Biological Principles

Implications of cell theory

• Functions of all cells are similar
• Life is continuous
• Origin of life was orgin of cells

Volume= amount of chemical activity in cell per uit time

Surface Area= amount of substance that can pass cell boundary per unit time

Conversions                                            Magnification = increase apparent size

• 1m = 10 -2m                                      Resolution = clarity of magnified objects
• 1mm = 10 -3m
• 1nm = 10 -9m (nano)            Two types of microscopes:
• 1pm= 10 -12m (pico)             Electron = electromagnets focus on electron beam

                                                    Light = glass lense and light

Prokaryotic: individual single cells -chains or clusters -> diverse energy source

• DNA constained in the nucleoid
• Ribsomes - sites of protien synthesis 
• Bactiera have pili - protect from surface 
• Some swim flagella- made of protein

Eukaryotic: Have compartments which specific reactions occur -> allow diversification of functions

• Compartments called organelles
• Has specific role in cell functioning
• Ribosome-free in cytoplasm attach to endoplasmic reticulum or inside mitochondria & chloroplasts 

Ribsomes: site of protein synthesis 

• RNA and protien molecules

Compartmentalisation: allow euk cells to specialise & form tissues & organs of multicellur organisms

Plasmic Membrane: Outer surface of every cell -> made of phospholipid bilayer, selectively permeable barrier and allows cells to maintain a constant internal environment

Golgi Apparatus: composed of flattened sacs and small membrane enclosed vesicles -> recieves protiens from RER and sorts proteins

Endoplasmic Reticulum: network of interconnected membrans in cytoplasm; large surface area

• Rough ER: ribosome attached -> proteins are modified and transported to other regions
• Smooth ER: no ribosomes -> chem modifies small molecules e.g drugs or pesticides, synthesis of lipids & steroids

Nucleus: Assembly of ribosomes, surrounded by 2 membranes, some proteins have amino acid sequence- nuclear localization signal -> DNA + proteins = chromatonin. Nucleoplasm surrounds chromatonin and nuclear matrix - helps organise chromatonin

Primary Lysomes: golgi app -> constains digestive enzymes, macromolecules are hydrolysed into monomers. Food molecules enter by phagocytosis ( fuse with prim lys = sec lys)

Mitochondria: energy in fuel molecules is transformed to bonds of energy-ATP->needs loads of energy=lots of mitochondria. The membranes create large SA for celluar respir reaction

Mitochondria matrix: enzymes DNA and ribosomes

Peroxisomes: collect and break down toxic products of metabolism e.g. H202 using specialised enzymes

Glyoxysomes: only in plants- lipids are converted into carbs for growth

Plastids: occur only in plants and protists -> chloroplates: site of photosynthesis - has doub memb

Cilla and eukaryotic flagella are made of microtube

• Cilla: short, usually flex recovery stroke
• Flagella: long, 1 or 2 movemet is snakelike

Grana: Stacks of thylakoid- made of circular compartments of inner membrane

Thylakoid: contain chlorophyll and pigments which harvest light energy -> photosynthesis

Stroma: fluid grana is suspended contains DNA and ribosomes

Leucoplasts: store of fats and starch

Vacuoles: store pigments in flowers and fruit -> digestive enzymes- store food for growth 

Cytoskeleton: supports main cell shape -> holds and moves organelles -> interacts with extracellualar structures to hold cell in place.

Has 3 Components:

• Microflaments: helps cell to move, determine cell shape, made from protein actin
• Intermediate flaments: resit tension, tough, ropelike protein assemblages, anchor cell structure in place
• Microtubules: form rigid internal skeleton, made from protein tubulin, framework for motor protiens

Structure known as "fluid mosaic model". Phospholipids form bilayer where protieins float

Phosphlipid bilayer are flexible and interior is fluid allowing lateral movement of molecules

Two types of membrane protiens:

• Peripheral MP: lack exposed hydrophobic groups and do not penetrate the bilayer
• Integral MP: have hydrophobic and hydrophillic regions

Membranes have fatty acids or other lipid groups attached and referred to as anchorced membrane proteins 

Transmembrane Proteins: extend all the way through the phosphalipid bilayer

Membranes have selectively permeability - not all substances can pass through

• Passive transport- no outside energy required (diffusion)
• Active Transport- energy required 

Glycolipids= carb+lipds          Glycoproteins= carbs+protiens

Def: The process of random movement toward equilibrium

Equilibrium: particles continue to move but there is no net change in distribution -> net movement is directional until equilibrium is reached

Diffusion rate depends on:

• Diameter of the molecules or ions
• Temp of solution
• Concentration gradient
• Depending on the membrane properties 

Simple Diffusion: small molecules pass through the lipid bilayer

• Water and lipid- soluble molecules can diffuse across the membrane
• Electrically charged and polar molecules can not pass through easily

Facilitated Diffusion: of polar molecules (passive)

Def: The diffusion of water

If two solutions are seperated by a membrane that allows water but not solutes to pass through: water will diffuse from region of higher wter concen (low solute concen) to a region of low water concen (high solute concen)

Isotonic: Equal solute and water concentration

Hypertonice: Higher solute concetration

Hypotonic: Lower solute concentration

Water will diffuse from a hypo solution across membrane to a hyper solution

Plants cells with rigid cell walls bulid up internal pressure- turgor pressure

Channel protiens: have a central pore lined with polar amino acids

Carrier proteins: bind some substances and speed their diffusion through the bilayer

Ion Channels: specific channel protiens with hydrophillic pores -> most gated (closed or open to ion passage). Gate opens when protien is stimulated to change shape ( can be a molecule or electrical charge=ions+)

All cells maintain imbalanceof ion concentration across thebplasma mem = small voltage

Membrane potential: is a ccharge imbalance across a membrane

Rate of reaction depends on concen gradient and distribution of electrical charge

Glucose binds to protiens=change shape and release glucose on other side

Active Transport: move substances against a concentration &/or electrical gradient required (energy adenosine triphosphate ATP)

Active Transport is directional & involves 3 protiens

• Uniporters
• Symporters
• Antiporters

Primary AT: requires hydrolysis of ATP

Secondary AT: enerfy comes from ion concen gradient established from primary AT

Sodium potassium pump: (PAT) integral membrane (antiporter)

SAT energy can be "regained" by letting ions move across membrane wth concen gradient -> uptake in amino acids and sugars -> use symporters and antiporters

Macromolecules: too large to cross membrane-> screted by membrane vesicles

Endocytosis: processes that bring molecules and cells into a eukaryotic cell

• Plasma Membrane folds in around the mateiral forming a vesicle

Phagocytosis: Molecules or entire cells are engulfed, some protists feed this way, white blood cells engulf foreign substances

• A food vacuole or phagosome forms which fuses with a lysosome

Exocytosis: material in vesicle is expelled from  a cell

• Other materials leave cells such as digestive enzymes and neurotransmitters

Some membranes transforms energy:

• Inner mitochondria membranes- energy from fuel molecules is transformed to ATP
• Thylakoid membranes of chloroplast transform light energy to chemical bonds

Order: the highly ordered structure that typifies life

Reproduction: the ability of organisms to reproduce their own kind

Growth & development: consistent growth & development contolled by inherited DNA

Energy processing: the use of chemical energy to power an organism's activities & chem reactions

Regulation: an ability to control an organisms internal business

Responses to the environment: an ability to respond to environmental stimuli

Evolutionary adaptation: individuals with traits best suited to their envirnoment have greater reproductive success and pass their traits to offspring

Two key observtions by darwin:

• Individual variation: individuals vary and pass on traits to off spring
• Overproduction of offspring: all species can produce more offspring than the environment can support

Natural selection:

• Unequal reproductive success: individuals that have an advant over others and reproduce
• Accumulation of favourable traits overtime: over many generations these traits will take over with in the population - "a species"

Atom: smallest component of matter

• Have a dense and charged nucleus (protons + neutrons) around which are -charged electrons

Element: a pure substance that contains only one kind of atom

• Atoms of each element have specifc characteristics or properties

Atomic number: determines how an element behaves in a chemical reaction

Atomic weight: average of the mass numbers of a represent sample of atoms of that element

Isotopes: Different number of neutrons, some are unstable and some behave in the same way in chemical reactions

Radioisotopes: spontaneously give off energy in the form of radiation from the atomic nucleus

• unstable and known as radioactive decay, this releases energy and transforms the cells
• Can be used as tracers

Number of electrons in an atom determines how it will combine with other atoms

Behaviour of electrons explain how chem reactions occur

Can only describe a volume of space within an atom where the electron is likely to be (orbital)

• 1 orbital= 2 electrons

Octet Rule: an atom will always tend to become stable by filling the outermost shell with 8 elect

Energy level in a shell which is further away is higher

Def: sharing of electrons

Forms when two atoms attain stable electron numbers in their outermost shells by sharing one or more pairs of electrons

Very strong= takes a lot of energy to break

At temp where life exists, the CB of biological molecules are quite stable

1 bond = 2 electrons shared

IA def: when an atom gains or looses one or more electrons to achieve stability

• They are formed as a result of the electrical attraction between ion bearing opposite charges
• Ions can form bonds result in stable solid compounds which are called salts
• e.g sodium chloride (table salt) cations and anions are held together

IB def: when one interacting atom is much more electrobegative than the other, a complete transfer of one or more electrons may take place.

• Ions are electricity charged particles that form when atoms gain or loose one or more electron
• electron lost= +charge
• eletron gained= -charge
• when attraction holds the ion together it is called an ionic bond

Compound: is a pure substance made up of two or more different elements bonded together in a fixed ratio

Every compound has a molecular weight ( relatively molecular mass) that is the sum of the atomic weights of all atoms in the molecule

When two different atoms with incomplete outer shells react, each atom will share donate or recieve electrons so that both partners end up with completed outer shell

These atoms will stay close together = a molecule

A chemical bond is an attractive force that links two atoms together in a molecule e.g chemical and ionic bonds/attractions

Def: a substance produced by a living organism which acts as a catalyst to make a biochemical reacion happen

Catalyst: speed up rate of reaction and isnt altered by the reaction

Some reactions slow because of an energy barrier (amount of energy required to start a reaction) - activation energy

Reaction rate depends on:

• frequency at which the reaction collide
• energy of the reactants ( must collide with a certain mount of energy in order to react)

Activation energy: changes the reactants into unstable forms with higher free energy -> can come from heating ( have more KE)

Bio catalysts are highly specific, reactants are called substrates and they bind to the active site of an enzyme. 3D enzyme determines the specificity.

Shape of enzymes active site allows a specific substrate to fit (lock and key)

Many enzymes change shape when they bind to the substrate - induced fit

Some enzymes require "partners":

• Prosthetic groups: non amino acid groups bound to enzymes
• Cofactors: inorganic ions
• Coenzymes: small carbon - containing molecules; not bound permanently to enzymes

Rate of catalysed reactions depends on substrate concentration - this is lower than concent of substrate. At saturation all enezymes are bound to substrate

Max rate is used to calculate enzyme efficieny molecules of substrate converted to product per unit time (turnover)

Ranges from 1-40 mil molecules per sec

Reactions are organised in metabolic pathways, each reaction is catalysed by a specific enzyme. Regulation of enzymes helps maintain internal homostasis rates

inhibitors: regulate enzymes - molecules that bind to the enzyme and slow reaction rates - naturally occuring inhibitors regulate metabolism

Irreversible inhibition: inhibitor bonds to side chains in the active site - permanently inactivities the enzyme e.g nerve gas

• inhibits ocetylchlorine esterase so preventing nerve transmission

Resversible inhibtion: inhibitor bonds to the active site and prevents substrate from binding

Competitive inhibitors: compete with natural substrate for binding sites

• when concentration of competitive inhibitor is reduced it detatches from the active site

Non-competitive inhibitor: bind to the enzyme at a different site (not the active site)

• enzymes change shape and alter the active site.

Every enzyme has an optimal temp

High = bonds break

Low = bonds made

Enzymes can loose tertiary structure and become denatured

Isozymes: enzymes that catalyse the same reaction but have different properties i.e optimal temperature

Organisims can use isozymes to adjust to temp change

Enzymes in humans have higher optimal temp than enzymes in most bactiera ( a fever can denature the bactieral enzymes)

Inhibition depends on a lack of specificity of enzyme active site

If it binds to inhibitor substrate is denied access to active site (no product) CL:

• resemble substrate chemically
• compete for same active site
• if enough, substrate displaces inhibitor

Many micro orgs make folic acid from paraminobenzoic acid but humans cannot and require folic acid as a vitamin

Genetics: field of biology associated with inheritance and variation in organisms - heredity determinants (genes) housed in chromosomes

Blending inheritance: Heredity determinants from parents 'blended' in resulting offspring and can never be seperate

Particulate inheritance: Heredity determinnants from parents remain intact in resulting offspring (retaining the dermants for both characteristics)

Gregor Mendel (1822-1884)- did a study on common garden peas

• many varieties with easily recognizable characteristics
• character: observable physical feature e.g shape, colour
• trait: form of character e.g round, wrinkled

Conclusion: F1 offspring were not a blend of two traits only one trait present

• F2 offspring showed other trait hadnt gone 
• Mendel referred to more abudant trait as dominant the other trait recessive

Genes: is a unit of heredity it is a section of DNA sequence

Alleles: are different forms of a gene that occupy the same position on a chromosome that cover the same character

• A gene that has two alleles the same is homozygous (AA, aa)
• A gene with two alleles is hetrozygous (Aa)

Dominant allele: suppresses the expression if an alternate allele (AA,Aa)

Recessive allele: suppressed by the dominant allele and only expressed when homozygous (aa)

The physical appearence is known as the phenotype which is the result of the genotype

Genes are subject to mutuations - an allele can mutate to become a different allele = a variety, the raw material for evolution

Allele present in most individuals in nature referred to as wild type other referred to as mutant alleles. These alleles reside on the same genetic locus (location on the chromosomes)

If locus has a cetain frequency of mutant alleles, called polymorphic

Random mutations= 2+ alleles of a given gene may exist in a group of individuals

Epistasis: occurs when the phenotypic expression of on gene is affected by another gene

Environmental effects on genes: the phenotype of an individual does not result from it's genotype, genotype and environment interact to determine the phenotype of an organism

• Qualitative: variation generally describes simple binary varaition i.e one trait or another, medels peas
• Quantitative: variation describes phenotype which vary on a continuous basis i.e human height

Any changes in the nucleotide sequence of an organisms DNA

Occur randomly with respect to their costs/benefits to an organism

It is natural selection acting on these random changes that = adaptation

Mutations add new alleles to the gene pool altering the allele frequency, selection acting on genetic variation =new phenotypes

Adaptation: a particular envirnment is demonstrated when a different organism reproduces ans survives less well

Selection for a beneficial change - positive selection

In small populations, random changes in allele frequencies from on generation to the next - may produce large changes overtime

Harmful alleles may increase, advantageous alleles may be lost

Gene flow may change allele frequencies:

• migration of individuals (or gametes) between populations (gene flow) can change allele frequencies
• few populations are completely isolated

Individuals don't choose mates at random

Sexual selection: occurs when individuals of one sex mate preferentially with particular individuals of the opposite sex

Conspicuous that inhibit survival:

• intrasexual selection: improves the ability of individuals to compete for access to mates
• Intersexual selection: makes individuals more attractive to members of the opposite sex

Measuring evolutionary change: evolution occurs through the gradual change in allele frequencies from one generation to the next

allele frequency = number of copies of an allele in a population

                             Total number of all alleles for that gene in a population

The conditions that must prevail if the genetic structure of a population is to remain the same over time:

• No mutation
• No selection among genotypes
• No gene flow
• Infinite population size
• Random mating

No change in allele frequencies therefore evolution will not occur

Deviations from HWE show evoultion is occuring, natural populations don't follow strict assumptions

Useful for predicting genotype frequencies of a population from it's allele frequencies

Specific patterns of deviation from HWE help us identify the various mechanisms of evolutionary change

Acts directly on the phenotype and indirectly on the genotype

Stabilizing selection: preserves the average characteristics of a population by favouring average indivdual

Directional selection: changes the characteristics of a populations by  favouring individuals that vary in one direction from the mean of the population

Disruptive selection: changes the characteristics of a population by favouring individuals that vary in both directions from the mean of population

The fitness of a phenotype is determine the realtive rates of survival and reproduction of individuals with that phenotype.

Sexual Recombination: amplifies the number of possible genotypes

Disadvantages:

• May break up adaptive gene combination
• Reduces female rate pass on their genes
• Overall reproductive rate is reduced with offspring of different sexes

Advantages:

• Facilities repair of damaged DNA
• Eliminates deleterious mutations
• Creates variety of gentic combinations

Self: the animals/organisms own molecules

Nonself: foreign molecules, 3 phases

• 1. Recognition phase: discriminate between self and non self
• 2: Activation phase: mobilisation of cells and molecules to fight invader
• 3: Effector phase: the destruction of the invader

Innate response: first line of defense -> non specific defences acts against broad classes of organisms -> typically act very rapidly within minutes or hours -> all animals have some level of innante immunity and some are shared between plants and animals

Adaptive Response: aimed at specific pathogens -> activated by the innate immune response -> typically slower to respond but are longer lasting.

Skin: intact skin is rarely pentrated -> may be inhospitable (salty & dry) -> protection from 'normal' bactiera flora

Mucas: traps micro organisms

Lysozyme: enzyme made by muscus membranes that attacks bactieral cell wall causing them to lyse

Defensins: peptides that make pathogen membranes permeable thus killing them

Triggered by non self molecules, Patteren Recognition Receptors (PRR), Pathogen Associated Molecular Patterns (PAMP) -> Toll like recpetors -> Complement protiens

Proteins attach to surface of microbe/antibody on microbe surface -> act as a cascade fashion (each protein activating after the next)

• This helps phagocytes to recognise and destroy microbe
• Activates inflammatory response attracts phagocytes
• Lyse invading bactiera cells

Interferons: signalling protiens -> increase resistance of neighbouring cells, class of cytokines

• First line of defence against viruses and bind to receptors on membranes of uninfected cells, inhibiting viral reproductions
• Hydrolyze bactiera/ viral proteins to peptides an initial step in adaptive immunity

Phagocytes: Travel freely in circulatory and lymphatic systems, adhere for certain tissues

• Ingest pathogens, viruses by phagocytosis

Natural Killer Cells: Can distinguish virus infected cells and some tumour cells from their normal counterparts

• Initiate apoptosis in these target cells
• Can lyse antibody- labelled cells

Dendritic Cells: 'messenger' phagocyte between innate and adaptive responses

• Can endocytose microbes viruses and even virus infected host cells
• Secretes signals that activate adaptive response

Response to infections or injury (external and internal)

Isolates and stops spread of the damage

Recruits molecules and cells to the damaged loacation to kill invaders

Promotes healing

First reponse are mast cells which adhere to the skin and linings of organs and release numerous chemical signals

Ability to distinguish self between non self

Ability to respond to a large diversity of nonself molecules

Immunology memory

Specificity: Lymphocytes (B&T cells)

• T cell receptors and antibodies (B cells)
• Antigenic determinants - (epitopes) are small portion of antigens
• Antibodies - react with antigenic determinants

Ability to distinguish self between non self

Ability to respond to a large diversity of nonself molecules

Immunology memory

Specificity: Lymphocytes (B&T cells)

• T cell receptors and antibodies (B cells)
• Antigenic determinants - (epitopes) are small portion of antigens
• Antibodies - react with antigenic determinants