•

The normal prion protein present PrP can ‘spontaneously’ adopt the PrP form
...
Therefore the disease-causing from can be
passed from parent to offspring
...


Prion diseases include:
•

Scrapie that affects sheep
...






13


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
...


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
14


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
...

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
...
/ribosome where protein synthesis takes place
...


•

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
...


Process of DNA Replication
•

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


•

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
...








16


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
...

15

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
...

•

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

•

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

•

One generation after transfer to nitrogen-14

•

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
14

the other half contained only N
Note: In the third generation the pattern would be the same as with the second generation
...
Electron microscopes can resolve
points to 0
...
2µm because electrons have a shorter
LIGHT MICROSCOPE

ELECTRON MICROSCOPE

Cheap to operate
...


Small and portable
...


Vacuum is not required
...


Natural colour of sample maintained
...




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



19


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
...
The chromosomes are visible but are organised in chromatin which when densely packed appears
dark on electron microscopes
...

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
...
The outer
membrane of the nuclear envelope is encrusted with ribosomes and it the origin of rough endoplasmic
reticulum
...










20


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
...
Other parts of the ER do not
have ribosomes attached
...

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)
...




21


Lysosomes:
Lysosomes are tiny vesicles usually about 0
...
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
...

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
...
The inner membrane is folded to form cristae that extend into the matrix of the
mitochondrion
...

The mitochondrion is the ‘powerhouse’ of the cell
...

Mitochondria are particularly common in cells that have high energy requirements, such as muscle cells
...
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
...

Note: Cytoplasm is a general term that means the all parts of the cell including organelles between the
surface membrane and the nucleus
...


22


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
...
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
...

Secondary Cell Wall: the secondary cell wall has additional layers of cellulose can be deposited to form the
secondary wall
...
This
lattice type arrangement gives the great strength necessary in cell wall function
...
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
...


Chloroplasts:
Chloroplasts are large organelles and are usually intermediate in size between the nucleus and mitochondrion
...

Within the stroma is a system of membranes called thylakoids that are arranged in stacks called grana
...

The thylakoids contain chlorophyll, which is most densely concentrated in the grana
...

Chloroplasts are the sites of photosynthesis and are located in photosynthesising cells, in particular cells in the
palisade layer of leaves
...

23


Large Vacuole
Plant cells have a large vacuole within the cytoplasm
...
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
...
They have other plant-like
features such as the presence of a vacuole
...
They are more similar to animal cells in having glycogen as the carbohydrate store and also
though the presence of lysosomes
...








Prokaryotes
Prokaryotic cells are simpler
...
Bacteria is an
example of a prokaryotic cell





24


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
...









25


Proteins:
Proteins are very important molecules in the membrane
...



•

They may also act as enzymes
...



•

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
...




26


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
...
In general, they do not exhibit the characteristics normally
associated with living organisms
...
These differences include:
•

They have different shapes and phages have tail fibres attached to a base plate
...


•

In HIV the protein coat is within a phospholipid bilayer unlike phages

•

Glycoproteins are present in HIV but not phages

•

Bacteriophages normally contain DNA while HIV contains RNA
...
Inside their
host cells (bacteria) the viral DNA codes for the production of new protein (for new protein coats)
...
In due
course the bacterial cell is destroyed as it ruptures and many new viruses are released to continue the cycle
...
Outside the RNA core they have the typical protein coat, but
in addition, have a lipid bilayer containing glycoprotein
...
The reverse
transcriptase catalyses the synthesis of DNA from viral RNA
...


27


In human’s HIV invades a type of lymphocyte called helper t-cells
...
As progressively more t-cells are destroyed, the immune
system becomes critically compromised and the medical condition AIDS can develop
...
The phases of Mitosis begin ending in cytokinesis
Cell in Resting State





G2 Checkpoint



G1 Checkpoint


Cell in G0





Cell differentiated for specialist

Cells damaged beyond repair or too ‘old’

functions like neurons

Doesn’t return to the cell cycle

Doesn’t return to the cell cycle

Note: There is also a checkpoint at the end metaphase the cell checks that all the chromosomes have
attached properly to the spindle fibres

Control of the Cell Cycle:
There are number of checkpoints within the cell cycle
...
The checkpoints include:
G1 checkpoint This checkpoint is at the end of the G1 phase
...


•

There are enough nutrients available for the next stages to take place
...


•

There is no DNA damage
...


29


If not, the cell enters a resting state or phase, G0 phase
...

What happens depends on a range of internal and external factors
...

Highly differentiated cells such a neurons do not return to the cell cycle whereas cells in epithelial tissue may
not enter G0 at all
...
The cell checks that DNA replication has taken place
accurately and that there is no DNA damage
...

Note: Many Lymphocytes are in G0
...

Note: The G1 checkpoint is a logical position for cells that normally become very differentiated to move out
of the cell cycle
...


Cell Cycle Regulation and Cancer
Cancer is caused by uncontrolled cell division; in effect, it is mitosis out of control
...

Many modern anti-cancer drugs work by disrupting the cell cycle and stopping the process of mitosis
...
Examples of how these work include;
•

The inhibition of microtubule formation(vincristine): vincristine binds to the tubulin in
microtubules and prevents them from functioning properly
...
Vincristine and drugs
that act in a similar way are described as mitotic poisons


•

Antimetabolites that act as S phase inhibitors preventing DNA synthesis
...






30


DNA and The Cell Cycle
In preparation for mitosis, the DNA content of a cell doubles
...
The DNA doubles during the S phase and only returns to its normal
cellular level during cytokinesis













Chromosomes
Chromosomes consist of an extended DNA molecule supported by special proteins called histones
...
The histone proteins are folded into compact stacks and the DNA
coils tightly around the stack to form a structure called a nucleosome
...
Diploid organisms have their
chromosomes arranged in homologous pairs within their cells which are very similar to each other; they carry
the same genes in the same sequence along their length
...


31


The Process of Mitosis
•

Prophase: The chromatin in the nucleus becomes condensed given it a much greater strength, to
prevent damage during mitosis
...
At this stage the
nucleolus disappears, in animal cells the centrioles move towards opposite poles of the cell
...


•

Anaphase: The centromeres attaching the two chromatids of each chromosome split and the
contraction of the spindle fibres pulls the chromatids apart
...
The nucleolus reappears, the nuclear membrane reforms around the two
groups of chromosomes and the spindle disappears as it is broken down
...


In animal cells, a cleavage furrow forms as the cell surface membrane invaginates and eventually splits the cell
in two
...
The

Golgi apparatus plays an important role in synthesising the materials needed in the formation of the new wall
...
It is one chromosome from each homologous pair that enters a gamete
...
Therefore, meiosis can only
take place in diploid cells, cells that have homologous pairs to start with
...


During the first meiotic division (meiosis I), the chromosomes are separated into two sets
...

Meiosis I:
Prophase I: homologous chromosomes have paired up to form bivalents (Pairing happens in in interphase)
the chromosomes behave as homologous pairs
...
The nucleolus disappears
...

Metaphase I: pairs of homologous chromosomes(bivalents) align along the ‘equator’ of the cell
...

Telophase I: The chromosomes are pulled to opposite ends of the cell, with each chromosome still consisting
of two chromatids and the nuclear membrane reforms
...
Nucleolus reappears
...


Prophase


Metaphase

Anaphase
33

Meiosis II
Normally prophase II continues immediately after meiosis I
...
In effect meiosis II is very similar to mitosis
...
Therefore, meiosis
produces four haploid cells, each different from each other in two cell
divisions















34


Meiosis and Genetic Variation
...

Variation is produced as a consequence of two specific processes, independent assortment and crossing over
...
However, for any one gamete it can be either
of the two homologous chromosomes from any particular pair
...
The way one
chromosome pair lines up is totally independent of how any other pair aligns
...
This process if independent assortment is very important in producing variation in the next
generation
Crossing Over: As each chromosome separates into two chromatids, following DNA replication, the resulting
bivalent consists of 4 chromosomes lying side by side
...
This happens during
prophase I and is called crossing over
...
However, the alleles may not be
...


•

Some chromatids, may contain unique sequences of alleles that did not exist in the parental
chromosome
...
In reality there are many in a bivalent
Note: The diagram shows the effect of crossing over in one homologous pair
...
The process of
fertilisation itself adds to the variation, as it is totally random which gamete from each parent is actually
involved in fertilisation





36


Cell Physiology
Simple Diffusion
Non–polar molecules such as soluble oxygen and carbon dioxide can pass through the membrane unaided
...
Water soluble
substances generally are unable to pass through by simple diffusion due to the hydrophobic nature of the
centre of the phospholipid bilayer
...
Diffusion is not restricted to occurring across membrane surfaces
...



•

The size of the molecule: small molecules diffuse faster than larger molecules


•

The temperature: Diffusing is faster at higher temperature due to molecules having more kinetic
energy
...



•

The surface area of the membrane: the greater the surface area, the faster the diffusion
...









37


Facilitated Diffusion
This is the type of diffusion involved when the diffusion process is supported or ‘facilitated’ by proteins
...

These protein carriers have binding sites that match specific
molecules and they assist the movement of these molecules
across the membrane
...

Some of these ion channels are permanently open but others are
gated
...
e
...

Because of this energy is required
...
The substance to be
transported binds to the carrier protein
...
Again with facilitated diffusion, the carriers are
specific to a particular type of molecule or ion
...


38


Cytosis
Some substances can be transported into or out of the cell without having to pass through the membrane
itself
...
When the vesicles are taken into the cell, the fluid nature of the cell surface membrane allows it to
reform and close the gap created by Cytosis
...
The contents of the vesicle are then
released outside the cell
...

Water potential is measured in kilopascals (kPa)
...
e
...

The water potential is an indication of the free energy of the water molecules
...

In solutions some of the water molecules are not ‘free’ as they form hydration shells around the solutes
...
The
more concentrated a solution is, the more negative its water potential is, as more water is bound up in
hydration shells and not ‘free’
...
A solution with a
water potential of 600kPa will take in less water by osmosis from pure water than a solution of -1000kPa

40



There are other terms relating to water potential that you need to be familiar with:
Solute potential this is the potential of a solution to take in water
...

The potential relates to the solute concentration only but the tendency is affected by other factors, such as the
space available within a cell
...
A plant cell that is turgid will exert
considerable pressure on its cell wall, whereas one that is not will exert much less pressure
...
The pressure potential is
usually positive although it can be 0
...
Herbaceous plants are almost totally reliant on turgor pressure
...
The opposing forces of the cell membrane and cell wall on each other help
create the turgor support for the plant
...
The rant
hand side typically reflects the changes that take place in most plant cells as the gain and lose water

If plant tissue suffers a shortage of water, the cells will cease to be turgid and the tissue is described as being
flaccid
...

41


If a plant cell loses too much water by osmosis, its vacuole can shrink to the extent that the cell membrane can
pull away from the cell wall
...

In nature, plasmolysis seldom occurs, as plants are unlikely to survive if they have become plasmolysed
...

•

Plants growing in a field that has been given too much fertiliser

•

A seed from a woodland tree being carried to a salt marsh and starting to germinate in this
environment

The point at which the cell membrane just begins to lose contact with the cell wall is called incipient
plasmolysis
...
Lysis will take place if the animal cells are placed in hypotonic solutions
If animal cells are placed in a hypertonic solution, the cells lose water by osmosis, they will shrink and shrivel
up (crenation)
In healthy animals, the blood and tissue fluid are kept at the correct water potential to ensure that neither
lysis or crenation











42


Enzymes
The Structure and Function of Enzymes
Enzymes are biological catalysts that speed up metabolic reactions
...
Enzymes are also globular proteins

Activation Energy
In chemical reactions there is an activation energy which is an energy barrier that must be overcome before a
reaction can take place
...

The primary structure is the linear sequence of amino acids
...
Within this shape there is an area known as the active site
...

They are biological catalysts; enzymes lower the activation energy to overcome the energy barrier
...





43


Enzyme Action
Enzymes act on substrates
...

The enzyme and the substrate interact with bonds forming between some of the amino acids of the enzyme
and parts of the substrate molecule
...

Enzymes are specific
...
Enzyme specificity is due to only one
substrate being an exact complementary shape to the active site
...
e
...






L

The Induced Fit Model of Enzyme Action
The induced fit model proposes that rather then being an exact fit, the active site of the enzyme very closely
matches the shape of the substrate
...

The active site is therefore flexible as it changes shape to fit the substrate and the enzyme is able to put
pressure on the substrate, breaking particular bonds
...
Like metal ions mg Ca
3+
...
They are not easily removed
...


Coenzymes:
Coenzymes are a particular type of cofactor
...
Unlike some other cofactors they are not permanently attached
...

Thus an increase in in substrate concentration will increase an enzyme’s rate of reaction as at low levels the
substrate concentration is the limiting factor
...

The same will occur for increasing enzyme concentration

45


Temperature:
o

As the temperature increases from 0 C to the optimum, the
reaction increases steadily
...
As the temperature
increases past the optimum, the rate of reaction
dramatically decreases until the rate of reaction is 0

Temperatures Effect on Enzymes
Increasing the temperature provides more kinetic energy, and so both the enzyme and the substrate move
faster, which results in more collisions, which results in more enzyme-substrate complexes being formed,
which therefore increases the rate of reaction
...
The enzyme
molecules vibrate more as the kinetic energy increases
...


pH

Changes in pH cause the ionic bonds in the tertiary structure of the enzymes to break which in turn changes

the shape of enzyme’s actives site This causes the active site to no longer be complementary to the substrate
and so no reactions occur
...
They reduce enzyme activity by either
directly or indirectly affecting the functioning of the active site
...
The effect of the inhibitor depends on the relative concentrations of the substrate
...


Non-competitive inhibition:
non-competitive inhibition is when the inhibitor attaches itself to a part of the enzyme other than the active
site
...
An increase in substrate concentration does not
reduce the effect of the inhibitor, as the two molecules are not indirect competition, but in effect, the number
of functioning enzymes has been reduced
...

Enzymes also have a second active site are known as allosteric enzymes

47


Enzymes as Biomarkers of Disease
Enzymes are useful biomarkers
...

Monitoring the levels of enzymes over a period of time allows the progress or recovery of a disease to be of a
disease to be monitored
...

Note: Enzymes can be monitored in blood, urine and sputum

Example of Enzymes as Biomarkers
Elastase is an enzyme released by white blood cells as a consequence of lung infection
...

Elastase also breaks down the protein elastin, an important component of lung tissue that contributes to the
elasticity of the alveoli the elastin helps the lung tissue stretch and recoil
...

However, cigarette smoke causes too much elastase to be released in the lungs and there is not enough A1AT
present to control the elastase effectively
...
If enzyme inhibitors are used to target
enzymes involved in causing disease, then disease progression can be reduced or stopped
...


•

Able to work well at low doses to prevent a build-up of the inhibitor to levels which may be toxic

A1AT: can be used medically to reduce harmful effects arising from lung infection
...
They work by inhibiting an enzyme that leads to the constriction of blood vessels
...

Some antiviral drugs inhibit the DNA/RNA polymerases essential in viral replication
...

48


Diagnostic Reagent Strips
Enzymes are very effective biosensors
...

Biosensors
Biosensors have a wide range of application in for example, industry, medicine and environmental monitoring
...

The general principal has the molecule being monitored reacting with immobilised enzymes and the reaction
produced cause a colour change Like glucose monitoring strips or pregnancy tests
...

In some pregnancy tests, antibodies react with specific proteins (hormones) to give a positive test
...
The
combination of the hormones with the complementary antibody results in the colour change in the test strip
Note: Specific active site directed inhibitors can be developed that are much more specific than the normal
substrate of some enzymes being monitored in medical and other diagnostic testing
...
They have become
increasingly important in biotechnology
...
Immobilised
enzymes are trapped within or attached to appropriate inorganic or organic molecules




Adsorption: the enzymes are
attached by weak forces to and
inert substance such as glass or a
matrix

Cross-linkage: the enzymes are
bonded covalently to a matrix,
such as cellulose, due to
chemical reactions








Encapsulation: the enzymes are
trapped inside a selectively
permeable membrane such as
nylon

Entrapment: the enzymes are
trapped within polymers such as
alginate beads or microspheres
...


•

The enzymes are more resistant to changes in pH
...


•

Commercial processes can be continuous, which is faster and produces less wastage
...


Disadvantages of immobilised enzymes
Using immobilised enzymes reduces the rate of reaction
...


•

Some enzymes are trapped in such a way that the active sites cannot be reached by the substrate
...
The cells in any one tissue are
often very similar in structure
...
Organs seldom work in
isolation they tend to work together as organ systems
...
It is highly adapted organs in specific regions
...

Serosa This outer layer of connective tissue provides a very thin protective and
supportive lining
...

Muscularis mucosa: This thin layer of muscle between the sub mucosa and the mucosa
...
The muscle has strands
of muscle extending up through the mucosa into each villus, with contractions of these strands producing the
characteristic ‘wafting’ movement of the villi
...
It is highly specialised with a substantially
increased surface area due to the presence of villi and micro-villi





51


The Villus







The Columnar Epithelial Cells
The columnar Epithelial cells of the villus have their surface area extended by the presence of numerous
micro-villi that give a brush border appearance
...

The columnar epithelium cells are particularly rich in mitochondria for the active transport of some absorbed
food products
...
Glucose and amino acids are taken
into the epithelial cells by active transport, and once there, can diffuse into the
capillary network due to the concentrations that can build up in the cells
...
Lipids are transported out to the villi by the lacteals, which are
part of the lymphatic system Pinocytosis is also involved in absorption of some
substances
...
These secrete mucus which provides a slimy
protective layer that lubricates the canal, facilitating the movement of food and also protects against the
effect of digestive enzymes on the epithelial cells

Capillaries
Capillaries within the villus are important for transporting amino acids and monosaccharaides out of the villi
...
Which transports digested
products to the liver
...


Crypts of lieberkühn
Crypts of lieberkühn are intestinal glands that lie embedded in the tissue between villi
...
By the time they reach the top of the villus, usually after a few days they are sloughed off and
replaced
...
Other cells lining the crypts are involved in mucus secretion
...
It is also well adapted for gas exchange to enable both
photosynthesis and respiration to take place in cells and many leaves are highly adapted to reduce water loss
by transpiration,

The Upper Epidermis
The upper protective layer of the leaf and it has no chloroplasts so it is not directly involved in photosynthesis
...


The Palisade Mesophyll
The primary photosynthesising region in the leaf and to maximise the harvesting of light energy
...
The palisade
cells are arranged regularly in order to pack in as many as possible
...

Depending on the species, there may be one or more layers of palisade cells in the palisade mesophyll
...
As well as
the benefits of maximising the incident light in each cell, there are other advantages with this arrangement
...


Orientation of


palisade cells




The Large Surface Area
Most leaves a further adaption for photosynthesis, both through providing more palisade cells in close
proximity to the upper leaf surface and also to facilitate gas exchange with no cell being too far from a gas
exchange surface
...

In plants such as cacti, adapted to arid habitats, needle shaped leaves have evolved to decrease the surface
area across which water loss can occur
...
The spongy mesophyll cells are much more loosely and more
irregularly arranged this leads to the formation of inter cellular air spaces that encourages the diffusion of
gases for gas exchange
...
They are
important in gas exchange and the carbon dioxide and oxygen required by the palisade cells diffuses through
the spongy mesophyll cells on their way to and from the palisade layer
...
Xylem vessels transport water and inorganic ions up through the plant and into
the leaves
...
Stomata are present and their
opening and closing is controlled by the presence of guard cells thereby facilitating gas exchange
...

In most cells the stomata are closed at night to reduce water loss
...

During darkness leaf metabolic activity is much reduced with only respiration taking place and there is usually
enough oxygen within the leaf to allow respiration to take place even when the stomata are closed
...
Such as water lilies have stomata
on the upper leaf surface only

55




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