Biol 130 - Chapter 3 Chemistry of Life

matter

is anything that has mass and takes up space

elements

are the basic building blocks of matter that cannot be broken down by chemical means

atoms

are the smallest units of an element that retain the element’s physical and chemical properties. these bond together to form molecules

parts of the periodic table of elements

• atomic number: how many protons are in the nucleus

• atomic symbol: letter abbreviation

• atomic mass: average weight of an atom’s isotopes

subatomic particles of atoms

• neutrons are neutral (uncharged)

• protons are positively charged

• neutrons and protons make up the nucleus

• electrons are negatively charged and orbit around the nucleus

isotopes

• are atoms that have the same atomic number but a different atomic mass because the number of neutrons differ.

radioisotopes

• a type of isotope that is useful in dating old objects through decay of C14, imaging body organs and tissues through alpha, beta, gamma rays and x-rays, and killing cancer

• any radiation can be harmful by damaging cells and DNA and/or causing cancer

molecules

• made of atoms that are bonded together

• can be made of the same atom N-N, or different atoms H2O

types of chemical bonds

• covalent

• hydrogen

• ionic

covalent bond

a type of chemical bond, atoms in this type of bond share electrons, result in a stable outer shell

• a polar BLANK bond results in a molecule that has slight charge separation

• a non-polar BLANK bond results in a molecule with no charge separation.

hydrogen bonds

occurs between two polar covalently bonded molecules (ie two water molecules)

the oxygen of H2O is slightly electronegative, the 2 H’s attached at an angle are slightly electropositive

opposites attract = the O is attracted to one of the 2 H’s on another water molecule

ionic bonds

atoms in this type of bond donate or take on electrons

result in a stable outer shell of each atom

occur between particles that are charges (ions)

typically is a solid until dissolved into solution: ie table salt, sodium chloride, NaCI, a white solid until dissolved into a solvent then it vanishes from sight.

properties of water

• water is liquid at room temperature

• solid at 0 degrees cel

• liquid water changes temperature slowly (high heat capacity)

• water has a high heat of evaporation (100degree cel_

• frozen water is less dense than liquid water, floats

• molecules of water cling together through H bonds

• water is a solvent for other polar molecules (like dissolves like = hydrophilic, ie NaCI) but not for non-polar ie fats/oils)

dehydration or condensation reaction

• making/breaking down organic molecules

• the removal of water that allows subunits to link together into larger molecules

hydration or hydrolysis

• making and breaking down organic molecules

• the addition of water that breaks larger molecules into their subunits

pH scale

• p either stands for power/potential of h = hydrogen

• it is unitless

• a measure of hydrogen ion (H+) concentration

• working scale is between 0 and 14, 7 being neutral

• a pH below 7 is acidic and above 7 is basic (vinegar is about 3, a mild acid)

• the concentration of hydrogen ions between each whole number changes by a factor of 10 = logarithmic: pH 3 = 10 times more acidic than 4.

acids

• substances that dissociate and release hydrogen ions (H+)

• ie CH3COOH, acetic acid found in vinegar, dissociates into free H+ and CH3COO-

bases

• are substances that take up hydrogen ions (H+) or release hydroxide ions (OH-)

• ie NaHCO3, sodium bicarbonate, baking soda, dissociates into Na+ and HCO3

example of acids and bases together

• add vinegar to baking soda and the reaction creates CO2, H2O and sodium acetate, + heat and foam

the four organic macro molecules found in living organisms

1. carbohydrates

2. lipids

3. proteins

4. nucleic acids

carbohydrates

• made of subunits called monosaccharides

• made of C, H, and O, in which the H and O atoms are in a 2:1 ratio

• function as short and long term energy storage

• found as simple and complex forms

monosaccharide

• a simple carbohydrate

• 1 carbon ring as found in glucose

disaccharide

• type of simple carbohydrate

• 2 carbon rings as found in maltose, created by a dehydration reaction

polysaccharides

• type of complex carbohydrate

• made of many carbon rings and are energy storage molecules

glycogen

• type of complex carbohydrate

• is the storage form in animals. up to 60,000 units long

starch

• type of complex carbohydrate

• is the storage form in plants

lipids

• molecules that do not dissolve in water = hydrophobic. will dissolve in non polar solvents

• multiple uses in the body

• found in cell membranes

• found as fats and oils, phospholipids, and steroids

difference between fats and oils

fats

• usually animal origin

• solid at room temperature

• function for long term energy storage, insulation from heat loss, and cushion for organs

oils

• usually plan origin

• liquid at room temperature

creation of triglycerides

• a glycerol molecule and 3 fatty acid tails when combined, become a fat molecule called BLANK, a non polar molecule.

understanding fats when reading a nutrition label

• recommendation for total amount of fat for 2,000 cal diet is 65g/day

• be sure to check the number of servings, 130g but two servings = 65 per serving (unless you eat both all by yourself. some serving sizes are too small)

• a % daily value of 5% or less is low and 20% or more is high

• avoid trans fats

understanding the nutrition facts

structure of a phospholipid

the structure is similar to a triglyceride

one fatty acid is replaced by a polar phosphate group

BLANK are the primary components of cellular membranes

steroids

• BLANK is a lipid

• the structure is four fused carbon rings

• some examples are cholesterol and sex hormones, testosterone and estrogen

proteins

• made of subunits called amino acids (AA’s) associated via dehydration reactions into long chains

• important for diverse functions in the body, including hormones, enzymes, antibodies and transport

• can denature

denature

• process of undergoing a change in shape that causes loss of function

3 of 700 known amino acids

• valine (val) (nonpolar)

• glutamic acid (glu) (ionized, polar)

• lysine (lys) (ionized, polar)

• but we typically use only 20 different AA’s commonly

the basic structure of an AA

• consistent across all AA’s

4 levels of protein organization

1. primary

2. secondary

3. tertiary

4. quaternary

• all proteins have primary, secondary, and tertiary structure, while only few have quaternary structure

primary

1. the linear order of amino acids

secondary

2. localized folding into pleated sheets and helices

tertiary

3. the 3d shape of the entire protein in space

quaternary

4. combination of more than one polypeptide

one major function of proteins

• enzyme activity

• enzymes lower activation energy to facilitate chemical reactions

• activation energy is that energy needed push a chemical reaction to completion

enzyme assisted reaction

protein purposes

• building blocks for things like hair and nails, muscles

• serve as fuel for normal metabolic processes

nucleic acids

• made of nucleotide subunits

• function in the cell to make proteins

• include RNA and DNA

3 parts of a nucleotide

the 5 bases found in nucleotides

• adenine (A) and guanine (G) are double ringed purines

• cytosine (C), thymine (T), and uracil (U) are single-ringed pyrimidines

• in DNA, A pairs with T and G pairs with C

• in RNA, A pairs with U and G pairs with C

DNA and RNA structural differences

• DNA

  • sugar is deoxyribose

  • bases include A, T, C, and G

  • double stranded

• RNA

  • sugar is ribose

  • bases include A, U, C, and G

  • single stranded

how nucleotides combine to form DNA