Chapter 2 - The Chemistry of Life

The matter that makes up every object consists of one or more elements that organize into atoms and molecules.

$Element$ - a substance that cannot be broken down by chemical means into other substances

$Living things are mostly composed of:$

• carbon
• hydrogen
• oxygen
• nitrogen
• phosphorus
• sulfur

Periodic Table lists all known elements

Each box shows:

• the elements full name
• the elements one or two letter symbol
• atomic number
• atomic weight
    * mass - things inside
    * weight - gravitational pull

Atoms make up all matter

$Atom$ - smallest piece of an element that retains the characteristics of the element

• composed of protons, neutrons, and electrons
• electrons - surround the atomic nucleus
• protons and neutrons - in atomic nucleus
• protons - positively charged (+), mass 1
• neutrons - neutral (0) mass 1
• electrons - negatively charged (-), mass 0
• Atomic number - number of protons
• Atom mass number - number of protons and neutrons
• Ion - charged atom
    * Atoms do not have charge

Isotopes are different forms of the same element

$The number of neutrons may vary which causes each isotope to have different masses.$

The atomic weight on the periodic table is the average mass

Chemical Bonds link atoms together

Atoms are organized into molecules

$Chemical bonds are determined by electrons$

• The number and distribution of electrons around an atom determines whether how the atom will react with other atoms

Energy shells, $orbitals,$ contain the atoms electrons

• The shell farthest from the nucleus is the most important for bonding
• Electrons are arranged in pairs on the shells
    * Unpaired electrons form bonds with other atoms
    * Atoms are more stable when their outer shells have $no vacancies$
    * The more vacancies, the more likely they are to bond with another atom
• $Covalent Bonds - when atoms share electrons$
    * Double bonds - share 4 electrons between atoms
• Noble gases - full and do not bond

Electronegativity measures an atom’s ability to attract electrons

• Differences determine chemical bonds
• The periodic table arranges atoms by electronegativity
• When atoms have similar electronegativity, neither will pull electrons more strongly than the other
    * $Nonpolar covalent bonds form during this$

Some atoms have a partial charge

Electrons spend more time - slightly negative charge (atom)

Electrons spend less time - slightly positive charge (atom)

$This charge difference gives the bonds polarity$

$Different electronegativity - polar covalent bonds$

Polarity in water molecules creates hydrogen bonds

Slightly positive charge on the hydrogen atom attracts the negatively charge of a neighboring water molecule

Hydrogen bonds pull water molecules close to each other

• This gives water unique properties
• This is important to DNA structures and proteins

Very high electronegativity forms ionic bonds

Some bonds have such different electronegativities that one atom completely pulls an electron away from each other

• electrons can completely transfer over to highly electronegative atoms
• atom that loses an electron - positively charged
• atom that gains - negatively charged
• charge difference attracts the atoms to each other, forming ionic bonds

In ionic bonds, both atoms get full outer shells, so both atoms become stable

• $Two elements with similar/moderately different electronegativities will - form nonpolar covalent bonds$
• $Two elements with very different electronegativities will - form ionic bonds$

Water Unique Properties

Cohesion - tendency of water molecules to stick to one another

• give high surface tension

Adhesion - allows water molecules to form hydrogen bonds with other molecules

$Cohesion and Adhesion allows water to “climb” from a trees roots to its highest leaves$

Water is an excellent solvent

Water dissolves hydrophilic (water - loving) substances

• polar solutes and ions

The polarity of water molecules help water dissolve most biologically important molecules

• Salt (NaCl)
    * Slight negative charge on water attracts positive charges (Na+)
    * Slight positive charges on water attracts negative charges (Cl-)

Only dissolved selected molecules

• Water does not dissolve hydrophobic (water - fearing) solutes
• Example: Lipids (butter) that have nonpolar covalent bonds

Water regulates temperature

Hydrogen bonds make water resist changes in temperature

• $water cools and heats up slowly$
• This is how sweating cools the body

Water expands when it freezes

Hydrogen bonds make water molecules spread out as the water freezes into ice

• This is why ice is less dense than liquid water and ice floats to the top
• In large bodies of water, a top layer of ice provides insulation to keep aquatic life and everything else from freezing underneath

Water participates in chemical reactions needed for life

Water is a reactant in reactions that build and break down all classes of biological molecules

$pH scale shows the amount of H+ ions in solutions$

• Acidic pH <7 - the lower the pH, the stronger the acid
• Neutral pH =7
• Alkaline (basic) pH >7 - the higher the pH, the stronger the base

$Acidic solutions have a low pH and a high H+ concentration$

$Basic solutions have a high pH and a low H+ concentration$

• Have more OH- ions than H+ ions

Many organisms maintain pH homeostasis close to pH=7

• $If an organism stray too far from its optimal pH, it could die$

$Buffer solutions - maintain a constant pH by absorbing or releasing H+ into a solution$

• pH too high - releases H+ to lower pH
• pH too low - absorbs H+ to raise pH

Organic Molecules

Contain both carbon and hydrogen (ex: methane)

They are $biologically important$

• they are needed for life’s processes and are categorized into four main categories
    * Carbohydrates
    * Proteins
    * Nucleic acids
    * Lipids

Organic molecules such as carbohydrates, proteins, and fats are common in our diets.

Organic Molecules are made of monomers

$monomers - single unit of carbohydrate, protein, or nucleic acid$

• form together to form polymers

$Dehydration synthesis - chemical reaction that joins monomers$

• enzymes form bonds between two monomers
• water is released as a part of the reaction

$Hydrolysis - chemical reactions that break polymers apart$

• enzymes break bonds between monomers
• water molecule is required

Carbohydrates include simple sugars and polysaccharides

Monosaccharides are simple sugars; they are the monomers that make up larger carbohydrates

• example: ribose, glucose, and fructose

Dehydration synthesis binds two simple sugars together, forming a $disaccharide$

• ex: sucrose

Hydrolysis breaks disaccharides into monosaccharides

Complex Carbohydrates

Polysaccharides are long chains of carbohydrates

• cellulose: structure
• starch: energy
• glycogen: energy

Proteins are made of amino acids

Monomers of proteins are amino acids

Dehydration synthesis binds two amino acids together, forming a $dipeptide$

• A long chain of amino acids is called a polypeptide

Hydrolysis separates dipeptides and polypeptides into individual amino acids

Proteins have many different structures and functions

• Proteins are the “workers” of the cell; they do almost everything
• Collagen - Create cellular structures
• Actin and Myosin - Produce muscle contractions

Each amino acid has its own chemical and physical properties

The 20 different amino acids have 20 different R - groups

These properties in turn determine the properties of the proteins

Polypeptides fold up into proteins

A chain of amino acids folds up into a unique 3 - D shape to become a protein

The function of a protein depends on its shape, or $tertiary structure$

• Denatured proteins lose their shape

Proteins Structures

1. Primary structure (sequence): Amino acid sequence of a polypeptide
2. Secondary structure (“substructure): Localized area of coils, sheets, and loops within a polypeptide
3. Tertiary structure (polypeptide structure): Overall shape of one polypeptide
4. Quaternary structure (protein shape): Overall protein shape, arising from interaction between the multiple polypeptides that make up the functional protein. Only proteins with multiple polypeptides have quaternary structure

Nucleic Acids carry genetic information

Nucleic acids include DNA and RNA

• DNA : Deoxynucleic Acid
• RNA: Ribonucleic Acid

The primary structure of each protein in a cell is determined by the nucleic acids

The monomers of nucleic acids are nucleotides

The 3 different parts of a nucleotide are a phosphate group, a 5 - carbon sugar and a nitrogenous base

• There are 5 possible nitrogenous basesz
    * DNA + RNA both incorporate Adenine, Cytosine, Guanine
    * Only DNA - Thymine
    * Only RNA - Uracil

Dehydration synthesis binds two nucleotides which creates DNA and RNA

Hydrolysis separates nucleic acids into individual nucleotides

$DNA Replication$

$Happens in the nucleus$

1. $DNA has to uncoil$
2. $Hydrogen bonds break$
3. $Sides separate$
4. $Floating nucleotides come in from the cytoplasm$
5. $Hydrogen bonds form$
6. $DNA recoils$
7. $2 DNA molecules as the result$

Lipids are a collection of different hydrophobic molecules

$All lipids are hydrophobic$

Different groups of lipids include molecules with varying structure and function

$THESE ARE NOT BUILT FROM CHAINS OF MONOMERS$

Classes of Lipids

• ^^Triglycerides (fats and oils)^^ - energy rich, needed for long term energy storage
    * formed by covalently attaching 3 fatty acid molecules to a glycerol molecule
    * Dehydration synthesis links fatty acids to glycerol
    * Hydrolysis separates fatty acids from glycerol
• Some fatty acids are saturated
    * All carbons of a saturated fatty acids are bonded to 4 other atoms which has a straight shape
    * Same fatty acids are unsaturated which contain at least one double bond and has a bent shape
• $Saturation gives triglycerides different properties$
    * Bends in the unsaturated fatty acids prevent them from packing close together so unsaturated fats like oils are therefore liquids at room temperature
• ^^Waxes^^ - second class of lipids
    * Composed of fatty acids combined with alcohols
    * Particularly hydrophobic
    * In nature, waxes from waterproof seals
• ^^Steroids^^ - third class of lipids
    * Cholesterol regulates the fluidity of animal cell membranes; it is also used to synthesize many sex hormones

==Check flow chart in notes==