Module 1

Atoms

the smallest unit of life.

Element

are defined as substances that consist entirely of a single type of atom.

Atomic number

is the number of protons in an element.

Mass number

is the sum of protons and neutrons in an atom.

Dalton

A unit of mass approximately equal to the mass of one proton or one neutron

Isotopes

Any of several forms of an element that differ in the number of neutrons contained in their nuclei.

Atomic weight

The average mass of an element that is based on the relative proportions of all its naturally occurring isotopes.

Radioactive isotope

A version of an element that has an unstable nucleus, which will release energy as it decays to a more stable form.Decay often results in the radioisotope losing protons and becoming a different element.

Orbitals

The region of space around an atomic nucleus in which an electron is present most of the time.Orbitals are grouped electron shells.

Electron shells

A group of electron orbitals with similar energies.Electron shells are arranged in roughly concentric layers around the nucleus of an atom, and electrons in outer shells have more energy, valence shells, often are involved in chemical bonding.

Valence shell

The outermost electron shell of an atom.

Valence electrons

An electron in the outermost electron shell, the valence shell, of an atom.Valence electrons tend to be involved in chemical bonding.

Valence

The number of unpaired electrons in the outermost electron shell of an atom is involved in covalent bonding, valence often determines how many covalent bonds the atom can form.

Chemical bonds

An attractive force bending two atoms together.Covalent bonds,ionic bonds,and hydrogen bonds are types of chemical bonds.

Covalent bond

A type of chemical bond in which two atoms share one or more pairs of electrons.Compare with hydrogen bond and ionic bond.

Compounds

Any substance that consists of more than one different type of element chemically bonded together.

Electronegativity

a measure of how strongly an atom pulls shared electrons toward itself in a bond.

Nonpolar covalent bond

A covalent bond in which electrons are equally shared between two atoms of the same or similar electronegativity. Compared with polar covalent bonds.

Polar covalent bond

A covalent bond in which electrons are shared unequally between atoms differing in electronegativity, resulting in the more electronegative atom having a partial negative charge and the other atom having an partial positive charge.Compared with nonpolar covalent bond.

Ionic bonds

A chemical bond that is formed when an electron is completely transferred from one atom to another. Resulting ions remain associated due to their opposite electric charges.Compared with covalent bond and hydrogen bond.

Ion

An atom or a molecule that has lost or gained electrons and thus carries a full electric charge, either positive(cation) or negative(anion) respectively.

Cation

A positively charged ion

Anion

a negatively charged ion

Solvent

Any liquid in which one or more solids or gasses can dissolve.

Solution

A liquid containing one or more dissolved solids or gasses in a homogenous mixture

Solutes

Any substances that is dissolved in a liquid

polar

(1) Asymmetrical or unidirectional.(2) Carrying a partial positive charge on one side of a mole and a partial negative charge on the other.Polar molecules are generally hydrophilic.

Hydrogen bond

A weak interaction between two molecules or different parts of the same molecule resulting from the attraction between a hydrogen atom with a partial positive charge and another atom(usually O or N) with a partial negative charge.Compare with covalent bond and ionic bond.

Hydrophilic

Interacting readily with water. Hydrophilic compounds are typically polar compounds containing partially or fully charged atoms.

Hydrophobic

Not interacting readily with water.Hydrophobic compounds are typically nonpolar molecules.

Hydrophobic interactions

Very weak interaction between nonpolar molecules or nonpolar regions of the same molecule, when exposed to an aqueous solvent.The surrounding water molecules support these interactions by interacting with one another and encapsulating the nonpolar molecules.

Van der Waals interactions

a weak electrical attraction between two nonpolar molecules or parts of a molecule that have been brought together, often through hydrophobic interactions. In proteins, it contributes to tertiary and quaternary structures.

Cohesion

The tendency of certain molecules to cling together due to attractive forces.

Adhesion

The tendency of certain dissimilar molecules to cling together due to attractive forces.

Surface tension

the cohesive force that causes molecules at the surface of a liquid to stick together, thereby resisting deformation of liquid's surfaces and minimizing its surface area.

Specific heat

the amount of energy required to raise the temperature of 1 gram of a substance by 1C; a measure of the capacity of a substance to absorb energy.

Heat vaporization

the energy required to change 1 gram of a liquid into a gas.

Chemical reactions

Any process in which substances combine or are broken down into other substances: involves the making and/or breaking of chemical bonds.

Reactants

any of the starting material in a chemical reaction.

Product

any of the final materials formed in a chemical reaction.

Hydrogen ion (H+)

a single proton with a positive electric charge of +1 typically, one that is dissolved in solution or that is being transferred from one atom to another in chemical reactions.

Hydrogen ion (OH-)

An oxygen atom and a hydrogen atom joined by a single covalent bond and carrying a negative electric charge of -1.

Chemical equilibrium

a dynamic but stable state of reversible chemical reactions in which the forward reaction and reverse reactions proceed at the same rate, so taht the concentrations of reactant and products remain constant.

Acids

Any compound that gives up protons or accepts electrons during a chemical reaction or that releases hydrogen ions when dissolved in water.

Bases

Any compound that acquires or gives up electrons during a chemical ration or accepts hydrogen ions when dissolved in water.

Mole

the amount of a substance that contains 6.022 x 1023 of its elemental entities.This number of molecules will have a mass equal to its molecular weight expressed in grams.

Molecular weight

The sum of the atomic weights of all the atoms in a molecule; the total number of protons and neutrons in the molecule.

Molarity

The number of moles of a solute present in 1 liter of solution.

PH

a measure of the concentrations of protons in a solutions and thus of how acidic or basic the solutions is.defined as the negative of the base 10 logarithm of the proton concentration: pH = log[H-]

Buffers

a substance that, in solution, acts to minimize changes in the pH of that solution when acid or base is added.

Homeostasis

the tendency toward a relatively stable equilibrium between interdependent elements, especially as maintained by physiological processes.

System

A defined set of iterating chemical components under observation.

Endothermic

Referring to a chemical reaction that absorbs heat.

Exothermic

Referring to a chemical reaction that releases heat.

Energy

The capacity to do work or to supply heat.May be stored(potential energy) or available in the form of motion(kinetic energy)

Potential energy

Energy stored in matter as a result of its position or the position of electrons that form electrons that form chemical bonds between atoms.

Chemical energy

The potential energy stored in chemical bonds between atoms.

Kinetic energy

the energy of motion.

Thermal energy

The total kinetic energy of a system that includes the motion of matter and is measured as temperature.

Temperature

A measurement of thermal energy present in an object or substance, reflecting how much the constituent matter is moving.

Heat

Thermal energy that is transferred from an object at higher temperature to one at lover temperature.

First law of thermodynamics

The principle of physics that energy is conserved in any process. Energy can be transferred and converted into different forms, but it cannot be created or destroyed.

Entropy

A quantitative measure of the amount of disorder of any system, such as a group of molecules.

Second law of thermodynamics

the principle of physics that the entropy of the universe or any closed system always increases.

Organic compounds

A group of molecules that include at least one carbon atom; most have carbon hydrogen bonds and carbon-carbon bonds.Organic compounds are widely used by living organisms.

Functional Groups

A small group of atoms bonded together in a precise configuration and exhibiting particular chemical properties that it imparts to any organic molecule which it occurs in.

Macromolecules

Generally, any large organic molecule made up of smaller molecules(monomers) joined together into a polymer.The main biological macromolecules are proteins, nucleic acids and polysaccharides.

Monomer

A small molecule that can covalently bind to other similar molecules to form larger macromolecules.

Polymer

Any large molecule composed of small repeating units(monomers) bonded together.The main biological polymers are proteins, nucleic acids, polysaccharides.

Polymerization

The process by which many identical or similar small molecules(monomers) are covalently bonded to form a large molecule(polymer)

Condensation reactions

A chemical reaction in which two molecules are joined covalently with the removal of an -OH from one and an -H from another to form water. In biology, most condensation reactions involve the joining of monomers t=into polymers.Also called a dehydration reaction.

Dehydration reaction

A chemical reaction in which two molecules are joined covalently with the removal of an -OH from one and an -H from another to form water. In biology, most condensation reactions involve the joining of monomers t=into polymers. Also called a condensation reaction.

Hydrolysis

A chemical reaction in which a molecule is split into smaller molecules by reacting with water. In biology, most hydrolysis reactions involve the splitting of polymers into monomers.

Organic compounds

A group of molecules that include at least one carbon atom; most have carbon hydrogen bonds and carbon-carbon bonds.Organic compounds are widely used by living organisms.

Functional Groups

A small group of atoms bonded together in a precise configuration and exhibiting particular chemical properties that it imparts to any organic molecule which it occurs in.

Macromolecules

Generally, any large organic molecule made up of smaller molecules(monomers) joined together into a polymer.The main biological macromolecules are proteins, nucleic acids and polysaccharides.

Monomer

A small molecule that can covalently bind to other similar molecules to form larger macromolecules.

Polymer

Any large molecule composed of small repeating units(monomers) bonded together.The main biological polymers are proteins, nucleic acids, polysaccharides.

Polymerization

The process by which many identical or similar small molecules(monomers) are covalently bonded to form a large molecule(polymer)

Condensation reactions

A chemical reaction in which two molecules are joined covalently with the removal of an -OH from one and an -H from another to form water. In biology, most condensation reactions involve the joining of monomers t=into polymers.Also called a dehydration reaction.

Dehydration reaction

A chemical reaction in which two molecules are joined covalently with the removal of an -OH from one and an -H from another to form water. In biology, most condensation reactions involve the joining of monomers t=into polymers. Also called a condensation reaction.

Hydrolysis

A chemical reaction in which a molecule is split into smaller molecules by reacting with water. In biology, most hydrolysis reactions involve the splitting of polymers into monomers.

Amino acids

A small organic molecule with a central carbon atom bonded to an amino group(-NH#), a carboxyl group(-COOH), a hydrogen atom, and a side chain.When amino acids are linked together to form proteins, they are referred to as residues.

R-group

Part of an amino acid's core structure that varies from a single hydrogen atom to large structures containing carbon rings.R-group variability is responsible for the variability in amino acid structure and function.Also called side chains.

Hydrophilic

interacting readily with water. Hydrophilic compounds are typically polar compounds containing partially or fully charged atoms.

Hydrophobic

Not interacting readily with water.Hydrophobic compounds are typically nonpolar molecules.

Peptide bond

the covalent bond formed by a condensation reaction between two amino acids.

Oligopeptide

a chain composed of fewer than 50 amino acid residues linked together by peptide bonds.Often referred to simply as peptide.

Polypeptides

A chain typically composed of 50 or more amino acids linked together by peptide bonds

Protein

A macromolecule consisting of one or more polypeptide chains.Each polypeptide has a unique sequence of amino acids and each protein generally possesses a characteristic three-dimensional shape.

Primary structure

The sequence of amino acid residues in a protein polymer; also the sequence of nucleotides in a single nucleic acid strand.

Secondary structure

in proteins, localized folding of a polypeptide chain into regular(i.e.,alpha-helices and beta-pleated sheets) structures stabilized by hydrogen bonding between atoms of the peptide backbone. In nucleic acids, elements of structure(e.g.,helices and hairpins) stabilized by hydrogen bonding between complementary bases and hydrophobic interactions with the aqueous environment.

Alpha helix

a secondary structure in proteins in proteins formed when the polypeptide backbone coils into a spiral shape stabilized by hydrogen bonding.

Beta pleated sheet

a secondary structure in proteins, formed when the polypeptide backbone folds into a sheetlike shape stabilized by hydrogen bonding.

Tertiary structure

the overall three-dimensional shape of a single polypeptide chain, resulting from multiple interactions among the amino acid side chain and the peptide backbone.In nucleic acids, three-dimensional shape is formed by hydrogen bonding between complementary bases and other interactions.

Hydrogen bonding

Hydrogen bonds form between polar side chain and opposite partial charges either on the peptide backbone or other r-groups.

Hydrophobic interactions

In an aqueous solution, water molecules interact with the hydrophilic polar side of a polypeptide forcing the hydrophobic nonpolar side chains to coalesce in the interior of the resulting globular mass. Water molecules surrounding the mass form more hydrogen bonds with each other and the polar residues on the surface of the protein increase the stability of their own interactions and disorder of the rest of the aqueous solutions.

Van der waal interactions

once nonpolar side chains are forced close to one another by hydrophobic interactions, their association is further stabilized by van der Waals interactions. A large number of these weak electrical attractions can significantly increase the stability of the protein.

Covalent bonding

covalent bonds can form between the side chains t=of two cysteines though a reactions between the sulfhydryl groups.The disulfide(two-sulfur) are frequently referred to as bridges, because they create strong links between distinct regions of the same polypeptide or two separate polypeptides.

Disulfide bonds

A covalent bond between two sulfur atoms, typically in the side chain of certain amino acids.Often contributes to tertiary and quaternary levels of protein structure.