Chapter 2

Chemistry of Life

Nature of Matter

MATTER• is anything that occupies space

and has mass• atom, element, molecule,

compound

• elements are pure substances composed of one type of atom (#p determines element)

• e.g.• molecules are two or more atoms (same or

diff)• e.g. • compounds are substances in which molecules

have more than one type of element• e.g.

THE ATOM

• the center is the nucleus• in the nucleus are protons (+) and neutrons• electrons (-) surround the nucleus in the

electron cloud • they are found in orbital which are further

arranged in energy levels• energy levels can only hold a certain # e

(2,8,18…)

THE ATOM

• atomic number = # protons•mass number= #p + #n• Atomic mass is the weighted

average of all the isotopes of that element

BONDING BETWEEN ATOMS

• an atom is said to be chemically stable when its last energy level is full (max for the level)• Recall term valence electrons• if an atom’s last level is not full it will

gain, lose, or share electrons depending on its need to fill that level

IONIC BONDS• when atoms have low # of valence electrons,

tend to give them up• when atoms have high # of valence electrons,

tend to gain them• lose a few or gain a few to be stable• now atom is + or – charged• atoms are attracted to each other• groups 1and 2 AND 16 and 17 on the PT will

tend to form these bonds

• ionic molecules usually dissolve easily in water because water molecule wedges between the ion and force them apart - dissociate• molecules that form ions when

dissolved in water are called ELECTROLYTES• be aware of notations for ions

COVALENT BONDS

• when atoms have mid range number of valence electrons will not loose or gain, but rather share electrons• atoms found in the middle of the PT

tend to form covalent bonds• eg. Oxygen

Water and Solutions

• H2O is a very unique molecule• Because of its structure and bonding

water takes a long time to heat, but holds onto the heat longer than other molecules

• Our cells are filled with water and this ability to hold heat helps cells maintain homeostasis• Due to its polarity and hydrogen

bonding• Water is also very important in most

biochemical reactions

Water’s Atomic Structure

• Water consists of one large oxygen atom and two small hydrogen atoms

• Electrons are attracted to the oxygen nucleus more than the small hydrogen nucleus

• Hence oxygen tends to be negative and the two hydrogen tend to be positive- POLAR MOLECULE

HYDROGEN BONDS

• One H2O molecule is attracted to another H20 molecule due to this polarity

• Water molecules are attracted to each other

COHESION

• Is the attractive properties between substances of the same kind• A water molecule is attracted to

another water molecule because of hydrogen bonding• This results in surface tension• Raindrops, insects, insulation

ADHESION

• Is the attraction of a substance to another substance• Water is attracted to other substance

because of its polar charges• Meniscus, capillary action

SOLUTIONS

• Is a mixture of two substances in which one (solute) is dissolved in another (solvent)• Water is known as the universal solvent

as most chemicals dissolve in water• Without water many substances could

not flow through the body/ blood easily

ACIDS AND BASES

• inorganic compounds (no carbon)• acids and bases can effect reactions• at times water molecules dissociate to form

the H+ and OH- ions• generally in pure water the balance between

these ions are equal and no problem• Since many compounds disassociate in water

they can disrupt this ratio

ACID• Compounds that produce surplus of

H+ when dissolved in water• in blood CO2 forms carbonic acid

H2CO3 when it dissolves in water• this will add surplus of H+ in blood

and make blood acidic

BASE• compounds that produce surplus of

OH- when dissolved in water

pH• the relative conc. of acids and bases in

solution• high ph = low H+ • low ph = high H+

• ph =7 neutral, balanced

• the pH of body fluids affects body chem. greatly

• usually body function can only be maintained within a narrow range of pH

• body can remove excess H+ ions by excreting them in urine or increasing the loss of CO2 in respiration• also body can produce buffers• Buffers help neutralize a strong acid• In the stomach there are natural

buffers that help raise the pH after digestion

ORGANIC COMPOUNDS

• very complex molecules• Contain the C-C double bond• major types are carbohydrates,

lipids, proteins, and nucleic acids

CARBOHYDRATES

• basic unit is monosaccharide• composed of C, H, O• glucose important mono. and it used

as a primary energy source at the cellular level• potential energy stored in the bonds

and when cell breaks down E released

GLUCOSE

• if you put two mono. together = disaccharide (e.g. sucrose, and lactose)

• the body must break up these sugars into mono.

• large carbs. made of many mono.’s are called polysaccharides (e.g. glycogen = starch)

• they are chains of glucose molecules joined• liver and muscle cells form glycogen when

there is an excess of glucose in the blood and stores it for later use

LIPIDS

• fats and oils• fats solid at room temp., oils liquid

like carbs bonds store E • very important for storing E for later

use

• TRIGLYCERIDES are lipid molecules formed by a glycerol unit joined to three fatty acids

• PHOSPHOLIPIDS are similar to trigl. but have P• the P unit is the head and attracts water

(hydrophilic)• the fatty acid tail repels water (hydrophobic)• this allows the formation of a stable bilayer in

water• foundation of cell membrane

• CHOLESTEROL is a steroid lipid (multiple ring) • it combines with phospholipids to make

membrane stronger• base ingredient to make steroid hormones:

estrogen, testosterone, and cortisone

PROTEINS• large molecules made of amino acids• contain C, H, O, N• can combine with other organic molecules• sequence of AA is held together with peptide

bonds• difference atomic charges of molecules have +

and – attractions throughout the chain that cause it to coil

• shape = role

• STRUCTURAL PROTEINS = shaped to form structures in the body like collagen, keratin

• FUNCTIONAL PROTEINS = shaped to from role in chemical process like hormones, receptors, enzymes (lock and key)

• ENZYMES are chemical catalysts that speed up a process without being used up themselves• no reaction in the body occurs fast

enough unless there is a specific enzyme • each enzyme is very specific like a

lock and key model

NUCLEIC ACIDS

• high molecular weight substances• direct the formation and structure of

all proteins/ overall body• DNA and RNA• basic building blocks are nucleotides

= phosphate unit + sugar + nitrogen base

• nitrogen bases : cytosine, guanine, adenine, thymine • in RNA uracil replaces thymine• DNA is double helix• on DNA sequence of nucleotides

determines genetic code for putting together proteins• RNA is needed to make proteins (m-

RNA and t-RNA)

Organic Compound Monomer Polymer Function (s)

Carbohydrate

Lipid

Protein

Nucleic Acid

Energy and Chemical Reactions• ENERGY is the ability to move or change matter• Different forms:

• Light• Heat• Chemical• Mechanical• Electrical

Law of Conservation of Energy

• Energy is neither lost or gained, it is simply converted from one form to another

• Kicking a ball• Bioluminescent fire fly• Cellular respiration

• Chemical reactions are summarized by symbols and equations

• Reactants → Products• NaCl →Na+ + Cl-

• C6H12O6 + 6O2 → E + 6CO2 + 6H2O

Energy in Chemical Reactions

• Energy is absorbed (endothermic) or released (exothermic) when chemical bonds are broken and new ones are formed

ACTIVATION ENERGY

• The energy needed to start a chemical reaction

• E.g. spark from a spark plug ignites gasoline• Match transfers enough energy to ignite the

logs on a fire• Pushing a ball at the top of the hill to get the

ball rolling

ENZYMES

• Enzymes reduce the activation energy of a chemical reaction, thereby speeding up the reaction

http://www.youtube.com/watch?v=hoBhOdQV7vw&feature=related

• Enzymes help organisms maintain homeostasis

• Without enzymes chemical reactions would not occur quickly enough to sustain life

• A substance on which an enzyme acts during a chemical reaction is called a SUBSTRATE

• Enzymes act on specific substrates• E.g. the amylase assists in the breakdown

of starch to glucose

• The enzymes shape determines its activity

• Most often an enzyme is a large protein with one or more deep folds on its surface shape

• These folds form pockets called ACTIVE SITES

• The substrate fits into specific enzymes because like puzzle pieces only certain enzymes and substrates match together

Steps of Enzyme Activation

1. When an enzyme first attaches to a substrate during a chemical reaction, the enzymes shape changes slightly so that the substrate fits more tightly in the enzymes active site.

2. At an active site, an enzyme and a substrate interact in a way that reduces the activation energy of the reaction, making the substrate more likely to react.

3. The reaction is complete when the products have formed. The enzyme is now free to catalyze further reactions.

Factors in Enzyme Activity

• Any factor that changes the shape of an enzyme can affect the enzyme’s activity

• Things that effect activity:• Temperature•pH•Other chemical reactions