Chapter 2 Biochemistry of Life

Matter

Anything that takes up space

Element

Substance that can’t be broken down by chemical means into other substances

90% of life consists of

Carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur

Atom

Smallest piece of an element that retains the characteristics of the element

The 3 subatomic particles

Protons, neutrons, electrons

Protons

Positive charge, mass of 1, found in the core

Electrons

Negative charge, no mass, floats around the core

Neutron

No charge, 1 mass, found in core

Atomic number

Number of protons

Charge

P-e

Atomic weight

P+n

Isotope

Atom with different neutrons, affects the weight

Chemicals bonds do what

Link atoms together

Atoms form

Molecules

Valence shell

Outermost shell of an atom

Ion

Charged atom

Cation

Positively charged atom

Full valence shell

Stable, won’t bond

Not full valence shell

Unstable, reactive

Period

Rows, number of electron orbits

Group

Columns, number of valence electrons

the 3 chemical bonds

Nonpolar covalent, polar covalent, ionic

Covalent bond

Each atoms unpaired electrons are shared by both nuclei

Non polar covalent bond

Electrons are evenly shared between 2 atoms, the bond is symmetrical

Polar covalent bond

Electrons are asymmetrically shared

Ionic bond

Electrons are transferred from 1 atom to another

Electronegativity

Measure of an atoms ability to attract electrons, helps determine the type of bond

Period table arranged atoms by electronegativity

Low to high

Elements with similar electronegativities will form

Nonpolar covalent bonds, right

2 elements with moderately different electronegativities will form

Polar covalent bonds, middle

Elements with very different electronegativities will form

Ionic bonds, left

Hydrogen bond

Atom with a partial negative charge attracts a hydrogen atom with a partial positive charge. These bonds form between adjacent molecules or between different parts of a large molecule.

Water is

cohesive, adhesive, an excellent solvent, only dissolves selected molecules, regulates temperature, expands when it freezes, has a neutral pH, is necessary for chemical reactions for life

Water is cohesive

this creates high surface tension

Cohesion

tendency of water molecules to stick to one another

surface tension

caused by cohesion between molecules on the surface

Adhesion

water bonds from hydrogen bonds with other molecules

Transpiration

cohesion, adhesion, condensation, evaporation, and surface tension allow water molecules to climb from a trees roots to its leaves

hydrophillic

water loving (polar solutes, ions)

water does what when it freezes

expands

Why does water have unique properties

hydrogen bonds pull water molecules close to eachother

Why is water an excellent solvent

it dissolves hydrophillic substances

hydrophobic

doesnt dissolve (nonpolar)

Excellent solvent for salt

slight negative charge on water attracts positive charges

solution

liquid mixture

solvent

liquid portion

solute

stuff in solvent

Water regulates temperature

it heats and cools slowly (hydrogen bonds make it resist changes in temperature)

ice is

less dense than water

Water has a neutral pH

7

acidic

0-6, more left you go more acidic. Adds H to the solution

Basic

8-14, more right you go more basic. OH exceeds H.

Buffer solution

Helps maintain a constant pH by absorbing and releasing H into a solution

Organic molecule

contains both hydrogen and carbon
(methane, glucose, Carbs, proteins, nucleic acids, and lipids)

Water is essential in many chemical reactions

photosynthesis, respiration, dehydration, hydrolysis

Macromolecules

Carbs, proteins, lipids, and nucleic acids

Monomer

single unit

polymers

multiple monomers

Dehydration synthesis

Joins monomers together

Hydrolysis

breaks polymers apart

Carbohydrates (polysaccharides)

Provide quick energy, simple sugars/monosaccharides

Monosaccharides

simple sugars (ribose, glucose, fructose)

Disaccharides

contain 2 monosaccharides, joined by dehydration synthesis (Lactose and Sucrose)

Lactose

composed of galactose and glucose. Found in milk.

Sucrose (carb)

table sugar. Composed of glucose and fructose.

polysaccharides (carbs)

multiple monosaccharides joined together. (starch, glycogen, cellulose, chitin, and peptidoglycan)

starch

Carb; provides energy storage in plants

glycogen

protein; provides energy storage in animals

cellulose

Carb; found in cell walls of plants

Chitin

Carb; found in cell walls of fungi and exoskeletons of some animals

Peptidoglycan

Carb; found in cell walls of bacteria

Proteins

Have many different structures of functions. Made of amino acids .

protein structures

defense antibodies, storage (hemoglobin), structural (collagen), transport, contractile (actin and myosin), enzymes

Collagen

Structural protein; creates cellular structures

actin and myosin

produce muscle contractions

Dipeptide

2 amino acids binded together by dehydration synthesis

polypeptide

long chain of amino acids

What determines a proteins function

its shape

Denature

removes its nature, changing the shape of something (irreversible)

5 sugar carbs (pentose)

ribose, deoxyribose

6 sugar carbs (hexose)

glucose, fructose

R groups

each amino acid has its own

Protein primary structure (sequence)

amino acid sequence of a polypeptide

Protein secondary structure (substructure)

Localized areas of coils, sheets, and loops within a polypeptide (amino acids change position to go where they are attracted)

Tertiary structure

overall shape of the protein

Quaternary structure (protein shape)

overall protein shape of multiple polypeptides all interacting

Lipids

collection of different hydrophobic molecules not built from monomers

Lipids include

fats, oils, phospholipids, steroids, waxes

fats

long term energy storage and insulation in animals

oils

Lipid; Triglyceride; 3 fatty acid chains attached to a glycerol molecule; Unsaturated fatty acid; long term energy storage in plants and their seeds

phospholipids

Lipid; derived from triglycerides; has 2 fatty acids attatched to a phosphate group; component of plasma membrane

steroids

Lipid; component of plasma membrane/ sex hormones; ex cholesterol for animals

waxes

Lipid; composed of fatty acids combined with alcohols; protection, prevent water loss

Triglycerides (fats and oils)

3 fatty acid chains attached to a glycerol molecule.

Fatty acids are either

saturated or unsaturated

Unsaturated fats

one or more double bonds between carbons (liquid at room temp)

saturated fats

No double bonds between carbons; solid at room temperature

Phospholipids

derived from triglycerides. 2 fatty acids attached to a phosphate group

Fatty acids are

nonpolar and hydrophobic

phosphate groups are polar and hydrophillic