Monday, 30 January 2017

Metabolism All chemical reactions in a cell → arranged into metabolic pathways



Intermediates in these pathways are called metabolites
Catabolic reactions (e.g. respiration) release energy
Anabolic reactions (e.g. photosynthesis) use up energy
Leaf Structure
Phototropism → growth towards light
Large leaf surface area → captures more light
Thin leaves → few cell layer → more light captured by chlorophyll
Leaf mosaic increases leaf exposure to light
Internal Structure
Cuctile → reduces H2O loss by evaporation
Palisade mesophyll → chloroplast can move around cell for max light absorption
Spongy mesophyll → allows diffusion of gases through leaves
Phloem sieve tube → removes products of photosynthesis
Chloroplast
Thylakoid membrane: light-dependent → large surface area
Associated with chlorophyll, accessory pigments, ETC, enzymes
Grana: stacks of thylakoid membranes
Enclose hydrogen reservoir used in chemiosmosis
Lamella: tubular extensions forming a network between grana
Stroma: RuBP carboxylase catalyses light independent reaction
Starch granule → insoluble storage carbohydrate product of photosynthesis
Light Dependent Reaction
In Thylakoid Membrane / Granum
IMG 5-14-6
Chemiosmosis/Photophosphorylation produces ATP
//H+ from photolysis remain in thylakoid space

ETC releases energy
Used to pump H+ from stroma into thylakoid space
By active transport and electrochemical gradient
H+ conc in thylakoid space > stroma
H+ ions pass back from space between two mitochondrial membranes
Through pores which are associated with the enzyme ATP synthetase
Energy from the ETC will be used to produce ATP
Diffuse down conc gradient across thylakoid membrane
Produces ATP by photophosphorylation
Light Independent Reaction
In Stroma (Calvin Cycle)
IMG 5-14-6
Summary WITH IMG!!!!!!!!!!!!!!!
The light dependent reaction takes place in the chloroplast and is important to produce ATP and NADPH + H+. Both molecules and carbon dioxide (CO2) are needed in the light independent reaction (Calvin Cycle) to produce a hexose sugar, such as glucose, from RuBP.
Glucose is used to in the mitochondrion to produce the energy molecule ATP. NAD+ is also needed for respiration, but is not produced by photosynthesis.
PARP (Poly-ADP-Ribose-Polymerase) and PARG (Poly-ADP-Ribose-Glycohydrolase) are important if the plant is exposed to excessive stress factors (such as extreme temperatures). Note: knowledge about PARP and PARG is not required for your exam.
IMG
Picture 5-1 from Bayer research.
Genetic engineering improves crop yields,
Braving the drought [view article]
Energy Transfer
Ecological pyramids
Pyramids of numbers
Total number of organisms in a food chain at each trophic level
Highest number at the bottom (usually producers, then consumers)
Pyramid will be inverted if lots of small animals are feeding off one large plant
Pyramids of biomass
Total biomass of organisms in a food chain at each trophic level
Always pyramid shaped
Organisms multiplying rapidly may have biomass less than primary consumers
Dry mass is measured / H2O stores no energy and varies in different organisms
Pyramid of energy
Amount of energy transferred to each level of a food chain in an ecosystem
Always pyramid-shaped / no energy loss
Transfer of energy between trophic levels
Food chains and food webs
Energy is used to produce new cells / remains fixed in that organism
Energy is passed on to the next trophic level through feeding
Producers are photoautotrophs (plants)
Transduce light energy into chemical P.E. by forming new tissues and storing organic compounds (starch, glucose, lipids, proteins)
Consumers are herbivores, carnivores and omnivores
Decomposers are detritivores and saprophytes
Break down dead complex organic molecules into simple inorganic molecules
Food chains are feeding relationships and linked with each other to form complex food webs
Some organisms feed on different trophic levels / leaves and insects
Some organisms feed on different foods when they are larvae (leaves) and when they are adult (nectar produced by different flowers)
Energy transfer and efficiency
2% of light energy is converted to chemical P.E. by photosynthesis
Rest is lost reflection from leaves / heat loss / not all wavelengths are utilised / light strikes non-photosynthetic structures
10% of that are passed on along trophic levels
Rest is lost in respiration / as heat/faeces/urine
Chemical P.E. / generates heat / stores energy by forming organic matter (new cells)
Mammals are homeothermic / must maintain constant body temp
Warm environment / less energy maintains body temp / more organic matter stored / more transferred to consumer
Small organisms / large surface area:volume ratio / lose high amounts of energy
Carnivores fix organic matter more efficiently than herbivores
Herbivores feed on plants
Thus, take up cellulose and lignin / difficult to digest
Thus, more food passes through gut and is lost as faeces
Trout fix organic matter most efficiently, they are
Poikilotherms → must NOT maintain constant body temp
More energy is used to fix organic matter
Carnivores are harvested while they are still young and grow rapidly
Trout transfer most energy to consumer (human) in terms of food
[EXAM] Number of food chains is limited
Due to energy losses (at each trophic level)
In respiration/egestion/excretion/movement/as heat
(Too) little energy is left to sustain higher trophic levels/to be passed on




Ecosystem

Ecosystem
Five Kingdoms
Human Activity
Inheritance
Nutrient Cycle
Photosynthesis
Selection
Variation
Content

Metabolism
Leaf Structure
Chloroplast
Light Dependent Reaction
Chemiosmosis/Photophosphorylation produces ATP
Light Independent Reaction
Summary WITH IMG!!!!!!!!!!!!!!!
Energy Transfer
Ecological pyramids
Transfer of energy between trophic levels

DNA replicates → Identical sister chromatids form







Meiosis I

Meiosis II (same as mitosis)

Prophase

//Spindle forms
Nuclear envelope disappears
- Chromosomes shorten/thicken/condense
- Form bivalents/tetrads
- Crossing-over of homologous pairs

//Spindle forms
//Nuclear envelope disappears

Metaphase

//Spindle complete
- Bivalents at equator
- Join to spindle (fibres) via centromere

//Spindle complete
- Chromosomes at equator

Anaphase

//Cytokinesis begin
Random segregation of homologues
- Intact centromeres
- Two chromatids on one chromosome

//Cytokinesis begins
Random segregation of chromatids
- Chromatids are pulled to opposite poles
- Centromeres divide

Telophase

//Spindle disappears
//Nuclear envelope reforms
- 2 haploid cells
- Chromosomes still duplicated

//Spindle disappears
//Nuclear envelope reforms
- 4 haploid daughter cells

Principles of Mendelian Inheritance
Mendel's 1st Law of Segregation (Anaphase I and II)
During gamete formation, allele pairs (Gg) of one gene separate (G)(g)
Thus, only one of the alleles of one gene is present in a single gamete
Monohybrid inheritance (single gene - 3:1 ratio)
Recessive alleles can cause genetic disorders (e.g. cystic fibrosis)
Mendel's 2nd Law of Independent Assortment (Anaphase I and II)
Alleles for one gene segregate independently with the alleles of another gene (GgBb)
Two genes for each characteristic segregate during gamete production (GB)(gb)(Gb)(gB)
Independent assortment means either G / g can go with either of B / b
Meiosis separates alleles / homologous chromosomes
Dihybrid inheritance (two genes - 9:3:3:1 ratio) → occurs at different loci
Multiple Alleles
Human ABO group is controlled by the immunoglobulin gene I
The immunoglobulin gene has 3 alleles IA, IB, I0
These alleles code for antigen A, B, neither A/B, respectively
Only 2 alleles can be present in a diploid cell → IAIB is codominant, I0 recessive
Codominance (1:2:1)
Heterozygous allele is neither dominant nor recessive → both alleles are expressed
Sex Linkage
e.g. Haemophilia → clotting time of blood is longer than usual
Inheritance of sex in humans
Females are homogametic sex (X: or XX)
Males are heterogametic sex (XY) / Y chromosome is shorter
Involves whole chromosomes instead of individual genes
Phenotypic characteristic is inherited on X, not on Y chromosome
Thus, more common in males / females can be heterozygous (XAXB)
Thus, sex linked characteristic is never passed from father to son
Evidence from a tree diagram which suggests that a disease is
Sex linked: only seen in males / not in females
Recessive: unaffected parents
Application of Chi-Squared Test (x²) to Data Obtained
Observed Expected value
IMG 5-14-1
Degree of freedom = n - 1
Shows if differences between sets of data are significant or not
Null hypothesis states that there are no significant differences between sets of data
Small value / probability higher than the level of significance 0.05/5%
Little difference between observed and expected value
Likely to be extremes of the same population
Null hypothesis accepted
Large value / probability is less than the level of significance 0.05/5%
Significant difference between observed and expected data
Likely to be two distinct populations
Null hypothesis rejected




Ecosystem

Ecosystem
Five Kingdoms
Human Activity
Inheritance
Nutrient Cycle
Photosynthesis
Selection
Variation
Content

Stages of Meiosis
Principles of Mendelian Inheritance
Multiple Alleles
Codominance (1:2:1)
Sex Linkage
Application of Chi-Squared Test (x²) to Data Obtained

Definition of species (basic unit of classification):




Members of a species are similar (phenotype) to each other but different from other species
Similarity of organisms in same species can be
physical (branching pattern of trees)
biochemical (haemoglobin structure)
immunological (antibody against an antigen equally effective)
development (similar growth of embryos)
ecological (occupy identical ecological niche)
(Group of) organisms able to interbreed/reproduce giving fertile offspring
Each species is reproductively isolated from every other species
The five-kingdom classification of organisms
Nomenclature: Naming of organisms
Binomial: Biological name of an organism → Genus species
Taxon: Set of organisms within a category / Taxonomy / Study of biological classification
Different levels of taxons: SPECIES, GENUS, FAMILY, ORDER, CLASS, PHYLUM, KINGDOM
Most number of species on right
Most similar organisms on left
Unicellular: Single cell; Colonial: Groups of cells; Multicellular: Many cells
Autotrophs produce energy from inorganic sources
Phototrophs from photosynthesis/sunlight
Chemotrophs from simple inorganic (oxidative) processes
Heterotrophs digest and absorb organic molecules
Prokaryotae (prokaryotes)
Cell structure:
Prokaryotes, unicellular
Prokaryotes lack cytoplasmic organelles found in eukaryotes
Cell wall: murein
Nutrition: autotrophic (photosynthesis, chemosynthesis), aerobic heterotrophs
Divide by binary fission, not by mitosis
≈10μm in size (bacterial cell, filaments of blue-green bacteria)
Mutualistic nitrogen-fixing bacteria live in nodules on the root of legumes / symbiotic
Protoctista (protoctists)
Cell structure: eukaryotes, unicellular and multicellular
Cell wall: (sometimes) polysaccharide
Nutrition: autotrophic, heterotrophic
Placed in this category by exclusion / cannot be placed in any other kingdom
Slime moulds / fungi characteristics
Protozoa / heterotrophic and ingest food
Algae / photosynthesis
≈10μm (amoeba) - 1m (Laminaria / large brown alga)
Fungi
Cell structure: eukaryotes, multicellular and unicellular (yeast)
Cell wall: chitin
Nutrition: heterotrophic / saprotrophic decomposers or parasitic
Genus Penicillium
Body of a fungus is composed of thin filaments called hyphae / form a mycelium
Secret enzymes / external digestion / absorbs resulting nutrients
Erect hyphae that grow upwards from the mycelium carry their reproductive spores
Chains of spores on the erect hyphae / coloured mould visible on stored food
Break down organic matter
Plantae (plants)
Cell structure: only multicellular, eukaryotic; large vacuoles
Cell wall: cellulose
Nutrition: autotrophic (photosynthetic)
Growth is restricted to meristems (layers/patches of dividing cells)
Non-motile; adapted to land / strong tissues, leave gas exchange system, waterproofed
Eg mosses, ferns, conifers, angiosperms (flowering plants)
Plant kingdom has two different types of adults in their life cycle
Gametophytes, hidden in plant / sexual reproduction forms multicellular zygotes
Sporophytes, what we call plant / asexual reproduction to form spores that germinate into gametophytes
Gametophyte (n) → gamete (n) → fertilisation → zygote (2n) → mitosis → sporophyte (2n) → meiosis → spore (n) → mitosis → gametophyte (n)
Animalia (humans, animals)
Cell structure: eukaryotic, multicellular, no cell wall
Develop form a blastocyst / embryo
Have nervous and hormonal control systems
No cell wall!
Nutrition: heterotrophic, involving a digestive system
Are motile and grow throughout tissues (no mersitems)
Viruses → acellular → not included in classification system → pathogenic





Ecosystem

Ecosystem
Five Kingdoms
Human Activity
Inheritance
Nutrient Cycle
Photosynthesis
Selection
Variation
Content

Definition of species (basic unit of classification):
The five-kingdom classification of organisms
Prokaryotae (prokaryotes)
Protoctista (protoctists)
Fungi
Plantae (plants)
Plant kingdom has two different types of adults in their life cycle
Animalia (humans, animals)

The Hardy-Weinberg principle



The Hardy-Weinberg principle
Allele frequency → p (A) + q (a) = 1 (total gene pool)
Genotype frequency p2 (AA) + 2pq (Aa) + q2 (aa) = 1 (gene pool)
Allele frequency must be constant / population must be stable [EXAM]
Large population
Prevents large swings in frequencies
Anomalies and chance variation less significant
Random mating
Equal chance of alleles being passed on
No mutations / no immigration/emmigration / no natural selection
Prevents addition or removal of new alleles
Baseline by which to judge whether allele frequency of population's gene pool has changed
Gene pool: all the alleles in a population
Selection and change of allele frequency
Natural selection
New environmental factor affects survival rate of phenotype before reproduction
//otherwise population may become extinct
Organisms better adapted to the environment survive, reproduce, pass on their alleles/genes
Allele frequency of the advantageous gene increases
Changes frequencies of alleles in gene pool / phenotype in population
Population becomes adapted to environment
Stabilising selection
Natural selection favours "average" organisms best adapted to that environment
Organisms with extreme forms of characteristics/mutations are selected against
Heaviest and lightest babies have highest mortality
Less likely to survive, reproduce, pass on their alleles
[Graph] Normal distribution curve with thinner bell-shaped curve
Directional selection
Natural selection favours organisms with one extreme form of a characteristic
Pesticide resistance (warfarin - poison used to kill rats)
Resistant rats / need a lot of vitamin K / stabilising selection
New environmental effect: warfarin / kills normal rats
Resistant rats survived, reproduced, pass on resistance gene
New population forms by directional selection
Antibiotic resistance (penicillin resistance)
Resistant bacteria / unnecessary enzymes / selected against
New environmental factor: penicillin / kills normal bacteria
Resistant bacteria survived, reproduced, passed on resistance gene
[Graph] bell-shaped curve shifted to the right
Disruptive selection
Natural selection favours organism with two extreme forms of a characteristic
Balanced polymorphism: equilibrium of non-carriers and carriers of a characteristic caused by natural selection
Sickle-cell anaemia
Abnormal Hb makes red blood cells sickle-shaped / stick in capillaries
People homozygous for this recessive allele die before reproducing
People heterozygous for the allele should be at a disadvantage / red blood cells can sickle during exercise / allele should be selected against and rare
Where malaria is found, people heterozygous for sickle-cell have an advantage (resistant) and are likely to survive, reproduce and pass on the allele; people without the allele also have an advantage, because their red cells behave normally
Balanced polymorphism is produced / carrier is heterozygous for sickle cell
[GRAPH] Acts against the mode in a range of variation producing a bimodal distribution (two new modes) / might result in two distinct forms of the species (→morphs)
Reasons for a high incidence of a (dominant) rare disease/allele in a population [EXAM]
Allele frequency stays constant due to
Common ancestor/no migration/genetic isolation/small gene pool/in-breeding
High probability of mating with person having the allele
Reproduction before symptoms of the disease are apparent
No survival/selective disadvantage (no elimination by natural selection)
Speciation
Splitting of one into more species/transformation of one into a new species over time
Emigration/immigration moves alleles between populations
Changes allele frequency by genetic variation in meiosis
Reproductive Isolation Mechanisms
Premating
Habitat isolation / populations inhibit different local habitants within one environment
Temporal isolation / same environment but are reproductively active at different times
Behavioural isolation / two populations have different courtship patterns
Geographical separation / populations inhabit different continents, islands, �
Postmating
Gametes mortality / sperm cannot reach or fertilize egg
Zygote mortality / fertilisation occurs, but zygote fails to develop
Hybrid sterility / hybrid survives (viable) but is sterile and cannot reproduce (no meiosis)
Hybrid inviability / F1 hybrid has reduced viability: incomplete development
Allopatric speciation (geographical isolation)
Physical barrier (H2O, mountains, dessert) divides a population
Two different environments (abiotic, biotic)
Natural selection
Genetic drift changes genotype and phenotype
Two populations evolve separately
Reproductively isolated / 2 distinct species
Sympatric speciation (reproductive isolation)
Genetic isolation by mutation / reproductively isolated / but inhibit same habitat
Drift can cause further divergence between isolated gene pools
Hybridisation in plants
Offspring produced from parents of two different species
Chromosomal number doubles / polyploidy
New species is reproductively isolated by a postmating mechanisms
Can only reproduce with other polyploids, backcrosses with (2n) parents are sterile




Ecosystem

Ecosystem
Five Kingdoms
Human Activity
Inheritance
Nutrient Cycle
Photosynthesis
Selection
Variation
Content

The Hardy-Weinberg principle
Selection and change of allele frequency
Reasons for a high incidence of a (dominant) rare disease/allele in a population [EXAM]
Speciation
Reproductive Isolation Mechanisms