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3. CHEMISTRY

MAIN TOPICS OUTLINE

3.1 BASIC CHEMISTRY (inorganic chemistry fundamentals)
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3.11 Matter & Elements
3.12 Atoms, Ions & Isotopes
3.13 Chemical Properties of Elements
3.14 Molecules
3.15 Chemical Reactions
3.16 Chemical Bonds

3.2 WATER CHEMISTRY
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3.21 Importance of Water
3.22 Unique Properties of Water
3.23 Acids & Bases
3.24 Acids Precipitation ("Acid Rain")

3.3 ORGANIC CHEMISTRY
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3.31 Carbon Chemistry
3.32 Carbohydrates
3.33 Lipids
3.34 Proteins
3.35 Nucleic Acids



3.1 BASIC CHEMISTRY


LECTURE OBJECTIVES:
Explain the difference between an element and an atom.
Explain the difference between an atom and an ion.
Name and describe the subatomic particles of an atom, indicating which one accounts for the occurrence of isotopes.
Describe and discuss the energy levels (electron shells) of an atom, including the orbitals of the first two levels.
Draw a simplified atomic structure of any atom with an atomic number up to 20.
Name and describe the most common bonds in biological molecules.
Draw representative atomic structures for ionic and covalent molecules, and distinguish between ionic and covalent bonds.
Define selected key terms.


Key Terms

def. Atom: The smallest part of an element that still acts like that element, that cannot be divided by chemical means. (It can be divided by physical means into subatomic particles.)
def. Chemical bond: A union between the electron of two or more atoms or ions. (Attractions that hold molecules together.)
def. Compound: A substance with more than one element in which the relative proportions never vary.
def. Covalent bond: Bond formed by the sharing of one or more electrons between atoms or group of atoms.
def. Electron: Particle in the orbital around the atomic nucleus that has a negative charge.
def. Element: Matter [substance] consisting of only one type of atom, that cannot be broken down to any other substance.
def. Hydrogen bond: Bond formed by the weak charged attractions when an electropositive hydrogen atom in a polar covalent bond is attracted to a neighboring electronegative atom, and therefore interacts weakly with this neighboring atom.
def. Ion: Electronically charged (unbalanced) atom, or compounds.
def. Ionic bond: Bond formed by the force between ions of opposite charge.
def. Isotope: One of several atomic forms of an element, each containing a different number of neutrons
def. Matter: Anything that has weight (mass) and takes up space (volume).[‰ a substance you potentially can touch]
def. Molecule: Two or more atoms held together by chemical bonds.
def. Naturally occurring element: A substance with only one element in which the relative proportions never vary.
def. Negatively charged ion: An atom or a compound that has gained one or more electrons, hence has acquired an overall negative charge.
def. Neutron: Particle in the atomic nucleus that has no electrical charge
def. Noble gas: Inactive, inert gas that does not participate in chemical reactions.
def. Periodic table: A tabular arrangement of the elements according to their atomic number (= number of protons).
def. Positively charged ion: An atom or a compound that has lost one or more electrons, hence has acquired an overall positive charge.
def. Proton: Particle in the atomic nucleus that has a positive charge.
def. Valence shell: The outermost shell of an atom, the shell that participates in chemical bonds



3.11 Matter & Elements

http://www.webelements.com/webelements/scholar/index.html

• Everything, both living and nonliving things, is made of matter

def. Matter: Anything that has weight (mass) and takes up space (volume).[‰ a substance you potentially can touch]

Matter is made of basic substances called elements.
-- There are 92 naturally occurring chemical elements.
-- About 25 of the natural occurring elements are essential to life.

There are at present 112 recognized (confirmed) chemical elements. They can be organized into different groups in a table, called a periodic table, according to a number called the atomic number. Each element is composed of a specified number of particles called subatomic particles -- protons, neutrons, and electrons, and the elements are numbered according to the number of protons (the atomic number). Elements cannot be broken down to form other substances with different properties (Properties are things like density, solubility, melting point, reactivity). Both the earth's crust (rocks) and organisms are made of chemical elements, but they differ as to which ones are predominant. There are 92 elements found in nature in either a solid, liquid, or gaseous form. Many of the elements that are not found in nature (made artificially in a laboratory or an industrial process) are extremely unstable and decompose within seconds (or microseconds

Four (4) elements account for 96% of chemicals in the human body, and eleven (11) elements accounts for 99.9%.


• Elements in the human body


i. The 4 most important elements in the human body (‰96%).

Symbol Name %
1 O oxygen 65
2 C carbon 18
3 H hydrogen 10
4 N nitrogen 3


ii. An additional 7 elements are also very important (‰3.99%)

5 Ca Calcium 2
6 P Phosphorus 1.1
7 K Potassium 0.35
8 S Sulfur 0.25
9 Na Sodium 0.15
10 Cl Chlorine 0.15
11 Mg Magnesium 0.05


-- These 11 elements make up nearly 100%.

iii. 14 Trace Elements required in very small amounts (< 0.01%)

12 Fe Iron 0.004
13 I Iodine 0.0004



3.12 Atoms, Ions & Isotopes

• The atom is the smallest part of an element.

def. Atom: The smallest part of an element that still acts like that element, that cannot be divided by chemical means. (It can be divided by physical means into subatomic particles.)

Atoms are composed of 3 sub-atomic particles.

NEUTRON -- no charge, 1 AMU (atomic mass unit)
PROTON -- + charge, 1 AMU (atomic mass unit)
ELECTRON -- - charge, negligible weight (much less than an AMU)

http://www.webelements.com/webelements/scholar/index.html

If separated these particles will no longer act like the element they used to form:

e.g., the element hydrogen is an explosive gas, but if split up into subatomic particles, it will no longer be an explosive gas.
This is why the ATOM is considered the smallest part of an ELEMENT -- not these particles.

def. Neutron: Particle in the atomic nucleus that has no electrical charge
def. Proton: Particle in the atomic nucleus that has a positive charge.
def. Electron: Particle in the orbital around the atomic nucleus that has a negative charge.
def. Ion: Electronically charged (unbalanced) atom, or compounds.
def. Negatively charged ion: An atom or a compound that has gained one or more electrons, hence has acquired an overall negative charge.
def. Positively charged ion: An atom or a compound that has lost one or more electrons, hence has acquired an overall positive charge.


Normally an atom is neutral in charge.

When electrons are added to or removed from the atom it becomes positively or negatively charged -- an Ion

-- Protons (+ charge) are balanced with the electrons (- charge)


Example: the elements forming table salt, NaCl, Sodium Chloride
(Sodium Na, and Chlorine Cl)

gained electrons = negative ion Cl- Chlorine
lost electrons = positive ion Na+ Sodium

def. Isotope: One of several atomic forms of an element, each containing a different number of neutrons


Review:
Different # of electrons:
Ion
Different # of neutrons:
Isotope
Different # of protons:
Element


http://www.webelements.com/webelements/scholar/index.html

If you wish to learn more about the periodic table and elements use your Web browser type in the following URL: http://www.webelements.com/webelements/scholar/index.html

(Or click on the link above.)



Dr. Thinkwell ../Thinkwell_f/03_IntrElemAtom_2653_2676.mov












































































3.13 Chemical Properties of Elements

• Atom do usually not exist alone -- the react (bind) to other elements.

-- e.g., H. Naturally occurring hydrogen: H2
Noble gases: Inactive elements, also called inert gases, that does not participate in chemical reactions. do not have room for extra electrons -- they cannot form bonds with other elements, with "filled" outermost shells tend to be non-reactive with other atoms.

-- Helium He, Neon Ne, Argon Ar, Krypton Kr, Xenon Xe, Radon Rn all occur as single atoms.

http://www.webelements.com/webelements/scholar/index.html

Other elements: have one or more unfilled spaces for electrons (orbitals) form bonds with other atoms

-- these elements with atoms with "unfilled" outermost shells tend to be reactive with other atoms, and form molecules held together with chemical bonds.


• Electron behavior influences atoms.

Atoms other than the inert gases may form chemical bonds with other elements. -- They acquire, share or donate electrons -- valence electrons, from their outer shells to another atom.

Elements with different behaviors are placed at different locations in the periodic table.

def. Chemical bond: A union between the electron of two or more atoms or ions. (Attractions that hold molecules together.)


Electrons fill space, orbitals, around the atomic nucleus. An orbital can have two electrons.

Orbitals make up shells around the nucleus of the atom:


-- innermost shell (1 orbital) = 2 electrons
--
all other shells (4 orbitals) = 8 electrons



The most important shell is the Valence Shell, the outermost shell -- the shell that participates in chemical bonds.



Dr. Thinkwell ../Thinkwell_f/03_electrule_2654bio027a_1.mov













































































3.14 Molecules



def. Molecule: Two or more atoms held together by chemical bonds.

• There are two types of molecules


i. Naturally occurring elements

H2 Hydrogen gas (H-H)

O2 Oxygen gas (O-O)

Note: Inert gases are also naturally occurring elements but occur as single atoms.


ii. Compounds

H20 Water (H-O-H)

CO2 Carbon dioxide (O-C-O)

NaCl Sodium Chloride (Table salt)





def. Naturally occurring element: A substance with only one element in which the relative proportions never vary.
def. Compound: A substance with more than one element in which the relative proportions never vary.



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3.15 Chemical Reactions
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• Molecules interact and rearrange their chemical bonds in chemical reactions.

Life depends on these chemical reactions!

Types of chemical reactions:

reactants product(s)

i. Synthesis (put together): A + B -----> AB

-- e.g., sucrose (table sugar) synthesis in plants


ii. Decomposition (break down): AB -----> A + B

-- e.g., digestion of sucrose (table sugar) in the human body



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3.16 Chemical Bonds
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Chemical bond is a union between the electron structures of two or more atoms or ions -- attractions that hold molecules together.




• Ionic Bond


def. Ionic bond: Bond formed by the force between ions of opposite charge.

-- one atom attracts the electrons more than the other atom

one atom gains one or more electrons ‹ positively charged
one atom loses one or more electrons ‹ negatively charged

-- opposite charged ions positive & negative attract each other bond

-- strong bonds in crystal form (salt crystals hard as rock)
-- weak bonds in water (salt crystals dissolve in water)

Dr. Thinkwell ../Thinkwell_f/03_ion_isotope_2655_2678.mov

• Covalent Bond

def. Covalent bond: Bond formed by the sharing of one or more electrons between atoms or group of atoms.

-- both atoms attract the electrons equally

-- always strong bonds
e.g.,
-- water H
2O
-- many organic compounds

i. nonpolar covalent bonds

-- atoms share the electrons equally, e.g., oils.

ii. polar covalent bonds

-- atoms share electrons unequally ‹ slight difference in charge between the two poles of the molecule, e.g., water.



• Hydrogen Bond

def. Hydrogen bond: Bond formed by the weak charged attractions when an electropositive hydrogen atom in a polar covalent bond is attracted to a neighboring electronegative atom, and therefore interacts weakly with this neighboring atom.

-- bond between a slightly positive hydrogen atom & another slightly negative atom in a POLAR COVALENT BOND

-- weak bonds
-- biologically important:

-- properties of water, e.g., surface tension
-- shape and function of proteins: allow the protein molecule to twist and bend
-- shape and function of DNA: strong enough to allow the DNA molecule to twist and weak enough to split
-- chemical signaling of hormones: allow hormones to temporarily attach to other molecules




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3.2 WATER CHEMISTRY
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LECTURE OBJECTIVES:
1. Discuss why water is important.
2. List and describe the unique properties of water that make the molecule indispensable to living systems.
3. Explain the difference between an acid, a base, a salt and a buffer, and recognize that it is important that pH remains within natural limits (explain how these properties are related to hydrogen bonding).
4. List potential damage caused by acid precipitation, and recognize that changes in natural pH impacts natural ecosystems.
5. Define selected key terms.

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Key Terms

def. Acid: A substance having a sour taste that releases H+ ions in water (having the ability to turn litmus red, and the ability to react with bases to form salts).
def. Acid rain: The falling to earth of rain, snow or fog, that is more acidic than pH 5.6, that contains sulfur (S)
and nitrogen (N) oxides. (Also called acid precipitation, or wet acid deposition.)
def. Base: A substance having a bitter taste that releases OH- ions in water (having the ability to turn litmus blue, and the ability to react with acids to form salts).
def. Neutralization: the chemical process when an acid and a base is mixed, forming water and a salt.

def. pH: A measure of how acidic or basic (alkaline) a solution of water is (numerically equal to 7 for neutral solutions).
def. pH scale: A scale used to indicate the strength of an acid or a base (to measure the concentration of hydrogen ions in water solutions)

def. Salt: An inorganic compound formed when an acid reacts with a base.


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3.21 Importance of Water
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Many chemical reactions in living things require water (as a reactant).

Organisms on Earth are made mostly of water:
- adult human 40-60% of body weight
- infant human 75% of body weight

Water is a polar molecule (Oxygen slightly more electronegative than hydrogen)
[
-- forms Hydrogen bonds
[
IMPORTANT PROPERTIES OF WATER



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3.22 Important Properties of Water
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1. Solvent Properties
-- many imp. chemicals in the body dissolved in water -- polar molecules)
-- life on Earth rely on water

2. Temperature Properties

(temperature buffer) Example: continent vs. sea climate

-- because of hydrogen bond water needs to be heated up substantially before its temperature increases measurably
-- below 0°C hydrogen bonds resist breaking -- ICE

3. Cohesion Properties
(water molecules attracted to each other)

-- surface tension

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3.23 Acids and Bases
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def. Acid: A substance having a sour taste that releases H+ ions in water (having the ability to turn litmus red, and the ability to react with bases to form salts).
def. Base: A substance having a bitter taste that releases OH- ions in water (having the ability to turn litmus blue, and the ability to react with acids to form salts).
def. Neutralization: the chemical process when an acid and a base is mixed, forming water and a salt.

def. pH: A measure of how acidic or basic (alkaline) a solution of water is (numerically equal to 7 for neutral solutions).
def. pH scale: A scale used to indicate the strength of an acid or a base (to measure the concentration of hydrogen ions in water solutions)

def. Salt: An inorganic compound formed when an acid reacts with a base.


Acids and bases -- biologically important compounds

-- acids and bases destroy proteins (denature) -- important for living systems

-- acids and bases are corrosive (esp. strong acids and bases) -- environmental implications
-- acid - corrosive, e.g., Hydrochloric acid, HCl
-- base - caustic, e.g.,
Lye, NaOH, Sodium hydroxide

• pH Scale

The degree to which a solution is acidic or basic is measured by a quantity called the
-- pH

-- pH is a number that can be measured

-- Ranges from 0 (acidic) 7 (neutral) 14 (basic)


0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
_______________________________________
HCl H
2O NaOH

Low pH High pH

Tooth enamel dissolves at pH 5.5


pH of some solutions (many are highly variable!)

pH value Solutions

0 HCl
<1 battery acid
1 gastric juice (HCl + enzymes)
2.3 lemon juice
3 carbonated drinks, vinegar (sour wine), some acid rain, orange juice, beer
4 tomato juice, banana, grapes
5 black coffee
5.5 tooth decay start
5.6 normal rain
6
(5 - 7) urine
6.6 milk
6.2 -
7.4 saliva
---
7 pure water
---
7.35 - 7.45 blood
7.8 - 8.3 sea water
9 baking soda
9.5 tums
10 soap
10.5 milk of magnesia
11 Household ammonia
12.5 hair removers
13.5 oven cleaner
14 NaOH "lye"


• Neutralization Reaction

def. Salt: An inorganic compound formed when an acid reacts with a base.

reactants product(s)

A + B -----> C + D

Acid + Base -----> Salt + Water

HCl + NaOH -----> NaCl + H2O

pH 1 pH 14 solid pH 7

-- cannot measure pH in solids


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3.24 Acid Precipitation (Acid Rain)
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def. Acid rain: The falling to earth of rain, snow or fog, that is more acidic than pH 5.6, that contains sulfur (S)
and nitrogen (N) oxides. (Also called acid precipitation, or wet acid deposition.)

pH tolerance of organisms vary
-- normal pH for most organisms is around pH 7
-- acidophiles (lactic acid bacteria, most yeasts, most molds, Thiobacillus, Sulfolobus)
-- alkaliphiles (Vibrio cholerae)

Normal rainwater has few impurities (polluted rainwater may have several)

1. burning of fossil fuels (oil, coal, natural gas)

2. industrial gases, NO, NO2, and SO2, in the atmosphere

3. gases dissolve in rainwater forming acids H2SO4 (sulfuric acid) & HNO2 (nitric acid)

4. rain

5. acid damage foliage

6. acid runoff into lakes and rivers

7. lower pH in lakes and water


Damage caused by acid rain

a. Forest damage
(acidification may eliminate sensitive species)
b. Soil damage
c. Aquatic damage
d. Building damage
e. Visibility damage

Acidification can spread to relatively non-industrialized areas
or industrial areas with good environmental policies.



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3.3 ORGANIC CHEMISTRY
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LECTURE OBJECTIVES:
1. Recognize the difference between inorganic and organic molecules, and understand the importance of four valence electrons in a carbon atom.
2. List the major functional groups found in organic molecules.
3. List and describe the structure and function of the four major groups of organic molecules.
4. List the major groups of molecules within each of the four major groups of organic molecules, and give examples of each.
5. Recognize the importance of structure in organic molecules (e.g., molecular formula vs. structural formulas, importance of functional groups, importance of hydrogen bonds, primary, secondary, tertiary, and quaternary structures of proteins, and helical structure of DNA)
6. Define selected key terms.

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Key Terms

def. ATP (Adenosine triphosphate): The main energy carrying molecule in cells, made from a nucleotide (composed of adenine, 3 phosphate functional groups, and ribose sugar).
def. Amino acid: Small organic molecule with both amino & carboxyl groups; subunit (building block) of proteins.
def. Carbohydrates: Organic compound, a simple sugar or large molecule composed of sugar units, including sugars and starches.
def. Disaccharides: A type of carbohydrate with two sugar units (monosaccharides) covalently bonded (e.g., sucrose, lactose, maltose).
def. DNA (Deoxyribonucleic acid): For all cells the molecule of inheritance.
def. Enzyme: A class of proteins serving as catalysts, chemical agents that speed up chemical reactions without being consumed by the reaction.
def. Fat: A lipid with a glycerol head and three fatty acid tails. Also called a triglyceride.
def. Fossil fuel: Coal, petroleum, and natural gas, nonrenewable source of energy derived from the bodies of partly decomposed prehistoric organisms.
def. Fructose: A very sweet sugar, occurring in many fruits and honey and used as a preservative for foodstuffs and as an intravenous nutrient.

Def. Functional group: A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.
def. Galactose: A monosaccharide found in milk, forms lactose together with glucose.
def. Gene: A unit of information about a heritable trait that passes on from parents to offspring.
def. Glucose: A monosaccharide a digestive breakdown product (together with maltose a disaccharide) of polysaccharides (in part dextrose)
def. Hemoglobin: An iron containing protein in red blood cells.
def. Insulin: Protein hormone that lowers blood glucose levels.
def. Lactose: A disaccharide made from whey (the watery part of milk) and used in pharmaceuticals, infant foods, bakery products, and confections; milksugar (galactos and glucose)
def. Lipids: A greasy or oily compound of mostly carbon an hydrogen that shows little tendency to dissolve in water, including oils, fats, phospholipids, steroids, and waxes.
def. Maltose: A disaccharide a digestive breakdown product (together with glucose a monosaccharide) of polysaccharides; malt sugar.
def. Monosaccharides: The simplest carbohydrate, with only one sugar unit (e.g., glucose, fructose, galactose, ribose, deoxyribose).
def. Nucleic acid: Complex molecules, a long, single- or double-stranded chain of four different kinds of nucleotides, that store and transfer information.
def. Nucleotide: The structural unit (building block) of nucleic acids, and ATP
def. Organic chemistry: The study of carbon compounds (organic compounds).
def. Organic compound: Compound with a carbon backbone (carbon chain) found in "living" things.
def. Peptides: Short organic chains of at least two amino acids.
def. Peptide bond: The covalent bond between two amino acid subunits.
def. Phospholipid: A type of lipid that is the main structural component of cell membranes, a hydrophobic tail of two fatty acids and a hydrophilic head that incorporates glycerol and a phosphate group.
def. Polysaccharides: A type of carbohydrate with many, usually hundreds or thousands of covalently linked sugar units in straight or branched chains (e.g., glycogen, starch, cellulose, chitin).
def. Proteins: Large organic compound composed of one or more chains of amino acids held together with peptide bonds.
def. RNA (Ribonucleic acid): A category of nucleic acids that function in the process by which genetic instructions are used to build proteins.
def. Steroid: (‰ Sterol) A lipids consisting of a carbon backbone (carbon skeleton) of four carbon rings with various functional groups attached.
def. Sucrose: A disaccharide found in many plants, especially sugar cane and sugar beet, and widely used as sweetener, preservative, and in the manufacture of plastics and cellulose; table sugar (two glucose molecules)
def. Wax: A lipids with long hydrophobic fatty acid chains linked to long-chain alcohols or carbon rings.

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3.31 Carbon Chemistry
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In this chapter we will discuss the four macromolecules important for living organisms: Carbohydrates, Lipids, Proteins, and Nucleic Acids. First, however, we need to discuss the carbon atom, which make up the skeleton of all these macromolecules.


• Chemicals can be divided into two groups

1. Inorganic -- chemistry of inorganic molecules
-- molecules with none or at the most one carbon atom (e.g., water, carbon dioxide)

2. Organic -- chemistry of organic molecules
-- molecules containing one, or more carbon atoms (e.g., proteins)

one carbon atom
-- Carbon dioxide, CO
2 (by some inorganic, by some organic)
-- Urea, CO(NH
2)2

many carbon atoms -- bonded with covalent bonds
-- short chains: Simple sugar
e.g., glucose, C6H12O6, C-C-C-C-C-C
-- long chains: Hemoglobin, (C
738H1166FeN203O208S2)4

def. Organic chemistry: The study of carbon compounds (organic compounds).
def. Organic compound: Compound with a carbon backbone (carbon chain) found in "living" things.
def. Fossil fuel: Coal, petroleum, and natural gas, nonrenewable source of energy derived from the bodies of partly decomposed prehistoric organisms.


• The carbon atom is unique

1. Carbon can bind 4 other molecules


2. Carbon can form long chains (the "skeleton" of organic molecules)
C-C-C-C-C-C (C
6H12O6).
This "skeleton" can vary a great deal
-- variation important for living organisms

-- Variations in carbon skeletons:

i. Length
ii. Branching (branched or unbranched)
iii. Bonding (double bonds -- vary in location)
iv. Rings (carbon skeleton arranged in rings)
v. Other elements (bonded to the skeleton) -- FUNCTIONAL GROUPS

Def. Functional group: A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.


3. Carbon source for living organisms

CO2 in the atmosphere

+++ more about this in chapter 5: PHOTOSYNTHESIS



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3.32 Carbohydrates
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def. Carbohydrates: Organic compound, a simple sugar or large molecule composed of sugar units, including sugars and starches.
def. Monosaccharides: The simplest carbohydrate, with only one sugar unit (e.g., glucose, fructose, galactose, ribose, deoxyribose).
def. Fructose: A very sweet monosaccharide, occurring in many fruits and honey and used as a preservative for foodstuffs and as an intravenous nutrient.
def. Galactose: A monosaccharide found in milk, forms lactose together with glucose.
def. Glucose: A monosaccharide a digestive breakdown product (together with maltose a disaccharide) of polysaccharides (in part dextrose)
def. Disaccharides: A type of carbohydrate with two sugar units (monosaccharides) covalently bonded (e.g., sucrose, lactose, maltose).
def. Lactose: A disaccharide made from whey (the watery part of milk) and used in pharmaceuticals, infant foods, bakery products, and confections; milksugar (galactos and glucose)
def. Maltose: A disaccharide a digestive breakdown product (together with glucose a monosaccharide) of polysaccharides; malt sugar.
def. Sucrose: A disaccharide found in many plants, especially sugar cane and sugar beet, and widely used as sweetener, preservative, and in the manufacture of plastics and cellulose; table sugar (two glucose molecules)
def. Polysaccharides: A type of carbohydrate with many, usually hundreds or thousands of covalently linked sugar units in straight or branched chains (e.g., glycogen, starch, cellulose, chitin).


• Functions

a. Source of energy (to keep us alive)
b. Provide structural support (building material)

• Classification

a. Monosaccharides (Simple Sugars)
-- Building blocks: One single carbon chain or ring

Example: 6C -- glucose, fructose, galactose -- HEXOSES

--- same molecular formula, C6H12O6 (different structural formulas)
--- wh. dissolved in water (
as when inside cells) they circle up in a ring form.
GLUCOSE
GALACTOSE
FRUCTOSE



--- building block in RNA, and DNA

RIBOSE --- molecular formula, C5H10O5
DEOXYRIBOSE
--- molecular formula, C5H10O4



b. Disaccharides
-- Building blocks: 2 monosaccharides

Example: sucrose, lactose, and maltose
-- same molecular formula, C
12H22O11

SUCROSE: table sugar (Glucose + Fructose)
LACTOSE: milk sugar (Glucose + Galactose)
MALTOSE: malt sugar (Glucose + Glucose)



c. Polysaccharides
-- Building blocks: many glucose units "linked" (in ring forms).

GLYCOGEN: Animal polysaccharide
--- energy storage (carbohydrate storage molecule in animals)
--- usually in the liver & the muscles

STARCH: Plant polysaccharide (glucose subunits -- same side up)
--- energy storage (carbohydrate storage molecule in plants)
--- usually in roots & seeds

CELLULOSE: Plant polysaccharide
--- structural material (= of plants -- in cell walls) :
--- cannot be digested by most animals
--- fibers (addition to our diet, we cannot digest):

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3.33 Lipids
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def. Lipids: A greasy or oily compound of mostly carbon an hydrogen that shows little tendency to dissolve in water, including oils, fats, phospholipids, steroids, and waxes.
def. Fat: A lipid with a glycerol head and three fatty acid tails. Also called a triglyceride.

def. Phospholipid: A type of lipid that is the main structural component of cell membranes, a hydrophobic tail of two fatty acids and a hydrophilic head that incorporates glycerol and a phosphate group.
def. Steroid: (‰ Sterol) A lipids consisting of a carbon backbone (carbon skeleton) of four carbon rings with various functional groups attached.
def. Wax: A lipids with long hydrophobic fatty acid chains linked to long-chain alcohols or carbon rings.

• Functions

a. can be stored in adipose tissue (= fat tissue)
b. give high amount of energy
c. heat insulator
d. cushion
e. waterproofing (inability to dissolve in water)
f. component in cell membranes
g. vitamin D

• Classification

a. Triglycerides (fats & oils)
--- Building blocks: Glycerol + 3 fatty acids

b. Phospholipids
--- Building blocks: Phosphate group + Glycerol + 2 fatty acids
– major component in cell membranes

c. Steroids
--- Building blocks: 4 carbon rings (but no fatty acids)
– cholesterol (
necessary for prod. of vitamin D – react w. UV light)
– vitamin D
– some hormones – e.g., testosterone

d. Waxes
--- Building blocks: varies
– bee wax, ear wax

Animation

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3.34 Protein
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def. Amino acid: Small organic molecule with both amino & carboxyl groups; subunit (building block) of proteins.
def. Enzyme: A class of proteins serving as catalysts, chemical agents that speed up chemical reactions without being consumed by the reaction.
def. Peptides: Short organic chains of at least two amino acids.
def. Peptide bond: The covalent bond between two amino acid subunits.
def. Proteins: Large organic compound composed of one or more chains of amino acids held together with peptide bonds.


• Amino Acids and Peptide Bonds

BUILDING BLOCKS (structural unit of proteins)
-- held together by PEPTIDE BONDS (a kind of covalent bond)

Peptide Bond: Bond between the COOH group of one AA, & the NH2 group of another AA

AA - AA - AA - AA - AA - AA - AA

DIPEPTIDE
TRIPEPTIDE
POLYPEPTIDE
PROTEIN (> 100 AA)



• Functions
a. speed up chemical reactions (enzymes)
b. deliver signals (hormones)
c. transport agent (blood cells)
d. immunity (antibodies)
e. structural material

• Classification
a. Structural proteins
i. in cell membranes (egg white albumin)
ii. muscle cells fibers ("meat")
iii. in blood cells (e.g. antibodies, hemoglobin)
iv. spider silk
b. Regulatory proteins
i. enzymes (lactase – help digest milk, pepsin – in stomach)
ii. some hormones (insulin)

def. Hemoglobin
def. Insulin
• Levels of protein structure (Protein architecture)

1. PRIMARY STRUCTURE
--- Sequence of Amino Acids

2. SECONDARY STRUCTURE (superimposed on the primary structure)
--- the AA chain is coiled or pleated because of hydrogen bonds

3. TERTIARY STRUCTURE (superimposed on the secondary structure)
--- the coiled or pleated structure is folded
--- held in place by hydrogen bonds (weak)


--- If two or more polypeptide chains

4. QUATERNARY STRUCTURE
--- the single folded chain in many proteins is aggregated with other chains
e.g., Collagen (3 chains twisted), Hemoglobin (4 chains)

• Denaturation

Proteins may lose their unique structure and become biologically inactive, under extreme conditions

-- pH, salt, temperature e.g., egg coagulation


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3.35 Nucleic Acids
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def. Nucleic acid: Complex molecules, a long, single- or double-stranded chain of four different kinds of nucleotides, that store and transfer information.
def. Nucleotide: The structural unit (building block) of nucleic acids, and ATP
def. ATP (Adenosine triphosphate): The main energy carrying molecule in cells, made from a nucleotide (composed of adenine, 3 phosphate functional groups, and ribose sugar).
def. DNA (Deoxyribonucleic acid): For all cells the molecule of inheritance.
def. RNA (Ribonucleic acid): A category of nucleic acids that function in the process by which genetic instructions are used to build proteins.
def. Gene: A unit of information about a heritable trait that passes on from parents to offspring.

• Functions

a. DNA - store information – genetic blueprint, our hereditary material

b. RNA - transfer information from DNA so it can be used

• Classification


a. DNA – Deoxyribonucleic Acid

-- LONG, DOUBLE stranded molecule
-- Building blocks: Nucleotides with the following composition

Deoxyribose
Phosphate group
Nitrogen base (Adenine, Thymine, Guanine, & Cytosine)

b. RNA - Ribonucleic Acid

-- SHORT, SINGLE stranded molecule
-- Building blocks: Nucleotides with the following composition

Ribose
Phosphate group
Nitrogen base (Adenine, Uracil, Guanine, & Cytosine)

• ATP

def. ATP (Adenosine triphosphate): The main energy carrying molecule in cells, made from a nucleotide (composed of adenine, 3 phosphate functional groups, and ribose sugar).

The energy molecule of the body:

Building blocks: (nucleotide derivate)

Ribose
Phosphate groups
Adenine (the nitrogen base)

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