Introduction to Biochemistry(more in depth)

Atom Structural Review

Review of Atoms

Atoms have a nucleus that contains protons (p+), neutrons (n0) and electrons (e-). Atomic number = the number of p+. Atomic Mass is the number of p+ and n0.

Atoms and Chemical Reactions

%%Rearrangement of electrons%% when atoms/molecules collide. Electrons on the outer shell determines rearrangement.

$Water will be the most important$ molecule we observe in biochemistry.

Intramolecular Forces

%%Chemical bonds within a molecule%%. Also called covalent bonds.

Covalent bonds occur when %%2 non-metal atoms%% overlap so they can %%share valence electrons.%%

Electronegativity

An %%atoms ability to attract a shared pair of electrons wh%%ile in a covalent bond.

%%The higher the EN, the closer the electrons are to the nucleus.%%

%%If one atoms EN is higher than the others it will result in a polar covalent bond. If both atoms have an equal EN it will result in a non-polar covalent bond.%%

%%The atom with the lower EN gets a positive partial charge and the atom with the higher EN gets a negative partial charge.%%

The electronegativity difference between 2 atoms %%can be used to determine what bond will form%%. (Ionic, covalent, non-polar)

$Notes from the lesson homework.$

Page 13 #1-5 in McGraw-Hill Ryerson Biology12 Textbook.

• An atom is the smallest unit with elemental properties
• The difference between Carbon-12 and Carbon-14 is that Carbon-14 is a radioisotope and is unstable compared to Carbon-12. Carbon-12 is the most common carbon.
• Difference between ionic bonding and covalent bonding is that ionic bonds is when there is a transfer (gain or loss) of electrons, whereas covalent bonds is when the electrons are shared between atoms.
• Water is polar due to Intramolecular forces. Water is also hydrophilic and does not attract hydrophobes.

Factors Affecting Chemical Reactivity

1. The number of electrons in the outer shell
2. The number of energy shells
3. Electronegativity
4. Ionization and Valence

Chemical Bonds

Types of Chemical Bonding

• Ionic. %%Electrons are lost or gained%% between atoms, %%results in charged ions that attract%%. Ionic bonds are relatively weak and break apart in water.
• Covalent. %%Electrons are shared between atoms%%. Single, double and triple bonds may form. Energy in bonds depends on the EN of surrounding atoms. Molecules with double and triple bonds are “unsaturated”. Single bonds are “saturated”. $Bio molecules generally use covalent bonds. ⭐️$
• Polar covalent. %%Unequal sharing of electrons.%% Creates molecules that have polar sections. Eg. Water.

• Hydrogen bonds. A %%bond between molecules%%, created when a negative side of a molecule is attracted to a positive side of a molecule.

$Remember: Ionic and covalent bonds occur within molecules. Hydrogen bonds occur between molecules.$

Functional Groups

Groups of molecules that %%give specific properties to bigger structures.%% %%They are usually involved in chemical reactions%%.

Types of Functional Groups

• Hydroxyl group “OH”

Part of the alcohol family. Eg. Carbohydrates.

• Carboxyl Group “COOH”

Part of the carboxylic acid family. Eg. Fats and proteins.

• Carbonyl groups “C=O”

Aldehyde- carbonyl group is on a terminal carbon.

Ketone- carbonyl is located in the middle of the molecule.

Eg (for both). Sugars.

• Amino group “NH2”

Causes an amine. Amino group has a partial charge of its N which attracts the Hs. Animo Acids create proteins.

$Notes from the lesson homework.$

Page 17 #1-2, 4-13 in McGraw-Hill Ryerson Biology12 textbook

• Radioistopes emit gamma rays and are used in MRI, CT scans, etc.
• An example of a Intramolecular force would be the bond between H and O in an H2O molecule. An example of an intermolecular force is 2 H2O molecules bonded together.
• Intramolecular bonds are stronger because they make up molecules.
• H2O molecules attract together due to the polar side. The -ve sides attract the +ve sides and vice versa.

Metabolism

Chemical reactions in the cell that deal with energy.

3 Main Types

• Energy is released

When new bonds are formed %%reactants release energy as they form less energetic products.%%

Eg. Cell respiration

→ Exergonic- the process of energy being released.

• Energy is stored

Energy is %%absorbed by less energetic reactants creating more energetic product.%%

Eg. Photosynthesis

→ Endergonic- the process of energy being absorbed.

• Transfer of Energy

Most common reaction in biology. It occurs in both exo/endergonic reactions. $It is reversible..$

Redox Reactions (Reduction-Oxydation)

The %%process of losing electrons is called oxydation%% and the %%process of gaining electrons is called reduction.%%

$How to remember Redox???$

$OIL RIG → Oxydation is Losing, Reduction is Gaining.$

Molecular Reactions

%%Interactions of molecules with specific functional groups%%. It results in different organic molecules.

Types of reactions

• Condensation

Putting molecules together. A %%larger molecule is produced with an H2O.%%

• Hydrolysis

Taking molecules apart. %%Smaller molecules are produced%% with %%H2O being used to split them up.%%

Types of links

• Ether linkage

B/w between 2 hydroxyls

• Ester linkage

  B/w a hydroxyl and carboxyl

• Anhydride

B/w between 2 carboxylic acids

• Peptide(amide)

B/w between carboxyl with amino

$Notes on Lesson homework$

Page 36 #25-30 in the McGraw-Hill Ryerson Biology12 textbook

• a salt and a water are produced after a neutralization reaction
• Electrons are gained by another molecule in a reduction reaction
• Because electrons cannot float freely, if one molecule loses an e-, another molecule MUST gain the e-.
• A molecule in its reduced form has more energy that a molecule in its oxidized form due to the gain of an electron.

Carbohydrates

Functions: %%Energy and structure%%

Types of structures:

1. Simple Sugars(monosaccharides)

%%The building blocks%%. Identified by a ketone or aldehyde group and the # of carbons in the structure.

Eg1. Glucose C6H12O6 - %%if the “OH” on the C1 is below the midline of molecule it is called an alpha-glucose. If it is above the midline it is called a beta-glucose.%%

 %%A 6 sided pyranose ring is formed in water%%

Eg2. Fructose(isomer)C6H12O6

$Reminder: An isomer means it has the same chemical formula but different structure.$

Eg3. Ribose (5C sugars) (DNA) C5H10O5

2. More Complex Sugars