Gr.

11 Biology notes
Biology is the study of life. It examines the structure, function, growth, origin, evolution, and distribution of life.

In these diagrams, partial charges are shown in yellow. In Boron Trifluoride, the charges are equally distributed. However, in water they are not. Boron Trifluoride is an example of symmetrical attraction and water is an example of non-symmetrical attraction. Boron Trifluoride is non polar and water is polar. Levels of biological organization: Atoms Molecules (organic/inorganic) Cells Tissues Organs Organ Systems Organism Population Community Biomes Biosphere

Unit 1: Cellular functions

Cellular functions are functions that cells carry out. How do cells function? Dependent on organic and inorganic molecules ex. DNA, carbohydrates, salt etc.
*Note: Organic molecules have to have C+H. Inorganic molecules are all else

The study of biological molecules, chemical reactions, and the processes involved in chemical reactions is Biochemistry Cellular Respiration is an essential chemical reaction: 6O2 + C6H12O6 6CO2 + 6H2O + Energy This reaction provides energy for cells to carry out functions

In chemistry, there are three types of bonds: Ionic: when atoms give or take electrons to form ions

Covalent: attraction between + and -, repulsion - and -, + and + Rate of attraction increases faster than that of repulsion. Electron shells meld and each atom stable Polar Covalent: atom that has more protons pulls electrons more of the time making it negatively charged ex. water Because of partial charges, weak hydrogen bonds form between polar molecules Hydrogen bonds only form between H and O, N, or F
*Note: the special symbol means partial charge

Water: Is the most abundant molecule in any cell. It's functions are: -To carry dissolved materials in and out of the cell -Serve as a raw material (reactant) in many cell reactions -Act as a lubricant between cells, tissues, and organs -Regulate temperature What allows it to perform these functions? -Remains liquid over wide temperature ranges

Dissolves most substances important to living processes ex. O2, CO2, glucose, amino acid, NaCl, etc. (often called the universal solvent) -Changes temperature gradually when heated or cooled (high specific heat capacity) -Only pure substance to expand when solid floats when it freezes Water is polar covalent: other water and polar molecules are attracted to it

Macromolecules:
Macromolecules are large molecules (polymers) composed of smaller subunits (monomers) bonded together

Four main types: Carbohydrates, Lipids, Proteins, Nucleic Acids Chemical reactions are needed to make macromolecules. They are shown in the diagram above.

Carbohydrates: Basic Formula: CnH2nOn, where n is any whole number (ex. glucose is C6H12O6) Carb. functions: -Short and Long term energy storage (ex. glucose, starch) -Physical strength to the cell structure (ex. cellulose makes plant cell walls) Type Monosaccharide Basic Structure Function

Disaccharide Polysaccharide

One monomer: simple Quick source of energy sugar. Generally made of 56 carbon monomer Two simple sugars linked Quick source of energy Many simple sugars made Long-term energy storage, up of glucose subunits Structural support

*Note: the bond connecting the two sugar monomers is called a glycosidic bond

Remember the following Disaccharides: -Sucrose (glucose+fructose) -Lactose (galactose+glucose) -Maltose (glucose+glucose) On the right are three Polysaccharides. -Starch serves as energy storage in plants -Cellulose serves as a structural molecule in plants -Glycogen serves as energy storage in animals

Lipids

Features: -very diverse -do not dissolve in water (non polar) water hating (hydrophobic) Functions: -Long term energy/nutrient storage -Insulation, cushioning of internal organs -Hormones (chemical signals that send massages around the body) -Waxes (keep water in/out) ex. plants -Helps absorb vitamins Fats-solid at room temperature, Oils-liquid at room temperature both made of glycerol and 3 fatty acids On the right is the structure of a Triglyceride molecule.
*Note: the three fatty acids do not need to be the same

Fatty Acids may be: Saturated: has no double bonds (present in fats) more likely to be solid Unsaturated: has double bonds (present in oils) more likely to be liquid at room temperature due to "kinked" shape In the diagram on the right, the top two fatty acids are saturated and the bottom one is unsaturated. Trans fats: are unsaturated fats that have had hydrogen artificially added to them. They are linear and easy to pack together. Called Hydrogenation Trans fats raise risk of heart disease: -Raise blood levels of bad cholesterol, LDL. This is a risk to heart disease. -Lower blood levels of good cholesterol, HDL. HDL protects against heart disease.

Phospholipids-important in cell membranes (shown in diagram on right) -Made up of Glycerol, Phosphate, and 2 Fatty Acids -Head is polar (hydrophilic) -Tail is non polar (hydrophobic) Proteins Most diverse and complex of macromolecules Functions: -provide structure ex. hair, bones, muscle -facilitate chemical reactions as enzymes ex. amylase in saliva -transports substances ex. across cell membrane, hemoglobin in blood -acts as a chemical messenger ex. insulin regulates glucose Composition: -Made up of monomers called amino acids. There are 20 different Amino Acids -Amino Acids are linked by peptide bonds to form a polypeptide -Polypeptide folds into a 3D structure to form a specific shape

Primary Structure Is the order of amino acids Secondary Structure Hydrogen bonds between amino acids Tertiary Structure Super-folding due to other bonds Quaternary Structure Multiple polypeptides form Protein
*Note the different types of folding: Pleated sheet and Alpha helix

Nucleic Acids Functions: -determine what characteristics living things have ex. DNA -direct protein synthesis within the cell

-energy carrier within the cell Structure: -monomer called nucleotide (nt) -made up of phosphate sugar and nitrogenous base RNA is ribonucleic acid single strand of nucleotides, each nucleotide contains ribose sugar DNA is deoxyribonucleic acid double stranded nucleotide, each nucleotide contains deoxyribose
*Note: there are 4 different types of nucleotides

DNA: Adenine, Thymine, Guanine, Cytosine RNA: Adenine Uracil, Guanine, Cytosine

Cell membrane:
Functions: -acts as a barrier between cell and environment -permits passage of selected substances in and out of cell -flexible and able to change shape The fluid mosaic model: -Fluid: membranes are not static (able to move) -Mosaic: membranes consist of a mosaic of different components scattered throughout Cell membrane consists of: 1.Phospholipid bilayer -two layers -hydrophilic (water liking) region: "head" -hydrophobic (water hating) region: "tail" -small, neutral molecules can pass through spaces in the cell membrane

2.Proteins: -Peripheral proteins: external / internal surface (hydrophilic) Functions: -Enzymes carry out steps in a metabolic pathway (reactions) -Receptor sites, once a chemical binds, it initiates chain reactions of chemical changes in cell -Cell adhesion holds adjacent cells together -Integral proteins: embedded deep in the membrane (mostly hydrophobic) Function: -Transportation, move substances across the phospholipid bilayer

3.Cholesterol -a type of lipid -at low temperatures: allows for fluidity by preventing close packing of the phospholipids -at high temperatures: maintains rigidity of the phospholipids

4.Glycolipids / Glycoproteins -Carbohydrate chains attached to lipids and proteins -found only on external surface only

-each type of cell has it's own unique "fingerprint" of carbohydrate chains that distinguish it from other kinds of cells -Glycolipids attach to Phospholipids -Glycoproteins attach to Peripheral Proteins -Membrane carbs allow for cell - cell recognition. Allows cells to determine of other cells are similar of different. The identity of cell depends on carb composition

Passive Transport: The movement of substances across the membrane without the need for energy 1.Diffusion: the movement of small, uncharged particles from an area of high concentration to an area of low concentration

2.Osmosis: Diffusion of water across a semi-permeable membrane separating two solutions

*Note the names in the different solutions. Also note that for plant cells it is normal to be in a hypotonic solution *Note: Concentration gradient refers to the diffusion from areas of high to low concentration

3.Facilitated diffusion: Passive movement of a substance in and out of cell by embedded proteins -Channel proteins: Accept charged ions to pass through the cell membrane -Carrier proteins: Accept non-charged particles with specific shape

Osmosis and diffusion lead to equilibrium Some biological processes need to work against them

Active Transport: -moving substances against the concentration gradient energy is a must
*Note, diffusion is not enough to provide everything for cell

-many cells use up to 40% of energy on active transport ex. Kidneys use up to 90% Sodium-Potassium pump: -cells have high concentration of K+ on inside, high concentration Na+ on outside -Na+ and K+ move against concentration gradient with help of specific membrane protein and energy -this process brings glucose in at a faster rate as shown on the right Why go through all this trouble? -facilitated diffusion bringing Na+ back into the cell allows glucose to piggyback in

-facilitated diffusion of glucose by itself is not enough to provide the glucose needs of the cell

Bulk Transport: -requires the formation of vesicles to "swallow" or "expel" material -requires energy (active transport) Two overall types: -Endocytosis (take in) -Exocytosis (expel) Types of Endocytosis:

1.Pinocytosis: -means cell "drinking" -intake of small droplets of ECF (extracellular fluid) and dissolved particles -occurs in nearly all types of cells all the time (in humans) 2.Phagocytosis: -means cell "eating" -intake of large droplets of ECF (such as organic matter and bacteria) -occurs only in specialized cells ex. Ameoba, Macrophages (immune cells) 3.Receptor-Mediated Endocytosis:

-intake of specific molecules that attach to receptors (proteins on surface of cell membrane) ex. Cholesterol
*Note: the fluid contents still enter the cell

Exocytosis: -reverse of Endocytosis -vesicles form from inside cell and move to the cell surface -vesicles fuse with membrane, open up and release contents to ECF -ex. Secretory cells (Pancreas cells produce insulin)

Inside the cell:

Living cells must: -obtain food and energy -convert energy from external source -construct and maintain molecules that make up cell structures -carry out chemical reactions -eliminate wastes -reproduce -keep records Eukaryotes: have a complex internal structure -have organelles (organized, specialized structures) -organelles work as a team Prokaryotes: smallest type of internal organization -lack of a nucleus! -DNA is concentrated in an area inside the cell called nucleoid

Organelle
Cell membrane

Characteristics and functions

-fluid mosaic membrane separates cell interior from outside -controls movement of materials in/out of the cell -also allows for self recognition -gel like material made mostly of water contains dissolved materials -creates chemical environment for other structures -command centre for cell contains DNA blueprint of proteins -surrounded by double membrane with nuclear pores -pores in the nuclear membrane to allow macromolecules enter, ribosomes leave -uncoiled chromosomes (DNA) -specialized area of chromatin for producing proteins -two subunits that construct polypeptides -can be free or membrane bound

Cytoplasm Nucleus Nuclear pores Chromatin Nucleolus Ribosome

Endoplasmic Reticulum -rough ER: has ribosomes on surface -smooth ER: synthesizes phospholipids and packages macromolecules in vesicles Golgi Body -receives vesicles from the ER -contains enzymes for modifying proteins/lipids -packages finished products into vesicles for exocytosis Mitochondrion -powerhouse of the cell, organic molecules broken down into ATP -has double membrane + DNA -membrane bound vesicle with digestive enzymes -breaks down macromolecules and worn out cell components -membrane bound vesicle with enzymes -breaks down toxins, lipids converting waste into less harmful stuff -organelle located near nucleus -pair of centrioles that organize cell division -small membrane bound transport sac

Lysosome

Peroxysome

Centrosome (only in animals) Vesicle

Vacuole

-large membrane bound, fluid filled sac -temporary storage of food, water, waste products

Organelle
Cytoskeleton

Characteristics and functions

-network of three kinds of interconnected fibres -maintain cell shape and allow for movement of particles Microtubules Actin filaments Intermediate filaments -composed of cellulose fibbers for strength + rigidity -gaps called plasmodesmata allow movement of substances -membrane bound structure store starch, lipids, proteins -often needs light trigger -chlorophyll captures energy from the sun -has double membrane and own DNA

Cell wall (plants only) Plastid (plants only) Chloroplast (plants only)

Photosynthesis: Two main stages of photosynthesis 0. Photo Stage light dependent -occurs in thylakoids -chlorophyll absorbs light -ATP is synthesized -water is broken to produce O2 2. Synthesis Stage light independent (also known as Calvin Cycle) -occurs in the stroma of the chloroplast -ATP (from stage 1) used to make glucose molecules from CO2 Cellular Respiration Reactions: -occurs first in the cytoplasm then in the mitochondria First step, Glycolysis: anaerobic (no oxygen) -glucose split into 3 Carbon molecules (pyruvic acid) -net energy of 2 ATP

Second Step, Fermentation: anaerobic -no extra energy, helps recycle materials -Pyruvic Acid converted into Lactic Acid (muscle cells) or Ethyl Alcohol (yeast) Second Step, Citric Acid Cycle (Kreb's Cycle) Third step, Electron Transport Chain (ETC) 34 ATP released from these processes
*Note: steps two and three of aerobic respiration occur in the mitochondria

Unit 2: Diversity of living things

Why is it so important? -for the health of the biosphere: the more diverse the ecosystem, the greater it's stability Why does increased diversity increase the stability of the ecosystem? -it provides many options and alternatives ex. There are 30 million species of insects

Intro to classification:
To understand the diversity of living things, we classify organisms Why do we need a classification system? -to group things in an organized way -provides specific details to help identify organisms and represent relationships

Taxonomy: is the science of classifying living things It's two main purposes: -help identify organisms -represent relationships between organisms Early Taxonomy: -Aristotle proposed that all living organisms be arranged in a hierarchy

-simple organisms at the bottom, complex at the top Carl Linnaeus (1701-1778): -developed presently used classification system -system based on physical + structural features -the most features in common, the more related they are How are things classified? -hierarchy of groups (taxa pl. taxon sing.) Kingdom largest, most general taxa Species smallest taxa Binomial Nomenclature: -used for naming organisms by two names referred to as a scientific name

Scientific Names: -originate from Latin/Greek words -based on a characteristic ex. colour, habitat Genus: -first part of the name -refers to a group of organisms closely related with similar characteristics Species: -second part of the name -refers to a group of interbreed

organisms that look alike and

Domains or superkingdoms: -Prokaryotes (monera) -Eukaryotes -Archae

There are 7 levels of classification:

Kingdom Phylum Class Order Family Genus Species -Characteristics are more similar as you move down the chain. -The smaller the taxon, the more similar are the organisms within it

5 Kingdom systems: -plantae -monera -fungi -animalia -protista -archaebacteria

(bacteria)

Viruses:
Alive or not? -they do not fit in the kingdom system -they show very few characteristics of living things -viruses need living cells (hosts) to survive + reproduce -ex. bacteriophage, tobacco, mosaic virus, influenza, HIV What are the characteristics of living things? 1. 2. 3. 4. 5. 6. 7. Reproduction Growth Metabolism (controlled chemical Adaptation Response to stimuli Death Locomotion Viruses are not alive -they do not have -they do not have Structure of a virus: metabolism + growth organelles

reactions ex. ingestion, excretion)

consists of two main parts -Core: Nucleic Acid (RNA/DNA) Genome -Shell: protein coat Capsid Features of a virus: -very small, 20-400 um in size -consists of an inner nucleic acid core -comes in various shapes Viruses are specific Viral Specificity -each virus has a specific group of hosts that they infect -called host range - can be broad or narrow (depends on spikes)

Unit 4? Respiratory Systems:

The breath of life: -Recall: Aerobic organisms require Oxygen (O2) -O2 is necessary for cellular respiration Cellular Respiration releases energy to drive all cellular functions -CO2 is the waste product of cellular respiration Gas exchange: the process that ensures O2 enters each cell of an organism and CO2 leaves in order to meet metabolic needs of the organism
*Note: Breathing- physical forcing of air, Gas exchange- O2 coming in CO2 going out

Two gas exchange requirements: 8. 9. Surface area: must be large enough for O2 to enter and CO2 to leave Moist environment: allows gas exchange to take place (since O2 and CO2 must be dissolved in order to be transported) Simple gas exchange: Unicellular organisms ex. amoebae and algae -exchange gas through membrane by diffusion

-membrane must be moist (it must live in a moist environment) More complex respiratory systems: Large multi-cellular organisms -Require specialized cells greater need for O2 O2 must travel greater distances Problems with multi-cellular life: -The process of diffusion is only effective over a distance of a few cells -As the body surface becomes more specialized, surface area available fro gas exchange is reduced Solution specialized respiratory system Skin respiration: -Skin must remain moist -Skin lined with tiny capillary vessels -O2 carried to other cells of the organism Gills: -Structural changes: increase surface area of the body parts involved in gas exchange -Mechanism: has evolved which enables the organism to ventilate this surface Fish gills: -feathery structures of delicate -ensure a surface limited to system to O2 and and from Counter current gas exchange: tissue consisting numerous branches large area in a space connected vascular transport CO2 to cells

Terrestrial organism gas exchange -terrestrial organisms have an internal gas exchange system Breathing: -an important process as it forces O2 a cress the gas exchange surface -relies on a basic law of physics: air moves from regions of high pressure to regions of low pressure until equilibrium is reached