UNIT 1

Naturally occurring elements in the body 

Major Elements = 96%

Oxygen 65%

Carbon 18.5%

Hydrogen 9.5%

Nitrogen 3.3%

Essential Elements = 4%

Calcium 

Phosphorus 

Potassium 

Sulfur

Sodium 

Chlorine 

Magnesium 

Trace Elements = 0.01%

Copper: hair and skin 

Zinc: enzyme function 

Iodine: salt good for thyroid 

Iron: needed in transport O2 in blood 

Cofactor: Allows enzymes to function

Poly unsaturated: plant fat with many double bonds 

Monounsaturated: plant fat with one double bond 

Dietary Fiber: need 6 g to feel full 

Protein-rich: 5g-6g 

BHT: to pressure food and persevere food. It gives things shelf life 

Things to check on the nutrition label

Serving Size 

Calories 

Trans fat; toxic & manmade

Radioisotope: an isotope of an element that has an unstable nuclei

Radioactive decay: the process by which an unstable nucleus rearranges itself 

Electronegativity: Tendency of an atom to attract electrons

Partial charges: do not let electricity to pass through 

Ionic bonds: Transfer of electrons between two unstable atoms 

pH effect on the environment:

Acid Rain 

Coral reef

Carbon 

Element of life 

Bonds:  

Does not want to have charge; it only wants covalent bonds.

The double bond allows for fixed position

The single bond allows for rotation 

Hydrocarbon properties:

Length 

Double bonds

Branching 

Rings 

Methane: CH4

Ethane: C2H6

Ethene: C2H4

Most common Functional Groups attached to carbon

Methyl: R-CH3

UNIT3

Biomolecules (macromolecules)

• Carbohydrates *

• Lipids 

• Proteins *

• Nucleic Acids *

* Polymers: chemicals made up of many repeating units called monomers 

Dehydration RXN (condensation)

Short polymer with and H and monomer with OH connect to form a polymer with H2O

Hydrolysis RXN

Large polymer with H2O breaks into short polymer with and H and monomer with OH

Enzymes: proteins that allow rxns to take place

Hydrolytic enzymes: enzymes that use water to break down polymers 

Carbohydrates 

Empirical formula: CH2O 

Monomers of carbohydrates are called Monosaccharides. 

Functions:

• Provide energy for all organisms 

• Structure of plant fungi and bacteria 

• Communication for cells 

Glucose 

Structure of Glucose

If a B glu and B glu connect one of them has to flip. 

Polysaccharide 

1. Starch 

   1. Very long chains of A-Glu (1000>)

   2. Amylose - short chain 

   3. Amylopein - branch 

   4. Storage of energy for pants 

2. Glycogen 

   1. Very long branched chains of A-Glu (1000>)

   2. Highly branched 

   3. Storage of energy in liver/muscle cells

3. Chitin (CH2ON)

   1. Exoskeleton of insects 

   2. Makes up cell wall of fungi 

   3. Straight chain 

4. Cellulose 

   1. Only made up of B-Glu 

   2. Makes up the cell wall for plants 

   3. Made up of straight chains 

What makes cells strong and rigid?

H bonds between cellulose molecules 

Microfibril: a group of cellulose molecules holding onto each other 

When many are stacked, they form the cell wall

Adaptive tissue: fat tissue 

Our body stores sugar as glucose and excess sugar is stored as body fat 

Proteins 

All functions in the body are carried out by proteins

Protein could be used as energy once all other sources run out, this state is called starvation

Components 

20 different types of amino acids 

1. Nonpolar (hydrophobic)

2. Polar (hydrophilic) 

3. Electrically charged (ionic) 

Examples:

Nonpolar: Methionine 

Polar: All polar amino have O or N at it’s end 

Except for Cysteine, helps for 3D structure of proteins 

The basic structure of an amino acid:

Elements found in all proteins 

• Carbon 

• Oxygen 

• Nitrogen 

• Hydrogen 

• Sulfur

Structure level of proteins 

Primary structure 1°

1. Tells the number of amino acids 

2. Types of amino acids 

3. Sequence of amino acids 

Secondary structure 2°

1. Folding of the 1° structure using H-Bonds 

   1. α Helix (spiral)

• Exp: collagen, holds cells together 

2. β pleated sheets 

• Exp: keratin, for hair and nails 

Fibrous Protein

Proteins that have up to the 2° structure and they are insoluble in water, nonpolar, hydrophobic 

Tertiary structure 3°

1. Further folding and twisting of previous structures by using Intra molecular forces such as: 

• H Bonds

• LDF

• Ionic bonds

• Dip Dip

• Disulfide bridges 

2. Exp: hemoglobin or insulin 

Globalor proteins: 

They have 3° structure or higher, and they are soluble in water 

Quateunary structure 4°

1. Found in proteins that have 2 or more polypeptide chains held together by intra-MF

• Exp: 

  • Hemoglobin: 4 polypeptide 

  • Indulin: 2 polypeptide 

Denaturation

loss of protein structure leading to loss of functions 

Caused by:

• pH 

• Temperature 

• Pressure 

• Salt → have charged when dissolved in H2O, disrupts ionic bonds 

↑ maybe reversible or irreversible 

Structure of protein 

Defence → antibodies → protects from bacteria and viruses 

Enzymes → Alpha amylase → breaks down starch 

Structure → collagen → molecules have 2° fibers have 4° 

Communication → insulin (dec glucose) glucagon (inc glucose)

Storage → ferritin → stores iron 

Transport→ calcium pump → moves Ca^2+ across membrane

      HDL → lipids around body 

      Hemoglobin → transports O2 in blood 

Contractile proteins → myosin and actin → contract & move muscles 

Receptors → insulin receptor → detect hormones 

Nucleic Acid 

Central dogma: All life depends on DNA

DNA: 

• deoxyribonucleic acid 

• Double helix 

• It has 2 strands with H-Bonds in the middle.

RNA: ribonucleic acid 

• 1 strange with different types 

• mRNA (message) - carries the info from the nucleus to the cytoplasm 

• tRNA (transfer) - brings the correct amino acid during protein synthesis 

• rRNA (ribosomal) - needed in structure for ribosomes 

call structure that builds proteins 

• miRNA (micro) - regulates gene expression 

DNA → RNA → PROTEINS 

from DNA to RNA: Transcription                

from RNA to protein: Translation 

Transcription:

It happens in the nucleus 

Type of chemical remains the same but the structure changes 

Translation:

Happens in the cytoplasm 

Type of chemical changes and so does the structure 

Monomers of nucleic acids: nucleotides 

Made up of:

• Nitrogenous base ↓H⁺ attached to C1

• Pentose sugar      C5H10O5

• Phosphate group Always attached to C5

Lipids 

Fats

• Animal sources

• Solid at room temp 

• Saturated 

Oils

• Plant source 

• Liquid at room temp

• Unsaturated 

Basic functions of lipids

• Energy storage

• Insulation 

• Cell membranes (make new cells)

• Communication for hormones 

• Defence 

Triglycerides 

Used for energy storage

Made up of

• 1 glycerol

• 3 fatty acids 

  • Fatty: hydrocarbon 

  • Acid: carboxyl 

Structure 

Esterification: the process of creating an ester bond rxn between alcohol and fatty acid

Types of triglycerides 

Saturated triglycerides  

• All three fatty acids must have single bonds ONLY 

Monounsaturated  

• One and only one  

• double bond must be present, causing one of the fatty acids to move downwards, allowing it to be liquid at room temp. Because it leaves space for it to move and become a liquid  

Polyunsaturated  

• Has two or more double bonds present. It can be on the same fatty acid  

Vitamins

V. are special chemicals needed for proper metabolism  

Nonpolar are stored in adopost tissue 

Polar ones cannot be stored 

Retinol: V A1 alcohol nonpolar 

Retinal: V A aldehyde nonpolar 

VD: nonpolar cholesterol-based forms on skin 

Phospholipids 

Create the cell membranes. 

Made up of:

• Glycerol 

• 2 fatty acids

• Phosphate group 

Steroids 

• Creation of hormones 

• Membrane stability (flexibility) 

• Regulates fluidity 

  • More cholesterol more rigid 

Components

• Cholesterol 

Cholesterol Rings 

Waxes

For defence 

Made up of:

• Long chained alcohol 

• Long chained fatty acid 
  

UNIT 4

Microscopes

Light 

• Uses light as an energy source 

• Mirrors direct the light to your eyes 

• Lenses are used to enlarge and focus image 

Electron

• Uses electricity as energy source 

• Magnets direct flow of electrons for viewing 

• Scanning 

  • e- reflect off the specimen for 3d viewing 

• Transmission 

  • e- flow through providing an internal structure 

Structure of Cell membrane

Fluid mosaic model 

Fluid

Phospholipids: create flexible bilayers act as water barrier

Cholesterol: regulates the fluidity of the cell membrane 

Mosaic

Proteins: carry out various functions 

Transport proteins move substances from one side of the membrane to another.

Why are cells small in size 

Prokaryotic Cell

Cytoplasm: Gel-like fluid (cytosol) that contains chemicals (proteins) and cell structures (ribosomes) inner region of the cell contained by cell membrane

Bacterial chromosome: circular DNA that contains genetic information 

Nucleoiod: region of the cytoplasm where the bacterial chromosome is located 

Ribsomoes: Proton synthesis, creation of proteins for the cell 

Plasmid: extra small pieces of DNA that provide superpowers to cells

• Antibiotic resistance: cant be fought off by antibodies & neither will its offsprings 

• Motility: mobility by itself & spreads easily 

• Production of a capsule: proteins itself & moves around & sticks to surfaces 

• Fertility: ability to reproduce sexually, creation of new bacteria

Pathogenic: ability to cause infection or disease 

Cell membrane: made up of phospholipids, cholesterol proteins & carbohydrates, it creates the boundaries of the cell it acts as a barrier controlling what comes in & out 

Cell well: made up of a mixture of carbohydrates and proteins called peptidoglycan provies structure & shape 

Capsule: may or may not be present, attaches to surfaces to induce infections, strong enough to resist digestion by white blood cells 

Flagella: made up of protons, extending from the cell membrane, allow cells to move, moves by rotation. 

Fimbriae: made up of protons that extend from the cell membrane for attachment ot surfaces. 

Extracellular fluid: fluid on the outside of the cell

Eukaryotic Cells

Have compartmentalisation while prokaryotic don’t

The process of creating compartments closed off within the cell

Vacuole 

Large vesicles with specialised functions 

1. Food vacuole 

   1. Part of phagocytosis brings in large substances 

2. Central vacuole 

   1. Found in plants; usually the largest structure 

      1. Stores water to create ‘pressure’ that helps with structure & shape of the cell & plant

      2. Stores chemicals 

      3. Stores waste 

3. Contractile vacuole 

   1. Found in freshwater protists; like the paramecium 

      1. Removes excess water from the cell

Water always moves to regions that have more solutes. 

Paramecium 

Water rushes in to fill up the vacuole when it reaches a certain point it opens a trap dopr and push it out to maintain a certain pressure

Endomembranal System 

Nucleus

Controls the function of the cell & stores genetic material 

Nucleolus: stains deeply create rRNA & tRNA

Chromatin: unwinded DNA wrapped around proteins 

Nucleoplasm: the cytoplasm of a nucleus

Inner nuclear membrane: inner wall 

Outer nuclear membrane: outer wall 

Nuclear pores: openings between the membranes 

Proton complex control the opening and closing of the pores 

Ribosomes: made up of proteins & rRNA on outer membrane 

Nuclear envelope: where the nucleus is held

Ribosomes

Proteins synthesis 

Made up of two parts; large subunit and small subunit 

Made with proteins & rRNA

Bound ribosomes: attached to the membrane 

Free ribosomes: located in the cytoplasm 

Bound ribosome creates proteins for:

• Organisms they are attached to 

• Other organelles 

• Cell membrane 

• Exporting out the cell 

Endoplasmic reticulum (ER)

Endo: in 

Plasmic: thick fluid 

Reticulum: network

Smooth ER

Tubular network of membrane

Liquid synthesis stores Ca^2+ detoxification of harmful chemicals 

Rough ER

Flattened sack-like membrane covered with in bound ribosomes for protein synthesis 

Functions 

• Bound ribosomes release the polypeptide chain into the lumen of the RER

  • Lumen: space contained within a structure 

• Polypeptide chain twists & folds into 2 or 3-degree structure % sugar chains are attached to create glycoprotein. 

  • Sugar chains act as tags for sorting & delivering. 

• Glycoproteins are sorted into the ends of the RER for delivery when the transport vesicle is created by building 

  • Trans vesicle

  • Budding: a process that creates vesicles by pinching off segments from a membrane 

• Newly created transport vehicle packages with protons is delivered to the next destination. 

  • Vesicles: membrane-bound structures that have a spherical appearance and store or transport substances 

  • Big ones are called vacuoles 

Golgi Apparatus 

Functions

• Receives chemicals from other organelles 

• Modifies the chemicals 

• Sorts & packages the chemicals 

• Ships the chemicals to their final destination 

Possible destination 

• Other organelles 

• Cell membrane

• Export out of the cell 

• They become new organelles 

  • Exp: Lysosome 

Lysosome

Specialised vesicle filled with hydrolytic enzymes 

Breaking down… using water 

• Protons 

• Carbohydrates 

• Lipids 

• Nucleic acid 

Major functions

• Phagocytosis

  • A cell process that involves lysosomes which breaks down large structures 

• Autophagy 

  • A cell process where the cell digests…

    • Old worn-out organelles 

    • Damages organelles 

    • Uneeded organelles 

End of endomembranal system 

Energy organelles 

Mitochondrion 

Generates energy in the form of ATP 

Found in all eukaryotic cell 

Chloroplast 

Harvest light to produce food by photosynthesis found in plants & algae 

Chlorophyll is the chemical that absorbs light to provide energy to the chloroplast 

Cytoskeleton 

Skeleton of the cell located in the cytosol 

Cytoplasm = cytosol + organelles 

Components 

Flagells & cilia 

Flagella

Few and very long

Sperm cell

Cilia 

Many & very short 

Inside the throat 

Flagells & cilia have the microtubles in a 9 (doubles) and 2 (singles) arrangement 

Extra Cellular Matrix 

Located on the outside of the cell made up of a network of proteins and carbohydrates found in the extracellular fluid & attached to the cell membrane 

Fibronectin: holds cell matric to the membrane. 

Functions 

• Holds cells together, creating tissues using collagen 

• Communication between cells 

• Identification of self using immunoglobulins (glycoproteins) 

Cell junction

Attach cells together that are adjacent to each other. 

Functions:

1. Tight junction

   1. Holds cells tightly, preventing any substance from passing between them 

   2. Important for the skin & intestine 

   3. Made up of intermediate filaments (fibrous)

2. Desmosome (anchoring J.)

   1. Holds cells together in place but not tightly 

   2. Important for lung cells & cells in capillaries 

   3. Made up of intermediate filimates 

3. Gap junction

   1. Membrane protein (globular) that connects two adjacent cells to create tunnels 

   2. which allows the cytoplasm of one cell to mix with the cytoplasm of another

   3. Such as cardiac muscle 

Cell Wall Plants 

• Made up of cellulose (B Glu)

• Provides the shape of a structure of a plant cell 

• Resits pressure created by cells to become rigid 

• All plants have a primary cell wall, but some woody plants will also have a secondary cell wall

• Cell walls are always built on the outside of the cell membrane. 

Plasmodesmata 

• Plant cell junctions create opening which connect the cytoplasm of adjacent cells 

• Permit rapid movement & communication between plant cells 

Peroxisomes 

• Specialised vesicles filled with hydrogen peroxide (H2O2)

• Mainly found in plants (found only in our liver)

• Oxidation of amino acids & fatty acids 

• Detoxify poison 

*  not produced by Golgi apparatus 

Anatomy of a microscope

Handling

• Hold with 2 hands 

• Don’t slide the microscope 

• Rotate the head if someone wants to see

Parts 

• Eyepiece (ocular lens)

  • Magnifies specimen 10x 

• Diopter adjustment 

  • Zooms in & out 

• Head 

  • Tube w/ mirrors direct light to the eye 

• Nose piece 

  • Changes objective lens 

• Objective lens 

  • Scanning objective lens (4x)

  • Low-power objective lens (10x)

  • High-power objective lens  (40x)

  • Oil immersion lens (100x)

• Arm 

  • Holds upper structure 

• Course adjustment 

  • Moves stage up & down quickly 

• Fine adjustment 

  • Moves stage slightly up & down 

• Stage 

  • Where you place your specimen/ must be over the hole 

• Stage clip 

  • Holds specimen in place 

• Stage control 

  • Moves stage towards or away 

  • Moves stage left or right 

• Condensor 

  • Controls how much light is coming in (pupil)

• Brightness adjustment 

  • Dimmer switch 

• Illumination 

  • Light source 

• Light switch 

• Base 

  • Supports the microscope, keeps it sturdy 

How to draw your specimen 

• Use a pencil & unlined paper. 

• Take up most of the paper 

• Draw on the left side 

• Boundary structures of the specimen is more important than the secondary 

• Stipple method to show dark regions 

• Draw clear, continuous lines, no sketches 

• Draw part by part → look & draw 

• Label parts you can identify; lines need to be drawn by a ruler 

• Do not cross label lines; must touch what they point to 

• No arrowheads 

• Include descriptors 

• Include magnification used 

• Possible specimen descriptors 

  • Cross section 

  • Longitudinal section 

  • Dry mount 

  • Water mount 

  • Stained 

• Include the type of magnification bottom right 

UNIT 5

Membrane Proteins 

Transport proteins

May or may not use ATP for energy to move chemicals in or out of the cell

Signal transduction pathway: involves the use of signalling molecules (either protons or lipids that carry messages for the cell; maybe protein an exp is insulin) Which carry the message to target cells (cells that are able to receive the signalling molecules because they have the appropriate receptor) The receptor (protein that accepts the signalling molecule) locate don the target cells will then release a series of chemicals into the cytoplasm to carry the message to the nucleus. 

Extracellular matrix 

Cytoplasm 

Intercellular junctions 

Cell-cell recognition 

Relies on glycoproteins, macromolecules made up of proteins and carbohydrates. To helps cells in multi-cellular organisms identify each other as self  

Enzymatic activity  

Enzymes which are proteins that speed up or facilitate a reaction, can be located in the cell membrane.  

 Molecules are able to move because of their own kinetic molecular energy (KME) 

 What causes molecules to move the way they do? 

Transport proteins 

Channel & carrier → passive 

Pump                   → active 

1. Uniporters 

• Move chemicals in one direction 

• Either in or out of a cell 

• Exp: aquaporin 

2. Ssymporters 

• Move 2 different chemicals in one direction

• Both either into the cell or out 

• Exp: glucose/Na* contransport 

3. Antiporters 

• Move different chemicals in the opposite direction 

• One goes into the cell and the other goes out 

• Exp: Na* / K* pump 

Passive Transport 

Diffusion 

Diffusion 

• Movement of the substances from high [ ] to low [ ] movement of their substances down their concentrated gradient 

• When molecules move from a concentration to a less concentrated area  

• Electrical charge when molecules always move to balance charges 

Osmosis 

Selectively permeable membrane

Controls what goes from one side to another 

Through this membrane, water will move from an area of high concentration to an area of low concentration.

Type of solution when comparing 

1. Isotonic 

• A solution with a similar concentration of solutes 

2. Hypotonic

• A solution with a lower concentration of solutes than the ones around it 

3. Hypertonic 

• A solution with a higher concentration of solutes than the ones around it

Animal Cells 

Hypotonic 

Inside is hyper so H2O rushes in and it bursts, becoming Lysed

Isotonic *

Rate of water going in matches the rate of water going out (ideal)

Hypertonic 

Inside is hypo so H2O leaves making the cell shrivelled 

Plant Cells 

Hypotonic *

Water enters the cell while extra H2O enters the central vacuole creating pressure on the cell wall, making it turgid (ideal)

 Isotonic 

The rate of water going in equals the rate of water going out; leaves will be droopy because of the lack of pressure on the cell wall. The cell becomes Flaccid or deflated; it can survive, but it is ineffective. 

Hypertonic

The water leaves the cell, causing the cell membrane to get ripped off the cell wall, called plasmolysed. 

Facilitated diffusion 

Movement of soluted from high [solute] to low [solute] with the help of transport proteins 

Transport proteins: Allow cell membrane to be selective 

Channel Proteins 

• Create openings or tunnels for specific solutes 

  • Maybe gated 

• The nature & size of the tunnel allow what goes through 

• Exp: Na* channel / Aquaporin (allows water in)

Carrier Proteins 

• Change shape to carry specific solutes across the cell membrane 

• How it works 

  • When it is in the normal conformation, it will face either the outside or inside of the cell 

  • Specific solute enters the binding sight, which causes the carrier protein to flip counter motion and face the opposite side 

    • Binding sight is the region of a protein where a substrate attaches 

  • In the flipped counter motion the solute is repelled out of the character protein into the new region 

  • The carrier proteins will return back to its normal conformation because no solute is in the binding site 

Active Transport 

Cells must supply energy in the form of ATP to move solutes form low [solute] to high [solute], working against the concentration gradient 

Exp: sodium-potassium pump

Two forms of active transport 

Primary active transport 

• A pump uses ATP to move chemicals against their concentration gradient 

• Exp proton pump 

Secondary active transport 

• A carrier proton moves chemicals against their concentration gradient created by primary active transport 

• Exp: sucrose / H* conransporter 

Sodium Potassium Pump 

How does it work?

Bulk Transport

Using ATP, moves either large-size chemicals or large quantities of chemicals across the cell membrane using vesicles. 

Exocytosis

• Takes chemicals out 

• Exp: when Golgi apparatus produces secretory vesicles filled with proteins that are released out of the cell 

Endocytosis 

• Brings chemicals in

• Exp:

  • Phagocytosis 

    • Brings in large-sized substances into the cell 

  • Pinocytosis 

    • Brings in large quantities of solutes into the cell 

  • Receptor-mediated endocytosis

    • Brings in substances once a trigger (single molecule) active the reception on the cell membrane, which could be the solute itself
      

UNIT 6

Metabolism

All the reactions taking place in an organism 

Anabolism

• Anabolic rxn 

• Building up large molecules 

• Using dehydration rxn

Catabolism 

• Catabolic rxn 

• Breaking down large molecules 

• Using hydraulic rxn 

The first law of thermodynamics: 

Energy is neither created nor destroyed; instead, energy changes from one form to another 

The second law of thermodynamics:

Systems are not efficient; energy is always lost to the surroundings, resulting in disorder, which is called entropy, measured in temp 

Living things are constantly working against entropy by trying to maintain their homeostasis, a constant internal environment. We fight disorder and when we begin to lose, we start to age & die. 

Energy is the ability to do work.

Forms of energy 

• Kinetic: increate in KE → inc heat 

• Potential: stored energy located in the bonds; stronger bonds = more energy 

Heat: the amount of collisions particles form with each other & surroundings 

Temperature: the average movement of particles 

Different energy forms of chemicals 

• Ordered with high energy bonds; very reactivity 

  • Exp: ATP dec Δs

• Ordered with low energy bonds; low reactivity 

  • Exp: glucose, glycogen, lipids dec Δs

• Disordered with low energy bonds: low reactivity 

  • Exp: ADP, CO2 Inc Δs

Energy Graph

The most common chemical used in biology is ATP

ATP     → ADP           + Pi

Adenosine triphosphate → adenosine diphosphate + inorganic phosphate 

Coupling reactions

When two rxn are paired together, one is exergonic, supplying energy to the second rxn, which is endorgonic, allowing it to occur. 

Cellular Work

Most common forms of cellular work 

Chemical Work:

• Definition: Chemical work involves the synthesis of complex molecules, the breakdown of larger molecules into simpler ones, and the conversion of one type of molecule into another.

• Example: An essential example of chemical work is the synthesis of adenosine triphosphate (ATP), which serves as the primary energy currency of cells. During cellular respiration, cells break down glucose into carbon dioxide and water, releasing energy that is used to produce ATP.

Transport Work:

• Definition: Transport work involves the movement of substances across cellular membranes. This can include the active transport of ions or molecules against their concentration gradient, requiring energy input.

• Example: The sodium-potassium pump is a classic example of transport work. This pump actively transports sodium ions out of the cell and potassium ions into the cell against their respective concentration gradients, using energy derived from ATP hydrolysis.

Mechanical Work:

• Definition: Mechanical work involves the physical movement or mechanical manipulation of cellular structures. This includes activities such as muscle contraction and the movement of cilia and flagella.

• Example: Muscle cells perform mechanical work during contraction. The interaction between actin and myosin filaments, powered by ATP, leads to the shortening of muscle fibres and the generation of mechanical force.

Enzymes

Proteins (sometimes RNA) that lower the Ea to allow reactions to happen faster 

How is the Ea lowered?

• Enzyme brings reactants close to each other 

• Brings reactants together in the correct orientation 

• Places stress on bonds, allowing them to break and form more readily 

Catalytic cycle of enzymes 

1. Substrates (reactants) enter into the active site of the enzyme in the correct orientation 

   1. The active site is a specific region of the enzyme where the reaction takes place 

   2. receptors/transport proteins do now have an active site; they have a binding site instead. the binding site is for attachment, holding things

Each enzyme is specific to a substrate that is called the lock-and-key mechanism 

Substrates are attached to the active site, and as soon as they enter it, the active site will wrap tightly around the substrates; this is called induced fit

2. Once substrates are in the enzyme, the enzyme-substrate complex is formed, where the substrate is held by weak intermolecular force in the active site 

3. The enzyme lowers the Ea by placing stress on the bonds of the substrate using the weak intermolecular forces

4. The stress on the bonds created by the active site will allow bonds to break and new ones to form, generating products.

5. Products are repelled by the active site, causing them to leave the enzyme 

6. Enzyme returns back to its original conformation, ready to receive a new substrate 

Other chemicals can help enzymes function, such as…

Inorganic chemicals called cofactors 

Exp: zinc, manganese, copper 

Organic chemicals called coenzymes 

Factors that disrupt enzyme function (all stress)

• Pressure 

• Temperature 

• pH 

• Salt concentration 

• Electricity 

• poison/inhibitors 

These change the structure of the enzyme, resulting in denaturation 

Forms of enzymes 

1. In the active form (more common in bio)

   1. Always function and must be turned off when not needed (inhibited) 

2. Inactive form 

   1. Produced in a nonfunctioning form and must be turned on or activated

Controlling the function of active enzymes 

Inhibitors are chemicals that will inactivate enzymes 

Two types… 

1. Competitive inhibitors 

• Will compete with the substrate for the active site

• This can be controlled by changing the substrate concentration 

• More substrate, lower chance of activation 

1. Reversible competitive inhibitor 

   1. Inhibitor temporarily attaches to the active site and can leave 

2. Irreversible competitive inhibitor 

   1. Permanently attaches to the active site and will not leave 

2. Non-competitive inhibitors 

• Will attach to the enzyme at another location called the allosteric site, causing the active site to change in shape so that substrates will not fit properly

• Or blocks the active site so substrates can’t enter 

• Exists as reversible and irreversible 

Reactions are constantly regulated by feedback. 

Positive

• Feedback activation 

• As more products are created, this causes enzymes to work more and produce even more products 

Negative 

• Feedback inhibition 

• As products increase in amount, the enzyme will be inactivated 

  • The concentration of the product is the inhibitor 

• Example: threonine (amino acids) changes by a series of reactions to isoleucine, the isoleucine attaches have an allosteric site, inhibiting the cell. When isoleucine is used up, it will detach. 

UNIT 7

Overview:
Energy flows in a linear function; compounds are going to cycle between photosynthesis and cellular respiration

An ecosystem is made out of living things as well as nonliving things, with the main light source being the sun.
Photosynthesis needs sunlight as a fuel and then releases organic molecules and O2 as waste. The waste then acts as fuel for cellular respiration with the release of ATP for cellular work. Which has a waste product of CO2 and H2O which gets used up by photosynthesis, creating a cycle. 

Heat energy cannot be recycled.

Entropy is being generated in two ways, waste energy, and cellular respiration waste products. 

Simplified chemical formula for cellular respiration 

6O2 (g) + C6H12O6(aq) → 6CO2(g) + 6H20(l)

Coupling reactions:
ADP + Pi → ATP

Gets energy from Glucose, creating potential and chemical energy

Redox Reactions:
Split into 2 parts, oxidation & reduction

• OIL: oxidation is lost; losing an electron 

• RIG: reduction is gained; gain of electron 

Performed by dehydrogenase, a coenzyme that helps the reaction occur 

In the case of the formula, oxidation is happening from oxygen to carbondioxide and reduction is happening from glucose to water

Phosphorylation

When a chemical gains a phosphate group 

Two types:

• Substrate level phosphorylation 

  • When a phosphate group form an organic molecule is picked up by another organic molecule 

• Oxidative phosphorylation 

  • When a chemical gains a phosphate group using the energy from the oxidation of another chemical

Glycolysis 

Overall reaction 

Takes place in the cytoplasm

Glucose →→→→→→ 2 pyruvates 

Creates:
2 ATP by using 2 ADP & Pi

2 NADH & H* by using 2 NAD*

Ten RXNS of glycolysis 

Linkage Reaction

Krebs Cycle 

The goal of the krebs cycle is to trap as much energy as possible form Acetyl CoA in NADH. FADH2 & ATP

Two e- carrieres 

NAD* + 2e- + 2H* → NADH + H*

Nicotinamide Adenine Dinucleotide 

FAD +  2e- + 2H* → FADH2

Flavin Adenine Dinucleotide

For one glucose molecule 

Electron Transport Chain

Poisons 

Rotenone: 

Attaches to complex 1, stopping the flow of electrons, kills you 

Cyanide:

Attaches to complex 4, preventing the flow of electrons, stops the reduction of O2. it is irreversible, and can kill anyone with small amounts 

Carbon monoxide:

Attaches to complex 4, preventing the flow of electrons, stops the reduction of O2. reversible if caught early enough 

DNP:

Creates holes in the phospholipid bilayer, disrupting the H+ gradient. In large amounts can kill the person, overall stop the flow of ATP

Oligomycin:
Stops ATP synthase, stopping the flow of H+, which stops the creation of ATP

Producing Energy in the absence of O2

          ADP & Pi → ATP

Glucose →→→→→→ 2 pyruvates 

    NAD* → NADH + H*

If there is sufficiant oxygen, it goes through cellular/Aerobic respiration in the mitochondria

If not, it goes through fermentation, anaerobic respiration 

Fermentation 

Lactic Acid

Done by humans/animals/bacteria/fungi 

Lactic acid is a warning mechanism informing you that you are out of oxygen

Alcohol 

Done by plants/bacteria/fungi (yeast)

UNIT 10

Cell division When a cell divides, or splits in half, in order to create new cells

Reproduction when an organism creates new off springs 

Organism 

Unicellular: 

when they reproduce, they perform cell division. The mother  cell divides into two daughter cells 

Multicellular: 

Asexual; involves one parent, produces clone with no genetic difference 

Sexual: involves two parents, produces offspring with egentic differences 

Performs cell division for 

• Repair 

• Growth 

• Maintenance

Budding: when a unicellular organism has a growth appearing in one side that develops into a new individual and falls off; exp: Hydra 

Yeast

When conditions are favourable, yeast will reproduce by budding 

When conditions are not favourable, yeast will produce sexually  

Why? If they aren’t doing well and the condition is bad, they don’t want to clone themselves because they know their offspring will have the same bad condition. If they reproduce sexually, there becomes a chance that the mix of genetics can create a version that will survive the condition

Fragmentation: when a piece of an animal is cut off, and it will grow to become a new individual, exp, star fish 

Vegetative propagation: a survival mechanism where a broken piece of plant will grow to become its own individual 

Chromosomes

A molecule of DNA (double helix) 

Prokaryotic, 

Each prok cell will have one circular DNA molecule 

Eukaryotic,

Each euk will have several linear DNA double helices, each one wrapped around groups of proteins → histones to create chromosomes 

When one chromosome is duplicated, it becomes a set of sister chromatids held together at the centromere, the centre point. 

When it is duplicated, the information is no longer accessible 

Forms of DNA depending of cell activity 

When a cell is NOT dividing 

DNA exists in the form of chromatin, the chromosomes are spread out, and the information is easily accessible 

When a cell IS dividing 

DNA exists in the form of chromosomes that are condolences, wrapped up tightly. Information is no longer accessible 

Cell cycle 

The most basic function of the cell cycle is to duplicate accurately the vast amount of DNA in the chromosomes and then segregate the copies precisely into two genetically identical daughter cells.

Steps of the cell cycle 

Interphase 

1. G1 phase, first gap 

2. S Phase, synthase phase 

3. G2 phase, second gap 

Celldivision→ mitotic phase 

1. Prophase 

2. Prometa phase

3. Metaphase 

4. Anaphase 

5. Telophase 

6. Cytokinesis 

Functions in each step:

First Gap

• Brings in lots of nutrients 

• Generates lots of energy 

• Organelles/proteins & other structures will duplicate 

• Cells grow in size 

Synthase phase 

• DNA is duplicated 

Second Gap

• Everything in the first gap will continue if not finished 

• Checks and corrects any error found in DNA 

If the error cannot be fixed, the cell enters apoptosis; which is cell suicide 

Pro phase

• DNA condenses from chromatin into duplicated chromosomes 

• The nuclear envelope disintegrates, allowing access to the information 

• Centrioles begin to move away from each other to opposite poles

• Spindle fibres, microtubules, begin to form. (from the cytoskeleton) 

Prometa Phase 

• Nucleus disappears 

• Centrioles continue to move to the opposite pole

• Kinetachrome fibres from each centrosome connect to the centrosome of each duplicated chromosome and begin to move them to the equator of the cell

Meta Phase 

• Duplicated chromosomes are lined up at the equatorial plane 

• Centrioles have reached opposite poles 

Ana Phase

• Kinetochore fibres shorten, pulling sister chromatids apart & moving the chromosomes away from each other 

• Non-kinetochore fibres lengthen, stretching the cell

Tela Phase

• The appearance of the cleave furrow indicates the start of cytokinesis 

• Spindle fibres disintegrate 

• Formation of nuclear envelope around each set of chromosomes 

• DNA unwinds from chromosomes and into chromatin 

Mitosis 

• Duplication of the nucleus 

Cytokinesis 

The division of the cytoplasm of the cell

• Animal cells

  • rely on a belt of proteins known as the contractile ring, which is made from actin

• Plant cells

  • does not rely on a contractile ring because the cell is way too rigid.

  • Golgi apparati at each end of the cell will produce transport vesicles that fill with pectins that move to the centre of the cell

  • at the centre of the cell, the transport vesicles fuse with each other to create the cell plate

    • the cell plate lines up in the middle of the cell to become the new cell wall

  • the cell plate continues to grow and reach the cell membrane to become the cell membranes of the two new cells, the cells will be attached by the middle lamella that is filled with pectin

  • cellulose is secreted by each new cell to create its own cell wall

Drawing of the cells;

Factors that are controlling the cell cycle

• space is required around cell for them to divide; density-dependence

  • in tissues, cells form layers and not clumps; cells do not grow on top of each other

• a rigid surface is needed for attachment before cells can divide; anchorage dependence

• signal molecules called growth factors inform cells that they need to enter the cell cycle