CHAPTER 2 - Chemistry * level of organization

Chemistry

the science of the structure and interactions of matter

Matter

anyhthing that occupies space and mass

• mass - amount of matter in an object (never chanes)

  • It composes living and non living things

    • All matter is composed of chemical elements

      • Element - cannot be chemically broken down into simpler substances

        • composed of identical particles called atoms

96% of the human body mas is made up of..

1. Carbon

2. Hydrogen

3. Nitrogen

4. Oxygen

Atom

the smallest unit of matter that retains the properties and characteristics of matter

• atoms are electrically neutral (# of protons = # of electrons)

  • atoms of different elements contain diff # of protons

Atoms are defined by..

1. Atomic number (# of protons)

2. Mass number (protons + neutrons)

Isotopes

atoms of elements that differ in the number of neutrons

Ion

an atom that has gained or lost an electron

Protons

found in the nucleus and have a positive charge

• p+

Neutrons

found in the nucleus and have no charge

• N0

Electrons

these travel around the nucleus in orbitals (shells_ and have a negative charge (e-)

• each shell holds a specific # of electrons

  • outermost shell = valence shell

A molecule is formed…

when 2 or more atoms are joined by a chemical bond

• this can involve the same elements or different elements

Chemical bonds

these are formed to achieve complete shells of electrons and thus chemical stability

• 1st shell has 2 e- (nearest to the nucleus)

• 2nd shell has 8 e-

• 3rd shell holds 8 or more e- (max 18 e-)

Types of Chemical Bonds: Ionic bonds

these are formed by the transfer of electrons from one atom to another

• e.g. NaCl

Type of Chemical Bonds: Covalent Bonds

these are formed by the sharing of pares of electrons between two or more atoms

• Non-polar → e-'s are shared equally between atoms

• Polar → e-'s are not shared equally between atoms

  • One atom pulls the e- towards them b/c they are more EN

Types of Chemical Bonds: Hydrogen bonds

these are formed when a hydrogen atom with a partial positive charge attracts the partial negative charge of a nearby electronegative atom

• most often N or O

Chemical Reactions

these occurs when bonds are formed, broken or rearranged

Energy

the capacity to do work

• two forms:

  • Potential Energy → energy stored by matter due to it's position

  • Kinetic energy → energy associated with matter in motion

Chemical energy

a form of potential energy that is stored in the bonds of compounds and molecules

Activation energy

energy required to disrupt the electrons to get the molecules to interact

• aka start the reaction

Catalysts

These are enzymes that speed up reactions by lowering the activation energy

Synthesis reactions

Anabolic reactions

• where two or more atoms, ions, or small molecules join together to form a larger molecule

Decomposition reactions

Catabolic reactions

• where a larger molecule is broken down into smaller molecules, ions or atoms

Exergonic

a reaction where more energy is released than absorbed

Endergonic

a reaction that absorbs more energy than it releases

Exchange Reactions

this reaction involes both synthesis and decomposition

• parts of two different molecules trade positions with one another

Are chemical reactions reversible?

Yes they are

• they just require energy

  • doesn't happen often in biology

Biochemistry

the study of chemical composition and living matter

Inorganic compounds

these compounds lack carbon and are structurally simple

• e.g. water, salts, acids, and bases

  • except CO2

Organics compounds

these compounds always contain carbon & usually hydrogen and other functional groups

• formed via covalent bonds

  • Carbon forms 4 bonds w/ other elemenrs

    • built by joining monomers (small molecules) into polymers (macromolecules)

  • e.g. carbohydrates, lipids, proteins, nucleic acids, and adenosine triphosphate (ATP

Inorganic compounds: Water

The most abundant and important inorganic compound in all living organisms

• Has many important properties:

  • High heat capacity - gains and loses heat very slowly

  • High heat of vaporization - needs a lot of energy for it to be changed from liquid to gas (needs to break hydrogen bonds first)

  • polar solvent - universal, can dissolve most things

  • formed during dehydration synthesis reactions and required in hydrolysis reactions

  • cushioning and lubricating effect

Inorganic Compounds: Salts, acids and bases

All of these dissociate when dissolved in water

• gives rise to oppositely charged ions (electrolytes)

  • Salts - dissolve into + and - ions

  • Acids - dissolve into 1 or more H+ and 1 or more - ions (HCl → H+ + Cl-)

  • Bases - dissociate into 1 or more OH- and 1 or more + ions (NaOH → Na+ + OH-)

pH scale

range from 0-14

• based on the relative [ ] of H+ in a solution

  • 1 pH unit = 10x change in [H+]

• ph < 7 - acidic (H+ > OH-)

• ph = 7 - neutral (H+ = OH-)

• ph > 7 - basic (H+ < OH-)

Buffer systems

found in the body to minimize changes in the pH of solutions

• done by converting strong acids or bases into weak acids or bases

  • absorbs H+ or OH- so there is less from the strong acid/base

Dehydration synthesis

Monomers are joined by the removal of OH from one monomer and removal of H from the other at the site of bond formation

Hydrolysis

Monomers are released (broken apart) by the addition of water molecules

• Adds OH to one monomer and H to the other

Organic Compounds: Carbohydrates

used as fuel and structural purposes such as DNA

• Includes sugars, glycogen, starches, and cellulose

  • -composed of C, H, and O

• Main source of chemical energy for metabolism

  • classified by # of sugar units

Monosaccharides

simplest form with one sugar molecule

• general formula (CH2O)n

  • 1:2:1 ratio of C:H:O

    • e.g. pentose 5C → C5H10O5

Disaccharides

consists of 2 monosaccharides (2 sugars)

• formed by a dehydration synthesis

  • -e.g. sucrose

Polysaccharides

contains more than 2 sugars

• large chains of many monosaccharides joined tgt

  • e.g. glycogen → storage for glucose, broken down when blood sugar needs to be adjusted

Glucose vs Fructose vs Glacatose

all these sugars have the same formula, C6H12O6

• however they differe because they are bonded differently

  • this gives the different properties

    • known as isomers

Isomers

same molecular formula bonded differently

Organic compounds: Lipids

composed of C, H, and less O

• Non-polar compounds and are not soluble in water (hydrophobic)

  • includes: Triglycerides, phospholipids, steroids

• Can only dissolve in other non-polar solutions

Triglycerides

these are neutral fats

• composed of glycerol and 3 fatty acid chains

  • important for storage of energy, insulation and shock absorbtion

    • Can be saturated or unsaturated

Saturated fats

these fats have the maximum amount of hydrogens that can be bonded

• no c-c double bond

  • solid fat

Unsaturated fats

these fats have less than the maximum number of hydrogens that can be bonded

• bc of a c-c double bond

  • causes a kink/bend

    • makes it liquid (oil)

Phospholipids

composed of glycerol, 2 fatty acids and a phosphate grp (polar)

• main component of membranes

  • phosphate group will interact with water (hydrophyllic)

Steroids

consists of 4 interlocking carbon rings with various side groups

• includes cholesterol (important for membrane structure) and steroid hormornes

  • e.g. sex hormones for certain developmental characteristics

Organic compounds: Proteins

composed of C, H, O and N

• can also have sulfur and phosphorous

  • they are polymers build from the 20 diff amino acids

    • can be di, tri, and polypeptides

Amino Acids

these are joined by peptide bonds (covalent bonds) formed by dehydration synthesis to make proteins

• consists of an Amino group, Carboxyl group and a side chain

  • the side chain (r group) is the only thing that changes and gives diff chemical and physical properties to each amino acid

4 Levels of Proteins

1. Primary structure

2. Secondary structure

3. Tertiary Structure

4. Quaternary structure

Primary Structure

a linear sequence of amino acids

Secondary structure

alpha-helix or beta-pleated sheet

Tertiary structure

complex globular shape

• has a 3d shape

  • different charged atoms hold it tgt

Quaternary structure

interaction of 2 or more polypeptides

Proteins can be classified as…

can be classified as either:

• Structual (fibrous)

• Functional (globular)

Structural (fibrous) protein

these proteins are:

• stable and insoluble in water

  • provide mechanical support and give strength

    • e.g. collagen - holds the body tgt, Keratin - found in hair and fingernails, Elastin - gives elastic quality to connective tissue

Functional (globular) protein

these proteins are:

• Less stable and hydrogen bonds break easily

  • Are water soluble

    • has an outer layer where it interacts with water

      • inner layer (the protein) doesn't break

Denaturing

where proteins lose it's structure and unravel, causing them to lose function if their environment changes

• e.g. enzymes, important for reactions, are made of proteins and will denature

Enzymes

the biological catalysts which increase the rate of a specific chemical reaction

• they react with a specific substrate and inc the rate at which the product is formed

  • lock and key mechanism → enzymes will only fit with specific substrates

• They act to decrease the amount of activation energy needed for the reaction to proceed

  • does not get altered or used up

    • has -ase as a suffiv (lipase)

Organic Compounds: Nucleic acids

large molecules that are composed on C, H, O, N and P

• made of chains of nucleotides

  • Nucleotides - phosphate group + 5C sugar (pentose) + nitrogenous base

• 2 Kinds of Nucleic Acids

  • DNA

  • RNA

DNA

Deoxyribonucleic acid

• a double straned polymer (ladder-like shape), twisted into a double helix

• sugar is deoxyribose (no oxygen)

• Nitrogenous bases: Adenine, Thymine, Cytosine, and Guanine

• Hydrogen bonds join Nitrogenous bases tgt (rungs)

• Alternating sugar and phosphate molecules form the "uprights” of the ladder

RNA

Ribonucleic acid

• single nucleotide chain (single stranded)

• sugar is ribose (has oxygen)

• Nitrogenous bases: Adenine, Uracil, Cytosine, Guanine (replaces Thymine)

• several types of RNA, includes:

  • rRNA - ribosomal

  • mRNA - messenger

  • tRNA - transfer

Organic Compounds: ATP

Adenosine triphosphate (ATP)

• the molecule the cells use (energy) to perform various types of work

  • e.g. muscle contraction

• Consists of: Adenine, 5C sugar (ribose), & 3 phosphate groups

• ATP can be broken down to adenosine diphosphate (ADP), which releases energy to be used for cellular work

• Can be synthesized from ADP + P, which requires energy input provided by glucose breakdown.