Unit 1: Biochemistry - Grade 12 Exam Review

Dehydration Synthesis Reaction (Condensation)

• Assembly of macromolecules 

• Removal of an -OH from one reactant and -H from another reactant 

• The -OH and -H form H2O, while the two reactants join together forming a covalent bond 

• Type of Anabolic Reaction: Used to assemble small molecules together into larger ones 

Hydrolysis Reaction

• Reverse of dehydration reactions 

• Disassembly of macromolecules 

• Water is a reactant to split a large molecule into smaller subunits 

• A covalent bond in the reactant molecule is broken and the -H and -OH from the water are attached, forming two products 

Catabolic Reaction

• Macromolecules broken down into subunits (eg. digestion)

• Eg. Hydrolysis

Properties of Water

• Universal Solvent  

• Hydrogen bonds form between water molecules in both liquid and ice, forming a water lattice.

Liquid Water

• Hydrogen bonds that hold the lattice together, constantly breaking and reforming in new configurations. 

• This gives liquid water its ability to float.

Ice

• Water lattice is a rigid crystalline structure 

• Each water molecule in ice forms four hydrogen bonds with neighboring water molecules 

• This spaces water molecules farther apart that in liquid, so ice is less dense

Specific Heat Capacity

• Specific heat: Amount of thermal energy required to increase the temperature of a given quantity of water by a degree. 

• As heat is added to water, most is absorbed by the process of breaking the H-bonds in the water lattice, which increases water temperature slowly 

• Water stays liquid until 100 degree C

Cohesion (Water Sticks to Water)

• A property of water where H-bond lattice results in water molecules staying close together 

• This creates surface tension: how difficult it is to stretch or break the surface of a liquid 

• This allows small insects to walk on water

Adhesion (Water Sticks to Other Stuff) 

• Property where water molecules can form H-bonds with other polar molecules

• Eg. Water sticking to your skin when you get out of the shower

Aqueous Solutions

• Water molecules are small and very polar 

• They surround other polar and charged molecules and ions 

• This hydration shell, reduces attraction between these other molecules and promote their separation (breaks the ion apart) 

• This separation allow the substance to dissolve in the solution

Hydrophilic Molecules

Polar molecules or ions that are strongly attracted to and very soluble in water

Hydrophobic Molecules

Non-polar molecules that are not strongly attracted to and soluble in water

Three Types of Carbohydrates

Monosaccharides, Disaccharides and Polysaccharides

Monosaccharides

• “Mono” is single, “Saccharide” is sugar 

• Simplest sugar 

• Have ratio of C:H:O = 1:2:1 

• Distinguished from one another by: 

• Carbonyl group: either aldehyde or ketone 

• Length of Carbon chain

What happens when Carbohydrates dissolve in water?

• Monosaccharides with five or more carbons are linear in dry state, but form rings when dissolved in water 

• Example: When glucose dissolves in water, the -OH group at carbon 5 reacts with the aldehyde group at carbon 1 to form a closed ring 

Beta-Glucose

50% chance the -OH group at Carbon 1 will end up above the plane of the ring

Alpha-Glucose

50% chance the -OH group at Carbon 1 will end up below the plane of the ring

Disaccharides

• Sugars containing two (disaccharides) simple sugars 

• Linked together by a 1-4 glycosidic linkage: A covalent bond between 2 monosaccharides by a condensation reaction (dehydration synthesis) 

  • The hydroxyl group of carbon 1 of the glucose molecule links with the hydroxyl group of carbon 4 of the adjacent molecule:

Disaccharide Chart

Polysaccharides

• Formed by linking monosaccharides (several 100 to several 1000) by glycosidic linkages 

• Can be straight chained, or branched

• Very polar due to many hydroxyl groups 

• Hydrophilic but will not dissolve due to large size 

• Have two important biological functions: 

  • Energy storage (starch and glycogen) 

  • Structural support (cellulose and chitin)

Starch

• Main form of energy storage in plants 

• Plants produce starch by linking excess glucose molecules together

• Two types: Amylose & Amylopectin

Amylose

No branches, all 𝛂-1, 4-glycosidic linkages

Amylopectin

Branched, 𝛂-1, 4-glycosidic linkages for main chain and 𝛂-1, 6-glycosidic linkages for branches

Glycogen

• Storage polymer in animals (muscle and liver) 

• Glycogen stores small; depleted in a day if not replenished 

• Highly branches: (𝛂 1-4) linked glucose main chain with (𝛂1-6) linked branches 

• More branching and more compact than amylopectin (starch)

Cellulose

• Major component of cell walls 

• Straight chain polymer of beta-glucose held together by ꞵ-1-4 glycosidic linkages, where every other glucose molecule is inverted 

• Humans cannot digest cellulose because they lack an enzyme to hydrolyze ꞵ-1-4 linkage (roughage) 

• Provides rich supply of energy for organisms who can break it down

Lipids

• Lipids are nonpolar biological molecules  that provide long term energy storage, insulation, cushioning of internal organs and are the main component of the cell membrane 

• Lipids are the main structure of some hormones 

• All lipids are hydrophobic (do not dissolve in water) 

Five Main Types of Lipids

1. Fatty Acids

2. Fats

3. Phospholipids

4. Steroids

5. Waxes

Fatty Acid

• Consist of a long chain of carbon and hydrogen atoms with a terminal carboxyl functional group 

• Carboxyl gives its acidic properties 

• The longer the chain the more hydrophobic it becomes

What are the two types of Fatty Acids?

• Saturated

• Unsaturated

Saturated Fats

• Contain the maximum number of hydrogen atoms per carbon atom

• No double bonds - a straight chain

Unsaturated Fats

Contain a carbon double bond formed by removal of H from carbon skeleton - chain with a bend in it

Polyunsaturated

Contains more than one carbon double bond 

Fats

• Energy storage molecule - more than 2x energy than carbohydrates 

• The most common fat is the triglyceride which contain 3 fatty acid chains attached to a glycerol backbone. 

• They are linked with a dehydration synthesis reaction and are held together with an ester linkage.

Phospholipids

• The main component of cell membrane 

• Composed of two main parts, a phosphate head and two fatty acid tails 

• Amphipathic: The phosphate head is polar and hydrophilic while the fatty acid chains are nonpolar and hydrophobic (similar to soap) 

• Ester and Phosphate ester linkages to a glycerol

Steroids

• Consist of four linked carbon rings 

• Different steroids have different functional groups attached to the rings 

• Steroids rings are hydrophobic 

• Group of steroids Sterols, have a single polar -OH group at one end 

• Gives molecule dual solubility properties 

• Includes Cholesterol(component of the cell membrane), and sex hormones

Waxes

• Waxes are composed of long-chained fatty acids that are attached to an alcohol or a carbon ring

• Waxes are hydrophobic, non-polar and are firm yet pliable 

• EX. Cutin: Water resistant coating on plants, bird feathers, and beeswax

Proteins

• Make up 50% of the dry mass of most cells 

• Structural value: Collagen (tendons, bones) and keratin(hair, nails) 

• Enzymes that are used as catalysts in chemical reactions 

• Transport materials throughout the body like oxygen and carbon dioxide 

• Produce antibodies that destroy foreign bacteria and viruses 

• Form structures that allow transport across the membrane

Structure

• Proteins are large polymer units made up of amino acids monomers 

• The overall shape of a protein is determined by the amino acids that it is composed from 

• The structure of a protein is important in determining its overall function. It has to be the EXACT fit because if the shape changes, then the protein may not be able to perform its function properly

Structure of Amino Acids

• Consist of a central carbon bonded to four different covalent partners 

• Hydrogen atom 

• Carboxyl 

• Amino group 

• R group

• There are 20 different R groups which results in 20 different amino acids 

• R groups give amino acids their properties (polar, non-polar, acidic, etc) 

• 8 amino acids are considered essential - only obtained through diet

Amino Acid Linkages

• Amino acids are linked together through condensation (dehydration synthesis) reactions 

• The carboxyl group of one amino acid bonds to the amino group of a second amino acid to form a peptide bond. 

• When two amino acids bond, the resulting molecule is called a diepeptide.

• The chain of more than 50 aa’s(amino acids) is called polypeptide

Primary Structure

• Unique linear sequence of amino acids in a polypeptide chain 

• Changing a single amino acid will alter the overall structure of the protein 

• Unlimited combos of primary structure, specific to each protein (20 combos for each spot of the chain)

Secondary Structure

Results from hydrogen bonding between carboxyl group of one amino acid and the amino group of a neighboring amino acid

𝛂-helix

Coil structure held together by h-bonds between every fourth amino acids

ꞵ-pleated sheet

• Two separate polypeptide strands that run parallel to each other interact due to H bonds, an accordion shape appears 

• Ex. Strength of silk

Tertiary Structure

• The polypeptide chain continues to bend, fold and contort itself as a result of the interaction between the “R” groups. 

• Polar, non-polar and ionic “R” groups interact to form hydrogen, covalent, and ionic bonds 

• Forms a large globular arrangement 

• EG. Amino acid cysteine contains a sulfur atoms that will form a disulphide bridge with another cysteine atom

Quaternary Structure

• Some proteins consist of two or more polypeptide chains combined into one functional macromolecule 

• Same types of bonds/interactions as tertiary structure 

• The final structure of a protein (confirmation) is critical as its orientation and shape is directly related to its function. Many diseases and disorders are a result of an improperly functioning protein.

Protein Denaturation

• Results from changes in the 3D shape caused by temperature, PH or ionic concentration changes 

• Protein unravels and looses conformation 

• If peptide bonds break the protein is destroyed 

• Enzymes function best within a narrow range of the above conditions

Nucleic Acids

• Assembly instructions for all proteins in living organisms 

• Includes DNA and RNA 

• DNA and RNA are polymers that are made up of monomer units, these are called nucleotides

• Nucleotides have three parts: 

  • Nitrogenous base 

  • 5-C sugar 

  • Phosphate group (s)

DNA

• Source of genetic information for every living organism 

• Directs all cellular activities and is able to replicate itself so that new cells and organisms can be created

Nitrogenous Base

• Divided into two groups based upon the number of rings in the structure 

  • Purines: Two rings, adenine and guanine 

  • Pyrimidines: One ring, thymine and cytosine

Linkage and Phosphodiester Bonds

• DNA nucleotides are joined together at the phosphate group through phosphodiester bonds between carbon 5 of one molecule to the hydroxyl group at carbon 3 from another molecule 

• Additional nucleotides are always added in the 3 end of the previous nucleotide

Hydrogen Bonds

• DNA is a double stranded molecule where the 2 strands run anti-parallel to each other 

• Hydrogen bonds unite strands of DNA together 

• Adenine will always bind to thymine by 3 hydrogen bonds 

• Guanine and cytosine will always bond together by 3 hydrogen bonds 

• A purine will only pair up with its complementary pyrimidine

RNA

• Single stranded polymer 

• Involved in protein synthesis 

• Composed of: 

  • Ribose sugar 

  • Phosphate group 

  • 4 nitrogen containing bases (C, G, A and U) 

  • All of the bases are the same as those found in DNA except Uracil (uracil replaces thymine in RNA)

RNA Linkages: Phosphodiester Bonds

• Also synthesized in the 5’ to 3’ direction in a condensation reaction 

• A phosphodiester bond forms between phosphate group from one nucleotide and the hydroxyl group from the second nucleotide

Deoxyribose vs. Ribose

DNA vs. RNA

What is an Enzyme?

• Biological catalysts that increase the speed of biochemical reactions within cells. 

• Enzymes are proteins that are NOT consumed during reactions 

• They can catalyze the same reaction repeatedly 

• Each enzyme has a unique shape, which determines which reactions it catalyzes 

Induced Fit Hypothesis

• Initially the active site is not a direct fit for the substrate 

• Just prior to substrate binding, the enzyme modifies its shape to better accommodate the substrate 

• The enzyme binds to the substrate 

• Creates an enzyme-substrate complex 

• Enzyme converts substrate into product(s)

List the factors that affect Enzyme Activity

1. Enzyme and Substrate Concentration

2. Enzyme Inhibitors

3. pH and Temperature

Enzyme and Substrate Concentration

• If excess substrate, rate of reaction becomes proportional to enzyme concentration 

• If enzyme at a constant concentration, increasing substrate concentration will only increase reaction rate to a point called saturation level 

• At this point, all enzyme molecules saturated with substrate 

What are Enzyme Inhibitors? List the two types of inhibition

• Molecules that bind to an enzyme and lowers the rate at which it catalyzes a reaction 

• Competitive and Non-Competitive

Competitive Inhibitors

• Compete with the substrate for the enzyme’s active site 

• Shape/Mimics substrate 

• Enter the enzyme’s active site and prevent the normal substrate from binding

Non-Competitive Inhibitors

• Does not compete for active site 

• Attaches to enzyme on a site other than the active site (allosteric site) 

• Causes the enzyme to change shape, so that active site looses affinity for its substrate

Allosteric Regulation

• Allosteric regulation is a mechanism by which a molecule binds to an enzyme at a site other than its active site, called the allosteric site, altering the enzyme's activity.

• This binding can either inhibit or activate the enzyme, depending on the nature of the regulator.

• Regulatory molecules bind to a site located far from the active site called an allosteric site  

• Allosteric activator: keeps the active site of an enzyme available to its substrate 

• Allosteric inhibitor: Is a non-competitive inhibitor

Feedback Inhibition

• A product of a reaction acts as a regulator of the reaction 

• Used by cells to control metabolic pathways involving series of reactions 

• If the product accumulates in excess, its effect as an inhibitor automatically slows or stops the enzymatic reaction that produces it.

• If the product is scarce, the inhibition is reduced, and the rate of the reaction increases.

• Product formed later in sequence allosterically inhibits the enzyme catalyzing the first reaction of the pathway 

• Each reaction catalyzed by specific enzyme 

Temperature

• As temperature increases beyond a critical point, enzymes denature 

• Every enzyme has an optimal temperature at which it works best (humans -37 C)

pH

• Enzymes have optimal pH range 

• Eg. Pepsin works best at pH of 2 in stomach, inactive in small Intestine pH of 8

The Cell Membrane

• Separates the living cell from nonliving surrounding

• Selectively Permeable - Controls which substances can cross the membrane, allows some substances to cross more easily than others

• Keep nutrients in and waste products out

The Fluid Mosiac Model

• Membranes are not rigid, with molecules locked in place

• Instead molecules are in constant motion (Fluid Part)

• Membrane consists of a fluid phospholipid bilayer - proteins embedded into it float freely

• There are many types of proteins, lipids and carbohydrates embedded in the membrane (Mosiac Part)

Phospholipids

• Phosphate Group Head (Hydrophilic Polar Head)

• 2 Fatty Acid Tails (Hydrophobic Non-Polar Tails)

• Forms a lipid bilayer in aqueous (watery environments) that is two lipid molecules thick

• No water inside the lipid bilayer itself - water is present outside and inside the cell

Fluidity - Saturated Fatty Acids

• Saturated hydrocarbons - each carbon is bound to the maximum number of hydrogen atoms

• Single bounds cause the membrane to form a semi solid gel due to linear arrangement

• Have a straight shape - lipids are able to pack together more tightly

Fluidity - Unsaturated Fatty Acids

• Double bonds in an unsaturated fatty acid bend its structure - lipid molecules are less straight and more loosely packed

• Double bonds keep membrane fluid (less viscous)

Cholesterol

• A type of sterol (steroid with OH group at one end and hydrocarbon chain at the other)

• Plays a role in membrane fluidity

If temperature is High

• Phospholipids move quickly and membrane may become too fluid

• Cholesterol helps to restrain the movement of the lipid molecules in a membrane thus reducing the fluidity of the molecules

If Temperature is Low

• Phospholipids become tightly packed and membrane may become a highly viscous semi-solid gel

• Cholesterol occupies space between phospholipids

• Keeps the oil bilayer flexible in cold temps - prevents fatty acids from associating and forming a non-fluid gel

Integral vs Peripheral Membrane Proteins

All membrane proteins can be separated into these two additional categories

1. Integral Membrane Protein → Embedded in the lipid bilayer

2. Peripheral Membrane Protein → On the surface of the membrane

Integral/Transmembrane Proteins

• Span the entire bilayer and are exposed to the aqueous environment on both sides of the membrane

• Within Membrane - Non polar amino acids are hydrophobic which matches the hydrophobic region of the phospholipid tails

• Outer Membrane - Polar amino acids are hydrophilic and extend into the extracellular fluid on the outside and into the cytoplasm on the inside

• Transport Proteins → Acts as channels or pumps

Peripheral Proteins

• Loosely bound to the surface of the cell membrane

• Do not interact with the hydrophobic core of the membrane

• Outer Surface - They hold onto the surface of the membrane with ionic and H-bonds. Most are on the extracellular side of the membrane, but some are on the cytoplasm side as well.

• Act as cell identity markers (antigens) or receptors

• Inner Surface - Anchor points for microtubules or microfilaments

Membrane Carbohydrates

• Some of the membrane lipids and proteins have carbohydrates linked to them.

• Called glycolipids (any membrane lipid + carbohydrate) or glycoproteins (membrane component with sugar or carb + aa)

• Crucial for cell-cell recognition and signaling

• Allows the cell to distinguish one cell from another and to identify foreign cells or particles (bacterial or viral infections)

• Recognize and bind to carbohydrate receptors on adjacent cells and leads to attachment between cells

Passive Transport

• The movement of a substance across a membrane without the need to expend chemical energy (ATP)

• Universe tends towards disorder (entropy)

• If molecules are more concentrated on one side of a membrane, they will become equally distributed on both sides until equilibrium is reached

What are the three types of passive transport?

1. Simple Diffusion

2. Facilitated Diffusion

3. Osmosis

Simple Diffusion

• The ability of a substance to move across a membrane unassisted 

• Movement of a substance from high to low concentration (no energy needed) 

• Rate of diffusion depends on the concentration gradient between two sides of a membrane 

• Dynamic equilibrium - even after the concentration of molecules is the same on both sides, they continue to move from one side to the other 

What can Diffuse Through The Phospholipid Bilayer?

• Very small non-polar molecules can get through directly (eg. oxygen gas and carbon dioxide) 

• Small, uncharged polar molecules (eg. water and glycerol can also cross easily) 

What Molecules Cannot Can’t Through Directly?

• Ions (positively charged Cl, negatively charged K and positively charged Na) 

• Large uncharged polar molecules (polysaccharides and proteins)

Facilitated Diffusion

• Diffusion through transport protein channels 

• Channels help move specific molecules across cell membrane 

• Still driven by concentration gradient (high to low concentration) 

In what two ways does the membrane become semi-permeable?

1. Channel Proteins

2. Carrier Proteins

Channel Proteins

• A hydrophilic pathway in a membrane that enables water and ions to pass through

• Open tunnel

• Specific channels allow specific material across cell membrane

Carrier Proteins

• Protein changes shape and allows the solute to enter/exit the cell

• Form passageways through the lipid bilayer 

• Each binds to a specific solute and transports it across the bilayer

Osmosis

• Diffusion of water from high concentration of water (low amount of solute) to low concentration of water (high amount of solute).

• Water will move to the more concentrated side (more solute) to balance it out.

• Across a semipermeable membrane 

• Water will always chase the hypertonic side (high amount of solute) 

Concentration of Water

• Direction of osmosis is determined by comparing total solute concentrations 

• Hypertonic: More solute, less water 

• Hypotonic: Less solute, more water 

• Isotonic: Equal solute, equal water

Active Transport

• Cells may need to move molecules against concentration gradient 

• From low concentration to high concentration 

• Use of protein “pumps” 

• The term “active” refers to the fact that the cell has to expend energy = ATP

What are the two types of active transport?

1. Primary Active Transport

2. Secondary Active Transport Pumps

Primary Active Transport

• Pumps (carrier proteins) that move positively charged ions across the membrane 

• Electrochemical Gradient: 

  • Voltage across a membrane is a difference in electrical charge on either side of a membrane 

  • Forms as a result of many positive cations on one side of a membrane compared to the other 

  • Both the voltage difference and difference in ion concentration creates an electrochemical gradient 

  • It is a form of stored potential energy which is used in nerve impulse transmission or to make ATP 

Example of Primary Active Transport

• Sodium-potassium pump (Na+/K+ pump)

• Transports sodium ions (Na+) out of the cell and potassium ions (K+) into the cell, both against their concentration gradients.

• This process is essential for maintaining cell membrane potential and regulating cell volume and ion balance.

Secondary Active Transport Pumps

• Uses the concentration gradient of an ion set up by a primary active transport pump as its energy source 

• As the ion flows back along its concentration gradient, it brings a second molecule/ion along with it

Symport

A solute that moves through the membrane channel in the same direction as the driving ion

Antiport

The driving ion moves through the membrane in one direction providing energy for the transport of another molecule in the opposite direction

How are large molecules moved in and out of the cell?

Through vesicles and vacuoles

Endocytosis

• Phagocytosis: “cellular eating” 

  • Movement of large molecules or whole cells engulfed a cell 

• Pinocytosis: “cellular drinking”

  • Transports liquids into cell within vesicles

Exocytosis

• “Exit” 

• Exports large molecules out of the cell