Higher Biology Course Unit 1 Higher Biology Unit 1 Cell Biology: Cell structure in relation to...

Higher Biology Course Unit 1

Higher Biology

Unit 1

Cell Biology:Cell structure in relation to

function


• In a multicellular (many-celled) organism the cells are organised into tissues.

• A tissue is a group of similar cells which work together to carry out a specific function.


• Some tissues have only one type of cell (e.g. muscle). Other tissues have several types of cells (e.g. phloem contains sieve tubes and companion cells).


• The structure of a cell is related to its function (what the cell does).

• In a unicellular (one-celled) organism (e.g. amoeba, paramecium, euglena or yeast) all the processes necessary for life are carried out in a single cell.


Paramecium


Euglena


Root hair


Leaf epidermis


Phloem


Xylem


Leaf mesophyll


Parenchyma


Lining of kidney tubule


Return

Lining of trachea


Lining of trachea


Lining of mouth


Bone cell


Fat cell


Red blood cell


Muscle Cell


Nerve cell


Cell Ultrastructure


Cell Boundries

• Cell wall

• Outer boundary of plant cells• Made of cellulose fibres in layers• Strong, slightly elastic• Absorbs water, providing a pathway

for water movement through plant tissues.


•Plasma membrane

• Forms the cell membrane and forms or surrounds all cell organelles.


• Made of a double layer of phospholipid molecules with protein molecules embedded.

• Called “fluid-mosaic” model because

1. Molecules move around like fluid2. Proteins form a pattern on surface

(mosaic)

• Some protein molecules enclose a pore through which small molecules can pass in/out of the cell.


Functions of the plasma membrane

Molecules can enter or leave a cell, across the membrane, in 5 ways:

1. Diffusion2. Osmosis3. Endocytosis4. Exocytosis5. Active Transport


Diffusion

• Movement of molecules of (gas or) liquid from an area of high concentration to an area of low concentration down a concentration gradient.


• The concentration gradient is the difference in concentration between two areas.


Molecules cross the plasma membrane in two ways:

• Through the phospholipid layer• Through pores in the protein

molecules


Osmosis

• Diffusion of water molecules

• Through a selectively permeable membrane (e.g. plasma membrane)

• (S.P. Membrane is a membrane with pores which allows small molecules to pass but not large ones)


• Water moves from a high water concentration to low water concentration

HWC LWC


Effects of osmosis on cells


Hypotonic – higher water concentration

Hypertonic – lower water concentration

Isotonic – same water concentration


Turgid – cell swollen with waterFlaccid – cell limp through loss of waterPlasmolysed – in Plant cells, water loss

causes cytoplasm to shrink away from the cell wall.


Endo- and Exo-cytosisCells sometimes take in, or expel, large

quantities of material by forming a “pocket” in the membrane.

This is called endocytosis (taking material into the cell) or exocytosis (materials leave the cell).


An example of endocytosis is:


Phagocytosis


In this form of endocytosis the cell engulfs solid particles (e.g. amoeba) – like “eating” a bacterium.


Active Transport

Movement of ions across the plasma membrane against the concentration gradient

i.e. Low concentration → High concentration


Energy is needed.

Protein molecules transport ions across the membrane.


IN

OUT

Low conc. outside the cell

High conc. inside the cell

Low conc. inside the cell

High conc. outside the cell

Energy


Essay question

Discuss the role of the plasma membrane under the following headings:

1. The structure of the plasma membrane (4 marks)

2. The role of the plasma membrane in transport (6 marks)


Discuss the role of the plasma membrane under the following headings:1. The structure of the plasma membrane (4 marks)2. The role of the plasma membrane in transport (6 marks)

Plasma membrane:• Composed of phospholipid bilayer (two layers)• Contains proteins.• Some proteins form pores through the membrane.• Described as a “fluid mosaic”Role of plasma membrane:• Diffusion + movement of liquid/gas from area of high conc. to area

of low conc.• Osmosis + movement of water from area of HWC to area of LWC.• Endocytosis + description of engulfing a large molecule.• Phagocytosis is an example of endocytosis (eating bacteria).• Active transport + movement from area of low conc. to area of high

conc.• Active transport requires energy and a carrier protein.

1 mark for each bullet point. TOTAL 10 Marks

Higher Biology Course Unit 1Lives in the sea Lives in fresh water

Ion Fresh water

Sea Water

Lobster Mussel Cray-fish

Frog Fresh WaterM

ussel

Na 0.24 478.3 530.9 79 212 109 15.6

K 0.005 10.1 8.7 152 4.1 2.6 0.5

Ca 0.67 10.5 15.8 7.3 15.8 2.1 6.0

Mg 0.04 54.5 7.6 34 1.5 1.3 0.2

Cl 0.23 558.4 558.4 94 199 78 11.7

SO4 0.05 28.8 8.9 8.8 - - -

Concentrations in mM per kg


In the example above, the lobster actively transports sodium inwards (higher concentration in the body than the sea water), actively transports magnesium out (lower concentration in body than sea water), but does not regulate chloride (concentration equal).

Higher Biology

Unit 1

Cell Biology:Photosynthesis


Absorption, reflection and transmission of light by a leaf

Light shining on leaf (100

%)

12 % of light

reflected

5 % of light

transmitted

83 % of light absorbed but only 4 % of this is used for

photosynthesis


Light absorption by leaf pigments

Leaves contain several coloured pigments of which chlorophyll is the most important.

These pigments absorb light energy.


Which wavelengths of light are used

White light is made up of several different wavelengths of light from 400 nm to 700 nm.

Normal spectrum of white light:

violet blue green yellow orange

red


• Collect a leaf and cut into small pieces.

• Add some propanone and sand into a mortar and pestle.

• Grind this up, until the propanone turns green.

• Filter the mixture into a test tube.• Hold the spectroscope up towards the

test tube and look towards the light.



red


red

Spectrum viewed through Chlorophyll

The blue and violet are no longer visible and only some of the red is still seen. These have been absorbed by the chlorophyll.


The main wavelengths absorbed are violet and blue, and some red.

These are most important wavelengths for a plant in photosynthesis.


Absorbtion and Action Spectra

A leaf contains several pigments which can be separated by chromatography.

The main pigments are:1. Chlorophyll a (blue-green)2. Chlorophyll b (yellow-green)3. Carotene (yellow)4. Xanthophyll (yellow)


An absorption spectrum shows the absorption of light of each wavelength by each pigment.

An action spectrum shows the rate of photosynthesis at each light wavelength.

Comparison of absorption and action spectra reveals a close match – this is good evidence for the importance of leaf pigments in photosynthesis.


The presence of several pigments increases the range of wavelengths the plant can make use of.

Separation of photosynthetic pigments by thin layer

chromatography


Name Rf value

Carotene

Chlorophyll a

Chlorophyll b

Xanthophyll


Chloroplasts

The main pigments (chlorophyll a+b, carotene and xanthophyll) are contained in the chloroplasts.

Lamella


Chloroplasts have:

• A double plasma membrane• A liquid stroma• Stacks of flattened membrane bags

called grana (singular – granum) which contain chlorophyll

• Connecting tubes between grana called lamellae.


Chemistry of photosynthesis

Remember Standard Grade:

Carbon dioxide + water + light energy → glucose + oxygen

This takes place in 2 main stages:1. Photolysis (needs light)2. Carbon fixation (Calvin cycle)


Photolysis

Happens in the GRANA of the chloroplasts.

Light energy is absorbed by chlorophyll and used to split water molecules into hydrogen and oxygen.

Energy is released.


WATER

ENERGYOxygen Hydrogen


These products are treated like this:

OXYGEN – released as a by-product.

HYDROGEN – attached to a hydrogen acceptor molecule (NADP) to form NADPH2

ENERGY – stored as ATP


The hydrogen and the ATP play an important part in the second stage of photosynthesis, called CARBON FIXATION.


Lamella

2

3

4

5

6

Quick Quiz


1. Carbon dioxide + water + light energy → glucose + oxygen

2. Grana/Granum3. Outer membrane4. Lamellae5. Inner membrane6. Stroma7. Grana8. Water split to hydrogen & oxygen, energy released9. Picked up by NADP to form NADPH2/Picked up by

hydrogen acceptor10. In ATP

Answers


Carbon Fixation

Takes place in the STROMA of the chloroplast.

Molecules of carbon dioxide diffuse into the chloroplasts where they attach to molecules of 5-carbon Ribulose biphosphate (RuBP)


The resulting 6-carbon compound is unstable and breaks down into two molecules of 3-carbon glycerate-3-phosphate (GP).

In the next step, GP is reduced to triose phosphate (3-carbon) by the addition of hydrogen (from the NADPH2) and energy (from ATP).


CO2 (1C)

RuBP (5C)

6C unstable 2 x GP (3C)

Triose phosphate (3C)

NADPH2

NADP

ATP

ADP + Pi

Glucose

Complex carbohydrates + other organic molecules

CALVIN CYCLE


Triose phosphate has two possible fates:

1. Synthesis of glucose (6 carbon) which is then built up into other carbohydrates (e.g. starch and cellulose)

Plants also use carbohydrates to make other organic molecules (e.g. proteins, fats and nucleic acids)


2. Conversion to RuBP so that more carbon dioxide can be taken up.

The cycle of reactions involved in carbon fixation is know as the calvin cycle.


Limiting factors

A limiting factor is a factor which slows down the process of photosynthesis if is in short supply.

Limiting factors are light intensity , carbon dioxide concentration and temperature.


30°C

20°C

10°C

Carbon dioxide concentration

Rate of photosynthesis

A

B

B

B


At point A: Rate of photosynthesis depends on carbon dioxide concentration, regardless of temperature.

Carbon dioxide is the limiting factor.

At point B: Further increase in CO2 has no effect. The rate of photosynthesis is increased by raising the temperature.

Temperature is the limiting factor


Carbon dioxide concentration

Rate of

photosynthesis

Light intensity

Rate of

photosynthesis

Limiting factor = CO2 conc.

Limiting factor = Light intensity

Limiting factor either Light or Temp

Limiting factor either CO2 or Temp

Aerobic Respiration

Unit 1: Higher Biology


Energy storage in the cell

Chemical energy is stored in cells in molecules of ATP (Adenosine Tri-Phosphate).


(Pi = Inorganic phosphate)

In order to release the chemical energy, the bond attaching the third phosphate is broken (shown in red).


ATP formation

A molecule of ATP forms when a molecule of ADP (Adenosine Di-Phosphate) joins with an inorganic phosphate.

The energy required to join the Pi to the ADP comes from the chemical energy released from the breakdown of glucose during respiration.


The conversion of ADP to ATP is called Phosphorylation.


Summary


Aerobic respiration – S-Grade


Chemistry of Aerobic respiration

Aerobic respiration is the complete oxidation of molecules of glucose to release energy.

Oxidation is the removal of hydrogen with the release of energy.


Aerobic respiration takes place in 3 stages:

1. Glycolysis2. Kreb’s Cycle 3. Cytochrome system.


Stage 1: Glycolysis


Glucose molecules (6 carbons) are broken down into 2 molecules of 3-carbon molecule called Pyruvic acid.

Happen in the cytoplasm.

No oxygen is required.


There is a net gain of 2 ATP molecules.

Hydrogen is released and temporarily attached to a co-enzyme carrier molecule called NAD.

NAD + 2H NADH2 (reduced co-enzyme)


Stage 2: The Kreb’s Cycle

a.k.a. The Citric Acid cycle OR Tri-carboxylic acid (TCA) cycle.

This takes place in the mitochondria.


Mitochondria

Mitochondria (singular = mitochondrion) are sausage shaped organelles surrounded by a double plasma membrane.

The centre of the called the Matrix and is filled with fluid.


The inner membrane is folded into cristae which provide a large surface area for the stalked particles on which the cytochrome system takes place.


• The pyruvic acid diffuses from the cytoplasm into the mitochondrion.

• In the matrix, the pyruvic acid is converted to a 2-carbon compound called acetyl Co-A, releases CO2 and hydrogen. The hydrogen is bound to NAD.


• Acetyl Co-A now enters the Kreb’s cycle by combining with a 4-carbon compound to form 6-carbon citric acid.

• Citric acid is then broken down in a series of oxidation reactions to the original 4-carbon compound and the cycle begins again.

• The Hydrogen which is released binds with NAD.


Stage 3: Cytochrome system

• This takes place on the stalked particles on the cristae.

• Hydrogen is released from the NADH2 and passed along a “chain” of hydrogen carriers called the cytochrome system.


• As each pair of hydrogen atoms are passed along the chain enough energy is released to make 3 molecules of ATP. This is called oxidative phosphorylation.

• At the end of the chain the hydrogen combines with oxygen to form water.


Production of ATP

• Complete oxidation of one molecule of glucose produces 38 molecules of ATP (36 from oxidative phoshorylation in the cytochrome system and 2 from glycolysis).


As the organism respires it uses oxygen (and produces carbon dioxide which is absorbed by the sodium hydroxide). This causes the liquid level to rise and the syringe is used to find the volume of oxygen consumed.


Anaerobic respiration

Aerobic respiration only occurs if oxygen is available to accept the hydrogen at the end of the cytochrome system.

If no oxygen is available anaerobic respiration occurs.


During anaerobic respiration Glycolysis occurs as normal, but there is no Kreb’s cycle.


Glucose Pyruvic Acid Kreb’s cycle

ANIMALS PLANTS

Lactic Acid Ethanol + CO2

Oxygen available

Oxygen not available


Aerobic respiration

Anaerobic respiration

Oxygen required?

Total ATP production (per glucose molecule)

Other products (plants)

Other products (animals)


Anaerobic respiration is animals occurs during heavy exercise. After exercise stops the lactic acid can be converted back to pyruvic acid by repaying the “oxygen debt” by breathing heavily. It is therefore REVERSIBLE.

Anaerobic respiration is plants is IRREVERSIBLE as the CO2 diffuses out of the plants.


Measuring the rate of aerobic respiration

The rate of aerobic respiration can be measured using a respirometer.


Parts of this apparatus have the following purposes:

Glass beads: They are a control to show how it would be with something that does not respire.

Water bath: keeps the test tubes at a constant temperature, as the volume of gas would increase if the temperature increased.


Syringe: It measures the volume of oxygen used, by pushing down and returning the dye to the same level as before.

Sodium hydroxide: Absorbs carbon dioxide.


Synthesis and release of proteins

Higher BiologyUnit 1


Proteins

DNA

Replication

Transcription

Translation

Secretion

C,H,O,NGlobular

Fibrous

synthesis

Double helix

NucleotideGenes

Chromosomes

SugarPhosphate

Base

A,T,C,G

A-TC-G

DNA Polymerase

Genetic code

Golgi body

Rough ER

mRNA

UracilSingle stranded

RibosomestRNA

Codons

Amino acids

Peptide bonds


Structure and variety of proteins

• Proteins are composed of the following elements:• Carbon, Hydrogen, Oxygen, Nitrogen,

(often Sulphur) = HONCS• Atoms of these elements form amino

acids (20 different ones).• Amino acids link by peptide bonds to

form polypeptides.• Polypeptides link up to form Proteins.


Role of proteins

TYPE ROLE EXAMPLES

Globular Enzymes

Structural

Hormones

Antibodies

Fibrous Make hair and nails


Role of genes

• Chromosomes consist of many genes. These carry out their instructions by producing enzymes. Enzymes are made of protein.

• So, genes produce protein; Like this:


Protein Synthesis

• Genes contain a chemical code.

• This code is part of a molecule of DNA (Deoxyribonucleic acid).

• The structure of DNA enables the correct amino acids to be assembled in the correct sequence to make a particular protein.


Structure of DNA

• A DNA molecule is made of 2 chains of nucleotides.

• Each nucleotide contains:1. A deoxyribose sugar molecule2. A phosphate molecule3. A base molecule

Phosphate

Base

Deoxyribose sugar


Phosphate

Base

Deoxyribose sugar


• There are four different bases, and therefore four different nucleotides:

Adenine nucleotide

(A)

Guanine nucleotide(G)

Thymine nucleotide(T)

Cytosine nucleotide(C)


• Nucleotides are linked together by means of chemical bonds between phosphate and sugar molecules – called “sugar-phosphate bonds”:


• Two of these nucleotide chains are joined by means of hydrogen bonds between bases.

ADENINE always bonds with THYMINECYTOSINE always bonds with GUANINE


• The two, linked, nucleotide chains are twisted into a coil called a double helix.


• Each chromosome consists of one double-helix shaped molecule of DNA containing many thousands of base pairs.

• A gene is a section of DNA molecule whose base order forms the code to make one protein.


Replication of DNA

• Chromosomes must be able to copy themselves so that cells retain the same genetic information after cell divisions.

• This copying of the DNA in the chromosomes is called replication.


• Replication requires:(a)A DNA molecule(b) unattached nucleotides of 4 types(c) enzymes (DNA polymerase)(d) energy (in the form of ATP)


• Replication takes place in these stages:1. DNA uncoils2. The hydrogen bonds between bases

break (starting at the end like a zip)3. Free nucleotides attach to exposed bases4. Sugar-phosphate back bone reforms


The Genetic Code

• Proteins are made of a long chain of amino acid molecules.

• A gene contains a code (order of DNA bases) to ensure that the amino acids are joined in the correct order to make a specific protein.

• The order of the bases is called the genetic code.


• This is a triplet code because the sequence of three bases is needed to code for each amino acid.

• e.g. • AAG codes for amino acid Phenylalanine• GAC codes for amino acid Aspartic Acid• GGA codes for amino acid Glycine.


So a DNA strand with base sequence:

Would code for (part of) protein:

(one protein molecule may be hundreds or thousands of amino acids long)

A A AAG G GG C

A A AAG G GG C

Phenylalanine Aspartic acid Glycine


RNA (ribonucleic acid)

• Protein synthesis takes place on the ribosomes in the cytoplasm.

• The instructions in the genetic code are carried from the DNA (in the nucleus) to the ribosomes by a molecule of messenger RNA (mRNA)


• RNA differs from DNA in 3 ways:

1.RNA is single stranded

2.RNA contains ribose sugar

3.In RNA the base thymine is replaced by Uracil


There are two types of RNA:• Messenger RNA (mRNA) which

carries the genetic code from the DNA in the nucleus to a ribosome in the cytoplasm.

• Transfer RNA (tRNA) which carries amino acids to the ribosomes for assembling into polypeptide chains.


Transcription

• The piece of DNA containing the relevant gene uncoils and the base pairs separate.

• Complementary RNA nucleotides then attach to the exposed DNA bases.

• They link together (ribose-phosphate chemical bonds) to form a messenger RNA (mRNA) molecule.


A T T

C

GA

G G T C A C T A T A G G CT

AC

G

C G G A

T A AG

CT

CC A G T G A T A T C C G

AT

GCG C C T

DNA strand

One gene


Ribosomes and rough endoplasmic reticulum

• Ribosomes are:• Found in all cells• Free in cytoplasm or attached to rough

endoplasmic reticulum• Spherical, with two halves• Site of translation of mRNA into protein


Ribosomes

Sheets of endoplasmic reticulum

Fluid filled cavity between sheets


Assembling the protein = translation

• In the cytoplasm are molecules of transfer RNA (tRNA).

• These are composed to one triplet of bases and an amino acid molecule.

• e.g. Alanine Leucine

• Codon: triplet of bases on mRNA• Anti-codon: Complementary triplet of

bases on tRNA

G C A C U G


Stage 1

Stage 2

Stage 3


• The mRNA attaches to a ribosome.

• The ribosome moves along the mRNA with successive codons entering the “active site”.

• Here, a tRNA with the appropriate anti-codon is attached.

• Adjacent amino acids then link up by a peptide bond to form a polypeptide and eventually a protein.


Secretion of proteins

Nucleus

Nuclear membrane

Pore

Rough endoplasmic reticulum

Ribosome

Golgi Apparatus

Vesicle

Cell membrane


• The golgi apparatus is made up of many flattened fluid filled sacs.

• Vesicles containing newly made protein are pinched off the rough endoplasmic reticulum.

• These move towards the Golgi and use with the outermost sac.


• The contents then move down through the golgi from sac to sac, becoming modified in the process.

• The finished product (e.g. glycoprotein), in a vesicle, leaves the golgi and moves to the cell membrane and discharges its contents out of the cell.


Cellular Defence Mechanisms


Virus Structure


Reproduction of viruses

Viruses can only reproduce inside the cells of a host organism.

They use the host’s nucleotides for replication and the host’s amino acids to construct protein coats.


Defence against viruses


First line of defence

Mechanisms by which our bodies attempt to prevent entry of harmful microbes.


Second line of defence

Mechanisms by which our bodies attempt to kill harmful microbes which have succeeded in entering.


Immunity

Immunity is the ability of an organism to resist disease. The blood is usually involved.

There are two types:1. Non-specific immunity (phagocytosis)2. Specific immunity (antibodies)


1. Non-specific Immunity

Provides protection against a wide range of invading microbes e.g. by phagocytosis carried out by white blood cells.


Read page 70 of Torrance and make your own notes on “Phagocytosis”.

Then:• Prepare a 2-3 min illustrated presentation

to give to the class on the topic, explaining:

• How invading bacteria are detected• How invading bacteria are engulfed• What a lysosome is, what it contains and

what it does• What pus is


Phagocytosis

Phagocytosis is the process by which foreign bodies such as bacteria are engulfed and destroyed.

Cells capable of phagocytosis are called phagocytes.


A phagocyte detects chemicals released by the bacterium and moves up a concentration gradient towards it.

The phagocyte adheres to the bacterium and engulfs it into a vacuole formed by an infolding of the plasma membrane.


Lysosomes fuse with the vacuole and release their enzymes into it.

The bacterium becomes digested and the breakdown products are absorbed by the phagocyte.


During infection hundreds of phagocytes migrate to the infected area and engulf many bacteria by phagocytosis.

Dead bacteria and phagocytes often gather at a site of infection forming pus.


2. Specific immunity

A specific invading particle (e.g. A virus) is attacked by a specific defending chemical.


Antigen: a complex molecule recognised by our body as alien (e.g. A virus coat particle).

Antibody: a chemical produced a lymphocyte white blood cell to destroy antigens.


How antibodies work

An antibody is a Y-shaped molecule:


The binding sites on the arms attach to antigen molecules making them harmless:


There are many types of lymphocyte, each type targeting one antigen with specific antibodies.


Types of specific immunity

(a)Active immunity:We produce our own antibodies by:(i) Suffering from the disease and

retaining the antibodies in the blood – (natural)

(ii)Receiving a vaccine of treated antigen (e.g. Empty virus coats) which triggers antibody formation – (artificial).


(b) Passive immunityWe receive ready-made antibodies from:(i)Mother, across the placenta – (natural)(ii) Another mammal (e.g. A horse) which

has made the antibodies in response to treatment – (artificial).


Rejection of transplanted tissues

Make your own notes from Page 73 of Torrance.


Cellular Defence Mechanisms in Plants

Plants defend themselves from attack by:

(a) Producing toxic compounds(b) Isolating the infected area or

infectious organism


(a) Production of toxic compounds

(i) Cyanide• Made by clover plants by a process

called cyanogenesis.• Cyanide works by blocking the

cytochrome system of e.g. Slugs• It is produced when non-toxic

glycoside and an enzyme are mixed as a result of leaf damage.


(ii) Tannins• Tannins are toxic to micro-organisms• They defend by preventing pathogens

e.g. Fungi from gaining access to the plant organ under attack.

• The tannins act as enzyme inhibitors.• Therefore, they interfere with the

invading pathogen’s metabolism and render it harmless.


(iii) Nicotine• This is toxic chemical produced in the

root cells of tobacco plants and transported to its leaves.

• Since it is poisonous it protects leaves against attack by herbivorous insects.

• Nicotine can be extracted from tobacco plants and used as an insecticide.


(b) Isolation of the problem

(i) Insect galls• When a parasite penetrates the

cuticle of a leaf, the leaf produces a gall in response to a chemical stimulus.

• A gall is an abnormal swelling of plant tissue resulting from active division of cells at the site of the injury.


• The combination of the extra layers of cells and rich deposits of tannin in a gall provides the plant with a protective barrier where the parasite can be isolated.


(ii) Resin• Resin is a sticky substance produced

by many trees.• When a plant becomes wounded by a

pathogen the resin-secreting cells increase in activity, trapping pathogens.

Higher Biology Course Unit 1 Higher Biology Unit 1 Cell Biology: Cell structure in relation to...

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