temp

Structure of the atom

The nucleus is made up of protons and neutrons, electrons orbit the nucleus in energy shells

How to find the number of each subatomic particle

of protons = atomic number

of electrons in a neutral atom = atomic number

of neutrons = atomic mass - atomic number(# of protons)

Valence

Number of bonds that an element is able to form

Valence electrons

Number of electrons on the outermost shell

Isotopes

Atoms of an element that contain the same number of protons, but different numbers of neutrons

Similar chemical properties, but different physical properties

Radioisotopes

Nuclei of some isotopes are unstable and will decay Emits energy and particles which are detected as radioactivity Radiation is harmful to living tissue Transforms element into another element

Half-life

Amount of time it takes an element to decay to half of its original size

Diagnosis

Radioisotope tracing radioactive isotopes can “light up” organs and tissues of interest

E.g finding and destroying cells in the thyroid gland through the injection of radioactive iodine

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.

Ions

Elements or compounds with an electrical charge, due to the gaining or losing of electrons in order to form a stable shell

Electronegativity

The measure of an atom's ability to attract electrons in a compound Influenced by atomic number and distance between valence electrons and nucleus

ΔE values determine the type of bond

Intramolecular bonds

Bonds between atoms in a compound Ionic Covalent (Polar, Non-polar)

Ionic Bonds

Formed from giving or receiving electrons Attraction between cations and anions

ΔEN >1.7

Dissosicates in water

Polar Covalent

0.5 < ΔEN < 1.7

Similar to covalent, but the sharing of electrons is not equal, results localized electrical charge

Soluble in water

Non-Polar Covalent

ΔE < 0.5

Not soluble in water

Molecules share electrons equally

Intermolecular bonds

Bonds between molecules are weaker than intramolecular bonds Hydrogen bonds Dipole-Dipole forces London Dispersion forces

Hydrogen bonding

Force of attraction between an H atom of one polar molecule, and either a F, N, or O of another polar molecule Weak in small numbers, but strong in many Broken in heat

Dipole-Dipole

Holds polar molecules together

The partial positive side of one molecule attracts the partial negative side of another molecule

London Dispersion

Temporary attraction between nonpolar molecules when electrons in two atoms each align to create positive and negative poles, creating attraction between the molecules

These temporary poles can repel electrons of other adjacent atoms, creating more and more poles

Characteristics of Water

Cohesion

Adhesion

Highest density at 4O C

High specific heat capacity

High specific heat of vaporization

Cohesion

Attraction to other water molecules, forming up to 4 H-bonds

Contributes to high surface tension

Adhesion

Attraction to other polar or charged molecules through H-bonds

Water molecules follow eachother up in the xylem of plants, sticking to the side of it(capillary action)

Highest Density at 4OC

/Below 0OC, water molecules form a crystal lattice with other molecules, spreading them out more and thus taking more room up

High specific heat capacity

Due to the numerous and strong H-bonds found, more heat is needed to break these bonds Can store a large amount of thermal energy Contributes to regulating the temperature throughout night and day, absorbing thermal energy from the sun and expelling it in the night

High specific heat of vaporization

A lot of thermal energy is needed for water to evaporate Through panting or sweating, the water absorbs heat from the organism and evaporates, leaving it cooler

Acid

Proton donator Increases [H3O+] when dissolved in water Turns litmus red, sour, pH < 7

Base

Proton acceptor Increases [H3O+] when dissolved in water Turns litmus blue, bitter, ph > 7, slippery Dissociates into OH-

Strong vs Weak A&B

Strong acids fully ionize when dissolved in water Weak acids partially ionize when dissolved in water

Buffer

A chemical that helps resist sudden changes in pH through either accepting or receiving H+ ions Typically weak acids/bases, so they are able to release or absorb H+ ions as necessary

Carbonic Acid - Bicarbonate Buffer

If we need to increase the pH level, our body converts H2CO3 into HCO3- + H+, which raises pH If we need to decrease the pH level, our body converts HCO3- + H+ into H2CO3, and if needed, into H2O + CO2 and expels the CO2 to lower the pH more

Metabolic acidosis

The body is not able to remove enough acid, or it produces too much acid pH < 7.35

Symptom of metabolic acidosis

Rapid breathing, confusion, lethargy Severe cases → shock, death Treatment Giving individual NaHCO3-

Metabolic alkalosis

Too high bicarbonate (HCO3-) concentration. pH > 7.45

Dehydration Synthesis

Anabolic Reaction Creates water, and connects two molecules through an ether linkage

Hydrolysis

Water is used to break the bond between 2 subunits, and adds H to one side, and OH to the other

Reactions between functional groups

Alcohol + Alcohol → Ether + water Carboxylic acid + alcohol → Ester + water Alcohol + aldehyde → water + ketone Amino acid + amino acid → water + dipeptide

Carbohydrate linkage

The bonds that hold together monosaccharides are called glycosidic linkages Ether linkage

Lipid linkage

Functional groups that hold together lipids are called esters

Protein linkage

Peptide bonds hold together amino acids Contain amino and carbonyl groups

Nucleic acid linkage

phosphodiester bonds hold together nucleotides

Contain ether linkage, phosphate and nitrogenous bonds

Carbohydrate Composition

Composed of carbons, hydrogen, and oxygen in a 1:2:1 ratio Monomers are monosaccharides

Aldoses

Carbonyl group found at the end of the C chain

Ketose

Carbonyl group found within the C chain

Monosaccharides

Glucose → most abundant Fructose -> fruits, honey Galactose → dairy products

Disaccharide formation and examples

Formed through dehydration synthesis Matolse (glucose + glucose) Lactose (glucose + galactose) Sucrose (glucose + sucrose)

Polysaccharides

Large and insoluble Monosaccharides held together by glycosidic linkages, straight or branched Energy storage, and structural support

Open chain forms

Straight chain sugars, with one carbonyl group and hydroxyl groups on other carbons

Ring forms

Exist when open chain sugars dissolve in water Aldose’s C1 and C5 form a covalent bond, called a 1,5 linkage Ketoses C2 and C5 form a covalent bond, called a 2,5 linkage

Ring formation of glucose

Hydroxyl on C5 reacts with the aldehyde group on C1 to form a closed ring structure

A-glucose

OH group is below the plane, an alpha bond forms

B-glucose

OH group is above the plane, beta bond forms

Glycogen

Storage in animals Stored in livers and muscles

Glucagon

Hormone that breaks down glycogen

Starch

Glucose storage in plants, alpha glucose A mixture of amylose and amylopectin

Amylose

Alpha 1,4 bonds No branches, 1000’s of molecules long

Amylopectin

1,4 linkages in the main chain, along with 1,6 linkages to create branches 1,6 linkages form due to angles at which glycosidic linkages form

Cellulose

Fibre Straight chain polymer H-Bonds produce microfibrils, which intertwine to form tough cellulose fibres used in plant’s cell walls Beta acetal bonds, indigestible by humans

Chitin

Made from n-acetyl glucosamine Make up the outer skeleton of instances, crustaceans, and cell walls of fungi

Lipid composition

Made up of C, H, and O Hydrophobic Made of Fatty acids and glycerol

Functions of Lipids

NRG source and storage molecule Cushions internal organs Key components of cell membranes Act as raw materials for the synthesis of hormones and other chemicals Serve as insulation Aid in the absorption of vitamins

Neutral Lipids

Fats and oils Made up of triglycerides Non-Polar

Phospholipids

Made up of polar head, and nonpolar tails Phosphate head, glycerol and 2 fatty acid tails

Steroids

3 6C and 1 5C rings make up a honeycomb structure Ex. Cholesterol, testosterone, estrogen

Waxes

Alcohol or carbon chains with ester linkages to fatty acids Hydrophobic, used as a waterproof covering for plants or animals Ex. beeswax, carnauba, paraffin

Fatty Acids

Long hydrocarbon chains with a carboxyl group at the terminal end

Saturated fatty acids

Only single bonds are found Animal fats Solid at room temp Associated with heart diseases Chains are closer together, solid at room temperature

Unsaturated fatty acids

Contain at least one double bond between carbons Plant oils More kinks in the chain, liquid at room temp

Monosaturated fatty acids

Only one double bond

Polyunsaturated fatty acids

Multiple double bonds

Hydrogenated oils

Unsaturated fats with H-atoms fused to carbons with double bonds, making it harder to break down Liquid fats becoming solid

Bypass

Taking healthy blood veins from the chest or leg, and is connected under blocked heart artery, improving blood flow

Angioplasty

using a balloon to stretch open a narrowed or blocked artery

Arterioclerosis

Stiffening or hardening of the artery walls

Cholesterol

Precursor for important hormones Deposits in inner blood vessels Results in increased blood pressure, can lead to heart attacks and strokes LDL → bad HDL → good

Protein composition

Composed of C, H, O, N and sometimes S Monomers are amino acids Coded for by DNA

Protein Bond

Held together by peptide bonds

Structural Proteins

Sold material in the body E.g keratin, collagen

Functional Proteins

Hemoglobin – oxygen transport Myosin – helps muscles contract Insulin - helps to regulate the storage of glucose in the body Antibodies - help fight illness Cell Markers: major histocompatibility complex (group of genes) help the immune system recognize foreign substances Sub class of functional proteins – enzymes – help carry out specific chemical reactions in the human body Ex. amylase Found in saliva and pancreas, breaks down starch(amylose)

Amino acids

The # and arrangement of amino acids (the combinations) leads to formation of 1000s of diff proteins in the body 20 different a.a, 9 are essential Amino acids are amphiprotic Either side makes it polar or non polar

Primary Structure

Unique order of amino acids Determined by DNA Overall protein structure will be different

Secondary structure

Pattern of H-Bonds between carboxyl and amino groups creates unique shape α-helix: twisting causes helical coils Β-pleated sheets: parts of the polypeptide chain lie parallel to each other (non-helical)

Tertiary structure

Additional folding creates globular shape due to bonding between R groups 4 bonds responsible for this folding

Types of bonding in tertiary structure

Ionic bonds from opposing charges on acidic and basic R groups Disulfide bridges btw 2 sulfhydryl groups (-SH) on cysteine R groups H-bonds btw opposite partial charges on R groups Van der Waals (London Dispersion) forces between neutral R groups

Quaternary Structure

Two or more tertiary polypeptides join together eg. hemoglobin 4º structure is determined by 1º H-bonds hold it together

Conjugated Proteins

Proteins that need prosthetic groups to function E.g hemoglobin, 4 subunits of proteins form around heme, which contains a single iron molecule for oxygen to bind to

Prosthetic Groups

Tightly bound to conjugated proteins through covalent bonds Can be organic compounds, or metal ions

Factors that affect proteins

pH (acidic & basic) – H+ and OH- attract charged 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 NRG and break bonds solvents – such as organic solvents

Protein formation

Dehydration synthesis More than 50 a.a is called polypeptide chain

Nucleic acids

Genetic / Hereditary info Contains instructions for building proteins Made from monomers called nucleotides

DNA

Hereditery material with info that a cell needs to live Deoxyribonucleic acid

RNA

Ribonucleic acid Genetic messenger, carries genetic information from DNA through cytoplasm to ribosomes to create proteins

Nucleotides

Made from sugar, phosphate group, nitrogenous base Bonds to other nucleotides through the 3rd carbon and phosphate of another nucleotide Linked together with diphosphodiester bonds

Nucleotide sugar

Deoxyribose sugar, has one less oxygen than RNA Ribose sugar

Nitrogenous bases

Adenine (A) Guanine (G) These are purines they contain double rings Thymine (T) - DNA Uracil (U) - RNA Cytosine(C) These are pyrimidines they contain a single ring

Nitrogenous base paring

A binds to U in RNA, 2 H-bonds A binds to T in DNA, 2 H-bonds C binds to G in both, 3 H-bonds

DNA characteristics

Double stranded Long, stores all genetic information In the nucleus Sugar is deoxyribose

RNA characteristics

Single stranded Short, can only carry one gene at a time Copies DNA and travels to cytoplasm Sugar is Ribose

Basic components of cells

3 basic components Plasma membrane DNA-containing region Cytoplasm