IB biology

Unit 1: A: Unity and diversity

Molecules

A.1.1 Water

A1.1.1 Water as the medium for life

• Life needs chemical reactions to take place to gain energy, grow, and get rid of waste.

• Water is a liquid medium that allows the chemistry of life to take place.

• The first cells on the planet probably originated in water (hydrothermal vents)

A1.1.2 Hydrogen bonds as a consequence of the polar covalent bonds within water molecules.

• Water (H2O) is made up of two hydrogen atoms covalently bound to an oxygen atom

• While this bonding involves the sharing of electrons, they are not shared equally

• The number of protons in each atom is different; oxygen atoms have 8, whilst hydrogen atoms have just 1

• Having more protons, the oxygen atoms attract the electrons more strongly

• Thus, the oxygen atom becomes slightly negative and the hydrogen atoms become slightly positive (i.e., the oxygen has a higher electronegativity)

• Covalently bonded molecules that have a slight potential charge are said to be polar

A1.1.3 Cohesion of water molecules due to hydrogen bonding and consequences for organisms.

• Cohesion:

  • This property occurs as a result of the polarity of a water molecule and its ability to form hydrogen bonds

  • Although hydrogen bonds are weak, the large number of bonds present (each water molecule bonds to four others in a tetrahedral arrangement) gives cohesive forces great strength

  • Water molecules are strongly cohesive (they tend to stick to one another)

  • Water droplets form because the cohesive forces are trying to pull the water into the smallest possible volume, a sphere

A1.1.4 Adhesion of water to materials that are polar or charged and impacts for organisms

• Result of the polarity of a water molecule and its ability to form hydrogen bonds

• Water molecules tend to stick to other water molecules that are charged or polar for similar reasons that they stick to each other

• Single hydrogen bonds are weak but a large number of bonds give adhesive forces a lot of strength

• Capillary action

  • combination of adhesive forces that cause water to bond to a surface

  • Helpful in the movement of water during transpiration and when you drink using a straw

A1.1.5 Solvent properties of water linked to its role as a medium for metabolism and for transport in plants and animals

• Properties of water molecules

  • Solvent

    • Water can dissolve many organic and inorganic substances that have charged or polar regions

    • Water is often wrongly referred to as being the universal solvent, it is good for many substances though

    • Metabolic reactions

      • Happen most readily in solutions of water - water in cells dissolves the reactants/substrates

    • Cells are mostly water so diffusion into and out of them happens most easily if the substance is in solution

    • Soluble substances such as sucrose can easily be transported around the plant in the phloem. Once dissolved in the water of the phloem, the sucrose can be moved to where it is needed by mass flow

  • Hydrophilic

    • Substances that are chemically attracted to water

    • All substances that dissolve in water are hydrophilic, including polar molecules like glucose, and particles with positive or negative charges like sodium and chloride ions

    • Substances that water adheres to are also hydrophilic

  • Hydrophobic

    • Substances that are insoluble in water

    • Molecules are hydrophobic if they DON’T have negative or positive charges and are nonpolar

    • All lipids are hydrophobic 

    • Hydrophobic molecules dissolve in other solvents like propanone

  • Transport of molecules in the blood

    • Blood plasma consists of mainly of water, plus dissolved substances which it transports

    • Glucose

      • Polar molecule=freely soluble

      • Carried by the blood plasma

  • Amino acids

    • Positive and negative charges = soluble in water

    • Carried by the blood plasma

  • Oxygen

    • Non-polar molecule

    • Barely soluble

    • Water becomes saturated with oxygen at relatively low concentrations

    • As temperature increases, the solubility decreases

    • Hemoglobin in red blood cells carry the majority of oxygen

  • Fats

    • Insoluble

    • Non-polar

    • Carried in blood inside lipoprotein complexes

  • Cholesterol

    • Insoluble

  • Lipoprotein complex

    • Fats also need to travel in the blood but they’re nonpolar

  • Sodium chloride

    • Freely soluble in water

    • carried in the blood plasma

A1.1.6 Physical properties of water and the consequences for animals in aquatic habitat

• Thermal

  • Water has a high specific heat capacity

    • Water needs a lot of heat to warm up and cools down slowly because it can store a lot of energy.

  • Water has a high boiling point and latent heat of vaporization

    • It takes a lot of heat to boil and turn into steam

    • Latent heat is the extra energy needed to change from a liquid to a gas without changing its temperature

  • Water has a high heat of fusion

    • It takes a lot of heat to melt ice into water

• Water as a coolant

  • High temperatures damage tissues and denature proteins

    • enzymes don’t work

  • It takes a lot of energy for water to change temperature

    • Heats and cools more slowly than air or land

    • Useful for animals in hot climates who can use water to cool off

  • When water evaporates it removes a lot of energy from the system

    • Cooling sensation

    • Helps aquatic animals remain at fairly constant temperatures in hot weather

• Physical states of water

  • Water is less dense as a solid  because of hydrogen bonding

• Seals

  • Buoyancy helps them stay afloat without using too much energy

  • Water has a greater thermal conductivity than air so the seal needs to insulate itself with blubber

A.1.2 Nucleic acids

A.1.2.1 DNA as the genetic material of all living organisms

• Universal code

  • Every living thing uses DNA as the way of storing information

• Some viruses use RNA or DNA but never both as their genetic material but they are not considered to be living

  • Acellular

  • Can’t do any of the life stuff without invading a cell

A.1.2.2 Components of a nucleotide

A.1.2.3 Sugar- phosphate bonding and the sugar phosphate “backbone” of DNA and RNA

• DNA nucleotides are linked together by covalent bonds formed in condensation reactions into a single strand

A.1.2.4 Bases in each nucleic acid that forms the basis of a code

• State the names of the four bases in DNA

• Purines

  • Adenine

    • Always bonds with the T

  • Guanine

• Pyrimidines

  • Thymine

  • Cytosine

    • Always bonds with G

• Purines need to go with pyrimidines because they need to balance out the lengths

A.1.2.5 RNA as a polymer formed by condensation of nucleotide monomers

• Has Uracil instead of Thymine

• Function of RNA

  • Protein synthesis

    • Making a gene into a trait

  • It takes a copy of DNA out of the nucleus because DNA is too big to leave the nuclear pores and functions as a working copy of DNA

• Working copy of the DNA

  • Made through transcription

• RNA can go to a ribosome and create a protein

A.1.2.6 DNA as a double helix made of two antiparallel strands of nucleotides with two strands linked by hydrogen bonding between complementary base pairs

• Secondary structure of DNA is the double helix

  • Two strands of DNA

• How is the double helix structure maintained?

  • Hydrogen bonds hold sections together

  • Hydrogen bonds hold complementary base pairs together

  • Complementary base pairing ensures that mistakes are not made when copying or transcribing DNA

  • Covalent bonds

    • Sugar to phosphate

    • Sugar to nitrogenous base

  • Hydrogen bonds   

    • Base pair to base pair

    • Each line to each line

    • Sections of the backbone to each other that makes it twirly

    • Nucleotides to nucleotides

• DNA double helix is formed using complementary base pairing and hydrogen bonds

• C and G have 3 hydrogen bonds

• A and T have 2 hydrogen bonds

• Sequence of bases on DNA make up genes

  • Genes are heritable factors that control specific characteristics

  • Nuclear DNA contains single-copy genes and regions of highly repetitive sequences

    • Coding DNA and non-coding DNA

A.1.2.7 Differences between DNA and RNA

A.1.2.9 Diversity of possible DNA base sequences and the limitless capacity of DNA for storing information

• The human genome project which has decoded the case sequence for the whole 6 feet of the human genome requires a data warehouse to store the information electronically

• Entirety of all the genes inside a living organism

• Divided up the mapping of the human information code between many different universities

• About 500,000 dvds worth of data in 1 gram of DNA

A.1.2.10 Conservation of the genetic code across all life forms as evidence of universal common ancestry

• Strongest evidence in the theory of evolution is in the sharing of DNA across all life forms

• All life shares descent from a Last Universal Common Ancestor (LUCA)

  • First origin of life

  • Evidence that life has a common originCells

Cells

Cells

A2.2 Cell structure

A2.2.1 Cells as the basic structural unit of all living organisms

• Cell theory:

  • All living organisms are made of cells

    • Multi or unicellular

  • Basic unit of life

  • Come from pre-existing cells

• History of Cell Theory

  • Robert Hooke:

    • Colleague of Antoine

    • Physics, chemistry and biology

    • Named the cell

    • Tense relationship between Hooke and Newton

      • Hooke accused Newton of stealing his work

  • Matthias Schleiden

    • The Cell Theory

    • Botanist

    • Discovered every plant is made of cells

  • Theodor Schwann

    • Schwann cells

    • Studied animal cells

    • Discovered all animals were made of cells

    • The Cell theory

  • Zac Jensen:

    • First microscope

  • Antoine

    • discovered bacteria (animalcules)

  • Virchow 

    • figured out that cells came from cells

  • Louis Pasteur

    • Did an experiment to prove that cells came from cells

A2.2.3 Microscope

Developments in microscopy

• Staining

  • Improve visibility

  • Uses dye or iodine

• Immunofluorescence

  • made antibodies that bind to target areas and make them more visible

• Freeze fracturing

  • Freeze the specimen using liquid nitrogen, causing it to crack, exposing the insides of the specimen. Able to reform it.

• Cryogenic electron microscopy

  • Able to see the 3D structure of proteins

  • electron gun shoots electrons through the sample

  • high-tech camera catches the image and projects it

  • Specimen can be moving

• Calculating magnification

  • Scale bar=μm, so convert ruler to μm

  • 1mm = 1000 μm so 20mm = 20,000 μm

  • To calculate magnification

    • scale bar measurement/scale bar label = 20,000 μm/ 10μm

    • magnification = 2,000 times

• Calculating actual size

  • measure the part of the image you are instructed to and divide it by the magnification

  • convert to the most appropriate units

  • measured length/magnification

  • ex: 80mm/90,000 = 8.9 × 10^-4mm OR 0.00089mm

    • converts to 0.89μm

• Examples

  • A sperm cell has a tail 50μm long. A student draws it 75mm long. What is the magnification?

    • 1. Convert to μm

      • 75mm = 75,000 μm

    • 2. Drawing length/scale bar label

      • = 75,000/50

      • = 1500x magnification

A2.2.4 Structures common to cells in all living organisms

Prokaryotes

• Simplest type of cell

• The oldest type of cell appeared about four billion years ago

• The largest group of organisms

• Unicellular organisms that are found in all environments

• No nucleus

• Eubacteria and Archaea

• Simple cell structure without compartments

• Instead of a nucleus, they have a nucleoid

• Shapes

  • Cocci = Spherical

  • Bacillus = Rod shaped

  • Spirilla = Spiral

A2.2.5 Prokaryotic cell structure

• 1. Draw and Label (know at least 5)

• 2. annotate (explain their functions)

Peptidoglycan: The protein that makes up the cell wall of a prokaryotic cell

Pili: useful for conjugation (exchange of genetic material)

Plasmids: what is being exchanged through pilids

A2.2.6 Eukaryotic cells

• Organisms whose cells have a nucleus

• All animals, plants, fungi and many unicellular organisms are eukaryotes

  

Cell Membrane

• boundary of cell

• gatekeeper

  • prevents entry or exit of molecules

  • phospholipid bilayer

  • permeable to oxygen and co2

  • impermeable to water and charged particle, must enter through special proteins embedded in the membrane

Nucleus

• has chromosomes which make up most of the DNA in a cell

• largest organelle

• double layer membrane

• mRNA, transcribed from DNA in nucleus exits through pores

• can be multiple nuclei

Golgi apparatus

• packaging and delivery of proteins

Lysosomes

• simple, membrane bound organelles full of enzymes that digest engulfed bacteria and viruses and large molecules for recycling

• Breaks down things that shouldn’t be in the cell

Mitochondrion:

• Powerhouse of the cell

• Has a smooth outer membrane and a folded inner membrane

• Where aerobic respiration occurs

• Converts sugars into ATP

Free ribosomes

• 80s sized in eukaryotes (70s size in prokaryotes)

  • Ribosomes in bacteria have different ribosomes

  • ‘s’ is a unit

  • means bigger

• Proteins synthesized for use within the cell (enzymes used in the cytoplasm)

Chloroplasts

• Site of photosynthesis in plant cells

• Stacks of thylakoids

• exist in algae as well

Vacuoles and vesicles

• Animal cells sometimes have small vacuoles (vesicles) for digestion

• Unicellular organisms have contractile vacuoles for expelling water

• plant cells have large vacuoles that hold water and food

• vesicles are small lipid sacs used for transport

• vacuoles are large

Centrioles

• Bundles of microtubules found in animal cells

• Pull stuff in the nucleus to the side

• Help cells divide

Microtubules

• Separate chromosomes in cell division and make up cilia and flagella

• What centrioles are made out of

Flagella:

• occur in bacteria

• make bacteria move

• occur in eukaryotic cells some times

Cillia:

• Used for movement

• only in eukaryotic

A2.2.7 Processes of life in unicellular organisms

• Functions of Life

• Metabolism

• Reproduction

• Homeostasis

• Response

• Excretion

• Nutrition

• Growth

Paramecium

• Heterotroph

• surrounded by cilia

• take in food through specialized membranous feeding groove called a cytostome

• food particles are enclosed in vesicles

• solid wastes are removed through an anal pore while liquid through urine

• essential gasses enter and exit the cell via diffusion

• paramecia divide asexually (fission) although horizontal gene transfer can happen via conjugation (pili)

A2.2.8 Differences in eukaryotic cell structure between animals, fungi, and plants

• Eukaryotes have been classified into kingdoms, based on key structural and functional differences

  • Animal:

    • no cell wall and undertake heterotrophic (ingestion) nutrition

  • Plant:

    • have a cell wall (cellulose) and undertake autotrophic nutrition (photosynthesis)

  • Fungi:

    • Have a cell wall made of chitin and undertake heterophic nutrition (absorption)

• Protist:

  • Any eukaryotic organism that does not belong to the animal, plan, or fungal kingdoms (hetero and autotrophic)

A2.2.9 Atypical cell structure in eukaryotes

• Red blood cells don’t have a nucleus

• Striated muscle

  • Multinucleate

  • Composed of long muscle fibres that can measure 300mm or more and are larger than regular cells

  • Atypical, as each muscle fibre contains hundreds of nuclei, and each cell does not function independently

• Aseptate fungi

  • Normal fungi have thread-like structures

  • does not have individual/discrete cells

• Phloem

  • Sieve tube element

  • Comparison cell

  • Because sieve tubes do not contain a nucleus

• Sieve tube elements

  • Found in plants and transports liquid nutrients in phloem

  • Lack a nucleus and have very few ribosomes

A2.2.10 Cell types and cell structures viewed in light and electron micrographs

• Prokaryotic cells

  • single cells, sometimes arranged in chains

  • small size—cells usually less than 5µm

  • No vacuoles

• Plant cells

  • Multicellular

  • larger size- cells usually larger than 5µm

  • Large vacuole often present

• Animal cells

  • Multicellular

  • larger size- cells usually larger than 5µm

  • No cell wall

  • only small vacuoles are present

Genes

A.3.1 Diversity of organisms

A.3.1.4 Biological species concept

• Species

  • A group of organisms that can interbreed to produce fertile offspring

  • If the species are not closely related it is often impossible for individuals of the different species to breed

  • If members of two closely related species do interbreed and produce offspring the hybrids will be sterile

    • Horse and donkey = mule

A.3.1.7 Karyotyping and karyograms

• Chromosomes of an organism become visible when cells are dividing in metaphase

• To study the chromosomes of an organism, cells are stained and placed on a microscope slide

• Then they are burst to spread the chromosomes by pressing on the cover slip

• Chromosomes often overlap each other but with careful searching, you can find a cell with no overlaps

• Stained chromosomes can be photographed

• Karyotyping

  • Prenatal test used to check for trisomy disorders

  • Extract fetal cells by amniocentesis or chorionic villus sampling

  • Culture cells and stimulate mitosis

  • Stop division in metaphase

  • Take a picture under the light microscope or scan with a computer

  • Arrange chromosomes in homologous pairs based on size, banding patterns, and centromere position

  • Check for gender (XX or XY) or trisomy disorders

A.3.1.4 Biological species concept

• Species

  • A group of organisms that can interbreed to produce fertile offspring

  • If species are not closely related it is often impossible for individuals of the different species to breed

  • If members of two closely related species do interbreed and produce offspring the hybrids will be sterile (mules)

Ecosystems

Unit 2: B: Form and Function

Molecules

B.1.1 Carbohydrates and lipids

B1.1.1 Chemical properties of a carbon atom allowing for the formation of diverse compounds upon which life is based

• Carbon forms the backbone of every organic molecule

• Carbon atoms form covalent bonds

  • Strongest type of bond between atoms

  • Stable molecules can be formed

• Carbon atoms have 4 electrons in their outer shell 

  • Allows them to form 4 covalent bonds with 4 other different atoms

• Carbohydrates

  • Have carbon, hydrogen and oxygen

  • They have a monomer (little molecules) and a polymer (a bunch of monomers chain up together that form a polymer)

  • Monomers are commonly ring shaped molecules

• Lipids

  • Made up of fatty acids

  • Common lipids

    • Triglycerides

      • Glycerol + 3 fatty acids

    • Phospholipids

      • Phosphate + glycerol + 2 fatty acids

    • Steroids

      • 4 fused hydrocarbon rings

• Proteins

  • Contain carbon, hydrogen, oxygen, and nitrogen

  • Large organic compounds made of amino acids

  • Arranged into one or more linear chains

  • Structural or part of the plasma membrane

• Nucleic Acids

  • Contain carbon, hydrogen, oxygen, nitrogen, and phosphorus

  • Chains of subunits called nucleotides

    • Base, sugar, and phosphate groups covalently bonded together

B1.1.2 Carbon production of macromolecules by condensation reactions that link monomers to form a polymer

• Condensation makes bonds

  • water releasing

  • Anabolic reactions are those which build molecules

• Hydrolysis breaks bonds

  • water splitting

  • Catabolic reactions are those which break down molecules

• Monosaccharides (sugars) are the monomers of polysaccharides (carbs)

B1.1.3 Digestion of polymers into monomers by hydrolysis reactions

B1.1.4 Form and functions of monosaccharides

• Monosaccharide 1: Glucose

  • Forms a hexagonal ring

  • Form of sugar that fuels respiration

  • Forms base unit for many polymers

  • Highly soluble in water

• Monosaccharide 2: Ribose

  • Forms a pentagonal ring

  • Backbone of RNA

  • Deoxyribose differs as shown in the diagram and forms backbone of DNA

B1.1.5 polysaccharides as energy storage compounds

• Polysaccharides

  • Polymers with more than two molecules

  • Often long and may be branched

• Cellulose

  • The tensile strength of cellulose (the basis of cell walls) prevents plant cells from bursting, even under very high (water) pressure.

• Starch (amylopectin)

  • Contains hundreds of glucose molecules

• Glycogen

  • Found in animals and some fungi

  • Stored in the liver and some muscles in humans

  • Short-term energy storage

  • Made up of repeating glucose subunits

  • Excess glucose is converted into glycogen

  • Doesn’t affect the osmotic balance of cells

    • The way the water moves in a cell

• Energy storage by lipids and carbohydrates

  • Why is glycogen needed at all?

    • Fats in adipose tissue cannot be mobilized as rapidly

    • Easily transported by the blood

      • Adipose: fat storage tissue in mammals

    

B1.1.6 Structure of cellulose related to its function as a structural polysaccharide in plants

• Polysaccharide 1: Cellulose

  • Hydrogen bonds link the molecules together

  • Straight chain - not curved

  • Basis of cell walls

    • Very strong to keep plant cells from bursting even under very high water pressure

• Polysaccharide 2: Starch

  • Amylose and amylopectin

    • Forms of starch made from repeating glucose units

  • Curved molecule

  • Only made by plant cells

  • Hydrophilic but too large to be soluble in water

  • Easy to add or remove extra glucose molecules 

    • Short term energy storage

• Polysaccharide 3: Glycogen

  • Polymer made from repeating glucose subunits

  • Made by animals and some fungi

  • Stored in the liver and some muscles in humans

  • Good for energy storage

B1.1.7 Role of glycoproteins in cell–cell recognition

• Glycoprotein

  • Enable cells to recognize another cell as familiar or foreign 

    • Cell-cell recognition (labeling)

    • Naming of the cell

      • Liver cells, skin cells, etc. 

    • Carbohydrate tails

  • Ex. Blood antigens

    • A, B, O, AB

B.1.1.8 Hydrophobic properties of water

• Substances that are insoluble in water

• Molecules are hydrophobic if they DON’T have negative or positive charges and are NONPOLAR

• All lipids are hydrophobic, including fats and oils

• Hydrophobic molecules dissolve in other solvents such as propanone (acetone)

B1.1.9 Formation of triglycerides and phospholipids by condensation reaction

• Triglycerides formation

  • Condensation reaction between glycerol and fatty acids

  • Glycerol + 3 fatty acids = triglyceride

• Example of condensation

  • smaller molecules linking up to create a larger molecule

• Lipids are glycerol combined with 1, 2, or 3 fatty acids

  • Triglycerides are lipids

B.1.1.10 Difference between saturated, monounsaturated and polyunsaturated fatty acids

• Cis-isomers

  • Natural

  • Tend to be curved because the hydrogen atoms are on the same side of the two carbon atoms

  • loosely packed

  • Liquid at room temperature

  

• Trans-isomers

  • Artificial

  • Tightly packed

  • Solid at room temp

  • Increased chance of heart disease

  • Straight

B.1.1.11 Triglycerides in adipose tissues for energy storage and thermal insulation

• Functions of lipids

  • Structure: Phospholipids are a main component of cell membranes

  • Hormonal signaling: Chemical messengers, steroids are involved in hormonal signaling (estrogen, testosterone, etc)

  • Insulation: Fats in animals can serve as heat insulators while sphingolipids in the myelin sheath can serve as electrical insulators. Fat keeps them warm

  • Protection: Triglycerides form a tissue layer around many key internal organs and provide protection against physical injury. Cushioning. (The heart)

  • Storage of energy: Triglycerides can be used as a long-term energy storage source

B.1.1.12 Formation of phospholipid bilayers as a consequence of the hydrophobic and hydrophilic region

• Cell membrane is made up of phospholipids

• Phospholipids are amphipathic

  • Have a hydrophilic head

  • Have a hydrophobic tail 

  • Phospholipid bilayer is very stable, but also flexible

  • They form double layers (cell membrane)

B.1.1.13 Ability of non-polar steroids to pass through the phospholipid bilayer

• Hormones are chemical messengers that produce a response in the target cells of an organism

• Lipid based hormones are called steroids

• Steroids are nonpolar so they can pass freely through the cell membrane

• Ex: Testosterone

B.1.2 Proteins

B.1.2.1 Generalized structure of an amino acid

• The amino group is one of the reasons why nitrogen is an important element in living things

• The carboxylic acid group contains an oxygen double-bonded to the carbon and a hydroxyl group that can be lost to form new bonds

• In proteins there are 20 amino acids that build up proteins in different ways

B.1.2.2 Condensation reactions forming dipeptides and longer chains of amino acids

B.1.2.3. Dietary requirements for amino acids

• Obtained from nutrition

  • Basic things to make amino acids come from food

• Synthesized by the body

• Essential amino acids

  • The ones you can’t make

  • Need to get them directly from food

  • Valine

• Non essential amino acids

  • Once you break down food, your body can make them 

  • Serine

B.1.2.4 Infinite variety of peptide chains

• Polypeptides are chains of amino acids joined by peptide bonds

• Proteins are versatile

• There are 20 different amino acids

  • Can be combined in any order

  • Each amino acid has unique properties

    • Some a polar (hydrophilic)

    • Some are non-polar (Hydrophobic)

    • Some are positively or negatively charged

    • Some contain sulphur

  • Properties determine how a polypeptide folds up into a protein

• Why are there infinite variety of polypeptides?

  • Because there are 20 amino acids

    • many possibilities in how they are built

    • Many different lengths we can make proteins 

• If a polypeptide has 7 amino acids there can be 20^7 possible polypeptides generate

• Proteins have different levels of structure

• Once a chain is made, it can link with other polypeptide chains

• Proteins can fold and that gives them versatility

• Fibrous proteins tend to be structures in nature which means its building material

  • Keratin (hair), collagen

  • Insoluble

    • Doesn’t want to build things that would melt in water

• Globular proteins are functional in nature

  • Transport, have functions

  • Haemoglobin, insulin

  • Soluble

• Functions of proteins

  • Digestion

  • Keep us healthy

    • immunoglobulins

  • Muscles

  • Involved in DNA stuff

  • Support to the body

  • Coordination for bodily function

  • Move essential molecules around the body

• Immunoglobulins

  • Globular protein

  • Keep us healthy    

    • Fight off viruses and bacteria

  • Antibodies

• Spider silk

  • Structural protein

  • Very strong

B.1.2.5 Effect of pH and temperature on protein structure

• Denaturation

  • What happens to a protein when subjected to extreme conditions of heat or pH

  • If you burn a protein or drop it in acid it will denature

  • Breaks down

  • Loses shape

  • Loses function

  • Sometimes in high salt or heavy metals can denature proteins

• Genes are codes for making polypeptides

• DNA is stored in the nucleus

• Polypeptide made in the cytoplasm

Cells

Cells

B.2.2 Organelles and compartmentalization

B2.2.1 Eukaryotic organelles as discrete subunits of cells that are adapted to perform specific functions.

• NOS Progress in science often follows the development of new techniques

  • Differential centrifugation

    • Separation technique that includes spinning things very quickly

    • Used for cell fractionation

      • separates organelles

    • works because different stuff has different densities

B2.2.2 Advantage of the separation of the nucleus and cytoplasm into separate compartments

• Eukaryotes have their DNA safe inside the nucleus.

• Allows for multiple linear chromosomes, which efficiently pack the whole DNA.

• In eukaryotes DNA needs to be transcribed into RNA before it can leave the nucleus.

• Allows for modification of the RNA before translation.    

• Does not occur in prokaryotes

B2.2.3 Advantages of compartmentalization in cytoplasm cells

B.2.3 Cell specialization

B.2.3.1 Production of unspecialized cells following fertilization and their development into specialized cells by differentiation

• Following fertilisation, an unspecialised zygote will divide and develop into a mass of specialised cells (early embryo) via differentiation

• This process is driven by the release of gene-regulating chemicals

(transcription factors) called morphogens

• In humans, 220 distinct highly specialised cell types have been recognised

• All specialised cells and the organs constructed from them have developed as a result of differentiation

B.2.3.2 Properties of stem cells

• Properties of stem cells

  • Undifferentiated

    • cells with the ability to divide endlessly and differentiate along different pathways

  • A single cell that can replicate itself or differentiate into many cell types

  • No job

  • All cells in an organism share the same genome

  • Some cells differentiate, that is grow and mature into different specialized cells

  • By only activating some of the genes in the genome during differentiation, cells can become specialized cells

  • Video notes

    • What?

      • cells that are undifferentiated, no job or function

    • Why are they useful?

      • potential to become all other kinds of cells

      • replaces dead cells

      • regenerative medicine

    • How many types?

      • tissue specific (adult)

        • replace existing cells in organs

        • totipotent

        • differentiate into limited types of cells

      • embryonic    

        • pluripotent

          • can differentiate into any type of cell

      • induced pluripotent

        • can become any cell in the body

        • artificially created from adult stem cells and can differentiate into many other cells

    • Why is their use controversial?

      • certain religious groups are against using potential life for research and medical research

• All cells in an organism share the same genome (entire set of genetic

instructions)

• Some cells differentiate , that is grow and mature into different specialized

cells

• By only activating some of the genes in the genome during differentiation,

cells can become specialized cells

B.2.3.3 Location and function of stem cell niches in adult humans

• sites in the body where a pool of adult stem cells are maintained in preparation for future proliferation and differentiation

• in bone marrow, hair follicles, heart, intestines, and brain

• bone marrow

  • give rise to different types of blood cells (erythrocytes - red blood cell, and leukocytes - white blood cell)

  • commonly used to treat leukemia

• Hair follicles

  • have a range of epidermal stem cells that are used for hair growth, skin innervation, vascularization and wound repair

  • treat severe burns and hair regrowth

B.2.3.4 Differences between totipotent, pluripotent and multipotent stem cells

• Totipotent

  • can differentiate into any type of cell

    • zygote

• Pluripotent

  • can differentiate into many types of cells but not all

• Multipotent

  • can differentiate into a few closely related types of cells

    • bone marrow

• Unipotent

  • can regenerate but can only differentiate into their associated cell type

    • Liver stem cells can only make liver stem cells

B.2.3.5 Cell size as an aspect of specialization

• Red blood cells need to squeeze through narrow capillaries and are small

• neurons need to transmit signals throughout the body and can be very long

• striated muscle fibres consist of fused muscle cells

• A human ovum (egg) is one of the largest cells, while sperm is very small

B.2.3.6 surface area to volume ratios and constraints on cell size

• The larger the organism, the more exchange has to take place to meet its needs.

• substances move in/out of a cell through the plasma membrane

• Big SA:V = big movement across membrane

• Small SA: Vol = little movement across membrane

• When volume increases, so does surface area, but not to the same extent

• As a cell gets larger, the SA: vol ratio gets smaller

  • if the ratio gets too small, the particles won’t be able to enter and exit the cell fast enough

B.4.2 Ecological niches

B.4.2.5 Mixotrophic nutrition in some protists

• Mixotrophs

  • plants and algae use a combination of different modes of nutrition

  • venus flytrap

B.4.2.6 Saprotrophic nutrition in some fungi and bacteria

• Saprotrophs

  • Live in or on nonliving organic matter, secreting digestive enzymes into it and absorbing digestive products

  • Digest first, then absorb

Unit 3: C: Interaction and interdependence

Molecules

C.1.1 Enzymes and metabolism

C.1.1.1 Enzymes as catalysts

• Enzymes

  • A globular protein that increases the rate of a biochemical reaction (Biological catalyst) by lowering the activation energy threshold

  • Proteins

  • Speeds up chemical reactions

    • Lowers energy threshold and activation energy

      • Minimum amount of energy needed for a chemical reaction to start

  • Amino Group (-NH 2)

    • One of the reasons why nitrogen is an important element in living things

  • Carboxylic Acid Group (-COOH)

    • Contains an oxygen double-bonded to the carbon and a hydroxyl group that can be lost to form new bonds

  • 3D protein

  • Substrates (disaccharide) go into the enzymes active site where it breaks down the molecule/substrate reacts and turns into products

C.1.1.2 Role of enzymes in metabolism

• Web of all enzyme catalyzed reactions in a cell or organism

• Usually occur in cytoplasm

  • Made mostly of water so it allows reactions to happen

• Can be extremely complex with numerous steps

• Examples

  • Cellular respiration

  • Photosynthesis

C.1.1.3 Anabolic and catabolic reactions

• Anabolism

  • Synthesis of complex molecules from simpler molecules by condensation reactions

  • Making of molecules

  • Examples

    • Protein synthesis using ribosomes

    • DNA synthesis

• Catabolism

  • Breakdown of complex molecules into simpler molecules

  • Releases energy

  • Can be achieved by hydrolysis

  • Examples

    • Digestion of food in mouth

  • Metabolism = Catabolism + Anabolism

    • Sum of all building-up + breaking-down processes within in organism

• Condensation

  • Makes bonds

  • water releasing

  • Anabolic

• Hydrolysis

  • Breaks bonds

  • Water splitting

  • Catabolic

C.1.1.4 Enzymes as globular proteins with an active site for catalysis

• Enzymes are specific

  • Enzymes can only bind with one type of substrate molecule

  • Substrate

    • Material which enzyme bonds to

  • In digestion, enzymes that break down proteins have no effect on fats or carbohydrates

  • Every reaction has their own substrate

• Enzymes are reusable

  • Enzymes are not changed or used up in chemical reactions

  • They themselves are not reactants of products

• Enzymes, substrates, and active sites

  • Substrate

    • Reactant in a biochemical reaction

  • Enzyme

    • Globular protein which acts as a catalyst for biochemical reactions

    • Has a 3D shape

  • Active site

    • Region on the surface of an enzyme to which substrates bind and which catalyses the reaction

    • Has a shape that matches with the shape of the substrate

• Lock and key hypothesis

  • The substrate and the active site match each other in two ways

    • Structurally

      • 3D structure of active site is specific to the substrate

      • Substrates that don’t fit, won’t react

    • Chemically

      • Substances that aren’t chemically attracted to the active site won’t be able to react

  • Key

    • Substrate

  • Lock

    • Enzyme

C.1.1.5 Interactions between substrate and active site to allow induced-fit binding

• The induced-fit model does a better job of explaining enzyme activity

  

C.1.1.6 Role of molecular motion and substrate-active site collisions in enzyme catalysis

• The coming together of a substrate molecule and an active site is known as a collision

• All molecules dissolved in water are in random motion, with each molecule moving separately

  • Diffusion

• Collisions are the result of the random movements of both substrate and enzyme

• The substrate may be at any angle to the active site when the collision occurs

• Successful collisions are ones in which the substrate and active site happen to be correctly aligned to allow binding to take place

• Enzyme examples

  • Lipase: breaks down lipids

  • Lactase: breaks down lactose

C.1.1.7 Relationships between the structure of the active site, enzyme- substrate specificity and denaturation

• Denaturing enzymes

  • For enzymes a change in structure means a change in the active site

  • If the active site changes shape the substrate is no longer able to bind to it

C.1.1.8 Effects of temperature, pH and substrate concentration on the rate of enzyme activity of molecular motion and substrate-active site collisions in enzyme catalysis

• Temperature, pH and substrate concentration can affect all the activity of enzymes

• Increasing temperature increases the speed of both enzyme and substrate, resulting in higher enzyme activity (more collisions)

• At an optimum temperature the rate of enzyme activity will be at its peak

• If the temperature is too high the enzyme will become denatured and will stop working

• Changing the pH will alter the charge of the enzyme, which may change the shape of the molecule

• Enzymes have an optimum pH and moving outside of this range will always result in a diminished rate of reacting

• Remember the wrong pH can denature a protein

• The reaction plateaus because it levels out

  • When all the enzymes are working as fast as they can

C.1.1.9 Measurements in enzyme-catalysed reactions

• Measuring enzyme activity

  • The method of data collection will depend on the reaction occuring

  • Most reactions are measure according to

    • The amount/rate of substrate decomposition (e.g breakdown of starch)

    • The amount/rate of product formation (e.g formation of maltose)

C.1.1.10 Effect of enzymes on activation energy

• Activation energy:

  • The initial input of energy that is required to trigger a chemical reaction

C.1.2 Cell respiration

C.1.2.1 ATP as the molecule that distributes energy within cells

• The biological molecule of energy is Adenosine Triphosphate (ATP)

• ATP is a nucleotide

C.1.2.2 Life processes within cells that ATP supplies with energy

• Muscle contraction

  • Movement

• Active transport

• Protein synthesis

• Vesicle transport

• DNA/RNA replication

• Cell signaling

C.1.2.3 Energy transfers during interconversions between ATP and ADP

• When ATP releases energy it becomes ADP

C.1.2.4 Cell respiration as a system for producing ATP within the cell using energy released from carbon compounds

• Cell respiration

  • The controlled release (steps) of ATP from organic compounds (food) in cell

C.1.2.5 Differences between anaerobic and aerobic cell respiration in humans

• Process of cellular respiration

  • Anaerobic

    • 1: Glycolysis:

      • Break down glucose into 2 carbon molecules (Pyruvate)

        • Gives us 2 ATP

      • 6C to 2×3C

      • Happens in cytoplasm

      • Doesn’t require oxygen or mitochondria

      • Need 2 ATP to get it going in the first place

      • Need NAD+

        • Helps create pyruvate

      • NAD+ turns into NADH by getting a hydrogen

    • 2: Anaerobic respiration

      • Pyruvate gets broken down

      • In cytoplasm

      • Doesn’t produce ANY ATP

      • Regenerates NAD+ for reuse in glycolysis

      • Two types

        • Lactic acid fermentation

          • Animal cells

          • Used to produce yogurt and cheese

          • Causes soreness in muscle cells

          • Pyruvate is converted into lactic acid and NAD+

          • Equation

            • Pyruvic acid + NADH = Lactic acid + NAD+

          • As the pyruvate gets broken down, it doesn’t make any ATP and it regenerates NAD+ for glycolysis

        • Alcoholic fermentation

          • Fungal cells (yeast), also plants, and bacteria

          • Used to produce alcoholic beverages and to make bread

          • Equation

            • Pyruvic acid + NADH = Ethyl alcohol + CO2 + NAD+

  • Aerobic

    • 1: Glycolysis

      • In cytoplasm

    • 2: Pyruvate into the mitochondria

      • Into the matrix

        • liquid like substance where chemicals react

      • Inner membrane

      • Oxygen needed for aerobic respiration

    • 3: Krebs cycle

      • Krebs

        • In matrix

        • Regeneration of the starting molecule (4C)

        • 4C

          • Binds with Acetyl CoA (2C) from pyruvate

        • 6C

          • Loses a carbon to become CO2

          • Loses a hydrogen (stolen from NAD+ to become NADH)

        • 5c

          • Loses another carbon and another hydrogen to FADH2 and more NADH

        • 4C

          • Back to original molecule

          • Does whole process again

            • Have 2 pyruvates = 2 spins

        • Creates 2 ATP

        • Creates 6 NADH and 2 FADH2

    • 4: ETC   

      • Hydrogens deposited from the NADH and FADH2 created

      • Proteins take hydrogens and move them into the inner membrane space

      • Makes about 32 ATP

    • 5: ATP

      • Hydrogen moving creates ATP

        • ATP synthase

• Similarities and differences between aerobic and anaerobic respiration

  

C.1.2.6 Variables affecting the rate of respiration

• Temperature

  • As temperature increases, respiration increases

  • Until too high=denaturation

• Concentration of glucose

  • As glucose increases, respiration increases

  • Until maximum level

• Concentration of oxygen

  • As oxygen increases, respiration increases

  • Until maximum level

• Concentration of wastes (CO2 or alcohol)

  • As wastes increase, respiration decreases

• Respirometer

  • A device used to measure respiration rate

    • Amount of O2 consumed

  • Cotton wool

    • Separates the living organism from the soda lime

  • A sealed container to contain living tissue

    •  Reaction chambre

      • An Alkali to absorb CO2

        • Soda lime

  • A capillary tube or pipette connected to the container

    • As the oxygen is used up, the fluid moves toward the container

  • If you can measure the movement of the water, you can measure the oxygen being consumed

C.1.2.7 Role of NAD as a carrier of hydrogen and oxidation by removal of hydrogen during cell respiration

C.1.3 Photosynthesis

C.1.3.1 Transformation of light energy to chemical energy when carbon compounds are produced in photosynthesis

• Photosynthesis and Respiration: a cycle

  

• Plant captures sun’s energy

• Plant later burns that sugar to use its energy

C.1.3.2 Conversion of carbon dioxide to glucose in photosynthesis using hydrogen obtained by splitting water

• Photosynthesis occurs in two main stages in the chloroplasts of plant cells

• In the light dependent reactions, photolysis happens

  • Result is ATP and hydrogen atoms

  • Waste product is oxygen

    • Exists through the stoma

• Light independent reactions

  • Energy from ATP and Hydrogen is used to transform CO2 into carbohydrates

    • Process known as carbon fixation

      • Enzyme doing it is rubisco

  • Happens in the stroma

    • Calvin cycle

C.1.3.3 Oxygen as a byproduct of photosynthesis in plants, algae and cyanobacteria

• Plants (leaves)

  • Green tissue in the interior of the leaf (mesophyll) contains chloroplasts

  • CO2 enters the leaf and O2 exits through the stoma

  • Stomata = bottom of leaf

  • Where most of the photosynthesis happens

• Algae

  • Eukaryotic

  • Protists (not plants)

  • Some can perform photosynthesis in chloroplasts

  • Ex: Chlorella

• Bacteria

  • Prokaryotic

  • Some can perform photosynthesis

    • They work as chloroplasts themselves

      • Similar size

      • Similar structures

  • Specialized structures

  • Very small

  • Ex: Cyanobacteria

• Chloroplasts

  • Similar to mitochondria

  • Outer and inner membrane

  • Membranous sacs

    • Thylakoids

      • Concentrated in stacks called GRANA

      • Contain chlorophyll

      • First part of photosynthesis (captures light)

  • Filled with fluid

    • Stroma

      • Where Co2 is turned into glucose

C.1.3.4 Separation and identification of photosynthetic pigments by chromatography

• Chromatography is a method of separating out different pigment molecules based on their solubility

• It can be used to separate and distinguish chlorophyll and other accessory pigments (not main ones, help out) , such as carotene and xanthophyll

• 1. Grind up leaf

• 2. Mix with ethanol

• 3. Extract pigment

• 4. Put pigment on paper/filter

• 5. Put paper in solvent

• 6. Paper absorbs solvent and separates the pigments

• We can calculate the Rf value for each pigment

  • Rf= distance travelled by the substance/distance travelled by the solvent front

  • Bigger ratio = bigger distance travelled

C.1.3.5 Absorption of specific wavelengths of light by photosynthetic pigments

• Winter

  • Colder climate, less sun, shorter days, enzyme reaction rate lessens

  • Start to shut down photosynthesis, making less chlorophyll process

    • Leaves change from green to yellow to red because of accessory pigments (pigments that cannot be normally seen when chlorophyll is active) shutting everything

C.1.3.6 Similarities and differences of absorption and action spectra

• Absorption spectrum

  • Shows percentage of light being absorbed at each wavelength by a pigment or group of pigments

  • Higher in reds and blues

  • Lowest in greens

• Action spectrum

  • Graph showing the rate of photosynthesis at each wavelength of light

  • Higher in reds and blues

  • Lowest in greens

C.1.3.7 Techniques for varying concentrations of carbon dioxide, light intensity or temperature experimentally to investigate the effects of limiting factors on the rate of photosynthesis

• Varying light intensity

  • Grows up to a certain point

  • When all chloroplasts are working at maximum capacity and adding more light doesn’t increase rate of photosynthesis

  • Rarely limiting factor

• Varying carbon dioxide concentration

  • More CO2 = more photosynthesis

  • Until all active sites of rubisco are being used up it plateaus

  • Often limiting factor

• Varying temperature

  • As you increase temperature you increase rate of reaction because of the higher amount of successful collisions until optimum temperature

  • After optimum it denatures the rubisco and rate of reaction decreases

C.1.3.8 Carbon dioxide enrichment experiments as a means of predicting future rates of photosynthesis and plant growth

• Enclosed greenhouse experiments

  • Have the advantage of allowing more variables to be controlled

• Free Air Carbon-dioxide enrichment Experiments (FACE)

  • Have the advantage of better stimulating natural conditions

Ecosystems

C.4.1 Populations and communities

C.4.1.1 Populations as interacting groups of organisms of the same species living. inan area

• Ecology

  • The study of relationships between living organisms and between organisms and their environment

• Population

  • A group of organisms of the same species living in the same area at the same time

• Ecosystem

  • A community and its abiotic environment

• Community

  • A group of populations living and interacting with each other in an area

• Habitat

  • The environment in which a spexies normally lives

• Species

  • A group of organisms that can interbreed to produce fertile offspring

C.4.1.1 Populations as interacting groups of organisms of the same species living in an area

C4.1.2 Estimation of population size by random sampling

• Population: Total number of individuals in it

• Usually impossible to count every individual in a population

• Unless it’s small and easy to find, it’s hard to determine exact size and has to be estimated

• Estimates are based on sampling

  • Small portion of something

  • Better to use multiple to increase representation of whole population

• Random sample

  • Used to ensure that every member of a population has an equal chance of being selected

  • Must avoid unconscious bias to have a truly random sample

C.4.1.3 Random quadrat sampling to estimate population size for sessile organisms

• Quadrats are square sample areas, often marked by a quadrat frame

• Repeatedly placing a quadrat frame at random positions in a habitat and recording numbers of organisms present within

• Goal is to obtain realistic estimates of population sizes

• Not very useful for highly mobile organisms

• Quadrats

  • Provide calculation of three aspects of species distribution

    • Species density

      • Number of individuals of a given species in a given area

    • Species frequency

      • A measure of the probability of finding a given species with any one throw of a quadrat in a given area

      • If a species occurs once every ten quadrants, its frequency is 10%

      • Obtained by recording the presence or absence of a species in a quadrat

      • Depends on spatial distribution and quadrat size

    • Species cover

• Transects

  • A straight line along a biologically relevant gradient

  • Ex. amount of light in a forest

• Provide calculation of three aspects of species distribution

  • Species density

    • Number of individuals of a given species in a given area

  • Species frequency

    • A measure of the probability of finding a given species with any one throw of a quadrant in a given area

    • If a species occurs once every ten quadrants, its frequency is 10%

• Species cover

  • The percentage of the whole area that the species covers

C.4.1.4 Capture-mark-release-recapture and the Lincoln index to estimate population size for motile organisms

• Motile organisms

  • Organisms that move from place to place

• Steps:

1. Capture as many individuals as possible in the area occupied by the animal population

2. Mark each individual, without making them more visible to predators

3. Release all the marked individuals and allow them to settle back into their habitat

4. Recapture as many individuals as possible and count how many are marked and how many are unmarked

5. Calculate the estimated population size by using the Lincoln index

   1. Population size = (n1 x n2)/ nm

   2. n1: # of individuals caught and marked initially

   3. n2: # of individuals recaptured

   4. nm: # of individuals recaptured with marks

• Assumptions

  • Mixing is complete

  • Marks don’t dissapear

  • Marks are not harmful or advantageous

  • It is equally easy to catch every individual

  • There is no immigration, emigration, births, or deaths in the population between the times of sampling

  • Trapping the organisms does not affect the chances of being trapped a second time

C.4.1.5 Carrying capacity and competition for limited resources

• Populations take materials from their environment

  • Food, oxygen, water, etc.

• A large population needs more resources

• Resources vary in abundance but are all limited in the amount available or rate of production

• If a resource becomes scarce, the members of the population will compete for it

• If a population grows too large, there wont be enough for some individuals

  • These individuals are likely to die, reducing the population size

  • The maximum size of a population that an environment can support is the carrying capacity

• Limiting factors can be density dependent or density independent

  • Density dependent factors

    • Will increase or decrease the carrying capacity of a population based on the size of a population

    • Ex: the amount of food available

  • Density independent factors

    • Will increase or decrease the carrying capacity regardless of the size of the population

    • Ex: temperature

C.4.1.6 Negative feedback control of population size by density-dependent factors

• Population sizes can rise or fall over time

• If a population is successful, there may be a long-term increase

  • Could happen if a population fills an ecological niche that has been unoccupied

• May be long-term decreases due to ecological changes that have negative impacts on the population

• Populations more commonly fluctuate but overall the population remains relatively stable over time, due to negative feedback control

• Density-independent factors

  • Have the same effect regardless of the population size

  • Forest fires kill plants and animals however many there may be before the fire

• Density-dependent factors

  • Have an increasing effect as the population becomes larges

  • Basis for negative feedback mechanisms because they reduce larger populations and allow smaller populations to increase

  • Competition for limited resources

  • Predation becomes more intense if a population of prey becomes denser and therefore easier to find, and less intense if the prey becomes more scarce

  • Infectious disease, parasitism, and prey infestation increases with population density because it is easier for pathogens, parasites, and pests to spread from host to host.

C.4.1.7 Population growth curves

• Populations will be prevented from undergoing uncontrolled exponential growth by limiting factors.

  • Most populations will adhere to a sigmoid growth curve

• Exponential growth phase

  • Unlimited growth of the population due to the absence of limiting factors

• Transitional phase

  • Limiting factors start influencing the rate of increase of the population

  • The number of individuals is still increasing but no longer at an exponential rate

  • Transition from exponential growth to no growth

• Plateau phase

  • The number of individuals of the population no longer increases due to limiting factors

  • Natality + immigration = mortality + emigration

  • Natural selection is taking place

  • Population has reached the carrying capacity of the environment

    • Maximum number of individuals of a species that can be sustainably supported by the environment (green line (K))

• Reproduction tends to cause exponential growth in populations

• Is an example of positive feedback

  • Breeding increases number of individuals and a larger number of individuals can breed more

C.4.1.8 Modelling of the sigmoid population growth curve

• Sigmoid population growth in natural ecosystems

  • Can be modelled experimentally using an organism like yeast

  • A small number of organisms should be introduced initially, with abundant resources for growth and no other organisms that could limit the population

  • Numbers should be monitored

• Yeast

  • A saprotrophic fungus with ovoid cells that live on surfaces where sugars are available

  • Can produce asexually by budding

C.4.1.9 A community as all of the interacting organisms in an ecosystem

• All species depend on relationships with other species for their long-term survival

• A population of one species can’t live in isolation

  • So groups of populations live together

    • Community

      • Consists of hundreds or thousands of species living together in an ecosystem

      • A group of populations that are living and interacting together in the same area

• Interactions between organisms can be complex and varied

  • Benefits one species and harms the other

    • Parasite and host

  • Both species benefit

    • Hummingbird feeds on nectar from a flower and helps pollinate it

• Feeding methods

  • Autotrophy

    • Produce own food from organic molecules

    • Producers

      • Photoautotrophy (photosynthesis, green plants, algae, and phytoplankton)

      • Chemoautotrophy (Chemosynthesis, deep sea chemosynthetic bacteria

  • Heterotrophs

    • Derive energy from other living organisms

    • Decomposers

      • Derive energy from non-living organic matter

      • Detritivores

        • Ingests nonliving organic matter (earthworms, woodice)

      • Saprotrophs

        • Lives in or nonliving organic, secreting digestive enzymes into it and absorbing digestive products (bacteria and fungi)

    • Consumers

      • Ingest organic matter which is living or recently killed

      • Primary eat producers

        • Herbivores

      • Secondary eat other consumers

        • Carnivores, omnivores

C.4.1.10 Competition versus cooperation in intraspecific relationships

• Intraspecific relationship

  • One that exists between individuals of the same species, usually within the same population of a species

  • Competition and cooperation are categories of intraspecific relationships

• Competition

  • Individuals in a population are members of the same species so they share an ecological niche and are likely to need the same resources

  • Unless a resource is abundant, there will be competition for it

  • Some individuals will be more successful and gain more of the resource, helping them survive and reproduce

  • As a result, natural selection occurs over the generations for traits that allow individuals to compete more efficiently

  • Example

    • Competition for light in plants

    • Plants compete for light that is used in leaves for photosynthesis

• Cooperation

  • Individuals in a population may cooperate in many ways

  • Extent of cooperation can vary, with less between plants and more in social animals like termites

  • Cooperative relationships have strong advantages because all individuals benefit

  • Example

    • Feeding in animals

    • Hunting in groups can increase chances of success

C.4.1.11 Herbivory, predation, interspecific competition, mutualism, parasitism, and pathogenicity as categories of interspecific relationship with communities

• Herbivory

  • The act of feeding on plants

  • An animal who eats plants

  • Primary consumers feeding on producers

  • Producer may or may not be killed

  • Example

    • Bison grazing on grasses

• Predation

  • One consumer species (predator) killing and eating another consumer species (prey) which enhances fitness of predator but reduces fitness of prey

  • Example

    • Starfish eating oysters

• Interspecific competition

  • Two or more species using the same resource, with the amount taken by one species reducing the amount available to the other species

  • Example

    • Ivy climbing up oak trees and competing for light

• Mutualism

  • Two species living in a close association, with both species benefiting from the association

  • Example

    • Mycorrhizal fungi growing into the roots of plants in the Orchidaceae family and exchanging nutrients with the orchid

• Parasitism

  • One species (the parasite) living inside, or on the outer surface of, another species (the host) and obtaining food from them

  • The host is harmed and the parasite benefits

  • Example

    • Ticks living on the skin of deer and feeding by sucking blood from it

• Pathogen

  • One species (the pathogen) living inside another species (the host) and causing a disease in the host

  • Can be cellular (fungi, bacteria) or acellular (viruses)

  • Example

    • Tuberculosis bacteria infecting badgers

C.4.1.12 Mutualism as an interspecific relationship that benefits both species

• Root nodules in Fabaceae (legume family)

  • Bacteria live with legume (lentils)

  • Bacteria gets carbohydrates and carbon compounds from plants photosynthesis

  • Lentil gets nitrogen nutrients from bacteria which gets it from the air

  • Bacteria converts nitrogen into ammonia

  • Bacteria gets nitrogen from the air and turns it into nitrate in the ground so the plant can absorb it

• Mycorrhizae in Orchidaceae

  • Fungi absorbs nutrients from the plant (starch sugar carbon compounds)

  • Fungi gives plant nitrates and phosphorus

  • Plant gives fungi food in exchange (carbohydrates)

• Zooxanthellae in hard coral (sea animal)

  • Protists live within most types of corals

  • Provide coral with food from photosynthesis

  • Corals in return provide them with a protected home and the nutrients needed for photosynthesis

C.4.1.13 Resource competition between endemic and invasive species

• A species that has been moved from its original native environment to a new environment

• Competes with native species (endemic)

• Competitive exclusion

  • Outcompete the native species because they do life better

    • No predators

    • All the things that kept them in check in OG doesn’t exist

• Example

  • Cane toad

  • South american

  • Keep sugar (cane) healthy by eating bugs

  • Balanced with predators

  • In australia they grew sugar cane

  • Beetles ate all the sugar cane

  • Introduced Cane Toad

  • High reproductive rates

  • Population boom

  • Became invasive

  • Poisonous

• Example (Spain)

  • Raccoon

C.4.1.14 Test for interspecific competition

• Interspecific competition

  • Between different species

  • Indicated but not proven if one species is more successful in the absence of another

  • This can be studied by ecologists using:

    • Laboratory experiments

    • Field experiments by random sampling

    • Field manipulation (exclusion experiments)

• Plant them together and see if it impacts growth rates, then plant them seperate and see the relationship

• Example of exclusion experiment

  • Cover the coral with cage to protect from fish

  • Compare it to other corals that are not protected

• Example 2

  • Study 2 species of barnacles living together in the same intertidal zone

  • Removed one species from rocks to see what the other one would do

  • Species that was mostly dry moved down to lower tide area

  • They were competing

C.4.1.15 Use of the chi-squared test for association between two species

• Chis squared analysis

  • x²=Σ (O-E)²/E

  • O: the frequencies observed

  • E: the frequencies expected

  • : The ‘sum of’

• Testing for the association between two species using the chi-squared test

  • 1. Define the hypothesis

    • Null hypothesis: there is no significant difference between the distribution of two species

    • Alternative hypothesis: there is a significant difference between distribution in species

  • 2. Complete the contingency table of observed frequencies using the data provided

    

  • 3. Calculate expected values using the formula

    

    • (Row total x column total)/ grand total

  • 4. Calculate the Chi-squared value

  

• • 5. Determine the degrees of freedom

    • (rows-1)(columns-1)

    • (2-1)(2-1)=1

  • 6. Compare the X² value with the critical values and validate the hypothesis

    • X²> critical value = sufficient evidence to reject the null hypothesis

C.4.1.16 Predator-prey relationships as an example of density-dependent control of animal populations

• When a predator makes a kill and consumes its prey, the prey population is one less

• In most communities, the prey population doesn’t change much overall because new prey is being born at the same time some are being killed

• Birth and death rates of predators are also mostly equal so the population also maintains stable

• Sometimes relationships don’t show this

  • Increase in prey = increase in food availability for predators = increase in predators

  • Increase in predators = more prey killed = less prey

  • Decrease in prey = decrease in food availability = less predators

  • Decrease in predators = less predation of prey = more prey

C.4.1.17 Top-down and bottom up control of populations in communities

• Top down control

  • Populations of organisms at lower feeding levels are controlled by the organisms at the top

  • Predators control population

  • Predator-controlled food web of an ecosystem

• Bottom up control

  • Driven by the absence or presence of the producers in the ecosystem

  • Changes in their population will affect the population of all the species (along the food web)

  • Plant, algae

  • No fertilizer = less snails = less frogs = less foxes

  • Resource-controlled food web of an ecosystem

C.4.1.18 Allelopathy and secretion of antibiotics

• Allelopathy

  • Phenomenon where plants, sometimes microorganisms, produce chemicals to inhibit the growth and development of nearby competing species

• Example

  • Walnut trees

  • Toxic to a variety of crop and horticultural species including corn and soybean

  • Make it hard for other things to grow around there

  • Most allelopathic plants store protective chemicals in their leaves or roots

    • When leaves drop to the ground and decompose, the release the natural toxins onto the plants below which inhibit their growth.

• Antibiotic secretion

  • The production and release of substances, termed antibiotics, that inhibit or kill other microorganisms

• Example

  • Penicillin mold

    • Antibiotic that disrupts bacterial cell wall synthesis

C.4.2 Transfers of energy and matter

C.4.2.1 Ecosystems as open systems in which both energy and matter can enter and exit

• Open system

  • Nature

  • Both matter and energy go in and out

    • Water, oxygen, sunlight, heat

• Closed system

  • No matter going in and out

  • But energy going in and out

    • Heat, light

• Isolated system

  • One that is very separated from everything and doesn’t exchange energy or matter with anything

C.4.2.2 Sunlight as the principle source of energy that sustains most ecosystems

• Energy flows in an ecosystem and must be continuously replenished over time

• The sun is the ultimate source of energy for most ecosystems

C.4.2.3 Flow of chemical energy through food chain

• Consumers

  • Ingest organic matter which is living or recently killed

• Food chains

  • Show the flow of energy through the trophic levels of a feeding relationship

  • Trophic level

    • Feeding position of an organism in a food chain

C.4.2.4 Construction of food chains and food webs to represent feeding relationships in a community

• Food webs

  • Show all of the feeding relationships within a habitat

  • Contain many food chains

C.4.2.5 Supply of energy to decomposers as carbon compounds in organic matter coming from dead organisms

• Decomposers

  • Fulfil a vital role in an ecosystem of recycling nutrients back into the system

  • Get their energy from the waste products and death of other organisms

C.2.4.6 Autotrophs as organisms that use external energy sources to synthesize carbon compounds from simple inorganic molecules

• Producers

  • Responsible for using the sun’s energy to produce useful carbon compounds

    • Amino acids, sugars, fatty acids, organic bases

  • Plants use sun to synthesis glucose from CO2

C.4.2.7 Use of light as the external energy source in photoautotrophs and oxidation reactions as the source of energy in chemoautotrophs

• Chemoautotrophs

  • Use energy obtained from the oxidation of hydrogen sulfide, methane, or ammonium, to transform carbon dioxide into organic biomass

• Examples    

  • Hydrothermal vent bacteria

  • Iron oxidizing bacteria

C.4.2.8 Heterotrophs as organisms that use carbon compounds obtained from other organisms to synthesize the carbon compounds that they require

• Complex carbon compounds such as proteins and nucleic acids are digested either externally or internally and are then assimilated by constructing the carbon compounds that are required by heterotrophs

• Examples

  • Mushrooms

C.4.2.9 Release of energy in both autotrophs and heterotrophs by oxidation of carbon compounds in cell respiration

• All organisms gain energy (ATP) through respiration

• Carbon dioxide and heat are released as byproducts of this process

• Oxidation is respiration

• Sunlight is the initial energy source for almost all communities

  • Energy flows through the food chain, being lost at each stage due to respiration

  • Nutrients are recycled

  • Energy needs to be replenished

• In an ecosystem

  • Energy flows (continuously originating from sun)

  • Nutrients are recycled (by decomposers

C.4.2.10 Classification of organisms into trophic levels

• Producers

  • Autotrophic

  • Make their own carbon compounds using external energy sources

  • Start of the food chain

• Primary consumers

  • Herbivores

  • Feed on producers

  • Second in food chain

• Secondary consumers

  • Eat primary consumers

  • Third in the food chain

• Tertiary consumers

  • Eat secondary consumers

  • Fourth in the food chain

C.4.2.11 Construction of energy pyramids

• Fat at bottom and skinny at the top because energy is lost as you ascend in trophic levels

• More prey and consumers than there are predators

C.4.2.12 Reductions in energy availability at each successive stage in food chains due to large energy losses between trophic levels

• Pyramids of energy

  • show the flow of energy between trophic levels

  • Measured in units of energy per unit area per unit time

    • kJ m^-2 y^-1

    • m: meter

    • y: year

  • Transfer of energy is never 100% efficient

• Around 90% of energy is lost between trophic levels

  • not ingested

  • not digested or assimilated

  • excreted

  • lost as heat from respiration

C.4.2.13 Heat loss to the environment in both autotrophs and heterotrophs due to conversion of chemical energy to heat in cell respiration

• Energy transfer between trophic levels is typically only 10% efficient

  • 90% is lost as heat

• Production efficiency

  • Only fraction of energy stored in food

• Energy used in respiration

  • Lost as heat

• Energy flows within ecosystem

C.4.2.12 Primary production as accumulation of carbon compounds in biomass by autotroph

• Two types of productivity

  • Primary

    • Productivity of autotrophs (plants)

    • Measured as rate of photosynthesis

  • Secondary

    • Productivity of heterotrophs (animals)

• Conservation of energy into biomass for a given period of time is measured as productivity

• The units are mass (of carbon) per unit area per unit time and (g m^-2 yr^-1)

  • Biomass accumulates when autotrophs and heterotrophs grow or reproduce

• Biomes vary in their capacity to accumulate biomass

  • Areas with higher rainfall and higher temperatures are also the ones with the highest productivity

  • Primary productivity is very dependent on rainfall and temperature

C.4.2.14 Restrictions on the number of trophic levels in ecosystems due to energy losses

• Food chains are generally short because energy transfer from one level of a food chain to the next is very inefficient

C.4.2.15 Primary production as accumulation of carbon compounds in biomass by autotrophs

• Conservation of energy into biomass for a given period of time is measured as productivity

• Units

  • Mass (of carbon) per unit area per unit time

• Biomass accumulates when autotrophs and heterotrophs grow or reproduce

• Biomes vary in their capacity to accumulate biomass

C.4.2.16 Secondary production as accumulation of carbon compounds in biomass by heterotrophs

• Amount of plant being converted into animal

• Energy available in consumers

• Measure

  • (food eaten - energy in feces) - respiration

  • NPP OR NSP = GPP OR GSP - R

    • NPP: net primary production

    • NSP: net secondary production

    • GPP: gross primary production

    • GSP: gross secondary production

    • R: respiration

C.4.2.17 Constructing the carbon cycle diagrams

C.4.2.18 Ecosystems as carbon sinks and carbon sources

• All autotrophs convert carbon dioxide (from atmosphere or dissolved in water) or into organic compounds

• Carbon Sources

  • Things that release carbon

  • Decomposition of matter produces methane(CH4)

  • Respiration in all organisms produces CO2

  • Methane CH4: burns to give Water and CO2

  • Methanogenesis: Methane is produced from organic matter in anaerobic conditions by archaeans and some diffuses into the atmosphere

  • Archaea

    • Microorganisms that share some traits of bacteria and some of eukaryotes

• Carbon Sinks

  • Things that store carbon

  • The ocean

    • CO2 will move into ocean and dissolve into the water

    • Most CO2 will combine with water to become carbonic acid

  • Limestone

    • Animals such as reef building corals and mollusks have hard parts that are composed of calcium carbonate and can become fossilized in limestone

    • Calcium Carbonate

    • An aquatic carbon sink

C.4.2.19 Release of carbon dioxide into the atmosphere during combustion of biomass, peat, coal, oil, and natural gas

• Peat formation

  • Soil-like peat forms when organic matter (dead vegetation) is partially decomposed in anaerobic conditions in waterlogged soils

  • Burns well

  • Used as a fuel source

  • If not burning its an important sink

  • Conditions

    • Low oxygen

    • Slightly acidic soils

    • Anaerobic decomposition

      • slow

      • in absence of oxygen

• Fossil fuels

  • Coal, oil, and gas formation

  • Partially decomposed organic matter from past geological eras was converted into crude oil, natural gas, or into coal

  • How coal was formed

    • Swamp 300M y/ago

      • Before dinosaurs, many giant plants died in swamps

    • Water 100M y/ago

      • Over millions of years, the plants were buried under water and dirt

    • Rocks and dirt → coal

      • Heat and pressure turned the dead plants into coal

• Combustion

  • Reaction of hydrocarbons with heat and oxygen to release energy and produce CO2 and H2O

C.4.2.20 Analysis of the Keeling Curve in terms of photosynthesis, respiration and combustion

• Shows the general increase in CO2 over the years

• Cycles every year

  • Higher in May

  • Lower in September

• Plants in summer

  • Blooming

  • High photosynthesis

  • They’re absorbing all the CO2 so there’s less in the atmosphere

C.4.2.21 Dependence of aerobic respiration on atmospheric oxygen produced by photosynthesis, and of photosynthesis on atmospheric carbon dioxide produced by respiration

• It is not possible to measure the size of carbon sinks and the fluxes between them.

• Estimates are based on many different measurements are often published with large uncertainties as a result

C.4.2.22 Recycling of all chemical elements required by living organisms in ecosystems

• Nitrogen cycle

• All nutrients recycle

Unit 4: D: Continuity and change

Molecules

D.1.1 DNA Replication

D.1.1.1 DNA replication as a production of exact copies of DNA with identical base sequence

• Cell cycle

  • Every cell has a life span

  • They divide and grow

    • Before division they need to double up genetic material (interphase)

• DNA replication

  • The production of new strands of DNA with base sequences identical to existing strands

  • Required for two life processes

    • Reproduction

    • Growth and tissue replacement in multicellular organism

      • Before a cell divides into 2 daughter cells it must replicate all of its DNA

D.1.1.2 Semi-conservative nature of DNA replication and role of complementary base pairing

• Replication happens in a semi-conservative way

  • Each time DNA is copied, the new double stranded molecule consists of one old template strand plus a new complementary strand made from previously free bases

  • Conserving exactly 50% of the OG

• Replication

  • Making a new copy of DNA

• Complementary base pairing makes it so that mistakes rarely happen

  • Makes it very unlikely that they will bond with the wrong partner

  • If it goes wrong we get a mutation

D.1.1.3 Role of helicase and DNA polymerase in DNA replication

• Helicase

  • Unwinds and unzips DNA

  • An enzyme

  • Breaks the hydrogen bonds between complementary base pairs

  • ATP is needed by helicase to move along the DNA molecule and to break the bonds

  • The two separated strands become parent/templates for the replication process

• DNA polymerase

  • Creates complementary strands

  • Uses two original strands as templates

  • Moves along the template strands, adding one nucleotide at a time

  • Reads the code (A,T,C,G) and brings in the complementary base pair to create new strand

  • Moves in a 5’ to 3’ direction

D.1.1.4 Polymerase chain reaction and gel electrophoresis as tools for amplifying and separating DNA

• Polymerase chain reaction (PCR)

  • Amplifying small amounts of DNA

  • Useful for testing crime scene samples of blood, semen, hair, etc.

  • Process artificially recreates DNA replication

  • Taq DNA polymerase

    • Artificial way we do replication

    • Comes from heat-resistant bacterium, Thermus aquaticus, that lives in hot springs

      • Can resist denaturation at high temperatures required to separate DNA strands in PCR

      • Copies up to 1000 nucleotides per minute

• PCR process

  • 1: Denaturation

    • DNA sample is heated to 95 C to break hydrogen bonds and separate it into two strands

  • 2: Annealing

    • DNA sample is cooled to 54 C which allows primers to attach to opposite ends of the target sequence

    • Primers: signal molecules, guide the Taq polymerase to attach to the DNA fragments and start replication process

  • 3: Elongation

    • Taq polymerase sees primers and starts copying the strands

  • One cycle of PCR creates two identical copies of the DNA sequence

  • Cycle usually repeats 30 times to make larger amounts of DNA

• Gel electrophoresis

  • DNA samples are taken and amplified with PCR

  • Restriction enzymes cut DNA into fragments at specific base sequences in each samples

    • Different length fragments move different ways along the gel, the smaller ones go really far, ends up giving you a pattern

  • A fluorescent marker binds to a triplet in the DNA fragments

  • Added to a gel electrophoresis chamber, the electric current is passed through which pushes the fragments along,

    • Different length fragments move differently

    • Smaller fragments move farther

    • Larger fragments stay closer to the origin

  • DNA is negatively charged so it moves towards the positive side of the machine

D.1.1.5 Applications of polymerase chain reaction and gel electrophoresis

• DNA profiling

  • Forensic investigations

    • Straightforward, just look for a full match between the DNA sample and the potential suspects

  • Paternity investigations

    • Since offspring inherits a mix of DNA from parents, the child will show bands unique to each parent

    • Each band in the child’s profile must match to either a band in the mother’s profile or a band in the father’s profile

D.1.2 Protein synthesis

D.1.2.1 Transcription as the synthesis of RNA using a DNA template

• Transcription is the synthesis of RNA, using DNA as a template

• Because RNA is single stranded, transcription only happens along one of the two strands of DNA

• Transcription happens in the nucleus

• RNA polymerase is the enzyme that catalyzes the reaction

• 3 main types of RNA

  • Messenger RNA (mRNA): a transcript copy of a gene used to encode a polypeptide

  • Transfer RNA (tRNA): a clover leaf shaped sequence that carries an amino acid

  • Ribosomal RNA (rRNA): a primary component of ribosomes

D.1.2.2 Role of hydrogen bonding and complementary base pairing in transcription

• Transcription

  • Ribonucleotide triphosphates (NTP) bond to template strand

  • Phosphodiester bond between NTP

  • Used to copy the base sequence of one of the two strands in a DNA molecule

  • The DNA strand that needs to be copied is called the sense strand

    • The other strand which has the complementary base sequence to the sense strand is called the antisense strand.

      • Transcription of this strand results in a strand of RNA with the same base sequence as the sense strand of DNA except that uracil is replaced with thymine

• The copying of base sequences during transcription depends on complementary base pairing

• Each nucleotide added to the growing RNA strand by RNA polymerase must have a base that is complementary to the corresponding base on the template DNA strand

• Pairs of bases are complementary because of the hydrogen bonds formed with each other but not with other bases

• Transcription occurs in the nucleus, once made, the mRNA moves to the cytoplasm (where translation can occur)

D.1.2.3 Stability of DNA templates

• When RNA splits DNA into single strands and uses the template strand to guide transcription, there shouldn’t be any changes to the base sequence of the DNA

• After transcription the two DNA strands pair up again with each base linked by hydrogen bonds to its complementary base on the opposite strand

• The two strands are only parted for a little bit because the RNA polymerase moves along the gene, so the bases are only briefly vulnerable to chemical changes that would cause mutation

• Stability is essential because they may be transcribed many times during the life of a cell

  • Needs to last a long time

D.1.2.4 Transcription as a process required for the expression of gene

• Purpose

  • Genes are instructions for proteins or messages

  • The cell needs to take this instruction and carry it out

  • One gene is responsible for one protein

  • In transcription

    • The gene is converted into a mRNA messenger which is posted to the ribosomes

    • The ribosomes then translate the message into a polypeptide

    • The sequence of amino acids is determined by the gene, and in turn determines the properties of the finished protein

D.1.2.5 Translation as the synthesis of polypeptides from mRNA

• To make a specific polypeptide, amino acids must be linked together in the correct sequence.

• A typical polypeptide is a chain of hundreds of amino acids

  • Could be any of the 20

• Information needed to make a polypeptide is in the base sequence of an RNA molecule copied from a gene by transcription.

  • Information is held as a genetic code in RNA

  • Code is translated to make an amino acid sequence

  • This process is called translation

    • Happens in the cytoplasm, in eukaryotes, RNA is made in nucleus and then passed out to the cytoplasm

    • The RNA with the information for making a polypeptide travels from one place to another in a cell, so it’s called mRNA.

    • Translation is the synthesis of polypeptides from mRNA

D.1.2.6 Roles of mRNA, ribosomes and tRNA in translation

• mRNA has a site to which a ribosome can bind and a sequence of codons that specifies the amino acid sequence of the polypeptide

  • start and stop codons which indicate where translation should begin and end

  • One mRNA molecule can be translated many times but is broken down if it becomes damaged or if more copies of the polypeptides it codes for are not required

• tRNA translates the base sequence of mRNA into the amino acid sequence of a polypeptide.

  • tRNA molecules have an anticodon at one end which consists of three bases

  • they have an attachment point at the other end for the amino acid that corresponds to the anticodon

  • Each type of tRNA molecule has a distinctive shape that is recognized by a dedicated activating enzyme, which attaches the correct amino acid onto the tRNA

• Ribosomes are complex structures that have a large and a small unit.

  • Small subunit has a binding site for mRNA

  • Large subunit has three binding sites for tRNA and a catalytic site that makes peptide bonds between amino acids, to assemble the polypeptide

D.1.2.7 Complementary base pairing between the tRNA and mRNA

• Translation depends on complementary base pairing

• The three bases of an anticodon on tRNA must be complementary to the next three bases of the next codon on mRNA for the tRNA to be able to bind to the ribosome and deliver its amino acid.

D.1.2.8 Features of the genetic code

• DNA is well suited to data storage because it can hold long sequences of bases which can be arranged in any order and accurately copied

• Data commonly stored in DNA base sequences is amino acid sequences of polypeptides and is stored in a coded form

• There are four different bases and 20 amino acids, so one base cannot code for one amino acid

  • There are 16 combinations of two bases, which still isn’t enough,

  • Living organisms use a triplet code, with groups of three bases coding for an amino acid

    • 64 combinations of three bases

    • Sequence of three bases on mRNA is called a codon

    • Codon AUG acts as the start codon in translation

    • Codon UGA acts as the stop codon in translation

• Genetic code is universal

  • Used by all living organisms and viruses

• Genetic code is degenerate

  • Different codons can code for the same amino acid

    • GUU and GUC both code for valine

D.1.2.9 Using the genetic code expressed as a table of mRNA codons

• Look at slides

D.1.2.10 Stepwise movement of the ribosome along mRNA and linkage of amino acids by peptide bonding to the growing polypeptide chain

1. An activating enzyme with an active site that fits the tRNA binds to it and attaches the specific amino acid corresponding to the anticodon of the tRNA

2. The tRNA carrying a single, attached amino acid binds to the A site on the ribosome, with its anticodon linked by complementary base pairing to the next codon on mRNA

3. The single amino acid on the tRNA is linked to the end of the growing polypeptide by formation of a peptide bond. The tRNA is now holding the whole of the growing polypeptide

4. tRNA moves from the A to the P site as the ribosome moves along the mRNA by one codon. The anticodon of the tRNA is still paired with the codon on the mRNA

5. The polypeptide held by the tRNA is transferred to another tRNA that has arrived at the A site

6. The tRNA moves from the P site to the E site (exit) as the ribosome moves along the mRNA by one more codon, causing the anticodon of the tRNA to separate from the codon on the mRNA and the tRNA to separate from the ribosome

7. Cycle starts again with an amino acid being linked to a tRNA

D.1.2.11 Mutations that change protein structure

• Mutation

  • A change to the base sequence of a gene

  • A single base substitution changes the codon to another which may code for a different amino acid.

• Sickle cell disease

  • Change due to a base substitution

  • Mutated gene codes for the beta-globin polypeptide in haemoglobin

CellsCells

D.1.3 Mutation and gene editing

D.1.3.1 Gene mutations as structural changes to genes at the molecular level

• Gene mutations

  • A permanent change in the base sequence of DNA

  • It is the cumulative effects of millions of mutations and natural selection that have allowed all organisms to evolve from simpler ancestors

  • Not all mutations cause disease

  • Environmental factors can increase the probability of this happening

    • radiation

  • Happen randomly

• Substitution

  • One base in the coding sequence is replaced by a different base

  • Adenine for Cytosine, Guanine, or Thymine

• Insertion

  • A nucleotide is inserted, so there is an extra base in the sequence of the gene

  • More major change

• Deletion

  • A nucleotide is removed, so there is one base less in the sequence of the gene

D.1.3.2 Consequences of base substitutions

• In non-coding DNA between genes on chromosomes, base substitutions are unlikely to have any effect. Only changes to the coding sequences of genes cam affect the amino acid sequence of polypeptides

• Same-sense mutations are base substitutions that change one codon for an amino acid into another codon for the same amino acid

• Nonsense mutation change a codon that codes for an amino acid into a stop codon

• Mis-sense mutations alter one amino acid in the sequence of amino acids in a polypeptide. May not have much effect if the new amino acid has a similar structure

D.1.3.3 Consequences of insertions and deletions

• Frameshift Mutation

  • When there is an insertion or deletion of nucleotides that is not a multiple of three

  • If 3 nucleotides are inserted it will insert an additional amino acid

  • Most detrimental mutation

  • Alters amino acid sequence

  • Can change the stop codon to lengthen or shorten the polypeptide

D.1.3.4 Causes of gene mutations

• Radiation

  • Increases the mutation rate if it has enough energy to cause chemical changes in DNA

  • Gamma rays, X-Rays, alpha particles from radioactive elements such as radon are mutagenic

  • Short wave UV radiation in sunlight is also mutagenic

• Chemical substances

  • Mutagenic

  • Polycyclic aromatic hydrocarbons and nitrosamines found in tobacco smoke

    • Carcinogens

  • Mustard gas is also mutagenic

D.1.3.5 Randomness in mutation

D.1.3.6 Consequences of mutation in germ cells and somatic cells

• Germ cell mutations can be inherited

  • entire organism carries the mutation

• Somatic cell mutations can lead to cancer

  • not heritable

  • patch of organism carries mutation

D.1.3.7 Mutation as a source of genetic variation

• So evolution can happen

Cells

D.2.1 Cell and nuclear division

D.2.1.1 Generation of new cells in living organisms by cell division

• All organisms need to produce new cells

  • growth, maintenance and reproduction

• They do this by cell division

  • One cell divides into two, the cell that divides is called the mother cell and the result are two daughter cells

  • Mother cell disappears as an entity in the process, unlike reproduction by animal parents

• Cells need to divide so they don’t get too big

D.2.1.2 Cytokinesis as splitting of cytoplasm in a parent cell between daughter cells

• Cytokinesis

  • Cytoplasm of a cell is divided between two daughter cells

• In animal cells

  • All done by contractile proteins

    • Form up in the middle and release material that grabs onto opposite ends of the cell membrane and drag it together causing a cleavage furrow

    • When the cleavage furrow reaches the centre of the cells it is pinched apart to create two daughter cells

• In plant cells

  • Done by cell plate

  • Small pockets of cellulose are delivered to the centre by vesicles which makes the cell plate

    • Cell plate continues to develop until it reaches the cell membrane and completes division of the cytoplasm and forms two daughter cells

D.2.1.3 Equal and unequal cytokinesis

• Oogenesis

  • Production of a mature egg characterized by an unequal cytokinesis

• Budding in yeast

  • Yeast cells reproduce asexually by budding

D.2.1.4 Roles of mitosis and meiosis and eukaryotes

• Growth

  • Multicellular organisms increase in size by increasing their number of cells through mitosis

• Asexual reproduction

  • Certain eukaryotic organisms may reproduce asexually by mitosis

• Tissue repair

  • Damaged tissue can recover by replacing dead or damaged cells

• Embryonic development

  • A fertilized egg (zygote) will undergo mitosis and differentiation in order to develop into an embryo

• Mitosis

  • Human diploid number is 46

    • Haploid is 23

      • Gametes are haploids because they contain half the genetic material

  • Continuity

  • Used to produce genetically identical cells

  • Cells produced using mitosis have the same number of chromosomes as the parent cell

  • Have the same genes as the parent cell, so mitosis maintains the genome

    • Ensures that every cell in a multicellular organism has all the genes it needs

    • Ensures that the cells in an individual are genetically identical, preventing tissue rejection

  • Allows a successful genome to be inherited without changes by offspring in asexual reproduction

• Meiosis

  • Change

  • Used to halve the chromosome number from

D.2.1.5 DNA replication as a prerequisite for both mitosis and meiosis

• Interphase

  • The parts of the cell cycle that don’t involve cell division

  • Longest part of the cell cycle

  • Protein synthesis and DNA replication

  • G1

    • Increase the volume of the cytoplasm

    • Organelles produced

    • Protein synthesized

  • Synthesis

    • DNA replicated

  • G2

    • Increase the volume of cytoplasm

    • Organelles produced

    • Proteins synthesized

• Mitosis

  • Prophase

    • DNA supercoils, chromatin condenses and becomes sister chromatids, which ware visible under a light microscope

    • The centrosomes move to opposite poles of the cell and spindle fibres begin to form between them

    • The nuclear membrane is broken down and disappears

  • Metaphase

    • Spindle fibres from each of the two centrosomes attach to the centromere of each pair of sister chromatids

    • Contraction of the microtubule spindle fibre cause the sister chromatids to line up along the centre of the cell

  • Anaphase

    • Continued contraction of the microtubule spindle fibres cause the separation of the sister chromatids

    • The chromatids are now referred to as chromosomes

    • Chromosomes move to the opposite poles of the cell

  • Telophase

    • The chromosomes uncoil and decondense to chromatin and are no longer visible under light microscope

    • Chromosomes arrive at the poles

    • Microtubule spindle fibres disappear

    • New nuclear membranes reform around each set of chromosomes

    • Cytokinesis begins

D.2.1.6 Condensation and movement of chromosomes as shared features of mitosis and meiosis

• DNA supercoiling

  • It bundles up

  • It twists itself and when done a lot it does supercoiling

  • Done because it’s so long and needs to be managed

  • Done by wrapping the double helix of DNA around histone proteins to form nucleosomes, and linking the nucleosomes together

• Sister chromatids

  • duplicated chromosomes attached by a centromere

• Centromere

  • Part that links the sister chromatids

• Centrioles

  • Organise spindle microtubules

  • Release the fibres (spindle fibres) that divide the chromosomes

• Spindle fibres

  • Help separate the chromosomes

• Two centrioles

  • Centrosome

D.2.1.9 Meiosis as a reduction division

• Meiosis

  • Process that divides one diploid (2n) eukaryotic nucleus to form four haploid (n) nuclei

• The original 2n cell is divided twice in this process

• Meiosis I

  • Prophase I

    • Crossing over

    • Homologous chromosomes pair up and condense

    • Nuclear membrane breaks down

  • Metaphase I

    • Homologous chromosomes line up

    • Microtubules from the two poles link to different homologous chromosomes in each pair

  • Anaphase I

    • Homologous chromosomes separate from each other and pulled to opposite ends

  • Telophase I

    • Two haploid nuclei are formed and both prepare for second division of meiosis

• Meiosis II

  • Prophase II

    • Chromosomes move to opposite ends of the cell

  • Metaphase II

    • Spindle fibres align the chromosomes along the cell equator

  • Anaphase II

    • Sister chromatids are pulled apart from each other and move to opposite sides of the cell

  • Telophase II

    • Nuclear membranes form again around the chromosomes

    • Spindle fibres break apart

    • Cell undergoes cytokinesis

    • End up with 4 haploid cells

• Since the chromosome number is halved, meiosis is called a reduction division

D.2.1.10 Down syndrome nondisjunction

• Nondisjunction

  • Chromosomes fail to split properly in Anaphase I or II

    • Anaphase I: Affects all the gametes

    • Anaphase II: can affect all or some

  • A pair of homologous chromosomes might move to the same pole in Anaphase I, or both chromatids of one chromosome might move to the same pole in Anaphase II

  • Result is the production of a gamete with an extra chromosome or a missing chromosome

  • Trisomy

    • Extra chromosome

  • Monosomy

    • Missing chromosome

  • Ex: Down syndrome

    • Person having three copies

      

      of chromosome #21

    • Trisomy on the 21st chromosome

D.2.1.11 Meiosis as a source of variation

• The orientation of the bivalents (homologous pairs) is random and affects which of the homologous chromosomes and will be assorted into which sex cell

  • 2²³ ways the 23 pairs could arrange at this stage, giving more than 8 million possible ways of dividing the bivalents

  • In metaphase I

• Randomly you get 23 from mom and 23 from dad because of sexual reproduction

• Crossing over

  • In prophase

  • When a sister chromatid from each of the homologous chromosomes form a junction at a random point to exchange genes

  • They synapse (homologous chromosomes pair up)

  • Results in chromatids with new allele combinations

  • Chiasma

    • Kind of like a centromere

    • Allows for the exchange of genetic material

  • In asexual reproduction

    • Offspring have same chromosomes as parents and are genetically identical

    • Stickbugs

  • In sexual reproduction

    • Differences between parent and offspring chromosomes which creates genetic diversity

    • The fusion of a male and female gamete to form a zygote results in a mixture of alleles that has likely never existed before

Organisms

D.3.2 Inheritance

D3.2.1 Production of haploid gametes in parents and their fusion to form a diploid zygote as the means of inheritance.

• In meiosis each haploid gamete gets only one of the two alleles that a parent has for eac gene

• Which allele each sex cell receives is random

D.3.2.2 Methods for conducting genetic crosses in flowering plants

• Gregor Mendel

• Established pure breeding lines by breeding one trait until only that trait came out

  • and did cross breeding to see how genetics worked

• He noticed that certain versions of a trait show up when crossed with a purebred plant

  • Dominant versions of the trait

• Other versions of the trait only showed up in hybrid crosses or when the dominant trait was not present in either parent

  • Recessive traits

• Monohybrid cross

  • Using a punnett square

  • Crossing a single trait

D.3.2.3 Genotype as the combination of alleles inherited by an organism

• Phenotype

  • The outward characteristic

  • The trait you’re interested in

    • Green, tall, etc.

  • Alleles of the gene

    • Different versions of the trait

  • Expression of alleles of a gene carried by an organism

• Genotype

  • Combination of alleles of a gene carried by an organism

• Alleles

  • Different versions of a gene

  • Dominant alleles: capital letter

  • Recessive alleles: lowercase letter

• Homozygous dominant

  • Two copies of the same dominant allele

  • AA

• Homozygous recessive

  • Two copies of the same recessive allele

  • Only expressed when both are recessive

  • aa

• Codominant

  • Pair of alleles which are both expressed when present

• Heterozygous

  • Having two different alleles

  • The dominant allele is expressed

  • Aa

• Gene Loci

  • Specific positions of genes on a chromosome

• Carrier

  • Heterozygous carrier of a recessive disease-causing allele

• Gametes are haploid

  • Contain one copy of each chromosome and therefore one allele of each gene

  • When the male and female gametes fuse in fertilization, the resultant diploid cell — called the zygote — will have two alleles of each gene, one from each parent

D.3.2.4 Phenotype as the observable traits of an organism resulting from genotype and environmental factor

• Genotype

  • Organism’s genetic information

  • BB: homozygous dominant

  • Bb: heterozygous

  • bb: homozygous recessive

• Phenotype

  • The outward characteristic

  • The trait you’re interested in

  • Green, tall, etc.

  • Alleles of the gene

  • Different versions of the trait

  • Expression of alleles of a gene carried by an organism

D.3.2.5 Effects of dominant and recessive alleles on phenotype

• Dominant alleles always show their encoded trait when they present in an organism

  • Code for functional proteins

• Recessive alleles only express their encoded traits when no other alleles present

  • Code for non-functional proteins

• Codominant alleles can have joint effects if both are present

D.3.2.6 Phenotypic plasticity as the capacity to develop traits suited to the environment experienced by. an organism, by varying patterns of gene expression

• Phenotypic plasticity

  • The capacity of an individual organism to alter its behavior, physiology, and/or morphology in direct response to changing environmental conditions

  • Many genetic diseases in humans are due to recessive alleles of autosomal genes

  • Autosomal gene

    • A gene whose loci is on an autosome (not a sex chromosome)

  • Genetic disease

    • Disorder caused by a gene

    • A muted allele causes a protein to be altered with impairs normal function

    • Most disease causing alleles are recessive

    • Individuals can be carriers for these genetic disorders but are not affected

D.3.2.7 Phenylketonuria as an example of a human disease due to a recessive allele

• Autosomal gene is a gene who’s loci is on an autosome

• Genetic disorder

  • Disorder caused by a gene

• Huntington’s disease

• PKU

  • If you have PKU phenylalanine cannot be converted to tyrosine

    • Amino acid

    • Builds up in body

    • Brain seizures

D.3.2.8 Single nucleotide polymorphisms and multiple alleles in gene pools

• A gene consists of a length of DNA that can be hundreds or thousands of bases in length

• Alleles of a gene often differ only very slightly in their base sequence

• These base differences are called Single Nucleotide Polymorphism (SNIPS)

  • base pairs in genes that give rise to different alleles

D.3.2.9 ABO blood groups as an example of multiple alleles

• In humans, ABO blood group is determined by a single gene on chromosome #9 and is an example of multiple alleles (and codominance)

D.3.2.10 Incomplete dominance and codominance

• Incomplete dominance

  • Some genes have pairs of alleles where neither allele is fully dominant over the other

  • A mix of both come out

  • Red and white but neither is dominant, you get pink

• Codominance

  • Some Both alleles are dominant

  • ABO blood group is an example

  • Blood group AB is a dual phenotype and is not intermediate between group A and B

  • Different blood groups have different glycoproteins

D.3.2.11 Sex determination in humans and inheritance of genes on sex chromosomes

• The sex chromosomes are non-homologous

• There are many genes on the X chromosome which are not present on the Y chromosome

• Sex linked traits are those which are carried on the X chromosome in the non-homologous region

• They are more common in males

• Haemophilia

• Color blindness

D.3.2.12 Haemophilia as an example of a sex-linked genetic disorder

• A recessive X-linked mutation in people with haemophilia results in globular proteins called clotting factors not being produced

• The clotting response to injury and bleeding does not work and the patient can bleed to death

• Potential treatment

  • Injections of clotting factors produced industrially through gene transfer

  • 1. Find gene for healthy human clotting factors

  • 2. Insert into sheep milk gene in sheep embryos

  • 3. Extract clotting factor from sheep milk

  • 4. Purify and produce injections for patients

D.3.2.13 Pedigree charts to deduce patterns of inheritance of genetic disorders

• Used to trace family histories and deduce genotypes and risk in the case of inherited gene-related disorders

• Sex of person

  • Square: male

  • Circle: female

• Presence of trait

  • Shading: affected

  • Unshaded: unaffected

  • Half shaded: carrier

  • Crossed out: dead

• Rows represent generations

• Sex linked, recessive

  • Trait can skip generations

  • Males are predominantly affected

• Autosomal recessive

  • Trait can skip generations

  • No major sex-bias in expression

• Autosomal dominant

  • Trait can’t skip generations

  • No major sex-bias in expression

D.3.2.14 Continuous variation due to polygenic inheritance and/or environmental factors

• Polygenic inheritance

  • Many genes making up one trait

• Skin color

  • Continuous variation in the phenotype

  • 4 separate genes

  • You get a mix and blend of skin colors

D.3.2.15 Box-and-whisker plots to represent data for a continuous variable such as student height

• Displays:

  • Outliers

    • 1.5 x IQR

  • Minimum

  • Maximum

  • 1st Quartile

  • 3rd Quartile

  • Median

D.4.3 Climate change

D.4.3.1 Anthropogenic causes of climate change

• Greenhouse effect

  • CO2 and other gases in the atmosphere trap heat, keeping the earth warm

• Greenhouse gases

  • Water vapour

  • CO2

  • Methane

  • Nitrous oxide

• Elevated levels of greenhouse gases are strongly correlated with an enhanced greenhouse effect

  • CO2, methane, water vapor, and oxides of nitrogen increase, more radiation is reflected back to earth instead of being lost to space

• Anthropogenic

  • et Human caused

• Increase in global temperature as CO2 increases

  • Ice core data over the last 400,000 years

  • Temperature shows greater variation than CO2

  • Most but not all rises and falls in CO2 have correlated with temperature rises and falls

• Link between human emissions and atmospheric levels of CO2

  • Strong correlation between human emissions and atmospheric levels of CO2

  • As atmospheric CO2 levels have increased the amount of CO2 absorbed by carbon skinks has increased

• Climate science controversy

  • Some claim human actions are not main reason for recent increases in carbon and global temperatures

• Anaerobic decomposition

  • Methane formation

• Aerobic decomposition

  • CO2

D.4.3.2 Positive feedback cycles in global warming

• Climate feedback loops can be positive or negative

• Example: Albedo

  • Measure of how reflective a white surface

  • Ice has a high albedo and therefore arctic regions can reflect back a lot of the suns radiation and keep the earth cool

  • A reduction in this ice, therefore leads to a reduction in cooling

• Example: decomposing organic matter

  • Once exposed due to melting of permafrost can lead to an increase in methane emissions as a result of decomposition

  • Its thawing releases methane which warms up the earth which melts the permafrost and it becomes a cycle

• Example: forest fire feedback loop

  • High temp = more forest fires

  • More forest fires = more CO2 in atmosphere

  • More CO2 in atmosphere

  • = warmer earth

  • Warmer earth = dryer forest

  • Dryer forest = more forest fires

D.4.3.3 Change from net carbon accumulation to net loss in boreal forests as an example of a tipping point

• Boreal forest

  • Originally carbon sink

• Warmer temperatures and decreased winter snowfall has led to increased incidence of drought and reductions in primary production in taiga, with forest browning and increases in the frequency of forest fires, which result in legacy carbon combustion

• Tipping point

  • System becomes destabilized and can’t come back to its original state

  • Point of no return

  • At some point the slightest push makes it fall off the edge and becomes irreversible

D.4.3.4 Melting of landfast ice and sea ice as examples of polar habitat change

• Emperor penguins

  • Make babies on big sheets of ice that extend into ocean

  • Sheets are melting so there’s less ice

  • Over years colonies decide to not make babies

  • Penguin population reduced

• Walrus

  • Rest and catches its breath on ice and can’t do that with no ice

• Polar bears

  • Need ice to hunt and feed themselves

D.4.3.5 Changes in ocean current altering the timing and extent of nutrient upwelling

• Temperature is an important factor for driving the currents in our oceans

• Currents    

  • Super important

  • Affected by temperature and salinity

  • Transport nutrients

  • Give stable climate to many countries

• Upwelling

  • Process that occurs in some of the world’s coastlines when cold nutrient rich water is brought to the Surface as a result of surface winds

  • Due to climate change, warmer surface water can prevent nutrient upwelling to the surface

    • This negatively impacts ocean primary production and energy flow through the entire marine food chain

  • No upwelling = no photosynthesis = no food = collapse of foodchain

D.4.3.6 Poleward and upslope range shifts of temperature species

• Peru

• 3 species of birds lived on separate parts of the mountain

• Top was cold but due to climate change it became warm

  • Other birds went up and outcompeted endemic species

D.4.3.7 Threats to coral reeds as an example of potential ecosystem collapse

• Threats to coral reefs

  • Dissolved carbon dioxide increases acidity of oceans which breaks down calcium carbonate that makes up reefs

    • pH decreasing = more acidic

  • Temperature is too high for survival