2 Chemistry of Biology

matter

anything that takes up space and has mass

atoms

the smallest chemical units of matter

what do atoms consist of?

neutrons, electrons, protons, nucleus

electrons

negatively charged subatomic particles circling a nucleus

nucleus

structure containing neutrons and protons

neutrons

uncharged particles

protons

positively charged particles

element

composed of a single type of atom

electron shells

energy rings

What does the nucleus contain?

protons and neutrons

where are electrons placed?

on the rings/shells

atomic number

equal to the number of protons in the nucleus

atomic mass

sum of masses of protons, neutrons, and electrons

valence electrons

electrons in outermost shell that interact with other atoms

-combining capacity of an atom (number of extra or missing electrons in outermost shell)

chemical bonds

attachment of atoms combined by sharing or transferring valence electrons

molecule

two or more atoms held together by chemical bonds

compound

a molecule composed of more than one element

ex) H2O

covalent bond

sharing of a pair of electrons by two atoms

electronegativity

attraction of atom for electrons; the more electronegative an atom, the greater the pull its nucleus exerts on electrons

-O & N super electroneg

Electronegativity Values (Linus Pauling)

F>O>N>C>H

types of chemical bonds

ionic bonds, non/polar covalent bonds, and intermolecular forces such as hydrogen bonds

Ionic bond

charged ions formed when electrons are transferred from one atom to another

-occur when two atoms with vastly different electronegativities come together

-Typically form crystalline ionic compounds known as salts

anion

A negatively charged ion

cation

A positively charged ion

Aqueous Interactions

hydrophilic, hydrophobic, amphipathic

Amphipathic

"feeling both" molecules have both hydrophilic and hydrophobic properties (polar and nonpolar parts)

hydrophobic

"water-hating" molecules repel water (nonpolar)

hydrophilic

"water-loving" molecules attract water to their surface (polar)

nonpolar covalent bonds

a chemical bond where atoms share electrons equally, resulting in a balanced molecule with no partial charges. (The most common bonds in living cells)

-Strongest covalent bonds in solution

what do nonpolar covalent bonds form between

Form between C, H, O, N, S, and P.

hydrogen bonding

weak attractions involving hydrogen and electronegative atoms that help hold molecules together and give many biological molecules their shape and properties

Polar Covalent Bonds

Unequal sharing of electrons due to significantly different electronegativities

-Most important polar covalent bonds involve hydrogen (Allows for hydrogen bonding)

which bond is weaker than covalent bonds but essential for life

hydrogen bonding

synthesis

to build

hydrolysis

splitting with water

what doesn't have a cell wall

animal cells

types of intermolecular forces

London dispersion, dipole-dipole, hydrogen bonding, ion dipole

what's the weakest force?

London dispersion forces

Common Elements in Living Organisms

CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur)

pH

Measures the acid concentrations of solutions

-Ranges from 0 (most acidic) to 14 (most basic); 7 is neutral pH = -log[H+]

functional groups of organic molecules

hydroxyl, carbonyl, carboxyl, amino group, phosphate, ester, ether

Chemical Reactions

the making and breaking of chemical bonds, leading to changes in the composition of matter (involve reactants and products)

Macromolecules

Many biological molecules are composed of monomer Units

what are polymers broken down by?

hydrolysis reactions

Organic Macromolecules

carbohydrates, lipids, proteins, nucleic acids

carbohydrates

Organic molecules composed of carbon, hydrogen, and oxygen (CH2O)n

function of carbohydrates

-Medium or Long-term storage of chemical energy

-Ready energy source

-Part of backbones of nucleic acids

-Converted to amino acids

-Form cell wall

-Involved in intracellular interactions between animal cells

types of carbohydrates

monosaccharides, disaccharides, polysaccharides

proteins

Mostly composed of carbon, hydrogen, oxygen, nitrogen, and sulfur

function of proteins

-Structure

-Enzymatic catalysis

-Regulation

-Transportation

-Defense and offense

what are proteins composed of?

amino acids

amino acids

monomers that make up proteins

amino acid structure

isomers

Compounds with the same formula but different structures.

stereoisomers

Compounds with the same structural formula but with a different arrangement of the atoms in space. ex) hands

protein structure

primary, secondary, tertiary, quaternary

primary protein structure

the sequence of amino acids

secondary protein structure

a localized (short distance) 3D structure based on hydrogen bonding on the peptide backbone

tertiary protein structure

a globular 3D structure of the protein based on the interaction of the R groups

quaternary protein structure

the association of more than one peptide

protein denaturation

when proteins are subject to heat, acid or other conditions that disturb their stability; protein uncoils, loses its shape, and loses its function

enzymes

proteins that act as biological catalysts (nearly always proteins)

Cofactors

non-protein chemical compounds that assist enzymes in catalyzing reactions

nucleic acids

dna & rna

DNA

genetic material of all organisms and of many viruses

-Carries instructions for synthesis of RNA and proteins; controls synthesis of all molecules in an organism

RNA

the genetic material of some viruses

-functions in protein synthesis (mRNA, tRNA, rRNA)

nucleotides

Monomers that make up nucleic acids

-Composed of three parts (Phosphate, Pentose sugar - deoxyribose or ribose, One of five cyclic nitrogenous bases)

lipids

Not composed of regular subunits, but are all hydrophobic

what 4 groups consist of lipids?

• Fats

• Phospholipids

• Waxes

• Steroids

unsaturated fats

liquid at room temperature (colder melting points)

-contain double bonds

saturated fats

solid at room temperature (warmer/higher melting points)

Phospholipids

a molecule with a hydrophilic head and hydrophobic tails that forms the structural foundation of all cell membranes

sterols

ring-structured lipids crucial for membrane stability and serve as precursors (transitions) for many important biological molecules like hormones, vitamins, bile acids

precursors

something that comes before and is transformed into another molecule through a biological process.

ex) "cholesterol is a precursor to steroid hormones", we mean that the body uses cholesterol as the raw material to chemically produce those hormones through metabolic pathways.

cells

fundamental unit of life

what do all cells have?

-a cytoplasmic membrane

-chromosomes made of DNA

-ribosomes for protein synthesis

-Reproduce to form progeny cells

-Obtain energy from their environment