Topic 3- Voice of the Genome

Electron microscope (EM)

Beam of electrons used to produce

magnified image Electron beam generated by electron gun, focused by electromagnets Membranes and other structures stained by heavy ions, stand out as dark areas EM better than optical microscope laser beam short than light rays

Cell

In multicellular organisms, cells are specialised for a

particular function
E.g. Epithelial cells, muscle cells

Tissue
Similar cell types from the same origin working

together for the same function

Organ
Several cell types working together for many functions Made up of tissues

Organ system
A group of organs working together to carry out a

particular function.
E.g. The circulatory system

Nucleus
Largest in Eukaryotic cell (10-20 micrometres in

diameter)
Double membrane with pores Contains chromosomes

Nucleus
Nucleoplasm Nuclear envelope Pore

Outer membrane

Nucleolus

Inner membrane

Chromatin

Histone

Highly alkaline, positively-charged proteins in the

nucleus of eukaryotic cells. Package and order DNA into structural units called nucleosomes. Main component of chromatin

Nucleolus
Site of ribosome synthesis Consists of protein and RNA

Mitochondria
Rod shaped/cylindrical organelles Large (0.5-1.5 micrometres wide, 3-10 micrometres long) Found in all cells, large numbers in metabolically active

cells (e.g. muscle fibres, hormone secreting cells.)

Surrounded by a double membrane

Mitochondria

Endoplasmic reticulum (ER)

Outer membrane of nucleus Rough Endoplasmic reticulum (RER) Smooth Endoplasmic reticulum (SER)

Endoplasmic reticulum

RER
Ribosomes attached to outer surface

Vesicles formed from swellings at margins that

become pinched off

Site of synthesis of proteins that are packaged in

vesicles and exit the cell (e.g. digestive enzymes)

SER
No ribosomes Site of synthesis of proteins needed by cells (e.g.

lipids)

Golgi apparatus
Stack-like collection of flattened membranous sacs Smooth (no ribosomes), curved cisternae One side formed by fusion of membranes of vesicles

from ER, other side vesicles are formed from swellings at margins that become pinched off
Modifies proteins by addition of carbohydrates

Golgi apparatus
Protein material moves from convex side to concave

Cisternae

RER and Golgi apparatus

Protein produced by ribosome
Ribosomes attached to RER Proteins stored within RER

Proteins folded with RER lumen

RER produces vesicles, packages proteins Vesicles fuse with Golgi Golgi modifies protein, carbohydrate added Water removed to concentrate Golgi produces lysosomes/ secretory vesicles

Lysosomes
Small spherical organelles, single membrane Contain concentrated mixture of hydrolytic enzymes

which are produced in Golgi apparatus or RER Breakdown contents of imported food vacuoles Then broken down into products of digestion which escape into cytoplasm Also fuse and digest broken-down organelles in cytoplasm

Lysosomes

Microtubules
Straight, unbranched, hollow cylinders (25nm wide)

In the cytoplasm of Eukaryotic cells

Consists of tubulin (a globular protein) Built up/broken down when needed

Microtubules

Centrioles
Centrosome= 2 perpendicular centrioles

Single centriole consists of 9 triplets of microtubules

Before nuclear division they separate, moving to the

poles of the cell

Centrioles

Eukaryotes
Eukaryotic cells = good nucleus True nucleus present

Plant and animal cells

Large 80s ribosomes present RNA polymerase made up of 14 subunits

Origin- mitochondria and chloroplasts

Prokaryotes taken up into food vacuoles of eukaryotes

for digestion
Useful, integrated into host cell Explains why mitochondria and chloroplasts have a

DNA double helix like bacteria and ribosomes like prokaryotes

Animal Cells

Plant Cells

Plant Cell Wall

Rigid Consists of cellulose fibres which run through other

polysaccharides (e.g. pectin, hemicelluloses) Sticky middle lamella holds neighbouring cells together Lignin makes wall strong and impermeable

Chloroplasts
Part of group of organelles known as the plastids

(which are only found in plant cells)

Large, green, biconvex Site of photosynthesis Double membrane

Chloroplasts

Vacuole
A fluid-filled space in the cytoplasm surrounded by a

membrane called the tonoplast

Contains a solution of sugars and salts called the cell

sap.

Prokaryotes
Cells containing no true nucleus

Before the nucleus

Bacteria and cyanobacteria (photosynthetic bacteria) Small 70s ribosomes present

Mitosis

Interphase
G1 = First growth phase. New organelles synthesized in

the cytoplasm, intense biochemical activity and accumulation of stored energy

S

= DNA synthesis, each chromosome copies itself by replication, forms chromatids

G2 = Second growth phase. Intense biochemical

activity and increase in the amount of cytoplasm

Prophase
Chromatids condense , forming bivalents
Nuclear envelope breaks down Nucleolus breaks down Spindle fibre begins to form Centrioles migrate to opposite poles

Metaphase
Centrioles move to opposite ends of the cell
Microtubules of the cytoplasm start to form spindle Microtubules attach to centromeres of chromatids

Chromatids line up on equator

Anaphase
Spindle fibres contract
Chromatids separate Centromere leads Spindle fibres attached to Kinetochores Move to opposite poles of the cell

Telophase
Chromosomes are in the process of decondensing and

are becoming visible Nucleus visible Nucleolus present Spindle broken down 2 separate nuclei visible Chromatin visible Evidence of cell plate formation

Cytokinesis
Cell organelles (e.g. mitochondria, chloroplasts) are

evenly distributed between the cells

In-tucking of plasma membrane at equator, pinching

cytoplasm in half
Two cells form

Chromatids
Daughter strands of a duplicated chromosome joined

by a centromere

Kinetochore
A protein structure on chromatids where the spindle

fibres attach during cell division to pull sister chromatids apart

Cell cycle
Mitosis

Used for growth and asexual reproduction

Meiosis
Gamete formation 2 stages: Meiosis I and Meiosis II Prophase I, Metaphase I, Anaphase I, Telophase I,

Cytokinesis, Prophase II, Metaphase II, Anaphase II, Telophase II, Cytokinesis

Four daughter cells produced, haploid Same as mitosis, repeats (no interphase on second cycle)

Genetic variation in Meiosis

Crossing over

Independent assortment

Crossing over
Pairs of homologous chromosomes (bivalent)
Bivalent coils and shortens continuously, chromatids

break Broken ends re-join at corresponding sites, chiasma forms Lengths of genes exchanged New gene combinations produced

Independent assortment
Bivalents line up randomly on equator during meiosis I

Orientation at the equator of the spindle is random

Possible gene combinations= 223

Gene locus
The location of a gene on a

chromosome

Sexual Reproduction
Fusion of two gametes (fertilisation) = zygote
Meiosis halves the normal chromosome number Gametes= haploid (contains half of the normal

chromosome number)
Diploid= cells that contain the full number of

chromosomes

Asexual Reproduction
Single organism produces offspring, clones No gamete formation, cells of new offspring produced by

mitosis
Advantage

Disadvantages

= a large number of individuals can be quickly produced by a single organism = no variation in offspring, genetic mutations will be passed on, exponential growth

Fertilisation in mammals

Occurs in upper part of oviduct Erect penis into vagina, ejaculation Vagina acidic, semen alkaline to neutralise so sperm can survive Waves of contractions by muscles in uterus walls to draw semen into oviduct Sperm reaches ovum, enzymes break acrosome Digests through zona pellucida Contents of cortical granules released by exocytosis to harden membrane and prevent other sperms entering (polyspermy) Meiosis II is completed Nuclei fuse

Haploid cells
Cells with half of the total number of chromosomes , n In humans, n= 23 Gametes When fertilisation occurs, zygote will have the full number

of chromosomes
Enables mixing of alleles

Sperm cell
Formed in seminiferous tubules in the testes Acrosome contains hydrolytic enzymes to

digest through ovum wall

Large no. of

mitochondria
Flagellum Streamlined Receptors

respiration, energy (ATP)for sperm mobility so sperm can swim down fallopian tubes to egg less resistance to motion bind to egg cell surface membrane

Enzyme release
Sperm comes into contact with zona pellucida

Acrosome swells
Vesicle/ acrosome fuses with sperm cell surface

membrane
Enzymes (e.g. acrotin) are released by exocytosis

Egg cell

Structure of a flowering plant (angiosperm)

Fertilisation in Flowering plants

Pollen grain germinates on the style, pollen tube grows

down towards ovary (growth controlled by tube nucleus) Pollen grain contains tube nucleus and generative nucleus Pollen germinates, division of generative nucleus, two haploid gamete nuclei form and move down pollen tube and enter embryo sac One fuses with egg cell (zygote) other with 2 nuclei ( triploid cell-seeds storage tissue, endosperm)

Stem Cells
Undifferentiated cell Can give rise to other types of cell Can proliferate Totipotent = can differentiate into any cell type Pluripotent = can differentiate into almost any cell

type Multipotent= is restricted into what type of cell it can become (e.g. bone marrow cell)

Stem Cell Sources

Umbilical cord blood Blastocyst Bone marrow

Brain/skin/liver cells
Addition of adult nucleus to enucleated egg cell

Reasons for stem cells research

Creates use for spare embryos from IVF, which

otherwise would be destroyed

Can obtain embryonic stem cells at eight-cell stage

without causing embryo death

Increases understanding of infertility, miscarriages

and diseases

Reasons against stem cell research

Potential life

Embryo should be considered full human status from

the moment of its creation

Not natural Stem cell research is expensive

IVF
In vitro fertilisation
Drug injected to block normal menstrual cycle steps Synthetic FSH injected superovulation

Male provides semen sample, processed to concentrate

healthiest sperms Laparoscope with ultrasound used to remove some egg cells from ovaries Mixed with sperms in dish and incubated Up to three embryos transferred back into uterus

Reasons for IVF

Enables couples with fertility problems to have

children
Enables cancer survivors to have children using

gametes harvested prior to treatment

Can avoid inherited diseases
Children will be much longed and cared for

Reasons against IVF

Not natural

May result in multiple births

Excess of unwanted children in orphanages and foster

homes
Excess embryos are potential human lives

Blastocyst

A hollow ball of cells that forms five days after

conception
Outer blastocyst cell layer goes on to form the placenta Inner cell mass goes on to form tissues of developing

embryo, pluripotent stem cells

Cloning
Produces genetically identical offspring
Somatic cell taken from donor sheep, egg cell taken

from second donor sheep Somatic cell nucleus placed inside egg cell nucleus Electric shock given to start mitosis, grown in culture Placed in surrogate, clone produced that is identical to somatic cell donor

Problems with cloning

Many attempts to produce live-born offspring has been

unsuccessful
High proportion of offspring produced by cloning have

health problems (Dolly the sheep developed arthritis at a fairly young age, had to be put down)

Gene Expression
Some genes are switched on (expressed), producing

active mRNA which is translated into proteins within the cell

However, others arent

- galactosidase

Enzyme
Produced by the prokaryote Escherichia coli Breaks down the carbohydrate lactose into glucose and

galactose

When lactose is absent

Lactose repressor molecule binds to operator gene in

the DNA
RNA polymerase cannot bind No mRNA produced Prevents transcription of - galactosidase gene

When lactose is present

Lactose molecule reacts with the regulator protein Prevents it from binding with the operator gene Lactose-metabolising enzyme is transcribed, lactose

metabolised
Once lactose is used up, repressor molecule blocks

transcription again

Regulator gene
A gene that is involved in the turning on or off the

transcription of structural genes

Operator gene
A sequence of bases when a repressor binds to it

Structural gene
A gene whose product is an enzyme, or protein that is

involved in structural functions

E.g. The gene which codes for -galactosidase

When gene expression goes wrong

FOP fibro dysplasia ossifcans progressiva Inherited, caused by gene mutation Genes that produce proteins needed to become a

specialised bone cell not switched off in white blood cells

Tissue damage wbcs produce protein, diffuses into

surrounding muscle cells, causes muscles to express other genes which turn them into bone cells

Master genes
E.g. Fruit flies Drosophila Control the development of each segment of the body Master genes discovered when mutations causing segments

not to develop properly were looked at

Produce mRNA which is translated into signal proteins Signal proteins switch on genes that produce proteins

needed for cell specialisation in each segment

Genes active in flower formation

When a plant starts to flower, cells in meristem

become specialised, forms organs that make up flower

Gene expression across meristem determines which

structures will form

Three genes (A, B and C) determine which organ type

will be produced in each area of meristem

A
Sepals Petals

Stamens Carpels

Apoptosis

Cell death When suicide genes are expressed, nucleus and

cytoplasm fragments

Polygenic inheritance
The inheritance of phenotypes that are determined by

the collective effect of several genes

These genes are often located at loci on different

chromosomes

Multifactorial
Phenotypes that are determined by several genes and

environmental factors
E.g. Skin colour

Discontinuous variation

Continuous variation

Height
Multifactorial Continuous variation Human height increasing

evidence that taller men have more children, greater movements of people (less inbreeding), better nutrition, improved health, end of child labour (more energy into growth), better heating of houses and quality of clothes (more energy into growth)

Melanin
Dark pigment in skin and hair (more melanin = darker) Made in melanocytes found in skin and hair follicle root Melanocyte activated by melanocyte-stimulating hormone

(MSH) Receptors for MSH on surface of melanocyte cells Melanocytes place melanin on melanosomes which are transferred to surrounding skin and hair cells Surround nucleus, protect DNA from harmful UV

Effect of UV on melanin
Increases amount of MSH on MSH receptors Melanocytes more active, skin darkens Hair not darker, UV light causes chemical and physical

changes to melanin and surrounding proteins in hair cells

Hair lightens as melanin is destroyed

MAOA
Monoamine oxidase A, gene that occurs on X

chromosome
Catalyses breakdown of neurotransmitter in brain

responsible for regulation of behaviour and stress

Mutation, no enzyme produced Studies suggest link between mutation and violent

behaviour

Cancer
Rate of cell division > rate of cell death

Causes growth of a tumour, often in tissue with high

mitosis rate (e.g. lung, bowel)

Caused by DNA damage (mutation) (e.g. UV light,

asbestos, carcinogens, in gametes)

Oncogenes
Code for proteins that stimulate transition from one

cell stage to the next

Continually active tumour

Tumour suppressor genes

Produce suppressor proteins, stop cycle Mutation cycle doesnt stop

Topic 4- Biodiversity and Natural Resources

Xylem
Water transport:
Lumen Waterproof Pores Support: Lignin Rings/spirals

enables vertical movement of water prevents water loss enables sideways movement of water strength strength and flexibility

Xylem

Water transportation in xylem

Water evaporates from all surfaces of plant, mostly from

leaves Water diffuses through stomata, down diffusion gradient (transpiration) Water that leaves is replaced by water from roots Water evaporation in substomatal cavities provide force needed to draw water up the plant by capillary action (surface tension) Transpiration stream stream of water passing through plant (continuous)

Phloem
Translocation movement of sugars up and down the plant,

requires energy
Sieve tube elements living, tubular cells, connected end to

end, cytoplasm is present but in small amounts, lacks a nucleus and most organelles for more space for solutes to move, cell walls made of cellulose so solutes can move laterally a well as vertically
Sieve plates formed by perforations in cell walls Companion cells controls the movement of solutes and

provides ATP for active transport in the sieve tube element.

Phloem

Sclerenchyma tissue
Dead cells

Form outer cap to vascular bundle

Impregnated with lignin Strength
Sclerenchyma

Vascular bundle
Vascular bundle

Phloem Stem

Parenchyma
Plant cells turgid, vacuoles filled with cell sap

Contents push hard against walls which push against

surrounding cells
Rigidity

Lignin
Polymer produced by plant cells to strengthen the cell wall Lignin impregnates cell wall, cells become lignified Entry of water and solutes into them become restricted Tonoplast breaks down, autolysis of cell contents (cell

contents broken down by enzymes and are lost)

Leaves an empty tube

Water

Solvent Thermal properties High surface tension and cohesion Density and freezing properties

Water - solvent
Many chemicals dissolve easily in water

Enables vital chemical reactions to occur in cytoplasm

E.g. NaCl Cl- ions attracted to +ve part of water

molecule whereas Na+ attracted to ive part

Polar molecules dissolve easily , hydrophilic

Water thermal properties

Specific heat capacity is very high

Large amount of energy needed to break hydrogen

bonds
Therefore, water heats up and cools slowly Avoids rapid temp. changes in organisms

Water- surface tension and cohesion

Hydrogen bonding strong cohesive forces

Cohesive forces between molecules surface tension

(useful, pond skaters)

Adhesion hydrogen bonds between water

molecules and cell wall

Water density and freezing properties

Water expands when it freezes

As it cools, molecules slow down, enables for max. no.

of hydrogen bonds to form

Hydrogen bonds hold molecules further apart than in

liquid ice less dense than water

Transpiration
Process in which water vapour is lost from the leaf

Diffuses through stomata, evaporates off of leaf

surface
Increase of rate of transpiration Increase wind

speed, increase temperature, increase CO2 concentration, decrease humidity

Starch

Branched chain of single glucose units

1,6 and 1,4 glucose linkages formed by condensation

reactions Composed of more than one type of molecule (amylopectin and amylose) All monomers have the same orientation

Structure and function of starch

Consists of many glucose monomers glucose is the

respiratory substrate
Large unreactive, in soluble, no osmotic effect Compact can be stored Branched increased mobilisation of glucose units

Cellulose
Straight chain of single glucose units
-1,4- glycosidic linkages formed by condensation

reactions Held together by hydrogen bonds between OH groups (micro fibrils) Alternate glucose units rotated by 180 Insoluble, tough, slightly elastic

Cellulose micro fibrils

Flexible, inelastic, tensile strength

Hydrogen bonding between OH- groups

Several layers Criss-cross arrangement

Plasmodesmata

Microscopic channels that link adjacent cells, enabling

for transport and communication to occur between them

Cytoplasm continuous between the cells

Middle lamella
Pectin layer which cements

two adjacent cells together

Dark line that is the

boundary between one cell and the next

Pits
The main channels by which water may enter and

leave the plant cell

Forms where only a single cellulose layer is deposited

in the cell wall

Pectin
Polymers of single galactose units Soluble dietary fibre, daily intake = five grams Become bound together by calcium ions, forming calcium

pectate (present in middle lamella, glues adjacent cells together) During fruit ripening, pectin broken down by pectinesterase and pectinase enzymes, fruit becomes softer as middle lamella breaks down Gelling agent, thickening agent and stabiliser in foods (e.g. in jam)

Hemicelluloses
Short, branched polysaccharide

With pectin, acts as the glue

Binds to surface of cellulose and each other Joins cellulose microfibrils together

Seeds
Adapted to protect embryo, aid dispersal and provide

nutrition for plant

Endosperm (storage)

Seed banks
Only seeds with a living embryo are taken, detected using

X-ray
Seeds are cleaned, dried
Stored at low temperatures Viability regularly tested If viability decreases, collect fresh seed for storage

Sustainability
Sustainability = resources that meet human needs

while preserving the environment

Starch is sustainable plant fibres can be regrown,

renewable, CO2 release is equal to CO2 removed when crop was grown
Oil isnt sustainable fossil fuel, non-renewable,

releases CO2 into atmosphere, non-biodegradable

Clinical trials
Animal testing (e.g. rats) legal requirement, to look Phase 1 Small dose of drug tested on a small no. of

for toxicity, well known metabolism, no harm to humans healthy individuals, check for side-effects effectiveness of drug patients

Phase 2 Tested on small no. of patients to measurement Phase 3 Double blind trial, testing on larger group of

Double-blind trial
Some patients are given the new drug whilst others are

given a placebo (e.g. sugar-coated dummy pill or old drug) Doctors and patients do not know which one is the new drug Reduces bias Can see if new drug works better than the placebo/ old drug

Three domains
Archaea

Eukaryote/ Eukarya
Bacteria

Taxonomy
The science of classification
Kingdom Phylum

Class
Order Family Genus Species
Used in the Binomial system

Remember : King Peter Called Out For Genuine Scientists

Species
A group of organisms with similar morphology,

physiology and behaviour, which can interbreed and produce fertile offspring and are reproductively isolated from other species

Habitat
A place where an organism lives

Ecosystem
A community of organisms and their surroundings

Community
The total of all populations living together in a

particular habitat

Population
A group of organisms, all of the same species, and all

of whom live together in a particular habitat

Adaptation
A process in which an organism becomes fitted to its

environment
Depends on: strength of selection pressure, size of

gene pool, reproductive rate of organism

Types of adaptation
Anatomical (e.g. ears of African elephants larger

than Asian elephant due to environment)

Behavioural (e.g. sheep ignoring sounds which are

not important to them)

Physiological (e.g. formation of sun tan when skin

is exposed to sunlight)

Genetic Diversity
The number of different alleles in a population Allele frequency

Niche
The role of a species within a community

Evolution
A change is allele frequency in a population over

time

Process of evolution
A population has some naturally occurring genetic variation with new alleles created through mutations. A change in the environment causes a change in the selection pressures acting on the population. An allele which was previously of no particular advantage now becomes favourable Organisms with the allele are more likely to survive, reproduce and so produce offspring. Their offspring are more likely to have the allele, so it becomes more common in the population.

Species richness
The total number of different species within a given

area or community
Calculated using Simpson Diversity Index:
Where

diversity

N(N-1) n(n-1)

= total no. of organisms of all species found = no. of individuals of each species

Allele
Different forms of a gene

Dominant the gene that is expressed, masks the

genotype of the recessive allele Recessive causes a phenotype only seen in a homozygous genotype

Punnet square
Shows the probability of an offspring having a

particular genotype

Homozygous
When identical alleles of the gene are present on both

homologous chromosomes

Heterozygous
When an organisms cells contain two different alleles

of a gene at a gene locus

Phenotype
The appearance of a cell or organism

Caused by a contribution of genotype

Can be affected by environmental factors

Abiotic factors
A non-biological factor that is part of the environment

of an organism (e.g. temperature)

Biotic factors
Associated with competition within a single

population or between the members of different populations.

Endemism

When an organism is exclusive to one geographical

location

Zoos
Maintain endangered species

Education
Captive breeding programmes Scientific research Reintroduction into the wild Studbooks

Genetic drift
Genetic drift = change in allele frequency overtime

In a small population, some alleles may not get passed

on by chance
Reduction in genetic variation

Inbreeding depression
In a small population, likelihood of closely individuals

mating increases
Frequency of homozygous genotypes rises, heterozygotes

lost
Offspring inherits recessive alleles from both parents Harmful effects, offspring less able to survive an reproduce,

smaller, not live as long, females produce less eggs

Experiments

Root tip squash

5mm of root tip cut, transferred to watch glass Add 30 drops of aceto-orecin stain, 3 drops HCL Heated 3-5 minutes (steam bath/Bunsen burner) Tissues transferred onto microscope slide, root tip gently pulled apart (mounted needles) More stain added, cover slip, tissue firmly squashed by thumb pressure Examined under high power microscope Safety precautions: Cut away from oneself, wear a lab coat

Mineral deficiency in plants

9 petri dishes (complete culture solution, minus

phosphorus, minus magnesium, minus nitrogen, minus potassium, minus iron, minus sulphur, minus calcium, distilled water) 15cm3 of water in each 5 healthy Lemna plants into each, add lids and incubate together for several weeks, examining twice a week Record no. of live plants, green leaves, dead leaves, length of longest root

Antimicrobial properties in plants

Crush extract (e.g. garlic or mint) in pestle with mortar,

10cm3 ethanol Filter off ethanol Add bacteria stain Bacteria need to be evenly distributed on sterile agar plate Incubate to encourage bacteria growth Measure diameter

Safety: Dont incubate at 37C (pathogens will grow),

aseptic technique (prevent contamination of pathogens)

Tensile strength of plant fibres

Soak stem (with no leaves or flowers) Extract bundles of fibres from stem and

dry them

Add same masses each time until fibre

breaks, recording the mass required

Repeat experiment, using same length,

diameter and fibre from same source case fibre snaps, be careful that the masses do not land on feet

Safety precaution: Wear goggles in