Unit 1

macromolecules

Carbohydrate protein lipids Nucleo acids

Glucose (monosaccharide) Amino acid (mon) Has no polymers Nucleotide (mon)

Lactose (mon)
Fructose (mon) Fibrous protein (poly) Fat (animal) DNA & RNA (poly)
Ribose (mon) actin, collagen, elastin, Solid, has no kink (saturated),
Xylose (mon) keratin, myosin, tubulin so it packs well and has
stronger intermolecular forces

Galactose (disaccharide) Globular protein (poly) Oil (plants)

Lactulose albumins, alpha globulin, Liquid, has a double bond
Cellobiose fibrin, hemoglobin (unsaturated) Creates a kink
chitobiose Which affects packing

Glycogen (poly) Membrane protein (poly)

Cellulose (poly) hormone receptors,
Starch-amylose, amylopectin (poly) hydrolases, transferases

Important small Covalent substances for life Ionic compounds

Water O2 high b.p & m.p

Universal solvent Diatomic, nonpolar some are soluble

Able to dissolve ionic and covalent concentration gradient between CO2 conductive when molten and
(Result of cellular respiration) and O2 exists aqueous
in capillaries surrounding alveoli

Solid form is less dense than liquid Reactant in Cellular respiration Mostly interact w/ protein

Readily experience all three states Oxidation ions = minerals = electrolytes

Has surface tension Oxidizing agent has a lot of O’s

high specific heat capacity 4.18J/gC

1. Introductory chemistry
- Isotopes​:
All atoms of an element have the same number of protons but may differ
in number of neutrons.
- Isotopes are different forms of the same element with different atomic
masses.
- Since isotopes have the same number of protons and electrons, they have
similar chemical properties

Radioactive isotopes:
- Nuclei of some isotopes of an element are unstable and tend to break down,
or decay, giving off particles and energy that
- can be detected as radioactivity.
- For example Hydrogen and Carbon have three isotopes, they all have the
same reaction.
- Carbon-14 is an unstable radioactive.
- Radioactive decay continues at a steady rate. The rate is independent of
chemical reactions or environmental conditions such as temperature or
pressure
- Applications of radioactive isotopes in biological research are:
- Dating fossils ​These isotopes break down at a constant rate over time through
radioactive decay. By measuring the ratio of the amount of the original (parent)
isotope to the amount of the (daughter) isotopes that it breaks down into an age
can be determined. We define the rate of this radioactive decay in half-lives. If a
radioactive isotope is said to have a half-life of 5,000 years that means after
5,000 years exactly half of it will have decayed from the parent isotope into the
daughter isotopes. Then after another 5,000 years half of the remaining parent
isotope will have decayed. Carbon dating is rarely applicable to fossils.
Carbon-14, the radioactive isotope of carbon used in carbon dating has a
half-life of 5730 years, so it decays too fast. It can only be used to date fossils
younger than about 75,000 years. Potassium-40 on the other hand has a half
like of 1.25 billion years and is common in rocks and minerals. This makes it
ideal for dating much older rocks and fossils.
- Tracing atoms through the metabolic process
- Radioactive isotopes react the same way in reactions as non-radioactive
isotopes
- Radioactive isotopes can follow the pathway of its corresponding
non-radioactive isotope in a chemical reaction while emitting radioactive
signal
- The radioactive signal can be used to detect how the isotope moves in the
organism
- Cite: Biology 12, page 10
- Diagnosing medical disorders:
 - A tracer in which a radioisotope, such as technetium-99m, is taken orally or injected
or is inhaled into the body.
- ​cobalt​-60 is extensively employed as a radiation source to arrest the development
of ​cancer​.
- ​carbon​-14, which is used in a breath test to detect the ​ulcer​-causing ​bacteria
Heliobacter pylori​.

2. Classification of matter:
Matter: pure substances and mixtures
Pure substances: Elements and compounds
Mixtures: Homogenous and heterogenous compounds
Substances: Ionic, covalent (Molecular, network), metals, alloys

3​. Polarity of small covalent substances

- All covalent bonds involve sharing valence electrons, they differ in the degree of sharing
that takes place
- Some atoms attract electrons more than the other
- The most EN the atom is, the more strongly it will attract shared electrons.
- EN depends and is influenced by the atomic number and size.
- EN increases as the distance between the electrons and the nucleus decreases
- Polar covalent bond:
- a bond between two atoms, made up of unequally shared electrons
- The more EN the atom is the strongly it attracts electrons and carries a partial
negative charge, so the other atom will carry the partial positive charge.
- As atoms are carrying partial charges, the overall atom may have a
non-uniform charge distribution.
 - This is the ​Polarity ​of the bond.

VSPER:
- Valence Shell Electron Pair Repulsion
- Is used to predict the geometric shape of a molecule
- The shape of the molecule determines the overall polarity of a molecule.
- If the dipoles cancel the molecule is nonpolar
- If the dipoles don't cross out the molecule is polar
VSPER theory (Molecular Shapes)
Hybridization:
- Atomic orbitals fuse to form newly ​hybridized orbitals:
- Hybrid orbital:
- An orbital that is formed by the combination of two or more orbitals in the
valence shell of an atom. To create identical bonds.
- For example:
- To create four identical bonds with H atoms, the C atom must form
four hybrid orbitals by combining the 2s orbitals and the three 2p
orbitals

Intermolecular Forces:
- The force of attraction between molecules
- Intermolecular forces, influences the physical properties, such as solubility, melting point,
and brittleness of a substance.

❖ Dipole-dipole (Van der waals forces )

- Very weak attractions between two molecules, or parts of molecules, when they are
close together
- The strength of these forces is dependent on the size, shape, and polarity of
molecules

❖ Hydrogen Bonds
- The attractive force between a partially positively charged hydrogen atom and a
partially negatively charged atom in another molecule.
- H → F, O, N
 Water
3. Why are living things mostly made of water? The importance of water?
Water has a high specific heat capacity due to its hydrogen bonds. Having this property allows the
environments of organisms to remain at an optimal range even when the overall temperature drops
or rises.
Water is also important for its ability to act as a universal solvent, and a buffer in biological
systems.
4. Draw a water molecule and indicate its polarity.

Water is a polar molecule as it consists of two different atoms.

Shape:
It has a tetrahedral structure with an angle of 104.5°. The difference in electronegativity
causes it to have partial positive and negative ends.

5. How does the structure of Water account for the following properties?
A. Cohesion​: (water attracted to water) water has strong cohesion forces due to its polarity.
The structure allows strong hydrogen bonding between water molecules causing them to
‘stick’ together. Strong intermolecular forces.
B. Adhesion: (​water attracted to other substances) works similarly to cohesion in that due to
its polarity, water molecules are attracted to other substances because of intermolecular
forces, especially ones with positive or negative charge. Water is polar so when interacted
with another polar substance, there is a dipole-dipole interaction (or H-bonding depending
on the substance). This explains water’s tendency to ‘stick’ to substances.
- An example of this is seen in plants where through cohesion and adhesion, water
can be brought from the roots and through the stems against gravity to cells all over
the plant.
C. High specific heat​: (specific heat capacity: the energy required to bring the temperature of
1 gram of a substance up by 1 degree Celsius (or 1 K) , J/g*C)
- The temperature of a substance is the average kinetic energy of the system. In
water, the strong intermolecular H bonds must be broken to allow the molecules to
move therefore it takes a lot of energy to raise the temperature of water.
D. Density: ​is the ratio of the mass to the volume of a substance.
 - The density of a substance is dependant on air pressure and temperature of the
environment that it is in.
- At SATP, water has a density of 1g/cm^3, meaning 1 cubic centimeter (1 mL) of
water weighs 1g
- Floating Ice
- Unlike most other substances, water in its solid form, ice, is less dense than
in its liquid form. This is caused by its polarity (intermolecular forces) and
structure. Therefore ice floats on water
- This is attributed to how Hydrogen bonds are oriented in a crystal lattice.
The H bonds between molecules in the crystal lattice become longer than
those in water. This means the molecules in ice cannot pack as closely
meaning the substance becomes less dense.
- In most other substances the transition from liquid to solid state through
lowering of temperature brings a higher density because there is lower
kinetic energy (temperature is a measure of the average kinetic energy of
the particles in a substance), allowing them to pack more tightly than in liquid
form.
- ​Applications in Nature/Biology
- ​During the winter, ice forms from the water in ponds, if it were not for the
properties of water the ice would sink and the plants and animals would not be able to
survive. But because of the polarity, intermolecular forces and structure, the ice is able to
float and act rather as a barrier that insulates the pond.
E. Good solvent properties
- Dissociation of soluble salts

- H- bonding with some polar molecules

F. Dissociation of water molecules:
- Water dissociates into H3O+ and OH-
- One hydrogen nuclei leaves its electron with the oxygen atom to become a
hydrogen ion, while the remaining oxygen and hydrogen become hydroxide
G. Heat of vaporization:∆H​vap
- The ​Heat of Vaporization, latent heat, or enthalpy of vaporization ​are all the same
terms to describe the amount of energy that must be added to a liquid substance to change
a specific amount of that substance from a liquid to a god state.
- Like Density, latent heat is dependent on air pressure and temperature of the surroundings.
- At 100 degrees Celsius the Heat of Vaporization of water is 40.65 kJ/mol
 - At 25 degrees Celsius: 44 kJ/mol
- The high latent heat of water is due to its strong intermolecular forces that stem from its
polarity and structure.
- Water molecules are attracted to one another through strong H- Bonds, therefore
high amounts of energy are required to break the intermolecular forces (vaporization
brings a breaking of IMF’s between molecules).
6. .Importance of water to living organisms:
-High specific heat capacity of water allows for:
-organisms to maintain stable body temperature
-aquatic environments to maintain stable temperature
-Cohesion of water allows for:
-transpiration pull
-surface tension: small insects can walk on the surface of water
-Water as a universal solvent allows for:
-water to transport substances within organisms
-dissolved substances to react more easily
-Density of water as liquid vs. Solid allows for:
-ice that floats on water acts as an insulator for aquatic organisms

7. Explain the relationship between the dissociation of water and the pH of a particular aqueous
solution.

- pH is a measure of the H+ ion concentration of a solution (pH = -log[H+])

- Water sets up an equilibrium (dissociation of water)
- 2 H​2​O(​l)​ ​H​3​O​+​(​aq​) + OH​-​(​aq​)
- Therefore the dissociation of water into H3O+ (hydrogen ion) and OH-
(hydroxide) are directly related to the pH of the solution because pH is a
measure of H+ ion conc.

Phys. Chem​.

Thermochemistry
Calorimetry the process of measuring the amount of heat
released or absorbed during a chemical
reaction, and determine whether it is an
endothermic or exothermic reaction.

Hess’ Law total enthalpy change for the reaction is the

sum of all changes
 Enthalpy Change(△H, J/kg) the amount of heat released or absorbed
during a reaction at constant pressure. Exo-,
Endothermic

Bond Enthalpy the energy it takes to break a specific type of

bond

Entropy A measure of molecular randomness or

disorder

Free Energy Exergonic, endergonic

1. ​Thermochemistry
Calorimetry: the process of measuring the amount of heat released or absorbed during a
chemical reaction, and determine whether it is an endothermic or exothermic reaction.
Hess’ Law: total enthalpy change for the reaction is the sum of all changes.
Enthalpy Change(△H, J/kg): the amount of heat released or absorbed during a reaction at
constant pressure. Exo-, Endothermic
Bond Enthalpy: the energy it takes to break a specific type of bond.
​ Entropy: A measure of molecular randomness or disorder
Free Energy: Exer-, Endergonic

Kinetic

Rx Rates The speed at which a reaction occurs, or the

change in the amount of reactants consumed
or products formed over a given time interval

Collision Theory The theory that a reaction occurs between two

particles (atoms, molecules, or ions) if they
collide at the correct orientation and with
certain minimum energy.

Activation Energy (Ea) The minimum energy required for a substance

to undergo a certain reaction

Catalysis Speed up chemical reaction(lower the

(Enzyme) activation energy);
regenerative(ready to have next round after
the reaction);
Mechanical of action may include bonding with
the reaction(s)
 Factors affecting rates Temperature;
Surface Area;
Pressure;
Concentration;
Catalyst

2. ​Kinetics
​ ​ Rx Rates:
- The speed at which a reaction occurs, or the change in the amount of reactants
consumed or products formed over a given time interval

​Collision Theory:
- The theory that a reaction occurs between two particles (atoms, molecules, or ions) if they
collide at the correct orientation and with certain minimum energy.

​ ​Activation Energy (Ea):

- The minimum energy required for a substance to undergo a certain reaction
​Catalysis:
- Catalysis is the modification of a chemical RXN, usually a speeding up, by the addition of a
substance that is not consumed during the RXN (a catalyst)
- A catalyst is a substance that is able to provide an alternate mechanism for a RXN usually
requiring a lower Ea than otherwise needed. Catalyst’s are regenerated ( not consumed)
- Catalysts do not affect the position of equilibrium of a RXN, only affects the rate at
which eq’m is reached
- Biological Catalysts are called ​Enzymes
- Work similarly to traditional catalysts

Factors affecting rates:

Increase in frequency of collisions and increase in number of effective collisions (sufficient
activation energy and correct orientation (mechanisms) speed up the rate of a RXN
- Temperature:
- increases frequency of collisions (particles are moving faster)
- Increases # of molecules with sufficient activation energy (increase in average
kinetic energy)
- Surface Area:
- Increases frequency of Collision
- Pressure: (increase)
- Increases frequency of collisions
- Concentration (increase)
- Increases frequency of collisions
- Catalyst
 - Increases the # of molecules with sufficient activation energy by providing alternate
pathway
- Lowers activation energy

Maxwell-Boltzmann Distribution Curve showing how a catalyst can increase the rate of a RXN
(​Chemguide. (2003). ​40​(07). doi:10.5860/choice.40-4021)

- Number of Bonds/Molecular size

- RXNs that involve the breaking of fewer bonds per reactant proceed faster that
those involving the breaking of a larger number of bonds per reactant.
- Enzymes:
- Enzymes speed up the reaction by lowering the activation energy.

3. ​Equil
Reversibility: where the reactants form products which in turn may react to give the reactants
back. Reversible reactions will reach an equilibrium where the concentration of both the reactants
and products will stay constant. (Notation: A + B ⇆ C + D)
Steady state: a reaction that remains constant over time requires continual work. A reaction in a
steady state can also be called dynamic equilibrium and they have a higher level of energy than
the surroundings.
Steady state:
- Also known as homeostasis
- Only applicable to living organisms.
- With constant usage and or generation of reactants and products to avoid natural tendency
for chemical equilibrium
- Basically, our mechanism to fight off chemical equilibrium. Living organisms avoid
equilibrium because ​If an organism is at equilibrium, it's dead.
 - For example:
- Aerobic respiration - energy for physical movement

Kc&△G
Kc: equilibrium constant which depends on the concentrations of both the reactants and
products at eq.
△G:

4.​ Redox Chem: (oxidation-reduction_ reaction is a type of chemical reaction that involves the
transfer of electrons between two chemical species.
4 definitions:
Agents:
- Reducing agent: causes reduction and in the process becomes oxidized
- Oxidizing agent: causes oxidation and in the process becomes reduced
- Reduction is ​GAIN ​ of electrons
- Oxidation is ​LOSS​ of electrons
Electrochem:

Organic Chemistry
1. An organic compound consists of one or more carbon atoms covalently linked to other
elements, mostly hydrogen,oxygen, nitrogen, sulfur, & phosphorus.

2. Features of org cmpds include a chain/ring of carbon atoms with hydrogens to fill up the octets.
If oxygen, nitrogen, sulfur, or phosphorus are bonded, then it is called a functional group

3. Classification and Functional Groups

Organic compounds
1. Hydrocarbons
○ Aromatics (benzene: ​https://goo.gl/images/LL8wzH​)​ ​Aromatics are based on benzene​,
​ as resonance
which are carcinogenic (react w/ DNA)​, h
○ Aliphatics
■ Alkanes (methane: ​https://goo.gl/images/SJfhQc​) ​Alkanes: C​n​H​2n+2 Ring: C​n​H​2n
■ Alkenes (ethene/ethylene: ​https://goo.gl/images/39L32c​) ​Alkenes C​n​H​2n
■ Alkynes (acetylene/ethyne: ​https://goo.gl/images/pHzN6K​)
2. Others
Family functional group

Alcohol OH hydroxyl

Ether -O-

Aldehyde C=O carbonyl

Ketones C=O carbonyl

Acids O=C-OH carboxyl

Esters O=C-O-

Amine C-Ņ- amine

Amide O=CーŅ- peptide bond

○ Alcohols => hydroxyl functional group:​https://goo.gl/images/s8HF6X

(Example; methanol: ​https://goo.gl/images/NiqmsX​)
○ Aldehydes => terminal carbonyl: ​https://goo.gl/images/xEeD7h
(Example; formaldehyde:​https://goo.gl/images/9nn7WT​)
○ Ketones => carbonyl:​https://goo.gl/images/Zn5LXn​)
(Example; acetone:​https://goo.gl/images/xyWp9J​)
○ Carboxylic/Organic Acid
=> carboxyl: ​https://goo.gl/images/qXyfpk​)
(Example; acetic acid: ​https://goo.gl/images/dcp2ma​)
○ Esters => carboxyl: ​https://goo.gl/images/bqLWVC​)
(Example; methyl acetate/ methyl ethanoate: ​https://goo.gl/images/2VEqvF​)

2. General features of organic compounds:

○ Covalent nature, Strong carbon-carbon covalent bonds. Mostly these compounds
are very stable.
○ Carbon forms single, double, and triple bonds to other C atoms
○ Some are chains and some are in rings
○ Do not ionize in solutions and are non-conductors of electricity
○ Non-polar C-H bonds, therefore most organic compounds are non-polar unless
elements such as chlorine or a hydroxyl group are bonded to it
○ Mostly insoluble in water due to non-polarity, unless the compound contains polar
groups. High solubility in non-polar solvents
○ Form aqueous solutions
○ Mostly LDF due to non-polarity
○ Low melting and boiling points which is caused by the weak intermolecular forces
(LDF).
 ○ Thermally unstable and tend to decompose into simpler molecules when heated
○ Are a main source of heat energy as they are highly flammable
○ Organic compound rxns are much slower than ionic rxns as they require heating,
constant mixing, or certain catalysts to help speed up the duration of reactions

3. Classification of Organic compounds:

( Chemistry assignment. General Classification of Organic Compounds.

http://www.chemistry-assignment.com/general-classification-of-organic-compounds​ )

4. Isomerism
Structural isomerism: 2 or more chemical compounds having the same molecular formula but
different structural formulas
(ex: 3-methylpentane & 2-methylpentane)
(ex: but-2-ene & cyclobutane)
(ex: hexanoic acid & 3,4-dimethylbutanoic acid)

Geometric isomerism: 2 or more chemical compounds that have the same molecular formula but
have a different geometric arrangement; in an unsaturated/ring compound where rotation around a
carbon bond is restricted (cis- and trans- configurations)
(ex: cis-pent-2-ene & trans-pent-2-ene)
(ex: E,1-chloro-2-fluoro but-1-ene & Z,1-chloro-2-fluoro but-1-ene)
(ex: E-but-2-ene & Z-but-2-ene)
5. Physical Properties
● Relatively low melting/boiling point
● Non-conductive
● If the nonpolar part of the molecule is smaller than the polar part then the molecule is water
soluble
● If nonpolar part >polar part, then the molecule is not water soluble
4. Chemical Properties/Reactions
● All organic compounds are flammable/combustible ex. C3H8 + 5O2 —> 3CO2 + 4H2O
Always Exothermic
● Alkanes can undergo substitution, cracking
Alkanes:
❖ Combustion: alkane + O​2​----->​ CO​2​ + H​2​O
❖ Cracking: alkane -----> alkane + alkene
❖ Halogenation: Halogen + alkene -----UV light→ haloalkane + HX

Alkenes:
❖ Oxidation reaction
➢ combustion: alkene + O​2​----->​ CO​2​ + H​2​O
❖ Electrophilic Addition reactions
➢ Hydrogenation: alkene + H​2 --Pt--->
​ ​alkane
➢ Halogenation: alkene + X​2​ → dihaloalkane
➢ Hydration: alkene + H​2​O → alcohol
➢ with HX: alkene + HX → haloalkane
- The final two reactions, use Markovnikov’s Rule- add H to the
carbon with the most hydrogens.
❖ Addition Polymerization alkene → polymer (long chain alkane)
Alkynes
❖ Combustion: alkyne + O​2​ → CO​2​ + H​2​O
❖ Addition reactions: see alkenes

Haloalkanes
❖ Substitution RX + Nu​-​ → R-Nu + X​-
❖ Elimination RX + Nu​-​ → alkene + NuH + X​-

Aromatics
1. Electrophilic Substitution ​ ​ ​FeX​ Or AlX​
3​ 3

a) Halogenation: Benzene + X​2 ​ → halobenzene + HX

Note: Alkyl side chains will readily undergo free radical halogenation without any addition to the ring.

b) Nitration Benzene + HNO​3​ → nitrobenzene + H​2​O

2. Hydrogenation aromatic + H​2 ​ → cycloalkane

Aldehydes and Ketones
1. Hydrogenation aldehydes + H​2​ → 1° ROH
ketones + H​2​ → 2° ROH

2. Oxidation aldehyde + KMnO​4​ → carboxylic acid

Carboxylic Acids
2. Elimination ​H​ SO​
2​ 4

alcohol + carboxylic acid → ester + H​2​O

​H​ SO​
2​ 4

amine + carboxylic acid → amide + H​2​O

Esters
1. Hydrolysis ​H​ SO​
2​ 4

ester + H​2​O → carboxylic acid + alcohol

Amides

1. Hydrolysis amide + H​2​O + H​+​ → carboxylic acid + amine

amide + H​2​O + OH​- ​ → carboxylate ion + amine

Alcohols
1. Oxidation
a) combustion:
b) mild oxidation 1° ROH (K​2​Cr​2​O​7​) alcohol → aldehyde
c) moderate oxidation 1° ROH (KMnO​4​) alcohol → carboxylic acid
d) 2° ROH (KMnO​4​) alcohol → ketone

1. Acid –Base

b) condensation / elimination 2 alcohols (or 1 in excess) → ether + H​2​O

​H​ SO​
2​ 4

alcohol + carboxylic acid → ester + H​2​O

c) halogenation HX + alcohol → haloalkane + H​2​O

Macromolecules

1. Why is carbon central to the structure of biological molecules?

Carbon is central to the structure of biological molecules because it can form 4 covalent
bonds. (Single bonds, double bonds, and triple bonds)
 2. ​Explain the concept of an isomer. As the number of carbon atoms in a molecule
increases, what happens to the number of possible isomers of that molecule? Make
sure to include SIMPLE examples to illustrate all 3 types of isomerism?
Isomers are compounds with the same molecular formula but different structures and
properties.
​Structural isomers:
​Have different covalent arrangements of their atoms.

​Geometric isomers:
​ Have the same covalent arrangements but differ in spatial arrangements

​ nantiomers:
E
​Are isomers that are mirror images of each other
- As the number of carbons increase there is more than one possible structure for that
molecule.
 -

https://www.compoundchem.com/2014/05/22/typesofisomerism/

3. Why is it significant that all biological systems use L-amino acids and D-sugars?
Amino acids acids occur in two isomer forms (except glycine): L- and D- however, cells only
use the L-amino acids which are manufactured in cells and incorporated into proteins.
The reason why biological systems L-a.a’s and D-sugars is because their structure allow
molecules to perform functions that are essential for living systems. Main ​significance is that the
energy in the form of these 2 isomers that organisms obtain can be used by other organisms as
sources of fuel for their body processes. This is because the same isomers function and have the
same properties in all organisms.
4. ​What is enantiomer?
​Enantiomers:
​Are isomers that are mirror images of each other
- As the number of carbons increase there is more than one possible structure for that
molecule.

5. Hydrocarbon? Hydrophobic or hydrophilic?

-Hydrocarbon: organic molecules made up of carbon and hydrogen atoms/ alkanes,
alkenes, and alkynes (ex. Methane and butane)
-Hydrocarbons are hydrophobic (non polar bonds and therefore nonpolar molecule)

6. What is the difference between an isomer and an isotope?

 Isotopes​: are two atoms with the same number of protons, but a different number of
neutrons. Due to the reason that they have the same number of protons they both belong to
the same element, but have different masses.

Isomers​: two or more compounds with the same molecular formula but the atoms are
arranged differently in the molecule resulting in different properties.

7. How are macromolecule polymers assembled from monomers? How are they
broken down? Names of linkages? Diagrams?

Assembling of Monomers
● In dehydration synthesis (condensation) monomers combine together via covalent
bonds to assemble polymers
● During dehydration synthesis either the hydrogen of one monomer combines with
the hydroxyl group of another monomer releasing a water molecule, usually
● Monomers that are joined through dehydration synthesis share electrons and form
covalent bonds with each other.
● As more monomers go through dehydration synthesis, it begins to form a polymer.
How Polymers are Broken Down
● Hydrolysis reactions use a water molecule and an enzymic catalyst to break down polymers
into monomers
● Cellular respiration is a catabolic rxn in which sugar and fat gets broken down to carbon
dioxide and water (not breaking of polymers, it’s breaking monomers)
● Polymers also get broken down into monomers in digestion, (see question 31)
○ carbs gets broken down in the mouth by saliva, in the stomach by gastric juice
(contains amylase), and in the jejunum by many many different enzymes resulting in
mono/disaccharides
lactose

■ Water--→ glucose+galactose
○ Proteins get broken down in the stomach by the enzymes in gastric juice and in the
second part of the small intestine jejunum, by Peptidases resulting in amino acids
○ Nucleic acid are
○ Fats are dealt with in the stomach and in the mouth
Lingual lipase

■ Triglycerides -----→ Free fatty acids/monoglycerides/diglycerides

8.Four commonly encountered rxs in biochem?
Neutralization reactions
● Acids and bases react to farm a water and a salt
● Acids dissolve in water to produce hydrogen ions (H+)
● Bases dissolve in water to produce hydroxide ions (OH-)
● When acids and bases are mixed water is produced
 ● Neutralization reactions can help control the pH of a solution

Condensation (Dehydration Synthesis)

● Dehydration refers to the removal of water
● In a dehydration synthesis reaction , a water molecule is removed from the reaction
molecule to create something new
● In carbohydrate synthesis removes a water molecule to create a glycosidic linkage
between two carbohydrates

Hydrolysis
● Hydrolysis reactions are the reverse of condensation reactions
● In these reactions water is added to a substance to cleave or split certain chemical
bonds to form new compounds

Oxidation Reduction reaction (Redox)

● Redox reactions refer to the change in oxidation state of the atoms involved
● The oxidation state is changed through a loss or a gain of electrons
● Oxidation refers to a loss of electrons which results in an increase of oxidation state
 ● Reduction refers to a gain of electrons which results in a decrease of oxidation state
● The oxidation and reduction occur simultaneously

Original site: ​http://sbi4u3.weebly.com/biochemical-reactions-and-enzymes.html

9. How can you tell whether a biological molecule is a carbohydrate?

All carbohydrates consist of either an alpha glucose molecule or beta glucose molecule
All carbohydrates are made of cyclic carbon structures, it only consists of C,H,O, and has
the molecular formula (CH​2​O)​N

10. Relationship between monosaccharides, disaccharides, and polysaccharides

Disaccharides are two monosaccharides joined together. Polysaccharides are made of the
monomer of glucose joined in different ways. Diag/eqn?
● sucrose+water→ glucose+fructose
● Maltose + water → 2glucose
● lactose+Water→ glucose+galactose
● Polysaccharide : ​line diagram of 2 types of starch.j​pg
● line diagram of Cellulose​ showing the glycosidic bond
● Disaccharide: ​Lactose-Disaccharide Showing the glycosidic bond
● sucrose disaccharide showing the glycosidic bond
● Monosaccharide:

11. Why are starch and glycogen useful as energy storage molecules while cellulose
is useful for structure and support? Why isn’t cellulose easily broken down?
Starch and glycogen are useful energy storage molecules because they can be easily
broken down while cellulose is useful for structure and support because it's made of
beta-glucose and these bonds are hard to break since animals lack the enzyme for
breaking cellulose bonds

12. How do herbivores solve the problem of cellulose production?

- Some herbivores are ​Ruminants m ​ eaning they can break down cellulose. They
have more complex stomachs that contain 4 compartments, one of which is called
the rumen.
- In the rumen resides microbes and microorganisms that are capable of
breaking down cellulose.
 - In cows, food may be passed back and forth between the mouth and rumen
until it is fully broken down

13. What is lactase? What causes lactose intolerance?

- Lactase is a type of enzyme which is produced by organisms. It is essential to break
down lactose (a sugar in dairy products)
- Lactose intolerance is caused by the lack/deficiency of lactase which is needed to
split lactose into smaller sugars (glucose and galactose) and allows lactose to be
absorbed from the intestine.

14. How can you tell if a biological molecule is a lipid?

Fatty acids: carboxyl group linked to hydrocarbon chain
Fats/Oils: three fatty acids and glycerol
Phospholipid: two fatty acids to two hydroxyl groups, one phosphate group to the last onel
Steroid: four carbon rings
Wax: A lipid that is formed when long fatty acid are joined to alcohols or carbon ring (cite:
Biology 12, page 37)

15. Saturated lipids vs. Unsaturated lipids (chemically)

-saturated lipids contain no double bonds
-unsaturated lipids contain double bonds
-double bonds in chain causes a bend in molecule
-This bend does not allow the molecules to pack as closely together as saturated
lipids
-This leads to a decrease in the intermolecular forces between unsaturated lipid
Molecules
-unsaturated lipids tend to exist as a liquid whereas saturated lipids tend to exist
as a solid
-saturated fats can lead to heart disease

16. How are triglycerides, phospholipids, and steroid similar? How do they differ?
- All 3 are lipids
- Triglycerides
- The main component of animal fat (saturated) and plant oils (unsaturated)
 - Phospholipids
- A major component of cell membranes
- Have a hydrophilic head (polar phosphate group) and hydrophobic tail (non
polar fatty acid chain)

- Steroids
- Very different in structure compared to phospholipids and triglycerides
- 4 linked carbon rings (general structure)
- Make up hormones
18. Why are proteins the most complex biological molecules?
This is due to the fact that they are made of 5 different elements: Carbon, Hydrogen, Sulfur,
oxygen, and nitrogen, and when compared to other molecules which have only 3 or 4 elements,
proteins will have a greater complexity.
19. Structure of general amino acid:

21. Formation of peptide bond between two amino acids:

The formation of peptide bond between two amino acids.
carboxyl group of one molecule reacts with the amino group of the other molecule,
releasing a molecule of water (H2O). This is a dehydration synthesis reaction (also known
as a condensation reaction), and usually occurs between amino acids.

The resulting CO-NH bond is called a peptide bond, and the resulting molecule is an amide.
The four-atom functional group -C(=O)NH- is called an amide group or (in the context of
proteins) a peptide group. Polypeptides and proteins are chains of amino acids held
together by peptide bonds, as is the backbone of PNA (PEPTIDE NUCLEIC ACID).
 22. ​How does the structure of the ‘R’ group affect the properties of a particular
amino acid?
The ‘R’ group will determine whether a molecule is polar or nonpolar, charged,
acidic, basic. It gives it each amino acid their individual properties

30. The importance of a balanced diet:

Nutrients: chemical substances used by organism
Essential nutrients: nutrients that the organism can’t produce
Vitamins: A, B1,B2, B3, B6, B12, C, D, E
Minerals: Fe​2+​, Ca​+​ , Na​+​, K​+​, Mg​2+​, Zn​+​, Cu​2+
fats: omega3
Amino acids: ​histidine, isoleucine, leucine, lysine, methionine, phenylalanine,
threonine, tryptophan, and valine

31. Digestion: break down large insoluble molecules into small water-soluble molecules.
Take place in mouth
Mechanical: chewing, forming bolus with your tongue
Chemical: poly/disaccharides+amylose→di/monosaccharide+water
Esophagus
Mechanical: peristalsis (not so much though, it’s more for transport)
stomach (chemical+mechanical)
Mechanical: churning
Chemical: protein+pepsin→ peptides+water
​ HCl
​

Nucleases + ribonucleic acids → water + Nucleotides

small intestine: jejunum
Chemical: α-Dextrins + α-Dextrinase → glucose + water
Sucrose + sucrase → glucose + fructose + water
Dipeptides + Peptidases → amino acids + water

Absorption: absorb nutrients from food into blood steam

Assimilation: ​absorbed food reaches the cells via the liver​,
once it reaches the cell it is used up in the cell by proteins or mitochondria
for cellular respiration or possibly kept in a vacuole for later use

From Biochem to Bio

1.What constitutes LIFE?

-Reproduction
-Response
-Homeostasis
-Nutrition
-Metabolism
-Cellular
● include nucleic acids (DNA & RNA)
● Include cellular membrane
● include cytoplasm & ribosomes
-Water
-Waste excretion

2.Levels of organization in nature

The levels, from smallest to largest, are: subatomic particles , atom ,molecule, cell, tissue,
organ, organ system, organism, population, community, ecosystem, biomes , biosphere.

3. The cell theory

All living organisms are composed of one or more cells.
The cell is the basic unit of structure and organization in organisms.
Cells arise from pre-existing cells.

Cell Parts
The FOUR main components of any cells:
1)Plasma membrane
Structure- a bilipid membranous layer composed of proteins and carbohydrates. It is fluid
like.
Function - the cell membrane separates the cell from its external environment, and is
selectively permeable (controls what gets in and out). It protects the cell and provides stability.

2)Cytoplasm
Structure - The jelly-like substance composed of mainly water and found between the cell
membrane and nucleus. The cytoplasm makes up most of the "body" of a cell and is constantly
streaming.
Function - Organelles are found here and substances like salts may be dissolved in the
cytoplasm.

3)Nucleic acids
genetic "control center" of the cell, for cell metabolism and reproduction.
Original website: ​http://www.edu.pe.ca/gray/class_pages/rcfleming/cells/notes.htm
4) Ribosomes
Structure - drawn as little circles, made out of proteins and RNA, it has two components, a
small subunit, and a large subunit. It has one mRNA binding site and 3 tRNA binding site.
Function - it produces and packages proteins, ​the small ribosomal subunits, which read
the RNA, and the large subunits, which join amino acids to form a polypeptide chain.
 Free ribosomes makes protein to be used in the cell, ribosomes attached to the
rough ER makes protein that are used outside the cell

4​.Themes of biology
1) All levels of life have systems of related parts.
2) Structure and function are related in biology.
3) Organisms must maintain homeostasis to survive in diverse environments.
4) Evolution explains the unity and diversity of life.
5. Tools of Biology
Microscope, Cell cultures, Computers and imaging systems,Basic Stockroom tools

20. Membranes and cellular Transport and Diffusion, Osmosis.

Membrane:
- It’s made up of a phospholipid bilayer and different molecules (proteins,
carbohydrates, cholesterol).

-
- phospholipid bilayer:
- Contains two fatty acid tails (hydrophobic) linked to polar (hydrophilic) head
group

cellular Transport and Diffusion, Osmosis.

-Cell membrane is ​selectively permeable​, meaning that it allows only certain

substances to pass through.
If a substance can pass through a membrane ​without expanding energy,​ it is called
 passive transport
If a substance passes through a membrane with the ​use of energy​, it is called ​active
transport
Passive vs Active Transport

Types of Passive Transport:

Three types:
1. Simple diffusion
2. Facilitated diffusion
3. Osmosis

1. Simple Diffusion
Movement of molecules from a high concentration area to a low concentration area
- Rate of Diffusion
- Depends on the concentration difference between the two areas
- The larger the gradient, the faster the rate

2.Facilitated Diffusion
diffusion of particles across a cell membrane with the assistance of ​protein complexes

Two Types of Transport Proteins:

1) ​Channel proteins
• hydrophilic pathways for water and ions to pass through
• voltage-gated channels – transport of ions (e.g. Na​+​, Ca​2+)
2) Carrier proteins
• binds to a molecule, changes shape, allows the molecule to cross the other
 side
3. ​Osmosis:
- passive movement of ​water​ across a selectively permeable membrane

- water moves from an area of lower solute concentration to an area of greater solute
concentration

- Osmosis stops when both sides of the membrane reach the same solute
concentration.

-
Active Transport:
- the movement of substances through a membrane against a concentration gradient using a
membrane-bound carrier proteins [​Energy is required!]

Fluid Mosaic Model​ of Cell Membrane

- “​Fluid​” means that the phospholipids and other parts of the membrane are not rigidly fixed
in position (it’s believed that they can move sideways across the membrane)
- “​Mosaic”​ refers to the arrangement of the different molecules in the membrane, making it
like a mosaic
 -

23. Define each of the following levels of protein structure and explain the bonds that
contribute to them
Primary:
- The structure of a protein is its unique sequence of amino acids
Secondary:
- Structure, found in most proteins, consists of coils and folds in the polypeptide
chain.
Tertiary:
- Structure is determined by interactions among various side chain (R groups)
Quaternary:
- ​Structure results when a protein consists of multiple peptide chains

Type of bond present in each level:

25. How do enzymes speed up the reaction.
Enzymes speed up the reaction by lowering the activation energy.
By binding the substrate molecule into a special environment called active site. Inside the
active site conformational change takes place that stabilizes not only the substrate
molecule but it also stabilize the transition state in the reaction. By stabilizing the
transition state it releases a certain amount of binding energy into the envior and that
decreases the energy of that transition state and lowers the energy of the energy state
and that's what lowers the activation energy.
By lowering the Ea we speed up the rate of reaction

Makes the reaction faster by:

making the reaction happen faster 
can stabilize an intermediate 
bring molecules together faster 
It creates an alternate pathway for the rxn to take place which leads to the lower E​a 
26. Draw a nucleotide. Label the phosphate, sugar, and nitrogen base? 

  
 
 
 
27. Structural differences between RNA and DNA
Three fundamental differences between RNA and DNA are:
1. RNA is single-stranded nucleic acid
2. RNA has a ribose sugar instead of a deoxyribose sugar like DNA.
3. RNA nucleotides have a uracil base instead of thymine.

DNA RNA

Structural Name: Deoxyribonucleic Acid Ribonucleic Acid

Function: Medium of long-term storage Transfer the genetic

and transmission of genetic code needed for the
information. creation of proteins from
the nucleus to the
ribosome. This process
prevents the DNA from
having to leave the
nucleus, so it stays safe.
Without RNA, proteins
could never be made.

Structure: Typically a double- stranded A single-stranded

molecule with a long chain of molecule in most of its
nucleotides. biological roles and has
a shorter chain of
nucleotides.

Bases/Sugars: Long polymer with a Shorter polymer with a

deoxyribose and phosphate
backbone and four different
bases: adenine, guanine,
cytosine and thymine.
ribose and phosphate
backbone and four
different bases: adenine,
guanine, cytosine, and
uracil.

Base Pairing: A-T (Adenine-Thymine), G-C A-U (Adenine-Uracil),

(Guanine-Cytosine) G-C (Guanine-Cytosine)

Stability: Deoxyribose sugar in DNA is Ribose sugar is more

less reactive because of C-H
bonds. Stable in alkaline
conditions. DNA has smaller
grooves where the damaging
enzyme can attach which
reactive because of
C-OH (hydroxyl) bonds.
Not stable in alkaline
conditions. RNA on the
other hand has larger
 makes it harder for the grooves which makes it
enzyme to attack DNA. easier to be attacked by
enzymes.

Unique Traits: The helix geometry of DNA is The helix geometry of

of B-Form. DNA is
completely protected by the
body i.e. the body destroys
enzymes that cleave DNA.
DNA can be damaged by
exposure to Ultraviolet rays.
RNA is of A-Form. RNA
strands are continually
made, broken down and
reused. RNA is more
resistant to damage by
Ultraviolet rays.

https://www.sparknotes.com/biology/molecular/structureofnucleicacids/section3/

28. Macromolecules in the cell

● DNA and RNA (nucleic acids) in the nucleus
● Cellulose (carbohydrate) in plant cell walls

29. Food and Nutrition (we are what we eat)

● Function of Nutrients
○ Build, maintain, and repair tissues
■ Cells play a critical role in growth and repairing damaged tissues
■ Cells are formed with materials that come from food. Body needs nutrients to
make new cells
■ Especially important during various phases of the life cycle: infancy,
childhood, puberty, pregnancy, old age, illness
○ Regulate body processes (systems)
■ Send messages for chemical reactions to occur
■ The circulation of body fluids requires a balance of essential nutrients
■ Digestion, Absorption, Metabolism rely on proper amounts of nutrients
○ Energy
■ Measured in calories and allows the body to perform its many internal
functions
■ Only the macros provide the body with energy
● Two types of Nutrients
○ Macronutrients (large quantities)
○ Micronutrients (small quantities)
● Energy Value of Food
○ Measured in units called kilocalories (calories)
■ 1 gram carbohydrate = 4 calories
 ■ 1 gram fat = 9 calories
■ 1 gram protein = 4 calories
● We are what we eat
○ Nutrients extracted from the foods digested provide the foundation of structure and
function of cells

30. Importance of a balanced diet

● Specific amounts of each nutrient (macros and micros) are required to prevent deficiency
● Health Canada has established Dietary Reference Intakes (DRI’s) as a set of nutrient
values for healthy individuals
● Carbohydrates
○ Deficiency
■ Puts the body into a state of ketosis (where the body uses protein for
energy) - Ketogenic diet (Fad diet)
● Fat
○ Deficiency
■ Dermatitis or skin inflammation
■ Lack of energy
■ Poor hormone production
■ Impired growth and body health
○ Excess
■ Heart disease
■ Obesity
■ Diabetes
■ Stoke
● Protein
○ Deficiency
■ Muscle weakness
■ Inability to fight off illness
■ Kwashiorkor disease (form of malnutrition)
○ Excess
■ Extra protein is converted into glucose or glycogen by the liver and the
remainder is filtered by the kidneys and excreted
● Long term, the extra work required by the kidneys and liver can result
in tissue damage - kidney and/or liver failure
■ High cholesterol
■ Osteoporosis and kidney stones
■ Increased cancer risks
■ Unhealthy metabolic state (ketosis)

31. Digestion, Absorption, Assimilation

Digestion: The process of breaking down foods by digestive enzymes when ingested
Absorption: Nutrients are absorbed by the small intestine and is sent into the blood to be carried
out by the body
Assimilation: Utilizing the absorbed nutrients by the movement of the substances into the cells or to
the tissues and organs of the body through ​diffusion​ and ​osmosis

Endosymbiotic Theory:
Is the hypothesized process by which prokaryotes evolved into eukaryotic cells. It attempts to
explain the origins of eukaryotic cell organelles such as mitochondria in ​animals​ and fungi and
chloroplasts in ​plants​. Based on the theory, the mitochondria and chloroplasts are organelles that
were once free-living cells. They were prokaryotes that ended up inside of other cells (host cells).
They may have joined the other cell by being eaten (a process called phagocytosis), or perhaps
they were parasites of that host cell. Rather than being digested, the inner cell survived and they
worked in correspondence to one another. The host cell provides a comfortable, safe place to live
and the organelles provide energy that the host cell can use.

Apoptosis:

Centrifugation:
Centrifugation is a separation process which uses the action of centrifugal force in order to settle
particles in a solid-liquid mixture. Substances are spun around in a rotor at high speeds. The
applied centripetal force causes the separation. In a solution, particles whose density is higher than
that of the solvent sink (sediment), and particles that are lighter than it float to the top. Usually, the
greater the difference in density, the faster they move.
A demonstration of the process:
http://www.flacktek.net/images/Animations/DualAsymmetricCentrifuge.gif

Cytology (cell parts)

The four most important parts of the cell:

Name Function Diagram

1)Genetic material DNA and RNA, they carry https://www.motifolio.com/1031114.html

hereditary information that
codes the cell.
 2)Cell membrane A semipermeable bilayer
membrane around the cell
that allows for passive and
active transport in and out of
the cell to take place
https://www.researchgate.net/figure/a-curre
nt-representation-of-the-plasma-membrane-
showing-the-same-basic-fluid-mosaic-mode
l_fig49_322724678

3)Cytoplasm A jelly-like material that fills

up the cell. It is mostly made
of water with a little salt and
proteins.

4)Ribosome They are the sites of protein https://courses.lumenlearning.com/wm-biolo

synthesis. There are two gy1/chapter/reading-ribosomes-mitochondri
schools of thought a-and-peroxisomes/
surrounding the production of
protein.
1: The protein folds after it is
completely spit out.
2: The protein folds as it is
spit out.

Parts of the cell that are common to both prokaryotes and eukaryotes
Name Function Diagram

5)Cell wall A hard wall that surrounds and

protects the cell. The animal
kingdom is the only kingdom
without cell walls.

6)Flagella and They are the motor of the cells https://microbiologyinfo.com/differences-bet

cilia ween-cilia-and-flagella/

7)Chlorophyll A photosynthetic pigment. It’s

essential for plants to absorb
light.

Membrane bound organelles

8)Nucleus Stores the genetic material

that tells the cell its function​.
Composed of:
Nuclear pores
Nucleolus
 has porous ​Nuclear
membrane​ that allows RNA to
pass, but traps DNA inside

9)Lysosome Stores digestive enzymes that

break down waste into parts
that can be reused in the cell.

When cells undergo

apoptosis(programmed death)
the membrane of the
lysosome opens and releases
enzymes to kill the cell.

10)Smooth ER The endoplasmic reticulum

and Rough ER manufactures and packages
proteins and lipids for export.
The proteins produced by the
ribosomes on the rough ER
are exported out of the cell.
An example is insulin

Endoplasmic reticulum is
located very close to the
nucleus.
lipids are produced by Smooth
ER

11)Vacuole Stores nutrients.

There are few large vacuoles
in plant cells.
There are many small
vacuoles in animal cells.

12)Golgi Processes and bundles Structure - looks like a stack of flattened

Complex macromolecules produced in water balloons that eventually lead to
the cell.​ It processes the vesicles
proteins produced by the
endoplasmic reticulum and
ribosomes, modifying and
storing them until it packages
them in vesicles. Lysosomes
also come from the Golgi
apparatus.
 lmao sry this is just here for lols :)
hope this cheers up whoever is doing the rest

13)Mitochondrion The location of cellular Emily did we answer all of the questions?
respiration From the worksheet?
Has a second folded inner
membrane