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BASIC CHEMISTRY AND BIOCHEMISTRY. BASIC CHEMISTRY. MEET THE ELEMENTS. http://www.youtube.com/watch?v=d0zION8xjbM. ATOMIC THEORY OF MATTER (vocabulary). Atoms = building blocks of matter that cannot be divided any further by ordinary chemical means

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Basic chemistry and biochemistry
BASIC CHEMISTRYANDBIOCHEMISTRY



Meet the elements
MEET THE ELEMENTS

http://www.youtube.com/watch?v=d0zION8xjbM


Atomic theory of matter vocabulary
ATOMIC THEORY OF MATTER(vocabulary)

  • Atoms = building blocks of matter that cannot be divided any further by ordinary chemical means

  • Molecule = two or more atoms combined that act as a single particle, the smallest particle that retains the properties

  • Elements = substances made of only one kind of atom


Atomic theory of matter vocabulary1
ATOMIC THEORY OF MATTER(vocabulary)

  • Compounds = two or more kinds of atoms in a substance in definite proportions

  • Isotopes = varieties in the normal number of neutrons on the nucleus

    (The atomic number stays the same, the mass number changes)

  • Radioactivity = a nuclear process in which an atom is undergoing changes by emitting charged particles


Structure of the atom
STRUCTURE OF THE ATOM

particle charge mass location

proton (+) 1 amu in nucleus

electron (-) 0 in orbitals

neutron ( ) 1 amu in nucleus

A “Happy Atom” has all its orbital places filled.

Atomic number = # of protons (also the number of electrons in a neutral atom)

Atomic mass or mass number = number of protons plus the number of neutrons in the nucleus.


Atomic orbitals energy levels
ATOMIC ORBITALS(energy levels)

Level 1

2 electrons orbit

nucleus

Level 2

8 electrons orbit

Level 3

8 electrons orbit

Remember: A “Happy Atom” has all its orbital places filled.


Chemical bonding
CHEMICAL BONDING

Chemical bond = force of attraction that holds atoms together

  • There are two kinds of bonds between atoms

    1. Covalent Bonds = chemical bond that is formed by the sharing of electrons

    • Ionic Bonds = chemical bond that is formed by transfer of electrons


Covalent bond
COVALENT BOND

HYDROGEN ATOM

HYDROGEN ATOM

OXYGEN ATOM

Covalent Bond = chemical bond that is formed by the sharing of electrons (covalent bonds form molecules)

Remember: A “Happy Atom” has all its orbital places filled.


Ionic bond
IONIC BOND

Ionic bond = chemical bond that is formed by transfer of electrons

Remember: A “Happy Atom” has all its orbital places filled

Sodium (Na) has 1 electron in its outer energy level – is it happy?

Chlorine (Cl) has 7 electron in its outer energy level – is it happy?


Ionic bond1
IONIC BOND

Sodium and Chlorine ions are formed –

What is an ion?

Ion = atom with an excess charge by the loss or gain of electrons

Sodium has lost one electron (one less (–) charge) so it now has a net charge of +1

Na

Cl

Na

Cl

Chlorine has gained one electron (one more (–) charge) so it now has a net charge of -1

The (+) charge of Na is attracted to the (-) of the Cl and this attraction forms an ionic bond!


Chemical formulas
CHEMICAL FORMULAS

Each element (symbol)

and its proportions (subscripts)

are represented information

All elements are listed in the periodic table

  • 6 atoms of Carbon (C)

  • 12 atoms of hydrogen (H)

  • 6 atoms of oxygen (O)

For example C6H12O6means:


Chemical formulas1
CHEMICAL FORMULAS

Examples are:

H2O

CO2

C6H12O6

CH4


Structural formulas
STRUCTURAL FORMULAS

A Structural formula shows the kinds and number of atoms as well as the chemical bonds

glucose

H

H

C

C

H

O

acetylene

H

water

benzene


Chemical equations
CHEMICAL EQUATIONS

Reactants = the original substances before a chemical reaction (left of the arrow)

Products = new substances formed after a chemical reaction (right of the arrow)


Law of Conservation of Mass = mass can neither be created or destroyed (chemical reaction formulas must balance)

+

2 molecules of hydrogen

(2H2)

+ 1 molecule of oxygen (O2)

2 molecules of water

(2H2O)



Biochemistry the chemical compounds of life
BIOCHEMISTRYThe Chemical Compounds of Life


Biologically important compounds
BIOLOGICALLY IMPORTANT COMPOUNDS

ORGANIC COMPOUNDS:

  • Species that naturally contain carbon and hydrogen (living organisms and their products)

  • Most also contain O (oxygen) and N (nitrogen)

  • Only a few elements are found in organic compounds

  • May also have P (phosphorous), S (sulfur), Fe (iron), Ca (calcium), Na (sodium), Cl (chlorine), Mg (magnesium), K (potassium)


Biologically important compounds1
BIOLOGICALLY IMPORTANT COMPOUNDS

INORGANIC COMPOUNDS:

  • DO NOT CONTAIN CARBON (with hydrogen)

  • May have carbonate compounds (CO2, CaCO, etc.) but not carbon with hydrogen.

  • Living organisms do contain inorganic compounds


Important inorganic compounds
IMPORTANT INORGANIC COMPOUNDS

  • WATER

  • The most important inorganic compound in living organisms

  • 65% of the body

  • Many biological processes require water

  • SALTS

  • Help maintain water balance in the cells

  • Provide ions for many biological processes

  • ACIDS and BASES

  • Help maintain homeostasis


The structure of organic compounds
The Structure of Organic Compounds

  • Organic compounds are large and complex because of the carbon atom

  • Four vacancies for electrons allow 4 covalent bonds

Carbon has an atomic # of 6 which means it has 6 protons and 6 electrons

It has 4 vacancies in the outer energy level

2.

1.

6 +

3.

4.


Chemical compounds of life
CHEMICAL COMPOUNDS OF LIFE

Living organisms depend upon a variety of molecules for their survival. Some are used to build complex parts of an organism; some supply energy; while others provide instructions for the operation of the organism.

There are many organic compounds found in organisms, but they can be classified into 4 main types:

  • CARBOHYDRATES

  • LIPIDS

  • NUCLEIC ACIDS

  • PROTEINS


Carbohydrates
CARBOHYDRATES

  • Carbohydrates are compounds of C (carbon), H (hydrogen), and O (oxygen)

  • They have the same ratio H:O as in water (H2O) = 2:1 (twice as many H as O)

    • Monosaccharides = simple sugars = C6H12O6

      • ALWAYS END IN “OSE”

        EX: MALTOSE, FRUCTOSE, GLUCOSE

      • RELEASE ENERGY WHEN BREAKING DOWN GLUCOSE INTO CO2 AND H2O

      • C6H12O2 CO2 + H2O

      • MOST ORGANISMS USE GLUCOSE AS A SOURCE OF ENERGY


Carbohydrates1
CARBOHYDRATES

THIS IS A MONOSACCHARIDE MOLECULE!

THIS IS A SIMPLE SUGAR!

THIS IS GLUCOSE!

THIS IS C6H12O6 !


Carbohydrates2
CARBOHYDRATES

DISACCHARIDE = two simple sugars joined

POLYSACCHARIDE = several simple sugars joined

POLYMERS = long chains of repeating molecules

(many) (molecules)


Carbohydrates3
CARBOHYDRATES

Sugars stored in plants are called STARCH

Sugars stored in the liver of animals are called GLYCOGEN

Glycogen will be changed into glucose when the body needs it for energy!


Carbohydrates4
CARBOHYDRATES

BUILDING BLOCKS OF CARBOHYDRATES ARE

SIMPLE SUGARS OR MONOSACCHARIDES


Lipids fats oils and waxes
LIPIDS(fats, oils, and waxes)

  • Made of carbon, oxygen, and hydrogen

    (there less oxygen in lipids than in carbohydrates)

  • Reserve energy supply in an organism

    2 times as much energy as carbohydrates

    • Plants store oils in seeds

    • Mammals store fats under the skin

  • Waxes are formed from fatty acids and substances similar to glycerol

  • Fats and oils are formed from fatty acids and glycerol


  • Lipids fats oils and waxes1
    LIPIDS(fats, oils, and waxes)

    BUILDING BLOCKS of LIPIDS (fats and oils) ARE

    1 GLYCEROL + 3 FATTY ACIDS


    The structure of a fatty acid
    The Structure of a Fatty Acid

    Lipid molecule

    The Fatty Acid has 2 parts:

    Chain of carbon atoms with hydrogen atoms bonded

    (hydrocarbon chain)

    Carboxyl group


    Saturated vs unsaturated fatty acids
    SATURATED vs UNSATURATED FATTY ACIDS

    • SATURATED FATTY ACIDS:

    • Fats that have all single carbon-to-carbon bonds

    • Tend to be solids at room temperature (ie. butter)

    • Tend to increase the amount of cholesterol in the body

    • Cause deposits that lead to hardening and narrowing of arteries


    Saturated vs unsaturated fatty acids1
    SATURATED vs UNSATURATED FATTY ACIDS

    • UNSATURATED FATS

    • Fats that have a double or triple carbon-to-carbon bond

    • Tend to be oils at room temperature

    • Tend to decrease blood cholesterol

    • Polyunsaturated fats = a chain that has more than one double or triple bond



    Nucleic acids
    NUCLEIC ACIDS

    • Compounds that contain phosphorus (P) and nitrogen (N)

    • Also carbon, hydrogen, and oxygen

      Two types of Nucleic Acids:

    • DNA

    • RNA


    Nucleic acids dna
    NUCLEIC ACIDS(DNA)

    DNA = deoxyribonucleic acid

    • Found in the nucleus of the cell

    • Directs and controls heredity information and the development and activities of the cell


    The structure of dna
    THE STRUCTURE OF DNA

    DNA is made of:

    Repeated chains of nucleotides

    Nucleotides are made of:

    • 5 carbon sugar (deoxyribose)

    • Phosphate group (PO4)

    • Nitrogenous base (A,T,C,G)


    The structure of dna1
    THE STRUCTURE OF DNA

    DNA

    • The DNA molecule is made of repeating chains of nucleotides

    • The sugar and phosphate groups are the sides of the ladder

    • Nitrogenous base pairs are the rungs of the ladder

    • The bases are adenine (A), thymine (T), cytosine (C), and guanine (G)

    • adenine (A) always pairs with thymine (T)

    • cytosine (C) always pairs with Guanine (G)


    RNA

    RNA = ribonucleic acid

    RNA structure:

    • A single strand or chain of bases

    • The sugar is ribose

    • The base thymine is replaced with uracil

    • RNA is involved with protein synthesis


    Proteins
    PROTEINS

    • Compounds that contain nitrogen, carbon, hydrogen, and oxygen

    • Many contain sulfur and phosphorus

    • Great range of properties that give live complexity

    • 20 different amino acids found in proteins

    AMINO ACIDS ARE THE BUILDING BLOCKS OF PROTEINS


    Structure of an amino acid
    STRUCTURE OF AN AMINO ACID

    One central carbon atom (C)

    One carboxyl group (COOH)

    One amino group (NH3)

    One hydrogen atom (H)

    One side chain (R)

    GLYCINE is the simplest amino acid – the side chain is only one H atom



    Protein vocabulary
    PROTEIN VOCABULARY

    Dipeptide = two amino acids bonded together

    The peptide bond = the bond between amino acids

    Polypeptide = a long chain of amino acids



    Dehydration synthesis
    DEHYDRATION SYNTHESIS

    DEHYDRATION = to remove water

    SYNTHESIS = to make more complex

    H and OH are removed from the glucose molecules (to make water), this is the dehydration part

    Then the two glucose molecules have open bonding sites so they can join together to make more complex, this is the synthesis part.

    Dehydration synthesis =

    to make more complex by removing water


    Hydrolysis
    HYDROLYSIS

    To break down by adding water



    Dehydration synthesis of a carbohydrate
    Dehydration Synthesis of a Carbohydrate

    In carbohydrates, two monosaccharides form a bond to create a disaccharide


    Dehydration synthesis of a protein
    Dehydration Synthesis of a Protein

    In proteins, two amino acids form a peptide bond to create a dipeptide molecule


    Dehydration synthesis of a fatty acid
    Dehydration Synthesis of a Fatty Acid

    In lipids, we remove 3 molecules of water!

    Then the glycerol molecule bonds with the 3 fatty acids


    Vocabulary review
    Vocabulary Review

    A small molecule that will combine with other small molecules to form a chain

    • monomer =

    • polymer =

    • dehydration synthesis =

    • hydrolysis =

    A large molecule (chain) formed from combined repeated smaller units (monomers)

    Combining molecules by the removal of water

    Breaking down molecules by the addition of water



    Enzymes
    ENZYMES

    The importance of enzymes:

    • Enzymes are proteins

    • Enzymes enter the chemical reaction temporarily and are not changed

    • Enzymes are used over and over again

    • Enzymes are organic catalysts


    Enzymes1
    ENZYMES

    A catalyst is a substance that brings about a chemical reactionwithout being changed itself

    The substrate is the substance the enzyme acts upon


    How enzymes work
    HOW ENZYMES WORK

    • The active site matches up with the substrate

    • Forms enzyme-substrate complex

    • Enzyme will either break down or bond molecules

    • Enzymes are very specific – one specific enzyme matches one specific substrate

    http://www.kscience.co.uk/animations/anim_2.htm


    Enzyme specificity
    ENZYME SPECIFICITY

    How do enzymes work?substrate: molecules upon which an enzyme acts. The enzyme is shaped so that it can only lock up with a specific substrate molecule.

    (enzyme)

    substrate -------------> product

    Each enzyme is specific for one and ONLY one substrate

    (one lock - one key)

    active site: part of the enzyme that fits with the substrate

    Note that the active site has a specific fit for this particular substrate and no other.


    Remember each enzyme is specific for one and only one substrate
    REMEMBER:Each enzyme is specific for one and ONLY one substrate

    If the substrate and enzyme are not a match – the reaction will not proceed


    Two enzyme theories
    TWO ENZYME THEORIES

    • LOCK AND KEY THEORY

    INDUCED FIT THEORY


    Naming the enzyme
    Naming the Enzyme

    • The prefix comes from the substrate (the material acted upon)

    • Enzymes end in “ase” (the suffix)

      For example:

      • Maltase (malt/ase) = an enzyme that breaks down ________

      • Lipases (lip/ases) = enzymes that break down ______

      • Proteases (prote/ases) = enzymes that break down ________

    maltose

    lipids

    proteins


    Factors affecting enzyme function
    FACTORS AFFECTING ENZYME FUNCTION:

    • REMEMBER…

    • Enzymes are powerful

    • one enzyme molecule can catalyze thousands of substrate reactions each second

    • enzymes speed up the reaction without raising the temperature of the environment

    • BUT…


    Enzyme reaction vs temperature
    ENZYME REACTION vs TEMPERATURE

    • Enzymes work the best at certain temperatures, usually the temperature of the natural environment

    Enzymes become denatured at high temperatures (the high temp will change the shape of the active site so the enzyme no longer fits)


    Enzyme reaction vs ph
    ENZYME REACTION vs pH

    • Enzymes work the best at a certain pH, usually the pH of the natural environment


    Enzyme reaction vs concentrations
    ENZYME REACTION vs CONCENTRATIONS

    • The rate of an enzyme controlled reaction depends upon theconcentrations of enzymes and substrates


    Coenzymes
    COENZYMES

    SOME ENZYMES NEED SUBSTANCES CALLED COENZYMES IN ORDER TO FUNCTION

    • Coenzymes are organic substances

    • Coenzymes are not proteins

    • Most coenzymes are vitamins

      A COENZYME ALLOWS AN ENZYME TO PERFORM ITS CATALYTIC FUNCTION



    Terms
    TERMS

    • Acids = any compound that produces hydrogen ions (H+)in solution

      HCl = H+ + Cl-

    • Base = any compound that produces hydroxide ion (OH-) in solution

      NaOH = Na+ + OH-


    Terms1
    TERMS

    • Neutralization = when quantities of acids and bases are mixed together and no extra H+ or OH- remain

      HCl + NaOH NaCl + H2O

      (acid) + (base) (salt) + (water)


    Terms2
    TERMS

    • Salts = the ionic compound obtained from the neutralization reaction between and acid and a base

      HCl + NaOH --- Na+ + Cl- + H2O Solid NaCl (salt) found if water is evaporated


    The ph scale
    The pH scale

    H2O --- H+ + OH-

    Neutral pure water, no excess of H+ or OH-

    (not an acid or a base)

    • If the H+ concentration increases, it becomes acidic

    • If the OH- concentration increases, it becomes basic


    The ph scale1
    The pH scale

    pH measures the concentration of H+

    Scale runs 0 - 14

    • if the [H+] > [H2O] = acid

    • if the [H+] < [H2O] = base

      The Scale

    • high [H+] = acids = low pH values = 0 - 6

    • neutral = 7

    • low [H+] = bases = high pH values = 8 – 14


    Indicators
    Indicators

    Indicator:substance that changes color when pH goes above or below a certain value

    • Litmus: Red = acid / Blue = base

    • Methyl orange: red to yellow indicates base

    • Phenolphthalein: colorless to red indicates base

      (compare to indicator paper to read actual pH)


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