Biochemistry

Biochemistry- The Basics

An Atom is the basic unit of a chemical element ( smallest unit for measuring chemical & physical properties)

Smallest particle of an element is an atom

A Particle is a small portion of matter

Matter is composed of elements___ Matter makes up everything in the universe.

An Element is a pure substance that cannot be broken down into a simpler substance. ex. carbon, hydrogen, etc

A molecule is a group of atoms bounded together ex O2

A chemical compound is a stable combination of different elements that are held together by chemical bonds.

All organic compounds in living organisms are composed primarily of CARBON, HYDROGEN, and OXYGEN( + sometimes NITROGEN)
This makes up 96% of the weight of living organisms
4% made out of calcium, phosphate, sulfer, Mg, Na, etc (occur as ions or in inorganic compounds within living organisms)
Rest of the elements required are founds in such small amounts (0.5-------->1.7----------> 3.2

0- exactly zero is purely covalent
0-0.5: covalent
0.5-1.7: polar covalent
1.7-3.2: Ionic( metal & non mental)

-3. Polar Covalent bonds: shared electrons are pulled closer to one of the elements than the other ( different in electronegativities does not surpass 1.7) : the atom that attracts the valence electrons more strongly carries a partial negative charge which results in the other atom carrying a partial positive charge. B/c the atoms carry partial charges, the whole molecule may have a non-uniform charge distribution. This is the polarity of the molecule. : partial charges called dipoles : a molecule's function is determined by the bond polarity and its overall polarity.

VSEPR( Valence Shell Electron Pair Repulsion) Theory: basically, valence electron pairs(usually 4) repel one another & will move as far apart as possible around a central atom.

Intermolecular Bonds( takes place between the atoms of two or more separate molecules): - very weak attraction between two molecules when they are close

Van der Waals forces:

London forces: temporary weak dipole moments( hold non polar molecules together)
Dipole-Dipole forces: the attractive force between two polar molecules
4. Hydrogen Bonding: extremely strong dipole-dipole force formed when hydrogen bonds to oxygen, nitrogen, or fluorine created hydrogen bonds are the strongest plus most biologically significant form of Van der Waals forces.
In small number are weak, but in large numbers strong hydrogen bonds between water molecules are responsible for many of the properties that make water a uniquely important molecule for all living organisms.
Importance of Water:

It is a highly polar molecule

Water forms hydrogen bonds with itself and with other polar or ionic molecules (intermolecular bonds) ex. NaCl is a hydrophilic(water loving) molecule.

Water is the most abundant liquid on earth & is known as the universal solvent.
Specific Heat: is the amount of thermal energy that is required to increase the temperature of a given quantity of water by 1 degree C.

High boiling point of water ensures that it's in a liquid state from 0 degrees to 100 degrees C.

Surface tension is the measure of how difficult it is to break or stretch the surface of a liquid.

Hydrophilic molecules (water loving): polar molecules or charged ions that are strongly attracted to water

Hydrophobic (water fearing): non-polar molecules that are not strongly attracted to water.

Aqueous Solutions- the surface coat of water is called the hydration shell. This shell reduces the attraction between molecules or ions of other substances and promotes their separation allowing substances to go into solution. This results in an aqueous(water based) solution in which the solvent and the molecules or ions of other substances are the solute. ex. Sodium chloride pg 21

pH of water is 7(neither acid or base)

Unique properties of water characteristics properties
Explanation
Effects
Examples

Water clings
Cohesion

Adhesion
When water molecules form hydrogen bonds with each other.

When water molecules form hydrogen bonds with other polar molecules.
High surface tension

Capillary action and solubility of polar compounds
A water strider walks on the surface of a pond

Capillary action causes water to move up the xylem tubes in plants.
Polar substances, such as sugars, are highly soluble in water.

Water absorbs thermal energy
High specific heat capacity

High specific heat of vaporization
Hydrogen bonding causes water to absorb large amounts of thermal energy as its temperature increases, or lose large amounts of thermal energy as its temperature decreases.

Hydrogen bonding causes liquid water to absorb large amounts of thermal energy and become a vapour(gas).
Temperature moderation

Evaporation and cooling
High heat capacity helps organisms maintain a constant body temperature

Many organisms including humans dissipate body heat by the evaporation of water from the surface of the body , often by sweating

Solid water is less dense( by 10 %) than liquid water

High density at 4 degrees C
As water molecules cool below 0C, they form an ice water lattice. The hydrogen bonds keep the water molecules spread apart, reducing the density so that it is below the density pf liquid water.

Ice floats on water
Fish and other aquatic organisms survive in winter because water freezes from the top down.
Snow is a very good insulator. It provides protection from extreme cold for many organisms.

All chemical reactions involve the breaking and formation of chemical bonds, thereby changing the arrangement of the atoms and ions.

4 major types of chemical reactions

Dehydration reaction: a chemical reaction in which subunits of a larger molecule are joined by the removal of water( most common method used by cells to join smaller molecules and to assemble extremely large macromolecules such as complex carbohydrates & proteins)

Hydrolysis reaction: a chemical reaction in which water is used as a reactant to split a large molecule into smaller subunits( are the reserves for dehydration reactions)

Neutralization reaction: a reaction in which an acid creates with a base to create a salt and water ex. Reaction between hydrochloric acid and sodium hydroxide. The product of these reactants are water and sodium chloride.

Redox reaction: the transfer of electrons from one atom to another.
Oxidation: a reaction in which a molecule loses electrons.
Reduction: a reaction in which a molecule gains electrons.

Acids, Bases, & Buffers

*When the concentration of hydronium ions(H3O) ina solution is greater than the concentration of hydroxide ions (OH-) the solution is an ACID. * ex. HCI
Properties of acids: sour taste, ability to conduct electricity, turns blue litmus paper red

*When the concentration of hydroxide ions (OH-) in a solution is greater than the concentration of hydronium ions( H3O), the solution is a BASE.* ex. NaOH
Properties of bases: bitter taste, slippery feel, conducts electricity, turns red litmus paper blue

Buffers: are molecules that resist changes in the pH level by absorbing or releasing H+( usually involves a weak acid & its conjugate base)

Strong & Weak Acids & Bases

The strength of an acid or base depends on the degree to which it ionizes when dissolved in water
Autoionization: the process in which a molecule spontaneously dissociates into ions.

Strong acids and bases ionize completely in water

Weak acids and bases partially ionize in water.

Organic acids and bases are weak.

ACID-BASE BUFFERS

There are 3 important buffer systems in our bodies(refer to textbook for image):
B. Carbonate buffer system
Phosphate buffer system
Protein buffer system

Organic Molecules(all are carbon based)

Properties of Carbon:
4 single valence electrons forms 4 stable covalent bonds

Molecules consisting only of carbon atoms bonded to hydrogen atoms are called hydrocarbons. smallest hydrocarbon is methane carbon always has 4 bonds
Alkanes(saturated**)
Alkenes & Alkynes(unsaturated) non polar (ED=0.4)
** maximum carbon-hydrogen bonds no double or triple bonds(all single)

Functional Groups: reactive clusters of atoms attached to the carbon backbone that affect the function of a molecule by participation in chemical reactions. (chart pg26 memorize)
CHECK & MEMORIZE CHART

Role of functional groups

Functional groups are more reactive and impart chemical properties to molecules to which they are attached. Ex.
OH & COOH are polar(negative oxygen)
OH group makes substances water soluble
COOH makes a molecule acidic
NH2 makes a molecule basic

BIOLOGICAL MACROMOLECULES

Molecules of living organisms almost invariably contain other elements in addition to C& H, giving them different functional properties. These molecules fall into 4 major groups:
Carbohydrates
Lipids
Proteins
Nucleic acids

1. Carbohydrates: a bio molecule that consists of carbon, oxygen, and hydrogen.

In photosynthesizing plants & organisms, carbon dioxide & water molecules are used as raw materials to build carbohydrates producing millions of tones of carbohydrates each year. carbohydrates are used as energy source, building materials, and for cell communication can be found in fruits, vegetables, and grains

Glucose most wildly used monosaccharide(produced my plants)

Monosaccharides that are composed of 3 carbons(triose), 5 carbons(pentose), and 6 carbons(hexose) are the most common in living organisms

When glucose forms a ring, there are 2 possible arrangements of the -OH group which is bound to the carbon at position one: alpha glucose, beta glucose(both isomers)

Isomer: a molecule that has the same composition as another, but a different arrangement of atoms. ex. Glucose, Fructose, and Galactose are isomers of each other.

Starch is composed of repeating units of glucose. They act as one immune energy source, two building materials(cellulose +chitin) and 3 surface makers.
Empirical formula (CH2O)n

Types of Carbohydrates (Pg15 memorize “Isomers of Glucose + Maltose”): monosaccharide: a single sugar unit oligosaccharide ( disaccharides)
Polysaccharides

Glycosidic bonds: a bond between two monosacch. ex. Milk -> lactose+B glucose
Chemical shorthand for representing a glucose bond between 1-carbon and 4-carbons is 1-----> 4
Condensation Reacts: AKA dehydration synthesis anabolic( build up) reaction: removal of an H and and OH to form water
Common to all macromolecules
* link two small molecules together, remove water*

Hydrolysis Reaction: catabolic(breaking down): addition of H and OH from water breaks bonds between molecules

Complex Carbohydrates: a molecule that is composed of hundreds to thousands of monosaccharides linked together( essential part of nutrition and valuable energy source) ex. Starch, chitin

Polysaccharides
100s of glucose molecules oriented in the same direction
NRG storage in plants every other glucose is “upside-down,” and we can not digest, therefore fibre more branching in starch... NRG storage in animals.

A polysaccharide is a small macromolecule (which is a very large molecule assembled by the covalent linkage of smaller subunit molecules).
Most common polysaccharides are starch, glycogen, and cellulose.
Polysaccharides are very polar, therefore, very hydrophilic( since they are huge, they attract water, but cannot dissolve in it)

Polymerization: a process in which small subunits are linked to form a large molecule ex. Dehydration synthesis reactions that assemble polysaccharides.

Monomers: a small molecule that can bind chemically to other molecules.

Polymer: a large molecule that is formed when monomers link together chemically in a chain. Ex DNA

LIPIDS a non polar compound that is made mostly of carbon and hydrogen smaller than complex carbohydrates, therefore they are not macromolecules functions energy source energy storage membrane components waxy protection can serve as hormones that regulate cellular activities

REFER TO DIAGRAMS ON PG16
There are 4 types of lipids: triglycerides phospholipids sterols waxes

Triglycerides(FATS): are lipids made from 2 types of molecules, fatty acids and glycerol molecules. they have 3 fatty acid chains linked to a glycerol molecule= “esterification” most well known lipids can have identical or different fatty acid chains very energy dense non polar therefore hydrophobic
Triglycerides function widely as stored energy(2x more energy than carbohydrates)

saturated fat: a lipid that is composed of saturated fatty acids with single bonds in their hydrocarbon chain. ex. Lard, butter

unsaturated fat: (usually referred to as oils) a lipid that is composed of unsaturated fatty acids with double bonds in their hydrocarbon chain. ex. Olive oil ( mostly derived from plants)

** saturated fats are solid b/c their chains are long and straight therefore can be packed together to form a solid structure at room temperature. Fatty acid chains that have kinks are bent and cannot be packed as tightly as saturated fats therefore these molecules stay more fluid and are liquid at room temperature.**

Phospholipids: a lipid that consists of two fatty acids and a phosphate group bound to a glycerol(pg35 textbook) main components of cell membranes they contain 2 hydrophobic fatty acids at one end attached to a hydrophilic polar group often called the head group.
Molecules that contain both hydrophobic and hydrophilic regions are called amphipathic molecules.

Steroids: a lipid that is composed of 4 carbon rings most abundant steroids are sterols which have a single polar- Oh group at one end of the ring framework and a complex, non polar hydrocarbon chain at the other end.
Hydrophobic
Cholesterol, a steroid, is an important component of the plasma membrane that surrounds animal cells.(phytosterols in plants)
- too much cholesterol can cause atherosclerosis
Sex hormones such as testosterone, oestrogen, and progesterone are all steroids.
Anabolic steroids used by athletes to build muscle mass, mimic the male sex hormone, testosterone and have harmful effects on the body

WAXES: are large lipid molecules that are made of long fatty acid chains linked to alcohols or carbon rings. are solid waterproof coatings on plants and animals hydrophobic, extremely non polar, and soft solids over a wide range of temperatures
Cutin is a type of wax made by plant cells for a water resistant coating. Cutin enables plants to conserve water, and it acts as a barrier to infections and diseases. Chart of lipids pg37

Proteins & Nucleic Acids

Proteins(comes from greek word “proteois” meaning first place): a large molecule that consists of many amino acid subunits that are joined together by peptide bonds folded into a specific 3-D shape. structural components of cells, muscles, fibres, hair, and enzymes all amino acids have the same structure except for “R” all proteins are polymers that are composed of amino acid monomers defensive proteins called antibodies help fight off infections hormones and other messenger chemicals in the cell are signal proteins haemoglobin is a special protein in red blood cells that delivers oxygen to the muscles and other tissues and organs
Motile proteins give cells and cellular structures the ability to move enzymes are proteins responsible for making almost every biochemical reaction possible(refer to pg 41 chart)

Peptides: a covalent bond that links amino acids into chains of subunits that make proteins formed by a dehydration synthesis reaction between the -NH2 group of one amino acid and the -COOH of a second amino acid.
Peptide: a chain of amino acid subunits that are connected by peptide bonds
Polypeptide: a peptide with more than 50 amino acids

** All proteins are polypeptides, but not all polypeptides are proteins**

Protein Structure: 4 levels of structure
1º (primary structure)= amino acid sequence
2º (secondary structure) = hydrogen bonding between peptide bonds
1. Common secondary structures include B-pleated sheet and alpha-helix
2. The beta- pleated sheet forms by a side by side alignment of amino acid chains ( play important role in the strength of silk)
3. An alpha-helix is a delicate coil that is held together by hydrogen bonds between every forth amino acid( found in filamentous proteins and trans membrane proteins and provides necessary structure for their function).

3º (tertiary structure)= interaction of R groups( 3D protein/ Globular)
4º (quaternary structure)= multiple polypeptide interact (refer to image on pg 17)
1. Haemoglobin molecules are composed of four polypeptides, each consisting of more than 140 amino acids.

Denaturation: the loss of both the structure and the function of a protein.

Many proteins require non-protein components, called prosthetic groups, to function. ex. Haemoglobin
Many enzymes require prosthetic groups that contain metal ions in order to function.
The shape of a protein influences and enables its function.

Amino Acid: a molecule that contains a carboxyl group and an amino group; serves as the monomer subunit of proteins attached to the central carbon atom is a variable side group, called a n R group, which gives each amino acid its distinct characteristics
20 types of amino acids

Nucleic Acid: a blueprint for proteins that are synthesized in cells; stores hereditary information carries our genetic information necessary for protein production in cells
Two types of nucleic acids:
DNA( deoxyribonucleic acid ): stores the heredity information that is responsible inherited traits in all eukaryotes and prokaryotes and in many viruses.
RNA(Ribonucleic acid): is the hereditary molecule of some viruses (a copy of DNA)
Nucleotide: the building block of nucleic acids; consists of 5-carbon sugars, a nitrogenous base, and 1-3 phosphate groups.
There are 2 general types of nitrogenous bases:
Pyrimidines (bases are single organic rings)
Purines (bases are two-ringed organic structures)

DNA & RNA are polymers of nucleotides.
The 3 pyrimidine bases are: uracil(U) thymine(T) cytosine(C) The 2 purine bases are:
Adenine(A)
Guanine(G)

DNA & RNA consists of chains of nucleotides called polynucleotide chains, with one nucleotide linked to the next by a single bridging phosphate group between the 5-carbon of one sugar and 3-carbon of the next sugar in line.
Phosphodiester bond: a link that is formed between nucleotides by a phosphate bridge. This forms the backbone of the nucleic acid chain.

In a DNA chain, each nucleotide contains deoxyribose, a phosphate group, and one of the 4 bases, A, T,G, or C. - Strands of DNA run antiparallel(oriented in opposite directions) to each other.

In a RNA chain, each nucleotide contains ribose , a phosphate, and one of the 4 bases A, U, G, or C.

Nucleotides perform many functions in cells, in addition to serving as the building blocks of nucleic acids. Two nucleotide in particular, ATP and GTP are the primary molecules that transport chemical energy from one reaction system to another. They also regulate and adjust cellular activity.

ENZYMES: a biological catalyst, usually a protein, that speeds up a chemical reaction. a catalyst is a substance that speeds up a reaction without being consumed by the reaction.
An uncatalysed reaction requires a higher activation energy than does a catalysed reaction the enzyme, lipase speeds up the hydrolysis of the lipid triglyceride.
Sucrose speeds up the hydrolysis of sucrose into glucose and fructose.
Enzymes bind to a specific reactant(s) called substrates, in doing so, they lower the energy barrier so that the reaction proceeds at a faster rate than it would without the enzymes.
Substrate: a substance that is recognized by and bins to an enzyme
In a reaction that uses an enzyme, the enzyme combines briefly with the substrate and after releasing the product, is unchanged.
The substrate interacts with only a very small region of the enzyme called the active site.
Active site: a pocket or grove in an enzyme that binds to the substrate(refer to pg 17 for image)

Induced-fit model: a model of enzyme activity that describes how an enzyme changes shape to better accommodate a substrate.

The Enzyme Cycle:

An enzyme binds to one or more substrates, forming an enzyme- substrate complex. The enzyme then converts the substrate(s) into one or more products. Since enzymes remain unchanged after a reaction, enzyme molecules can rapidly bind to other substrate molecules, catalyzing the same reaction repeatedly. (pg51)

What affects enzyme activity
[enzymes] & [substrate ] (square brackets mean concentration)
Inhibitors ( drugs, pesticides, poisons, antibiotics)
Allosteric regulation pH & temperature

Cofactor (inorganic): a non-protein group that binds to an enzyme and is essential for catalytic activity (often metals such as copper, iron, zinc, and magnesium) ex. Fe in haemoglobin. must bind to an enzyme for proper function essential for catalytic activity

Coenzyme(organic): are organic molecules that act as a cofactor of an enzyme (often derived from water soluble vitamins) - are needed for some enzymes to function (eg, coenzyme A in energy metabolism)

The concentration of both the enzyme and the substrate will influence the rate of a catalysis reaction.
Enzyme inhibitors lower the rate at which an enzyme catalyzes a reaction.

TYPES OF INHIBITORS

Competitive Inhibitors: a situation in which a competitor substance binds to a normal substrate binding site to block enzyme activity they compete with the substrate for the binding site on an enzyme.

Non-Competitive Inhibitors: a situation in which molecules bind to an enzyme at a site that is not the active site, thus blocking enzyme activity. they bind to a an allosteric site on an enzyme

Irreversible Inhibition: Some inhibitors bind so strongly to the enzyme through the formation of covalent bonds that they completely disable the enzyme include drugs, poison, pesticides, and antibiotics ex. cyanide

Allosteric Regulation: the body produces chemicals that change an enzyme’s shape to an active form(activator) or inactive form(inhibitor)
Molecules that naturally regulate enzyme activity in a cell often behave somewhat like a noncompetitive reversible inhibitor. These regulatory molecules bind to an enzyme on a site that is not its active site, called the allosteric site, and cause a change in the shape of the enzyme, thus affecting the active site.
Binding to an allosteric activator molecule stabilizes the enzyme in a shape that causes its active site to have a high affinity for its substrate.
Binding of an allosteric inhibitor stabilizes an inactive form of the enzyme. The inhibitor molecule changes the shape of the enzyme in such a way that the substrate is released from the active site.

Feedback Inhibition: the regulation of a pathway by one of the products of this pathway. control of metabolic pathways where the product of a series of reactions acts as an inhibitor of an enzyme earlier in the series.(pg 18 diagram)

read page 55 and understand it

Industrial uses of enzymes: starch production in laundry detergents to improve stain removal cheese making wine and juice

Chapter 2

Organelle: an internal functional structure that is located within the cytosol of a cell. Functions: some isolate toxic or harmful substances provide a favourable environment for a reaction that could not occur in the cytosol transport substances through the cytosol, maintaining fluid balance

*Each organelle adapted to perform a specific function therefore the shapes of some organelles are quite elaborate.*

The most complex of all cells are those of some single-celled protists.

Plasma membrane: a dynamic barrier that surrounds the cytosol of the cell.

An organelle rarely ever works alone, just like the organs in your body.

The Nucleus almost all eukaryotic cells have a nucleus the nucleus is an organelle that contains almost all the DNA in a eukaryotic cell and protects it
Small amounts of DNA are found in the chloroplast and mitochondria.

Nuclear Envelope the nucleus is surrounded by a double membrane called the nuclear membrane or nuclear envelope
It consists of 2 lipid bilayers that are folded together; the outer bilayer of the membrane is continuous with the membrane of another organelle, the endoplasmic reticulum(ER)
Different kinds of membrane proteins are embedded in the two lipid bilayers.
Some are receptors and transporters others collect in tiny pores that span the membrane
The membrane proteins work with the lipid bilayers as a system to transport various molecules across the nuclear membrane.
The nuclear envelope allows water and gases to cross freely.
The system of transporters and pumps controls the passage of molecules between the nucleus and the cytocol.

Memorize chart on page 73

NUCLEOLUS enclosed by the nuclear envelope, the nucleus contains nucleoplasm, which is a viscous fluid that is similar to cytosol the nucleus also contains at least one nucleolus( a dense irregularly shaped region where subunits of ribosomes are assembled from proteins and RNA).

The Endomembrane System: a group of interacting organelles between the nucleus and the plasma membrane. main function is to make lipids, enzymes, and other proteins for secretion or insertion into cell membrane
Other specialized functions include destroying toxins and recycling waste
Refer to diagram on pg 74

Endoplasmic Reticulum(ER): a membrane-bound organelle that is folded into flattened sacs and tubes, and is often an outgrowth of the nuclear envelope in a eukatyotic cell.
There are 2 types of ER: rough ER: areas of endoplasmic reticulum with ribosomes attached to the surface cells that make, store, and secrete a lot of protein have a lot of rough ER. ex. Pancreas cells smooth ER: areas of the endoplasmic reticulum without attached ribosomes( has no ribosomes therefore does not make protein)
Some polypeptides made in the rough ER end up in the smooth ER as enzymes which produce most of the cells lipids and also break down carbohydrates, fatty acids, and some drugs and poisons

Vesicles: a small, membrane-bound organelle that may transport, store, or digest substances within a cell (enclosed, sack-like organelles) form in great numbers
Many types of vesicles with many different functions.
Some types transport proteins from one organelle to another, or to and from the plasma membrane.
Another type called peroxisme contains an enzyme that digest fatty acids and amino acids
Plants and animal cells contain vesicles called vacuoles A vacuole is a liquid-filled organelle that stores waste and aids in cellular metabolism and water balance
Amino acids, sugars, ions, wastes and toxins accumulate in the water-filled interior of the central vacuole. Fluid pressure in the central vacuole keeps the plant cell, and therefore structures such as stems and leaves, form.
Usually central vacuole takes up 50-90 % of the cell’s interior.

Lysosome: a small, membrane-bound organelle that contains digestive enzymes that aid in waste disposal. are vesicles fuse with vacuoles that carry particles or molecules for disposal, such as worn out cell components

Golgi Bodies: an organelle with folded membranes where the final packaging of proteins occurs