Matter

Matter refers to anything that has mass and takes up space. All matter is composed of certain basic substances called elements.

Element a substance that cannot be broken down to simpler substances with different properties by ordinary chemical means

There are 92 naturally occurring elements, which serve as building blocks of all matter.

C, H, O, N, P, S the six elements that are basic to life and comprising about 95% of the body weight of organisms.

Types of Matter Solid -with definite shape and volume -molecules are compactly arranged so that no spaces exist between them.

Liquid - no definite shape. -assumes the shape of the container where it is placed. - molecules are loosely bound

Gas - tends to separate from one another and fills up any container where it is placed. - molecules are far apart from each other and are in constant motion. - no definite volume.

ATOMS ARE NATURES BUILDING MATERIALS

All substances are composed of tiny particles called ATOMS. ATOMS. ATOM the smallest part of an element, which displays the properties of the element. element.

Subatomic Particles
______________________________________________ Particle Electric Atomic Location Charge Mass ______________________________________________ Proton +1 1 Nucleus Neutron 0 1 Nucleus Electron -1 0 Electron shell/ orbital ______________________________________________

ATOMIC NUMBER -the number of protons in an element. ATOMIC MASS - the sum of the protons and neutrons in an atom.

ISOTOPES - atoms of the same element that differ in their number of neutrons but have the same number of protons. protons.

MOLECULES and COMPOUNDS

Molecule formed when two or more atoms bond together. Compound formed when atoms of two or more different bond together.

TWO TYPES OF BONDS

Ionic Bond a chemical bond formed by the transfer of electron(s) between atoms. This atoms. also formed by the attraction of anion (negatively charged ion) and cation (positively charged ion). ion).

Covalent Bond a chemical bond characterized by the sharing of electrons between two atoms. atoms. Types of Covalent Bonds: Bonds: a. Nonpolar Covalent Bond b. Polar Covalent Bond

CHEMISTRY OF WATER Water a polar molecule composed of 2 hydrogen and 1 oxygen atoms and constitutes 70-90 70% of living material. material.

Properties of Water:
high heat capacity high heat of vaporization high polarity molecules are cohesive and adhesive

high surface tension high heat of fusion

ACIDS and BASES

Acids - any substance that dissociates in water, releasing hydrogen ions (H+). - solution that has a high H+ concentration. concentration. Example: Example: Hydrochloric acid HCl H+ + Cl-

Bases
- any substances that either takes up hydrogen ions (H+) or releases hydroxide ions (OH-). -solution that has high OHOHconcentration. concentration.
Example: Example: NaOH Na+ + OH-

pH pH a measure to determine the acidity or alkalinity of solutions.

pH 0 6.9 (acidic) pH 7 (neutral) pH 7.1 14 (alkaline)

BUFFER
- a chemical or a mixture of chemicals that keep pH within normal limits - resists pH changes by taking up excess hydrogen ions (H+) or hydroxide ions (OH-).

BUFFER FORMATION
H2O + CO2 H2CO3 H+ + HCO3 -

Organic Molecules
- molecules that always contain carbon (C) and hydrogen (H). (H). the framework of biological molecules consists of carbon bonded to other molecules or other types of atoms. atoms.

Monomer - (simple organic molecule) are linked together with other monomers to form a POLYMER. POLYMER.

_________________________________

Polymer Carbohydrate Protein Nucleic Acid

Monomer Monosaccharide Amino Acid Nucleotide

_________________________________

Functional Groups
- specific groups of atoms attached to carbon backbones of an organic molecule. molecule. -determines the characteristics , solubility and chemistry of the molecule.

Important Functional Groups in Biological Molecules --------------------------------------------------------Group Chemical Properties Found Formula in --------------------------------------------------------Hydrogen H Polar and non- almost all nonpolar, involved organic in condensation molecules and hydrolysis

Continuation: --------------------------------------------Hydroxyl OHOH-

polar, involved in Carbohydrates, condensation and nucleic acids, hydrolysis alcohols polar Aldehydes, ketones

Carbonyl

-C=O

Carboxyl

-COOH polar, acidic, involved Amino acids, in Peptide bond fatty acids -----------------------------------------------------------------------------

Continuation -------------------------------------------------Amino -NH2 polar, basic, involved in peptide bond polar, acidic, links nucleotides in nucleic acids Amino acids nucleic acids Nucleic acids phospholipids Phosphates -PO4

Sulfhydryl -SH

forms disulfide bonds Thiols, Thiols, in some amino acids rubbers ----------------------------------------------------------------------------------

Synthesis and Breakdown of Biological Molecules: Molecules:

Dehydration Synthesis - removal of -OH and H during the equivalent services of a water molecule, synthesis of a new molecule.

Hydrolysis
- the addition of a water molecule to break down polymers.

Types of Macromolecules 1.) Carbohydrates

- contains carbon, oxygen and hydrogen in the general formula (CH2O)n - C H bonds hold much energy thus carbohydrates are good energy storage molecules

Glycosidic Bond
- binds monosaccharides together.

FUNCTIONS:
important energy source (e.g. glucose) principal sugar transported throughout bodies of land plants (e.g. sucrose) energy storage (e.g. glycogen in animals; starch in plants) structural material

Types of Carbohydrates :
a.) Monosaccharides - a simple sugar consisting of3 to 7 carbon atoms (e.g. glucose, fructose, galactose)

b.) Disaccharides - a sugar consisting of 2 monosaccharides that have been joined by dehydration synthesis. synthesis. Example: Example: Maltose (glucose + glucose) Sucrose (glucose + fructose) Lactose (glucose + galactose)

c.) Oligosaccharides - a sugar which usually consist between 3 to 10 monosaccharide units. units. Example: Example: stachyose raffinose

d.) Polysaccharides - polymers consisting of very long chains of monosaccharides that are joined by dehydration synthesis. synthesis. -used (plants use glycogen) for energy storage starch; animals use starch;

- also used for structural support (cellulose in plants; chitin in plants; animals) Examples: Examples:

cellulose starch chitin glycogen

2.) Proteins
- composed of one or more long chains of amino acids linked by peptide bonds. bonds. - have C, H, O, N and sometimes S in their molecules

- the building blocks of proteins are amino acids, which contain an amino group (-NH2), a carboxyl group (-COOH) and a hydrogen atom, all bonded to a central carbon atom

Cont. - a peptide bond (covalent bond) joins two amino acids together in a protein by linking an amino group of one amino acid and a carboxyl group of the second amino acid. acid.

20 Biologically Important Amino Acids

_______________________________________ Methionine Valine Threonine Isoleucine Phenylalanine Leucine Lysine Cysteine Tryptophan Alanine Glycine Asparagine Aspartic Acid Glutamic Acid Glutamine Proline Serine Histidine Arginine Tyrosine

Functions: Functions:
defense (e.g. antibodies, snake venom) transport (e.g. hemoglobin, myoglobin, cytochrome) support/structural (e.g. collagen, keratin, fibrin) motion (e.g. actin, myosin)

Functions:
regulation (e.g. insulin, vasopressin, oxytocin) storage (e.g. casein, calmodulin) enzyme catalysis (e.g. hydrolytic enzymes, proteases, kinases)

Protein Structure:
1.) Primary structure specific amino acid sequence that make up a protein and usually assumes a linear form. form. 2.) Secondary structure repeated regular structure assumed by protein chains produced by H bonding between the atoms of the polypeptide backbone. backbone.

2 Types of Secondary Structure:

a.) Helix spiral shape is due to the H bonding every fourth amino acid b.) Pleated Sheath results when a polypeptide turns back upon itself and H bonding occurs between extended lengths of the polypeptide. polypeptide.

Protein Structure:
3.) Tertiary structure shape of globular protein final folded

4.) Quartenary structure forms when two or more polypeptide chains associate to form a functional protein

Enzymes - most specialized classes of protein that speed up the rate of biological reactions - the name of the enzyme usually indicates its function. function.

Examples:
Sucrase degrades sucrose Lactase degrades lactose Maltase degrades maltose Phosphatase removes phosphate group from its substrate

Enzyme Structure
- determines the enzyme s particular function. function. Enzymes have one or more loci called active sites to which the substrates attaches. attaches.

Enzyme Specificity
- enzymes are usually specific, or unique to the reactions they catalyze and the substrates they are involved in these reactions. reactions.

Models of Enzyme Action

Lock an Key Model - assumes that the binding site of the enzyme has a particular shape into which the substrate(s) fit exactly. exactly.

Models of Enzyme Action

Induced Fit Model -assumes that the active site of an enzyme can be modified as the substrate interacts with the enzyme, creating an induced fit between enzyme and substrate.

3.) Nucleic Acids

- made up of polynucleotide chains which are formed by many nucleotides, nucleotides, the building blocks of nucleic acids.

- are formed when the phosphate group of one nucleotide is covalently bonded with the hydroxyl group of the sugar of another nucleotide forming a phosphodiester bond. bond.

Functions:
storage of genetic information transmission and use of genetic information

Components of a Nucleotide
1. 5 C sugar (pentose sugar) 2. phosphate group 3. nitrogenous bases

TYPES OF NITROGENOUS BASES

a.) pyrimidine bases - small, single ringed molecule 1.) cytosine (C) 2.) thymine (T) in DNA; uracil (U) in RNA

TYPES OF NITROGENOUS BASES

b.) purine bases - large, double ringed molecule 1.) guanine (G) 2.) adenine (A)

Nucleotide

Two Classes of Nucleic Acids

1.) Deoxyribonucleic Acid (DNA)
- found in all living things - encodes information used to assemble proteins - has a deoxyribose sugar and has thymine as one of the pyrimidine bases

Deoxyribonucleic Acid (DNA) ________________________________

- double stranded (composed of two strands held together by H bonds) - the two strands are twisted around each other forming a double helix

Deoxyribonucleic Acid (DNA) ________________________________

- the double helical structure of DNA was proposed by James Watson and Francis Crick in 1950 - primarily found in the nucleus but also present in mitochondria and chloroplasts

Deoxyribonucleic Acid (DNA) ________________________________

- pairing of nitrogenous bases is specific. specific. Specific purines always pair with specific pyrimidines (complementary base pairing) A = T (bonded by 2 H bonds) G = C (bonded by 3 H bonds)

2.) Ribonucleic Acid (RNA)

________________________________
- carries the genetic code into the cytoplasm - directs the synthesis of proteins - single-stranded single- contains ribose sugar instead of deoxyribose

Ribonucleic Acid (RNA)

________________________________
- contains uracil (U) in place of thymine (T) RNA Nitrogenous Pairing A=U G=C

Deoxyribose vs Ribose

Deoxyribose

Ribose

Kinds of RNA ___________________________________

1.) messenger RNA (mRNA) - carries the DNAs genetic code to the ribosome for translation. translation. tRNA) 2.) transfer RNA (tRNA) - brings amino acids to ribosome for protein synthesis

Kinds of RNA ________________________________

3.) ribosomal RNA (rRNA) (rRNA) - structural component of the ribosomes

Other kinds of Nucleotides ________________________________

1.) Cyclic Nucleotides - carry information from the cell membrane to other molecules in the cell

Other kinds of Nucleotides ________________________________

2.) Diphosphate and Triphosphate Nucleotides - high energy molecules that carry energy to different parts of the cell.

Example:
1.) ADP (adenosine diphospate) diphospate) 2.) ATP (adenosine triphosphate) triphosphate) - considered as the energy currency of the cell

Other kinds of Nucleotides ________________________________

3.) Coenzymes - assist enzymes in their activity. Example: NAD NADP

4.) Lipids
- loosely defined as groups of molecules that are insoluble in water - primarily composed of C, H, O and others have P and N - store twice as much energy as carbohydrates

Ester Linkage
- a covalent bond which binds the building blocks of lipids (fatty acid and a glycerol)

Fu c t i o n :
- energy storage - protection and cushioning of body organs - structural components of membranes - chemical messengers (hormones)

Components of Lipids