Unit 1 Biochemistry Study Guide

Unit 1: Biochemistry Review

Chemical Bonding
Three types of bonds
Ionic bond: 2 oppositely charged atoms (Na and Cl)
Polar covalent: Unequally shared electrons (H and O)
Non polar covalent: Equally shared electrons (C and C) or similar electronegativity

Electronegativity and chemical bonding
Electronegativity is a measure of the strength in which an atom can attract electrons.
A difference of < 0. 5 is non polar covalent bond
A difference of 0.5 – 1.7 is polar covalent bond
A difference of > 1.7 is ionic bond

Intermolecular forces force of attraction and repulsion BETWEEN molecules
Broken when solids melt into liquids and liquids evaporate to gas
Three types of forces are called van der waals: dipole-dipole: hold polar molecules together, one partial positive side attracts partially negative side to adjacent polar molecules. hydrogen bonding (dipole-dipole) - strongest bond, form between electropositive hydrogen (H) and electronegative N, O or F of neighboring molecule. london forces - weakest force, attraction between noble gas and between non-polar molecules. Temporary unequal distribution of electrons (Ch4), weak at room temperature.

Intramolecular bonds
Forces of chemical bond within a molecule between atoms/ions

Solubility Rule
Like dissolves like
Ionic/polar bonds dissolves with ionic & polar compounds (ex. water & alcohol)
Non-polar dissolves with non-polar
Nonpolar DO NOT dissolve with polar bonds (ex. oil & water)

Properties of Water
Polarity of water exhibits hydrogen bonding, bonds between molecules are intermolecular. water provides partial positive and partial negative charges to which other polar molecules can attach. When ionic solid dissolves, anions and cations dissociate.
In aqueous solutions (solutions where water is the solvent), solutes are generally divided into two categories:
Hydrophilic molecules: polar/charged molecules that are strongly attracted to water
Hydrophobic molecules: non-polar molecules that are not strongly attracted to water

Property
Explanation
Examples of benefits
Cohesion
Hydrogen bonds makes water molecules stick together.
Movement of water in a plant: water is taken in roots, moves through the plant till it reaches the leaves.
High specific heat
Water absorbs a lot of heat before it begins to get hot
Stabilizes temperature change between seasons.
High heat of vaporization
Hydrogen bonds are broken for water to evaporate
Cools body surfaces
Lower density of ice
Water molecules in ice are spaced far apart because of hydrogen bonding
Since ice is less dense than water, lakes do not fully freeze so fish can survive in the water
Solubility
Polar water molecules attracted to ions and polar compounds, making it soluble
Many kinds of molecules move freely in cells, permitting diverse array of reactions.

Functional groups of Biology
Organic Chemistry
Organic chemistry is sometimes called carbon chemistry since organic molecules form from a carbon frame.
Catenation: Carbon can form four bonds from a single atom and has a unique ability to make long chains with itself.
When carbon is bonded to hydrogen alone, the type of compound formed is called a hydrocarbon. Hydrocarbons are organic molecules.
Organic molecules: contain carbon & found in living organisms except hydrogen-carbon, carbonates & oxides of carbon
Inorganic molecules: do not contain carbon even if they are living

Functional Groups
Functional groups can be attached to hydrocarbons Carbons
Has 4 valence electrons
Can form single creating tetrahedral shape
Also form double or triple bonds
Crucial to the formation of multiple bonds to create long chains, ring structures
Most functional groups are either ionic/polar
Attracted to other ionic or polar molecules, including water
Causes many reactions to occur

Biological Reactions
Neutralization reaction: involves the reaction of an acid and base to produce a salt and water (similar to double displacement reaction) (NaOH must be in it)
HCl + NaOH --> NaCl + H2OHCl is an acid. NaOH is a base.
Redox (reduce oxidation) reactions: An oxidation-reduction reaction is any chemical reaction in which the oxidation number of a molecule, atom, or ion changes by gaining or losing an electron.
Cu + 2Ag+ --> Cu2+ + 2Ag
Condensation reaction (dehydration): a reaction in which two molecules combine to form a larger molecule, producing a small molecule such as H2O as a byproduct.
C6H12O6+ C6H12O6 -->C12H22O11 + H2O hydrolysis reaction: the chemical breakdown of a compound due to reaction with water.
ATP + H2O -->ADP + Pi adenosine triphosphate + water --> adenosine diphosphate + phosphate
Carbohydrates
Carbohydrates are composed of carbon, hydrogen and oxide
Ratio of C:H:O is 1:2:1
General formula is CH2O, CnH2nOn
Function of carbs is an immediate source of energy for cellular respiration
Also used for structural support in some organisms
Mostly hydrophilic (water loving)
There are THREE categories of carbohydrates: MONOSACCHARIDES, DISACCHARIDES & POLYSACCHARIDES
Monosaccharides
Single sugars, the building blocks of molecules
4 monosaccharides the human body uses/processes:
Ribose - important for DNA and RNA
Glucose - fuel for your brain, provides energy
Fructose - plant sugar, also found in honey
Galactose - part of milk sugar
Glucose, fructose, galactose are isomers (same molecular formula C6H12O6, but different structure)
Glucose has alpha/beta form

Disaccharides Chemical monosaccharides bond together by dehydration (condensation) reaction to form double sugar
When a disaccharide is formed, it is called glycosidic bond – for every bond formed, a molecule of water is released
For every glycosidic bond broken (through hydrolysis), a molecule of water is added in
There are THREE main types of disaccharides:
Sucrose (glucose + fructose)
Lactose (glucose + galactose)
Maltose (glucose + glucose)
All have the formula C22H22O11 and are all isomers (remember we miss the 2 hydrogen and one oxygen, this is why its not C6H12O16
Polysaccharides
Large molecules with many monosaccharides
So large that when ingested they go through hydrolysis to break glycosidic bonds to function
There are FOUR main types of polysaccharides:
Starch - storage molecule in plants (both hydrophobic), 2 types of starch: amylose – made of repeating glucose units in straight chains amylopectin made of repeating glucose units in straight chains with smaller branching chains
Glycogen – Animals store excess glucose using with amyloceptin, short term energy usage and stored in liver/muscles.
Cellulose - cell walls of plants. Straight chain of glucose with flip-flop pattern of bonding that produces long, rigid molecule.
The absence of side chains allows the linear molecules to lie close together allowing hydrogen bonding between adjacent chains and creating stiff, elongated fibers
Chitin – cell wall of fungi and exoskeleton of crustaceans

Lipids

Lipids made of carbon, hydrogen, oxygen (with different ratios)
Non-polar substances, meaning they are hydrophobic
There are FOUR main types of lipids: triglycerides (fats and oils) phospholipids steroids waxes Major functions of lipids
Long term energy storage
Fat in liquid state in cells as storage form of energy
When theres no more carbs left in body, fat provides 2x amount of energy per gram as carbs
Fat stores 2x amount of energy as glucose
Fat produces 2x number of calories when burned (twice as work needed to burn it)
Protection and insulation
Protects and insulates vital organs of body (like cushioning)
Insulation against heat loss, important to maintain body’s internal temperature.
Makes cell membranes (phospholipids)
Form a barrier between itself and water environment
Needed to absorb fat soluble vitamins (A, D, E, K)

Triglycerides - Definition
Lipid molecules composed of 3 fatty acids and 1 glycerol molecule
Fatty acids naturally come in 2 forms - saturated/unsaturated
Body makes triglycerides as long-term storage molecule of energy
Stored in adipose tissue (fatty tissue)

Saturated Fatty Acids – Triglyceride
Have a parent hydrocarbon chain that only contains single bonds
Saturated is used because every carbon is bonded to as many hydroge atoms as possible
General formula is CnH2n+1COOH
One end of every fatty acid has carboxylic group attached - COOH
Solid at room temperature & found in animal fats (butter, lard, any fat from meat)

Hydrogenated fatty acids – Triglyceride
Made by adding hydrogen atoms to unsaturated fatty acids
Creates trans-fatty acids
Solid at room temperature
Bad for peron’s health and most health professionals consider it worse than saturated fat

Unsaturated fatty acids – Triglyceride
Contain one or more double bonds in their parent hydrocarbon chain
These double bonds cause a “kink” in the general shape, making it bent
The formula depends on how many double bonds are present
These fatty acids are liquid at room temperature, found in plant fats (corn oil, olive oil, peanut oil, soybean oil, canola)
There are 2 types of unsaturated fatty acids – monounsaturated and polyunsaturated
Monounsaturated fatty acids have 1 double bond in parent chain
Polyunsaturated fatty acids have more than 1 double bond

FORMING A TRIGLYCERIDE
Triglycerides are formed when 3 fatty acids chemically bond to a glycerol molecule by three dehydration synthesis reactions (a.k.a. condensation reactions)
The bond formed between a fatty acid and glycerol is called an ester bond
For every ester bond formed, a molecule of water is released
The reverse process of separating fatty acids from glycerol requires a hydrolysis reaction
For every ester bond broken, a molecule of water is required

Phospholipids
Phospholipids are lipid molecules composed of 2 fatty acids, 1 phosphate group and 1 glycerol molecule
The phosphate group is attached to the third hydroxyl group on glycerol in place of a third fatty acid
This creates a molecule that has a hydrophilic region (phosphate head) and a hydrophobic region (fatty acid tails)
These phospholipids are the major component to forming cell membranes by creating a phospholipid bilayer
Cell membranes control what enters and exits the cell

Steroids
Steroids have 17 carbon atoms bonded into four carbon ring struture
They differ in (a) nature and location of the side chains, and (b) location of the double bonds within the rings
Some examples of steroids:
Cholesterol
Vitamin D
Bile salts
Estrogen
Progesterone
Testosterone
Cholesterol is the most abundant steroid (found in skin and reacts with sunlight to produce vitamin D)
High levels of cholesterol have been associated with heart disease

Waxes
Waxes are formed from the union of long saturated fatty acids and long chain alcohols
Some examples of waxes:
Beeswax
Spermaceti
Carnauba wax
Spermaceti is the oil from the head of sperm whales
Was once widely used in cosmetics, ointments, soaps and other products
Carnauba wax is used in floor waxes, shoe polish and car wax

Proteins
Functions of Proteins
Essential for growth and repair
Structural: muscles, skin, hair
Enzymes: chemical catalysts that speed up chemical reactions in the body
Part of cell membranes
Hormones (insulin), antibodies (fight infection)
Maintain pH balance

Structure of Proteins
Large molecules made up of long chains of amino acids (>1000)
Amino acids are joined by peptide bonds
Amino acids are made from C, H, O, N
20 different amino acids
Order and number of amino acids determine the protein
All amino acids have same basic structure, each one has a different R group that gives amino acid it's properties

Synthesis & breakdown of proteins
Through a condensation / dehydration synthesis reaction, two amino acids form a peptide bond and a molecule of water is produced
To break a peptide bond, a molecule of water is added through a hydrolysis reaction
Two amino acids bonded together are referred to as a dipeptide
Three or more amino acids bonded together are referred to as a polypeptide
Many polypeptides form a protein Levels of protein structure
1st structure (primary):
Sequence of amino acids specified by a gene
2nd structure (secondary):
Folding and coiling due to hydrogen bonds (weak bonds)
Either forms α-helix or β-sheet (β-pleated sheet)
3rd structure (tertiary):
Interaction between side chains (R groups) of amino acids
Include hydrophobic interactions, disulphide bridges, and hydrogen bonds
4th structure (quaternary):
Aggregation between two or more polypeptide chains
Often proteins are combined with metal ions to perform their functions
EX: hemoglobin requires iron to carry oxygen in the blood
Next page shows diagrams of the structures.
Nucleic Acids
3 main types of nucleic acids: DNA, RNA and ATP
DNA is the molecule that provides genetic instructions that are found in each cell in your body
RNA is similar in structure but makes proteins for your body

DNA Structure
DNA stands for deoxyribonucleic acid
Carries hereditary information passed on from one generation
Found in the nucleus of every cell
DNA is packaged tightly in the cell in a form of chromatin, when it is unwound and stretched out, it looks like a twisted ladder. This is called the DNA double helix.

RNA Structure
RNA differs from DNA in that it is single stranded. It has a hydroxyl group on carbon 2 of the ribose sugar while DNA does not. Also RNA does not contain the pyrimidine thymine. Thymine is replaced by another pyrimidine - uracil in its structure. RNA molecules are important in protein synthesis.

Adenosine triphosphate (ATP)
Unlike DNA and RNA, ATP is not found in long strands.
Single structure composed of adenine, ribose, and 3 phosphate groups. 
ATP is the “energy currency” in living organisms – it provides the energy required in cells

Nucleotides
Polymers have repeating monomer units called nucleotides
A nucleotide consists of a five carbon sugar (ribose), a nitrogen base, and a phosphate group.
A 5-carbon sugar (pentose): A nucleotide contains either: deoxyribose (found in DNA nucleotides) ribose (found in RNA nucleotides)
These sugars are part of the backbone of DNA and they attach to phosphate groups.
Phosphate group (PO4 3-): They form part of the DNA backbone, along with the sugars
Nitrogen bases: They form the “rungs” of the DNA ladder
5 nitrogenous bases: adenine, guanine, cytosine, thymine (DNA) and uracil (RNA)
The bases are either purines or pyrimidines.
Purines: double ring structures (guanine, adenine)
Pyrimidines: single ring structures (thymine, cytosine, uracil)

Enzymes
Proteins that act as catalyst to speed up chemical reactions
Without enzymes, reactions in the body occur too slow to sustain life
Substrate(s): what is being catalyzed, binds to the enzyme at the active site
Once the enzyme catalyzes the reaction, the substrate is turned into a product
Types of enzymes are classified based on reactions they catalyze:
Hydrolasses: catalyze hydrolysis reactions
Kinases: catalyze transfer of phosphate groups
Phosphatase: catalyze removal of phosphate groups

Lock & Key Model
Each enzyme is specific to a substrate, just like every key is specific to a lock
Shape of active site is determined by tertiary and quaternary structure of protein
Enzymes lower the activation energy (energy required for reaction to occur)

Induced Fit Model
A better explanation of enzyme activity
Active site is not as “rigid” as the lock and key model explains
Conformational change in the shape of the enzyme active site may occur once the substrate binds, “inducing fit of substrates”
Allows 2 substrates to bind to the same enzyme

Factors affecting enzyme action
Denaturation: occurs when there is a structural change that results in the loss of an enzyme's biological properties (thus enzyme no longer functions)
There are THREE factors that can cause denaturation:
Temperature
Rate of reaction increases as temperate increases
Enzymes have optimum temperate in which to function (usually body temperature)
Low temperature enzymes do not function well
High temperate enzymes denature pH Enzymes also have optimal pH (ex. Pepsin in the stomach = pH 2)
Outside optimal pH the enzyme will not function
Ionic interactions between R groups will be disrupted and enzyme denatures
Substrate concencation
Reaction rates increase if there's more substance until the amount of substrate exceeds amount of enzyme
Enzyme inhibition
Inhibitors are molecules that reduce or prevent enzyme reaction
There are TWO types of inhibition:
Competitive inhibition:
Blocks the active site by binding to it, thereby preventing substrate from binding
Slows enzyme activity by resulting in fewer collisions between substrate/enzyme
Must have similar structure to substrate
Adding more substrates reduces effect of the inhibitor (sulfa drugs, penicillin used in HIV treatment
Non-competitive inhibition
Inhibitor binds to a place on the enzyme that is NOT the active site called the allosteric site
Change the conformation of the enzyme (substrate may no longer fit) and reduces its ability to catalyze reaction
Adding more substance will have no effect

Plasma Membrane
The cell membrane is called the fluid mosaic model
Mosaic of various macromolecules that are fluid within the membrane
Functions include: gate keeping, cell recognition, transporting proteins, structural support, catalyze biological reactions

Phospholipid bilayer
Main component of cell membrane
Made of 2 fatty acids which are: hydrophobic (the tail) phosphate group that is hydrophillic (the head) when surrounded by water, phospholipids form a liposome, enclosed sphere so none of the tails come in contact with water
Proteins
There are TWO major types of proteins found in the cell membrane:
Integral: exposed on both sides of membrane
Peripheral: only rest on side of membrane

Passive Transport
Movement of solutes (ions or molecules) across a membrane from an area of higher concentration to an area of lower concentration
Movement down a concentration gradient
Requires no energy
There are THREE TYPES of passive transport: Simple diffusion, osmosis, facilitated diffusion

Simple Diffusion
Passive transport of small solutes: small non-polar molecules (gasses like O2 and CO2) small uncharged polar molecules (water molecules and glycerol) slightly larger non-polar molecules (steroid hormones)

Osmosis
Diffusion of water from an area of higher concentration to lower concentration
There are THREE specific terms we identify differences in concentration in cells
Isotonic solution: no net movement of water because intracellular concentration of solutes is the same as extracellular
Hypotonic solution: if concentrations of dissolved solutes are less outside the cell than inside, concentration of water outside if greater. There is net water movement INTO the cell. Cells without walls swell and may burst if excess water is not removed. Plant cells often benefit from turgor pressure.
Hypotonic solution: If concentrations of dissolved solutes are greater outside the cell, concentration of water outside is correspondingly lower. Water inside cell will flow outwards to attain equilibrium, causing shell to shrink.

Facilitated Diffusion
Since ions and larger polar molecules cannot pass through phospholipid bilayer through simple diffusion, they require help from transport proteins embedded in the membrane
Solutes still travel from an area of higher concentration to an area of lower concentrations
Channel proteins: allows polar molecules or ions to move through channel opening
Carrier proteins: molecules must bind to the protein and then transported across