The nuclei of some isotopes are unstable and break down or decay giving off particles of matter and energy that can be detected as radioactivity.
The decay transforms the unstable, radioactive isotope – called a radioisotope – into an atom of another element.
All have a characteristic half-life:
The time it takes for one half of the atoms in a sample to decay.
Constant for each isotope.
Applications of Radioisotopes
Diagnosis – radioactive isotopes can “light up” organs and tissues of interest.
Treatment – used to treat soft tissue disorders i.e., cancer.
Research – can be used to track changes to biological molecules in metabolic pathways.
Radiometric dating: provides the age of organic material, rocks, fossils, etc.
Chart pg.26 (or 29)
Bonding
Bonding allows atoms to form stable configurations as larger compounds.
A sharing or distribution of valence electrons in order to stabilize outer electron orbitals.
Electronegativity
Is the measure of an atom's attraction for the electrons it shares in a chemical bond with another atom.
It is influenced by the atomic # and the distance between valence ē and the nucleus of an atom.
Therefore, EN will increase as the distance between the ē and the nucleus decreases.
Scales ranges from 0 to 4.0
Cesium has the lowest value 0.7
Fluorine has the highest at 3.98
∆EN values determine the type of bond.
Types of Bonds
Intramolecular – bonds within a molecule
Ionic
Gaining or losing electrons
Force of attraction between cations and anions
∆EN > 1.7
Dissociate in water
Useful for biological reactions but not for creating biological structures
Covalent
Formed by the sharing of electrons
Can be single, double or triple
Most common form of bonding in biological molecules
Non-polar covalent
Molecule with evenly shared electrons
∆EN=0-0.5
Polar covalent
0.5 < ∆EN < 1.7
Similar to covalent, but the distribution of electrons is not equal resulting in a localized electric charge
Form H-bonds with each other
Intermolecular – bonds between molecules
Hydrogen bonds
A force of attraction between the electropositive H of one polar molecule and an electronegative N, O, or F of a neighboring polar molecule.
Individual H-bonds are weak but significant if in large numbers
Ex. DNA, surface tension of water
Dipole-dipole forces
Holds polar molecules together
Partial positive side of one molecule with the partial negative side of another molecule
London dispersion forces
Weakest (holds nonpolar molecules to one another)
Is a temporary attractive force that results when the ē in two adjacent atoms occupy positions that make the atoms form temporary dipoles (unequal distribution of ē as they randomly move about the nuclei of atoms).
Weak bonds between small molecules results in gases at room temperature.
Weak bonds between large molecules results in liquids at room temperature.
Due to the cumulative effect
WATER
Important biological molecule found in large percentages in all living things.
More substances dissolved in water than any other substance.
Each molecule has a partial positive and negative region, allowing it to readily penetrate or coat the surface of other charged molecules.
Surface coast of water (hydration shell)
Reduces the attraction between molecules/ions and promotes their separation into a solution (surrounded by water molecules).
Prevents molecules from re-association once in solution
“Like Dissolves Like”
“Like dissolves like” – polar substances dissolve in other polar substances.
E.g. oil and water do not mix because oil is nonpolar and water is polar.
Fats and oils are hydrophobic since they cannot form H-bonds with water.
Amphipathic Molecules
Amphipathic molecules: contain both hydrophilic and hydrophobic parts.
E.g. phospholipid
Properties of Water
Cohesion
The attraction between water molecules.
Can form up to 4 H-bonds with other water molecules.
Contributes to high surface tension of water.
I.e. a toothpick floats on water
Adhesion
H-bonds form between water molecules and other polar or charged molecules.
Capillary action of water depends on adhesion to “stick” water to ba surface.
I.e. xylem in plants (water to leaves)
Water sticks to sides (adhesion) but water molecules follow up the other water molecules which are lost at the leaves (cohesion).
High Specific Heat Capacity
Hydrogen bonding causes water to take in large amounts of heat before this temperature is increased.
Also causes water to lose large amounts of heat before its temperature is decreased.
Since the planet is mostly water, this acts as a heat sink or reservoir to moderate atmospheric effects.
Helps to maintain constant body temperature; ocean temperature.
High Specific Heat of Vaporization
Hydrogen bonds cause liquid water to absorb large amounts of heat to become a vapour (gas) resulting in evaporative cooling.
I.e. many organisms lose body by the evaporation of water from surfaces, such as the skin and tongue.
Highest Density at 4ºC
As water molecules cool below 0ºC, they form a crystalline lattice with hydrogen bonds spreading the molecules apart.
This reduces its density below that of liquid water leading to ice floating on water
BUFFERS Water
Pure H2o contains, H<em>2O, H</em>3O+, OH− (in equal amounts therefore, neutral)
Autoionization of Water: when 2H<em>2O molecules spontaneously react, 1H</em>2O molecule transfers an H+ ion to the other molecule, forming a H3O+ and OH−
2H<em>2O⇌H</em>3O++OH−
Acids
Increase the [H<em>3O+] when dissolved in H</em>2O
They donate protons
When more H3O+ exists = acidic
Sour: conducts electricity; pH < 7; blue litmus = red
Bases
Increase [OH−] in a water solution
They are proton acceptors that reduce the [H+] of a solution
When more OH− exists = basic
Bitter; slippery; conducts electricity; pH> 7; red litmus = blue
Neutralization Reaction
ACID + BASE → H2O + SALT
pH
The [H3O+] compared to the [OH−] ions determines the acidity.
pH scale – logarithmic scale
Why are Some Acids/Bases Strong, and Some are Weak?
Acids and bases may be classified as strong or weak according to the degree to which they ionize when dissolved in water.
Strong acids/bases: ionize completely when dissolved in water.
Weak acids/bases: ionize partially when dissolved in water.
Your Blood…
Operates best at a pH of 7.4 (acceptable blood pH range: 7.35 to 7.45)
When the pH of your blood drops:
H3O+ ions are able to do irregular things like bond to items (e.g. enzymes), impairing proper functioning.
When the pH of your blood increases:
OH− ions are able to do irregular things like vasoconstriction.
So how does your body maintain this optimal pH range? – buffers
Buf ers
Buffers: a chemical that compensates for pH changes in a solution by accepting or donating H+ ions
Many buffers are weak acids/bases or both because they will dissociate in a reversible reaction in water (therefore, absorbing or releasing H+ or OH− as necessary)
An important buffer in the human body (both in and extracellular fluid) is the CARBONIC ACID – BICARBONATE BUFFER
Carbonic acid – ACID
Bicarbonate – BASE
Carbonic Acid – Bicarbonate Buf er
The KEY here is that humans have the ability to control the amount of CO2 in their body through breathing.
H<em>2O+CO</em>2⇌H<em>2CO</em>3⇌HCO3−+H+
Water + carbon dioxide ⇌ carbonic acid ⇌ bicarbonate ion + hydrogen ion
How it Works
H<em>2O+CO</em>2⇌H<em>2CO</em>3⇌HCO3−+H+
Items in yellow – PART OF THE BUFFER
We ingest an acid, lowering the bodies’ pH
More H<em>2CO</em>3 is made to maintain equilibrium: I.e. H<em>2O+CO</em>2⇌H<em>2CO</em>3⇌HCO3−+H+
a) H<em>2CO</em>3 is a weak acid, raising the pH b) i) H<em>2CO</em>3 is converted to H<em>2O+CO</em>2 ii) this CO<em>2 is expelled from the body, so the body is forced to convert MORE H</em>2CO<em>3 to H</em>2O+CO2 to maintain equilibrium; this raises the pH even More
Metabolic Acidosis
Metabolic acidosis: occurs when the body produces too much acid, or when the kidneys and lungs are not removing enough acid from the body.
pH< 7.35
Diabetic acidosis: develops when ketone bodies build up in the body.
Hyperchloremic acidosis: excess loss of NaHCO3 from the body.
Lactic acidosis: build up of lactic acid
Metabolic Alkalosis
Metabolic alkalosis: occurs when there is an increase in bicarbonate (HCO3 -) concentration.
pH > 4.5
ORGANIC COMPOUNDS
Organic vs. Inorganic
With the exception of water, virtually all chemicals of life are carbon based
Organic compounds: compounds that contain primarily carbon and hydrogen (other than carbon dioxide and a few other exceptions)
Inorganic compounds: compounds that do not contain carbon and hydrogen together
The unique position of carbon in the periodic table allows it to combine with as many as 4 other atoms, forming 4 stable covalent bonds. This is possible because carbon has 4 unpaired valence electrons
Carbon
Valence of 4, so can form 4 covalent bonds
Any particle (element or compound) attached to a carbon atom is called a functional group
Will form single, double, or triple covalent bonds
C-skeletons can be either linear, branches, or form a closed ring shape
Molecules made up of only C and H atoms are called hydrocarbons
Examples of Hydrocarbons Carbon – Nomenclature
Generally, hydrocarbons have a two-part name;
Prefixes are named for the number of carbons in the longest continuous chain
1 meth 6 hex
2 eth 7 hept
3 prop 8 oct
4 but 9 non
5 pent 10 dec
Functional Groups
Organic compounds fall into various organic families
An organic family is a group of organic compounds with common structural features that impart characteristic physical properties and reactivity
These structural feature are particle combinations of atoms called functional groups
Functional group: a group of atoms that affects the function of a molecule by participating in chemical reactions
The usefulness of identifying functional groups on molecules is they have predictable chemical behaviours
This is why the characteristics of large biological molecules are determined by their functional groups since the functional groups will determine how they interact with other molecules
Unlike non-polar, hydrocarbon chains, they are usually ionic or strongly polar and therefore, very attracted to water
Molecules must interact in order for a chemical reaction to take place so functional groups play an important role in living systems
If a functional group is present a specific class of compound is formed…
Alcohols (family name)
Contain hydroxyl (name of functional group) group
General formula:
If only one OH group, called monohydroxyl alcohol
Aldehydes
Contain a carbonyl group (at the end of the molecules)
General formula:
Ketones
Contain a carbonyl group (not at the end of the molecule (within))
General formula:
Carboxylic Acids (or Organic Acids)
Contain a carboxyl group (-COOH)
Gives organic molecules pacific properties because the -OH group readily releases its H as a proton in a water solution (proton donor)
General formula:
Amines
Contain an amino group (-NH2)
Readily acts as a base by accepting H+ in a water solution
General formula:
Amides (linkage)
Produced from a carboxylic acid + amine
General formula:
Amino Acids
Contain both amino + carboxyl group
20 naturally occurring building blocks of protein
General formula:
Nucleotides, Nucleic Acids & Other Cellular Molecules
Contain a phosphate group (-PO4 2-)
General formula:
Thiols
Contain a sulfhydryl (-SH) group
General formula:
(seen in proteins)
Ether
(linkage)
Ester
(linkage)
Biological Reactions
Metabolism
A term used to refer to all the chemical reactions that take place in a living organism
There are two main categories of metabolic reactions
Catabolic reactions: those that break large molecules into small ones; exergonic
E.g. digestion of proteins; respiration (C<em>6H</em>12O<em>6+ O</em>2 → CO<em>2 + H</em>2O + energy)
Anabolic reactions: those that build larger molecules; endergonic
Involved the removal of a hydrogen atom, -H, from a functional group of one subunit and the hydroxide group, -OH, from the functional group of a different subunit
The -H and -Oh combine to form water
This is an anabolic reaction
Hydrolysis
Water is used to break the bond holding subunits together
Water is broken down and the hydrogen atom, -H, is added to the functional group of one subunit and the hydroxide ion, -OH, is added to the functional group of the other and the bond holding the subunits together breaks
This is a catabolic reaction
Opposite of dehydration synthesis
Neutralization Reactions
Acid + base → water + salt
Redox Reactions
Reactions in which electrons are exchanged between atoms; one atom is oxidized (loses ē) and the other is reduced (gains ē)
LEO says GER (OIL RIG)
BIOMOLECULES
Macromolecules
Large biological molecules
Made up of C, H, O and sometimes N
Made up of a few basic subunits (monomers) that join in specific sequences (polymers)
Made by attaching more units to create long chains
Created through dehydration synthesis reactions; broken down by hydrolysis reactions
Include carbohydrates, lipids, proteins, and nucleic acids
Micromolecules
Small biologically important molecules
Include vitamins and minerals
Carbohydrates
Known as ‘sugars’
Primary source of energy for living things
Obtained from food
Contain C, H, O in ratio 1:2:1
General formula – (CH<em>2O)</em>n (n= # of C-atoms)
Basic subunits – called simple sugars or monosaccharides
Simple sugars contain a single chain of carbon atoms to which hydroxyl groups are attached
3 main types: glucose (C<em>6H</em>12O6), fructose, galactose
2 types:
Aldoses (are aldehydes) and ketoses (are ketones)
Aldehydes
Carbonyl group – found at end of C chain
Sugar is called an aldose (general name)
E.g. glyceraldehyde
Ketones
Carbonyl group – found within C chain
Sugar is called a ketose (general name)
E.g. dihydroxyacetone
Monosaccharides
Simple sugars
Distinguished by:
The carbonyl group they possess
The length of the C-backbone
The spatial arrangement of their atoms
2 main forms:
Open-chain forms
Ring forms
Open Chain Forms
Are straight chain sugars
Contain one carbonyl group with hydroxyl groups and other carbonds
Pentoses and hexoses:
Exist as both straight chains (in a dry state) but readily form rings (more stable) when dissolved in water
Ring Forms
Non-linear molecules
Ring forms exist when dissolved in water
Aldose: the functional groups on C1 and C5 react forming a covalent bond; called a 1,5 linkage
Ketose: the functional groups on C2 and C5 react forming a covalent bond; called a 2,5 linkage
Ring Formation of Glucose
When glucose (a 6-C sugar; primary source of energy for humans) dissolved in water, the hydroxyl group on C-5 reacts with the aldehyde group on C-1 to form a close ring structure
If the OH group is below the plane of the ring an alpha bond forms → ⍺-glucose
If the OH group is above the plane of the rings a beta bond forms → β-glucose
Isomers
Glucose, galactose, and fructose are isomers:
Same formula – C<em>6H</em>12O6
Each has different shapes and physical and chemical properties
Disaccharides
Formed through dehydration synthesis when two monosaccharides are bonded together
Ether linkage in disaccharide = glycosidic linkage/bond
Examples:
Glucose + galactose → lactose
Glucose + glucose (both alpha) → maltose
Glucose + fructose → sucrose
Polysaccharides
They are large and insoluble
Monomers are held together by glycosidic linkages
Straight chained or branched (starch = straight, glycogen = branched)
They function in 2 important ways:
Energy storage (starch and glycogen)
Structural support (cellulose and chitin)
Starch
Glucose storage in plants
Made of ⍺-glucose
Is a mixture of amylose and amylopectin:
Amylose
Alpha 1,4 bonds – no branches; can be 1000s of molecules long
Straight chain with 1, 4 glycosidic linkages
Amylopectin
Similar to amylose, with 1, 4 linkages in the main chain
But has occasional 1, 6 linkages to create branches
The angles at which the glycosidic linkages form cause the polymers to twist into coils that make them insoluble in water
Glycogen
Glucose storage in animals
Stored in the liver and muscles
Branched structure; have more branches than amylopectin
Cellulose
Structural
Straight-chain polymer (allows the hydroxyl groups of parallel molecules to form many H-bonds – producing tight bundles called microfibrils which can intertwine to form tough, insoluble
Negative test: turns yellow/brown cellulose fibres used in the cell walls of plants) – also found in clothing and fabric
Beta-acetal bonds
These bonds cannot be broken down by human enzymes
Chitin
Made from a variant of glucose called N-acetylglucosamine
Repeating units make up a tough outer skeleton for insects and crustaceans and the cell wall of many fungi
Are Sugars in Your Food?
Monosaccharide (simple sugars)
Test: add Benedict's Reagent to the food sample
Heat in boiling water for 5-10 minutes
Positive test: turns a range of colours, depending on the concentration of monosaccharide
Negative test: blue coloured solution
Polysaccharide (complex sugars)
Test: add iodine to food sample
Positive test: turns black
Negative test: turns yellow/brown
Lipids
Made up of C, H, and O
They are hydrophobic
Become more solid as the number of carbons increases
Used primarily as long term storage of chemical energy
Store a greater amount of energy than carbohydrates
Function of Lipids
Energy source and storage molecule
Cushions internal organs
Key components of cell membranes
Act as raw materials for synthesis of hormones and other chemicals
Serve as insulation
Aid in the absorption of vitamins
Classes of Lipids
There are four classes of lipids:
Neutral lipids
Phospholipids
Steroids
Waxes
Neutral Lipids
Fats and oils
Also called triglycerides
Most common type of lipid
Consists of:
1 glycerol
3 fatty acids (can be the same or different)
Synthesis of a triglyceride:
Fatty Acids
Long hydrocarbon chains with one carboxyl group at the terminal end
2 main types:
Saturated fatty acids
Unsaturated fatty acids
Mono-unsaturated
Poly-unsaturated
Saturated Fatty Acids
Only single bonds between C-atoms
Each C has the max number of H-atoms stearic acid ←
Found predominantly in animal fats
Solid at room temperature
Chains are closer together (more Van der Waals attractions)
Associated with heart disease
Arteriosclerosis: the stiffening or hardening of the artery walls
Unsaturated Fatty Acids
Contain at least one double bond between a pair of C-atoms in the chain
Fewer than the maximum number of H-atoms oleic acid ←
Found predominantly in plant oils
Liquid at room temperature
Double bonds cause kinks in the chain (Van der Waals attractions)
Mono- & Polyunsaturated Fatty Acids
Monounsaturated fats – single double bond
Polyunsaturated fats – many double bonds Linoleic acid ← (polyunsaturated)
Hydrogenated oils
Unsaturated fats that have had H-atoms fused to carbons at the double bonds
Thereby making a very stable molecule (difficult to break down)
Results in liquid fats becoming solid (e.g. margarine)
Phospholipids
Major component in cell membranes
Consists of a:
Glycerol molecule
2 fatty acids
Water insoluble - nonpolar end
Phosphate group
Water soluble - polar end
Cytoplasm above bilayer sheet, extracellular fluid under
Steroids
Common feature
A multiple ring structure
Backbone of structure is 3 6C rings and 1 5C ring
Ex:
Cholesterol, stronger, testosterone ( hormones)
Cholesterol – one of the most important steroids
Precursor for many of the hormones
Will deposit itself on inner blood vessels
Results in increased blood pressure
May lead to heart attack and stroke
HDL – high density lipoprotein (good cholesterol)
LDL – low density lipoprotein (bad cholesterol)
Waxes
E.g. beeswax, carnauba, paraffin
Consists of alcohol or carbon rings with an ester linkage to a fatty acid
They are hydrophobic
Can be used by plants/some animals as waterproof coating
Formation
Lipids are created through dehydration synthesis
Lipids are broken down through hydrolysis
Are fats in your food?
Lipid (fats)
Tests: rub sample of food on brown paper
Positive test: the paper appears translucent (light can pass through)
Negative test: the paper is NOT translucent
Proteins
Largest percentage of body tissue is made up of protein
Composed of C, H, O, N and sometimes S
Coded for by DNA
Functions of Proteins
Can have a structural or functional role
Proteins are also components of membranes
Structural Proteins
Form most of the solid material in the human body
E.g. keratin is the main component of hair and nails
E.g. collagen is the main component of cartilage, bones, and tendons
Functional Proteins
Transport: hemoglobin – oxygen transport
Movement: myosin – helps muscles contract
Messengers: insulin – helps to regulate the storage of glucose in the body
Defense: antibodies – help fight illness
Cell markers: major histocompatibility complex (group of genes)
Help the immune system recognize foreign substance
Subclass of functional proteins – enzymes – help carry out specific chemical reactions in the human body
Ex. amylase found in saliva and pancreatic digestive juices
Breaks down starch
Composition of Proteins
Composed of amino acids
20 different amino acids
9 are essential because the body does not have the ability to make them
The number and arrangement of amino acids (the combinations) leads to formation of 1000s of different proteins in the body
Amino Acids
R = a variable group or side chain
20 different variable groups representing 20 different amino acids
Make the amino acid polar (hydrophilic), non-polar (hydrophobic), or charged (acidic/basic)
When dissolved in water the ‘carboxyl’ donates an H+ ion to the ‘amino’
Amino acids are amphipathic → contain both acidic (carboxyl) and basic (amino) functional groups
Structure of Proteins
Depends on the amino acids it contains, and the interaction between those amino acids
There are four levels of complexity:
Primary
Secondary
Tertiary
Quaternary
Primary Structure
The unique order of amino acids in a polypeptide chain
Determined by the DNA sequence
Determines the final conformation of the overall protein
E.g. pr-ala-val vs. ala-pro-val
Overall protein structure is going to be different
Secondary Structure
Shape of polypeptide chain is created by the pattern of H-bonding between carboxyl and amino functional groups
⍺-helix: twisting causes helical coils – every fourth amino hydrogen bonds with carboxyl
β-pleated sheets: parts of the polypeptide chain lie parallel to each other (non-helical) – hydrogen bonds form between different amino acids
Tertiary Structure
Additional folding creates globular formation due to interaction between R groups
There are 4 bonds responsible for folding:
Ionic bonds due to attraction of opposite charges on acidic (-) and basic (+) R groups
Disulfide bridges between 2 sulfhydryl groups (-SH) on cysteine R groups
H-bonds between opposite partial charges on R groups
Van der Waals (london dispersion) forces between neutral R groups
Proteins at 3º and 4º level are functional; e.g. enzyme
Quaternary Structure
Two or more globular or polypeptides come together forming a complex structure (functional protein)
E.g. hemoglobin
4º structure is determined by 1º
H-bonds are responsible for keeping globes together
Conjugated Proteins
Proteins that require non-protein parts called prosthetic groups to function
Prosthetic groups are tightly bound non-protein components
These non-protein parts can be metal ions or organic molecules
Example: hemoglobin transports oxygen and is made up of 4 polypeptide subunits, but each subunit contains a structure called heme which includes a single iron ion and it is the heme that binds the oxygen so each hemoglobin protein binds 4 oxygen molecules
Af ecting Proteins
The environment that the protein is in, has an effect on its tertiary structure
Disruption in the folding of a protein
Leads to unfolding
Causes change in shape of the protein and a subsequent loss in functionality!
This process is called DENATURATION
E.g. straightening/curling hair – exposing keratin proteins in hair to high heat
Factors That Af ect Protein Shape
pH (acidic and basic) – H+ and OH− attract charge R groups
Temperature – faster movement of molecules break H-bonds
Heavy metal ions – attract charged portions of R groups causing unfolding
Ultraviolet light – is high energy and break bonds
Solvents – such as organic solvents
Make proteins turn inside out
Formation
Proteins are created through dehydration synthesis
Proteins are broken down through hydrolysis
Peptide bond – a covalent bond that holds amino acids together