Biochemistry (Grade 12)

What are the organic molecules?

Carbohydrates, Lipids, Proteins, Nucleic Acids (Also vitamins and minerals)

Macromolecules

A very large compound containing Carbon, Hydrogen, Oxygen, Nitrogen

Carbohydrates

• Molecules containing carbon, hydrogen, oxygen, atoms in a 1 : 2 : 1

• Most are polar molecules that dissolve in water

• A source of energy and used for building material

• Polymer : Polysaccharide

• Monomer : Monosaccharide

Polysaccharide Examples

• Maltose : Glucose + Glucose

• Sucrose : Glucose + Fructose

• Lactose : Glucose + Galactose

Monosaccharide Examples

• Glucose, Fructose, Galactose, Deoxyribose, Ribose

Isomers

• Molecules with the same chemical formula but a different arrangement of atoms (Different structures)

Joining Monosaccharides

• Covalent bonds between two sugars is called a Glycosidic Linkage

Polysaccharides

• 3 glucose shapes = 3 polysaccharides with 3-D shapes and functions

Starch

• Means for storing energy in plants

• Humans digest starch for energy

• Structure : Has some branches coming off the main chain, some 1,6 Glycosidic Linkages (Mainly 1,4 Glycosidic Linkages)

Cellulose

• Component of cell walls

• Cannot be digested by humans but we need it (fibres) to aid  in the process of digestion

• Structure : Linear Polymer, each subunit flips orientation

Glycogen

• Means for storing glucose in animals

• Used to regulate blood sugar

• Structure : Many 1,4 and 1,6 Glycosidic Linkages, easily broken down due to numerous branching side chains

Chitin

• A polymer made from modified chains of glucose

• Found in exoskeletons of insects, cell walls of fungi, and certain hard structures in invertebrates and fish

Lipids

• Non-polar, hydrophobic

• Used for long term energy storage (more efficient than carbohydrates)

• Physical and thermal insulation

• Key component of cell membranes

• Used to make hormones

Triglyceride

• Most common type of lipid

• Composed of 1 Glycerol molecule and 3 Fatty Acids

• Function as long term energy storage in animals

Saturated Fatty Acid

• Have no double bonds between carbons

• Saturated with hydrogen

• Solid at room temperature

  • The straight chains are able to fit (pack) tightly together by stacking on top of each other

• Source : animals

Unsaturated Fatty Acid

• Have 1 or more double bonds between carbons

• Not saturated with hydrogen

• Liquid at room temperature

  • Bends created by double bonds and chains do not allow for them to be packed together nicely

• Source : Plants

Phospholipid

• A glycerol molecule attached to 2 fatty acids

• Form cell membranes (phospholipid bilayer)

Sterols

• Consists of four linked carbon rings

• Create hormones with the body 

Waxes

• Long fatty acids linked to alcohols and carbon rings

• Waterproof coating on plants and animals

Proteins

• Made of amino acid polymers (chains)

• 20 different amino acids, 8 are essential (must be consumed cannot be made)

• Number and order of amino acids determines type of protein

• Genetic information in the DNA codes for the production of proteins

Structure of Amino Acid

• Depending on R-group, can be polar, non-polar, or electrically charged

• Amino acids are joined by covalent bonds called peptide bonds (form between carboxyl of one acid and amino of another)

Protein Structure

• Proteins made by many amino acids are known as polypeptides

• There are four levels of protein structure that determines function

Primary Structure

• The sequence of amino acids held together by (covalent) peptide bonds

Secondary Structure

• The folding and coiling of a polypeptide chain as it forms alpha helices or beta pleated sheets

• Held together by hydrogen bonding in the main chain (N - C - C)

Tertiary Structure

• Additional folding due to interactions between the side chains (lots of side chain interactions where polar, soluble groups face out, and non-polar, insoluble groups face in) 

  • Hydrophobic interactions (non-polar side chains)

  • Electrostatic Interactions (+ / -)

  • Hydrogen Bonding

Quarternary Structure

• Two or more polypeptide chains come together, forming a multi-subunit protein (They become one big unit)

Function of Proteins

• Make cell structure required for growth and repair

• Act as enzymes to help in chemical reactions

• Help transport substances across the cell membrane or around the organisms

• Act as chemical messengers (Hormones)

Denaturation

• When a protein loses its structure (unfolds or changes shape) and it unable to carry out its biological functions

• Occurs due to extreme temperatures, changes in pH levels, and radiation

Nucleic Acids

• Found in DNA, RNA, ATP, etc

• DNA and RNA are nucleotide polymers

• Nucleotides consist of a nitrogenous base, 5 carbon sugars, and a phosphate group

Function of Nucleic Acids

• DNA codes for genetic information

• DNA and RNA code for and produce proteins

Nitrogenous bases

• Pyrimidines

  • Cystosine, Uracil, Thymine

  • Single ring structure

• Purines

  • Adenine, Guanine

  • Double ringed structure 

• Adenine + Thymine / Uracil = 2 Hydrogen bonds

• Cytosine + Guanine = 3 Hydrogen bonds

Neutralization Reactions

• An acid produces hydrogen (H⁺) ions in water

• A base produces hydroxide ions (OH^-) ions in water

• pH scale classifies substances as acidic or basic

• When an acid and a base react, they undergo a neutralization reaction that results in the formation of a salt and water

pH Buffers

• Normal pH range of the body is 7.35 - 7.45

• Maintain optimum pH ranges

• They are substance that minimizes changes in pH by donating hydrogen ions when fluid is basic or accepting hydrogen ions when fluid is acidic

• Carbonic Acid into Bicarbonate blood buffer is the most important

Oxidation Reduction (Redox) Reaction

• Molecule loses electrons → Oxidation

• Molecule accepts electrons → Reduction

• Oxygen is often a reactant

• In cellular respiration, sugar is oxidized.

Dehydration Synthesis (Condensation) Reaction

• A larger molecule is formed from two smaller subunits, a process that absorbs energy

• Two subunits link together through the removal of a water molecule

• Water is formed when a hydroxyl of one molecule reacts with a hydrogen atom from another molecule 

• Assembles long chains

Hydrolysis Reaction

• Smaller molecules are formed from a bigger molecule, a process that releases energy

• Two subunits break apart through the addition of a water molecule

• A water molecule provides the H atom for one subunit and the hydroxyl to the other subunit

• Breaks apart long chains

Types of Bonds / Linkages

• Carbohydrates - Glycosidic Linkage

• Lipids - Ester Linkage

• Proteins - Peptide Bonds

• Nucleic Acids - Phosphodiester bonds

Enzymes

• Protein catalyst (a substance that speeds up a chemical reaction without being used in the process)

  • All enzymes are catalysts, not all catalysts are enzymes

• Control many of the metabolic reactions (Condensation, Hydrolysis, Redox)

• Living things can not rely on high temperatures, they use catalysts to allow reactions to proceed

• The energy required to begin any chemical reaction is called the ‘activation energy’

• Cell manufacture specific protins (enzymes) to act as catalysts and increase the rate of reactions

Substrate

• The reactant that an enzyme acts on when it catalyzes a chemical reaction

Active Site

The locations where the substrate binds to an enzymes

How enzymes work

• Substrate and active sites must possess compatible shapes to bind (Substrate fits like a glove)

1. The substrate fits into the enzyme’s active site, creating an enzyme-substrate complex

2. Enzyme slightly changes shape and distorts the substrate

3. The enzyme releases the substrate after a reaction has occured. After this, it is called a product, not substrate

4. The enzyme remains unchanged and is free to combine with another substrate

Lowering Activation Energy

• Orients substrate correctly

• Straining substrate bonds

• Providing a favorable microenvironment 

• Covalently bonding to the substrate

Competitive Inhibitors

• Substance that compete with the substrate for an enzyme’s active site

Noncompetitive Inhibitors

• Substances that bind on the enzymes at different locations than the active site, causing the enzyme to change its shape (confirmational change in the active site) (substrate cannot bind)

Allosteric Regulation

• Control of enzymes activity (can inhibit or stimulate enzyme)

• Similar to non-competitive inhibitors

  • The inhibitor makes the inactive form of the enzyme

  • Activator binds and keeps all active sites available to substrates

Feedback Inhibition

• Controls a sequence of reactions

• A product later in a sequence of reactions inhibits the enzyme that catalyzes a reaction earlier in that process

  • The product (buildup) of the reaction inhibits the first reaction (earliest) but as it gets used up (as it’s blocked the body will eventually require the inhibiting substance, causing it to diffuse away freeing it), and then more of the initial substance is produced

Regulation by Location

• Cells can control metabolic processes by restricting the location of enzymes

Cell Theory

• All living organisms are made up of cells

• The cell is the basic unit of life

• All cells come from pre-existing cells

Types of Cells

• Prokaryotes : Single-celled with no nucleus

• Eukaryotic : Single or Multi-cellular with complex internal structure ( + nucleus)

Basic Features of a Cell

• Plasma (Cell) membrane

• Cytosol (Semi-fluid substance)

• Chromosomes

• Ribosomes (Makes proteins)

Cell Membrane

• Seperates the cytoplasm and its contents from the external environment

• Brings essential materials into the cell and excretes the metabolic wastes

• Composed of mainly phospholipid molecules

• Withing the cell membrane their are :

  • Cholesterol : A type of lipid that allows the cell membrane to maintain its fluidity

  • Integral Proteins : proteins in the cell membrane that span the entirety of its width (cross the entire thing) and are typically used to aid facilitated diffusion of large molecules

  • Peripheral Proteins : Found only on one side of the cell membrane

  • Glycoproteins : proteins that were modified to have carbohydrates within them, typically found attached to integral proteins on the cell membrane

Cytoplasm

• Jelly-like substance within the cell membrane that contains the organelles and RNA (nucleus excluded)

• Cytoskeleton is found in cytoplasm, made of tough stringy fibres that give support and aid in movement

Organelles

• Structures that perform certain functions within cells (Growth, metabolism, reproduction, etc)

Nucleus

• Contains nucleoplasm which fills up the nucleus and the nuclear matrix which functions as a structural component of the interior

• Controls and regulates cellular activities

Nucleolus

• Darker area of the nucleus

• Contains chromatin (DNA with protein wrapped around it) and RNA

• Where ribosomes are made

Nuclear Envelope

• Double phospholipid bilayer that contains nuclear pores (group of proteins forming openings in the nucelar envelope) which allow substances to travel in and out of the nucleus

Lumen

• Area between two phospholipid bilayers, where small particles and water can freely move around (enter/exit)

Endoplasmic Reticulum

• A folded membrane that is the passageway for moving materials to different parts of the cell

• Connected to the nuclear envelope

  • rough ER - rough surface due to ribosomes used for making proteins that LEAVE the cell - Muscles normally have more rER due to their need for proteins

  • smooth ER - No ribosomes on its surface, typically synthesizes lipids and has other functions based on its location in the body, makes transport vesicles - Liver has more sER due to its helpfulness in detoxifying substances

Ribosomes

• Area at which proteins are synthesized

Golgi Bodies

• Packages proteins and secretes them to outside the cell

• Responsible for making different types of vesicles (secretory, lysosomes)

• Cis-face receives transport vesicles

• Trans-face makes vesicles

Endomembrane System

• Consists of : Nuclear Envelope, sER + rER, Transport Vesicles, Golgi Apparatus, Lysosomes, Secretory Vesicles

• Steps :

1. rER makes polypeptides (proteins) from the ribosomes on their surface which is transported to the sER

2. sER receives these proteins and makes its own lipids

3. sER portions pinch off (containing the proteins or lipids) into Transportation Vesicles to be transported to the cis face for the Golgi Apparatus (cis face is the thinner side of the golgi apparatuse that receives vesicles)

4. Golgi Apparatus (cis) recieves vesicles and stores/packages/modifies the proteins/lipids further

5. Once done, these proteins/lipids travel to the trans face of the Golgi Apparatus, where they pinch off into various vesicles (Secretory Vesicles, Lysosomes (in animal cells), Vacuoles, etc.)

Lysosomes

• Pinch off the Golgi Apparatus

• Filled with enzymes that catalyze hydrolysis reactions

• Breakdown macromolecules

Peroxisomes

• Membrane enclosed sacs containing enzymes that catalyze redox reactions

• Pinch off the ER

• Essential for detoxifying things → commin in liver

Vacuole

• Membrane bound sacs used for transport and storage

• Vesicles are small, Vacuoles are larger

• Animal : Stores water, nutrients and waste

• Plants : Water collects in the cell vacuoles producing rigidity (without sufficient water the plant will wilt due to lack of pressure)

Mitochondri(on)a

• Smooth outer membrane and a folded inner membrane called cristae

• Fluid space inside the organelle is called the matrix

• Provides energy for the cell and is the site of cellular respiration

  • Glucose + O² → CO₂ + H₂O + energy

Centrioles

• Only found in animal cells 

• Involved in cellular division

Cell Wall

• Plants have cell walls

• Compositional compounds depend on the type of cell (elements)

• Shapes and supports the plant cell structuraly

• Made of cellulose and chitin

Chloroplast

• Found only in plants

• Contains chlorophyll which absorbs light energy for photosynthesis

• Uses sun’s energy to make food for the plant cell through photosynthesis

  • CO₂ + H₂O + sun’s energy → glucose of O₂

Cytoskeleton

• All cells contain this internal network of protein fibres

• It is structural support and is the route on which organelles and vesicles move along

Fluid-Mosaic Model of the Cell Membrane

• Made of a double layer of phospholipid molecules called the phospholipid bilayer

• Term ‘fluid’ is used because phospholipid molecules and proteins are free to drift around and fix any breaks in it’s membrane

• It is selectively permeable

  • Can regulate what enters and leaves the cell.

  • Hydrophobic (lipids) molecules can pass through freely (as they can move through the phospholipid tail)

  • Hydrophilic (carbs / proteins) molecules do not pass through freely and need to use transport proteins (cannot move through phospholipid tail without TP)

Passive Transport

• The movement of materials across a cell membrane without the use of energy from the cell

• 3 Different types : Diffusion, Osmosis, Facilitated Diffusion 

Diffusion

• Movement of molecules from an area of high concentration to an area of lower concentration (along the concentration gradient)

• Equilibrium is achieved when the particles are evenly spread out

Factors Affecting Rate of Diffusion

• State of Matter : Gas diffuses quicker than liquids

• Temperature : Diffusion is faster at higher temperatures

• Size of a molecule : Larger molecules cannot diffuse across a membrane

Osmosis

• Diffusion of water across a membrane

• Water moves from an area of high water concentration to an area of low water concentration until equilibrium is reached

Types of Solutions (RATIO not amount)

• Hypotonic : Solution that contains more water than inside the cell. 

  • Animal Cells : Water enters by osmosis, cell will swell + may burst (cytolysis)

  • Plant Cells : Water enters by osmosis, cell wall will swell and push on cell wall, creates turgor pressure, normal for plant cells

• Hypertonic : Soluton that contains less water than inside the cell

  • Animal Cells : Water leaves by osmosis, cells will shrink (called crenation)

  • Plant Cells : Water leaves by osmosis, cell membrane shrinks away from the cell wall (called plasmolysis)

• Isotonic : Solution that contains the same amount of water as inside the cell

  • Animal Cells : Water enters and leaves at the same rate, no overall change, normal for animal cells

  • Plant Cells : Water enters and leaves, no overall change, plant becomes flacid-limp

Osmoregulation

• Control of water balance

• Some fresh water organisms have the ability to pump out water so that they do not burst

Facilitated Diffusion

• Some molecules are too large to pass through the cell membrane

• Molecules enter the cell by diffusion along the concentration gradient with the help of a transport protein but no energy is required

• A particular transport protein will recognize a certain molecule and will undergo confirmational changes as they allow molecules through

Active Transport

• When cells need to move molecules against the concentration gradient, this process requires energy

• 3 Different types :

  • By carrier proteins

  • Endocytosis

  • Exocytosis

• Needed for :

  • Stockpiling nutrients inside the cell

  • Completely removing harmful wastes

  • Important for homeostasis (Maintains constant internal environment despite changes in external environment)

By Carrier Protein

• Membrane proteins that pump molecules against the concentration gradient

• Requires ATP to power the movement

Movement of Large Particles (vesicle formation)

• Endocytosis : a cell or single celled organisms surrounds a particle and encloses it in a vesicle to transport it inside the cell

  • Phagocytosis : ‘Cell-eating’ - engulfing solid particles

  • Pinocytosis : ‘Cell-drinking’ - engulfing liquid droplets / particles

• Exocytosis : a cell releases a particle by enclosing it in a vesicle that moves to the cell membrane, fusing with the membrane, and releasing the particles that were inside the vesicle