section 2.3 lipids fats/oils/steroids/wax 4 categories of organic molecules molecules of life...
TRANSCRIPT
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Carbon Compounds
Section 2.3
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Lipids
Fats/Oils/Steroids/Wax
4 Categories of Organic Molecules
Molecules of Life
Biochemicals
(CHON)
Proteins
Enzymes/Structure/ Movement/Protection
Nucleic Acids
(DNA/RNA)
Carbohydrates
Glucose/Fructose
Starch/Cellulose
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Carbon Compounds
Organic Compounds
Carbohydrates
Monomer:Monosaccharide
Made up of:Carbon, Hydrogen,
Oxygen (H:O in 2:1 ratio)
Lipids
Monomer: Glycerol and Fatty Acids
Made up of: Carbon, Hydrogen,
Oxygen(H:O not in 2:1 ratio)
Proteins
Monomer: Amino Acid
Made up of: Carbon, Hydrogen, Oxygen, Nitrogen
Nucleic Acids
Monomer: Nucleotide
1) 5 Carbon sugar, 2) phosphate group 3)nitrogenous base
Made up of: Carbon, Hydrogen,
Oxygen, Nitrogen and Phosphorus
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Organic Compounds All compounds are either
ORGANIC, containing carbon bonded to hydrogen and oxygen, or INORGANIC.
The chemistry of carbon is the chemistry of life.
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Organic Compounds >11 million compounds Contain a C-C or C-H bond in combination with
N, O, S, P or halogens Simplest = CH4
Most complex = DNA
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Organic CompoundsAllotropes of carbon
Allotropes: Different forms of an element in same physical state
Catenation: ability of an element to form chains and/or rings of covalently bonded atoms
Carbon has high bond energiesC-C 346 kJ/molC-H 418 kJ/mol
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Diamond tetrahedral array of C
atoms o sp3 hybridized
high mp (>3500°C) hardest material known
to man brittle most dense (3.5x that of
H2O) Industrial uses: cutting,
drilling, grinding
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Graphite layers of hexagonal
arrays of C atoms o sp2 hybridized (planar)
high mp no covalent bonds
between layers – C atoms too far apart from each other (London Dispersion forces)
layers slip past one another
lubricant and pencil “lead”
Graphite fibers (stronger and less dense than steel)- sporting goods and aircraft
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Soot amorphous form of carbon (no structure)
impure carbon particles resulting from incomplete combustion
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Carbon Bonding: How many protons does carbon have?
Electrons? Carbon has FOUR valence electrons
o Needs eight electrons to be stable Carbon readily forms four covalent bonds
with other atoms, including carbon
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Carbon Bonding Carbon can form straight chains, branched
chains, or ringso Leading to a great variety of organic
compounds
Isomers
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Arrangement of Atoms
Isomers – compounds that have the same molecular formula but different structures
More C atoms in formula, more isomerso 18 isomers for C8H18
o 35 isomers for C9H20
o 75 isomers for C10H22
Isomers of C6H14
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Ex #1) Butane, C4H10
Ex #2) Butene, C4H8
Ex #3) 2-Butene, C4H8
Ex #4) methyl propene, C4H8
ISO
ME
RS
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Structural Formula Indicates the number and types of
atoms present in a molecule and also shows the bonding arrangement of the atoms
One possible isomer of C4H10
Does not show 3D shape
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Structural Isomers Isomers in which the atoms are bonded
together in different orders. C4H10 (note continuous chain of C atoms)
butane
methylpropane
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Physical Properties of Structural Isomers
Melting Point (°C)
Boiling Point (°C)
Density at 20°C
Butane
-138.4 -0.5 0.5788
Methylpropane
-159.4 -11.633 0.549
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Hydrocarbons Only have carbon and hydrogen Simplest organic compounds From petroleum (crude oil)
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Carbon Bonding
Single Bond Sharing 2 electrons A single line
Double Bond Sharing 4 electrons Two parallel lines
Triple Bond Sharing 6 electrons Three parallel lines
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Naming Carbon Compounds
Organic PREFIXES Indicates the number of carbon atoms in the
hydrocarbon chain Hydrocarbon: any organic compound that
contains only the elements, hydrogen and carbon
# of C prefix # of C prefix1 Meth- 6 Hex-
2 Eth- 7 Hept-
3 Prop- 8 Oct-
4 But- 9 Non-
5 Pent- 10 Dec-
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Organic PREFIXES Prefixes for alkanes that have 1-4
carbons are rooted historically. o These are methane, ethane, propane,
and butane, respectively. o An easy way to remember the first four
names is the anagram Mary Eats Peanut Butter (methane, ethane, propane, butane)
Prefixes for 5 carbons and up are derived from the Greek language.
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Naming Carbon Compounds
Series EndingFormula determines the
# H atoms
Type of Bond(s)
Alkane -ane CnH2n+2 Single
Alkene -ene CnH2n Double
Alkyne -yne CnH2n-2 Triple
Organic SUFFIXES Indicates the types of covalent bonds that
are present in the hydrocarbon chaino Identifies the series to which it belongs
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Aliphatic Hydrocarbons- hydrocarbons without aromatic
ringsSaturated
Hydrocarbons: compounds that contain all SINGLE bonds
Alkanes: each carbon is bonded to 4 atoms– Only contain single
bonds– Skeleton: C-C Molecular formula:
CnH2n+2
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Unsaturated Hydrocarbons
Compounds that contain at least one double bond or triple bond
1. Alkenes: compounds that contain a double bond
• Skeleton: C=C
• Molecular formula = CnH2n
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Unsaturated Hydrocarbons
2. Alkynes: compounds that contain a triple bond
– Skeleton: CC– Molecular formula = CnH2n-2
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Naming Alkanes To give an alkane a name, a
prefix indicating the number of carbons in the molecule is added to the suffix aneo identifies both the kind of
molecule (an alkane) and how many carbons the molecule has (the prefix).
The name pentane tells you that the molecule is an alkane (-ane ending) and that it has 5 carbons (pent- indicates 5)
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Naming Alkenes1. Locate the carbon atoms in the longest carbon chain
that contains the double bond. Use the stem with the ending –ene.
2. Number the carbon atoms of this chain sequentially, beginning at the end nearer the double bond. If the parent chain has more than 3 carbons, insert the number describing the position of the double bond (indicated by its 1st carbon location) before the base name.
1-butene 2-butene
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http://wps.prenhall.com/wps/media/objects/476/488316/index.html
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Naming Alkynes Named just like the alkenes except the suffix –
yne is added
1-butyne
2-butyne
ethyne
propyne
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Write the names of the organic compounds
methane
propyne
1-pentene
2-pentene
nonane
3-hexene
2-butyne
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Give the structural formulas for the organic compounds
1. ethene2. heptane3. 3-
decyne4. butane5. 2-
octene
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Functional Groups An atom or group of atoms,
that replaces hydrogen in an organic compound and that defines the structure of a family of compounds and determines the properties of the family.
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Female lion
Estradiol(estrogen)
HO
OH
OH
OTestosterone
Male lion
Hydroxyl
Carbonyl(middle)
Carboxyl
Lactic Acid
{
Amino
Urea
Wohler1828
FUNCTIONAL GROUP - a cluster of atoms that influence the properties of the molecules that they compose, and determine the characteristics of the compound.
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Hydroxyl Group
Structure
Compound Name Alcohols
Properties
Polar, attracts water (good
solvent)
Naming -ol
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Carbonyl Group
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Carbonyl (end):
Structure
Compound Name Aldehydes
Properties
Structural isomers with
different properties
Naming -al
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Carbonyl (middle):
Structure
Compound Name Ketones
Properties
Structural isomers with
different properties
Naming -one
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Carboxyl Group
Structure
Compound Name
Carboxylic acid
(organic acids)
Properties
Acidic properties
Naming -oic acid
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Amino Group
Structure
Compound Name Amines
Properties
Basic properties
Naming -amine
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Phosphate Group
Structure
Compound Name Phosphates
Properties
Makes the molecule and
anionTransfer energy
DNA
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Methyl Group
Structure
Compound Name
Methylated compounds
Properties
May affect gene expression
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Sulfhydryl Group
Structure
Compound Name Thiols
Properties
Stabilize proteins
Some can have a stinky odor –
skunk, rotten eggs, garlic
Naming -thiol
Methanethiol - It is a colorless gas with a distinctive putrid smell. It is a natural substance found in the blood and brain of humans and other animals as well as plant tissues. It occurs naturally in certain foods, such as some nuts and cheese. It is also one of the main compounds responsible for bad breath and the smell of flatus.
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Large Carbon Molecules: In many carbon compounds, the molecules are built
up from smaller, simpler molecules known as MONOMERS.
Monomers can bind to one another to form complex molecules known as POLYMERS. o Large polymers are also called MACROMOLECULES o The process of reacting monomer molecules together in a
chemical reaction to form polymer chains or three-dimensional networks - POLYMERIZATION
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Biological Reactions WATER is the most important
inorganic compound in the body and it participates in two biological reactions:o Hydrolysis o Dehydration Synthesis
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Hydrolysis Breaking down polymers by adding a
water molecule.
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Hydrolysis Breaking down polymers by adding a
water molecule.C12H22O11 + H2O C6H12O6 +
C6H12O6
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HydrolysisPolymers are broken down to monomers
Animation: Hydrolysis of sucrose
H
H2O
OH
H OH
OH H
Hydrolysis
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Dehydration Synthesis Build up large molecules by releasing a
molecule of water.
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Dehydration Synthesis Build up large molecules by releasing a
molecule of water.
C6H12O6 + C6H12O6 C12H22O11 + H2O
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Dehydration Synthesiso Cells make most of their large molecules by
joining smaller organic molecules into chains called polymers
o Cells link monomers to form polymers H
OH H
OH
H OH
Unlinked monomer
Dehydration reaction
Longer polymer
Short polymer
OH H
H OH
Unlinked monomer
Dehydration reaction
Short polymer
H2O
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Energy Currency: Energy necessary for processes is available in the
form of certain compounds that contain a large amount of energy in their overall structure.
One of these is adenosine triphosphate or ATP
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Energy Currency: ATP has three linked phosphate groups ( PO4
-2) attached to one another by covalent bonds.
The bond holding the last one is easily broken and when broken much more energy is released then was required to make the bond.
This conversion of energy is used by cells to drive chemical reactions that enable organisms to function.
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Molecules of Life The four main classes of organic
compounds essential to all living things are made from CARBON, HYDROGEN, and OXYGEN atoms, but in different ratios giving them different properties.
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Carbohydrates: Made of carbon, hydrogen, and oxygen
with H to O in a 2:1 ratio Monosaccharides are a single sugar -
MONOMER Source of energy Can be in straight or ring form -ose ending for sugars Glucose (C6H12O6) Ribose (C5H10O5)
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Carbohydrates: Glucose, galactose, and fructose all have the same
molecular formula but differ in the arrangement of atoms = ISOMERS
General formula for the monomer = (CH2O)n
o Molecular formula = C6H12O6 (hexoses)
C5H10O5 (pentoses)
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Carbohydrates:Type of Sugar
Name of Sugar Description of Sugar
Pentose ribose Found in RNA
Pentose deoxyribose Found in DNA
Hexose glucose In blood; cell’s main energy source (ATP)
Hexose fructose In fruit; sweetest of monomers (honey)
Hexose galactose In milk
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Carbohydrates Disaccharides are double sugars Two monosaccharides condense to form
disaccharideso Formed by dehydration synthesiso Molecular formula = C12H22O11
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Carbohydrates: Bond that joins monosaccharides
(carbohydrates) = glycosidic bond
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Carbohydrates
A disaccharide is produced by joining 2 monosaccharide (single sugar) units.
In this animation, 2 glucose molecules are combined using a condensation reaction, with the removal of water.
Glucose molecules joining to form a disaccharideCondensation of Monosaccharides
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Enzyme Catalytic Cycle
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Common Disaccharides
Name of Disaccharide
2 single sugars that join to form the
disaccharideDescription of Sugar
Sucrose Glucose + Fructose
Table Sugar; transportable energy (sugar beets, sugar
cane)
LactoseGlucose + Galactose
In milk of mammals; provides energy for
suckling animals
Maltose Glucose + GlucoseIn malt (grains)
From starches (cereal, pasta, potatoes)
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Carbohydrates Polysaccharides many sugars: General formula – (C6H10O5)n plus H2O (n = #
monomers) Formed by dehydration synthesis Long chains of glucose molecules
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Carbohydrates:Name of
Polysaccharide
Description of Sugar
Glycogen(animal starch)
• Animal polysaccharide - stores excess sugar
• Stored in liver and muscles • Muscle contraction & movement
• Broken down into glucose and released into blood for quick energy
Starch• Plant polysaccharide• Stores excess sugar
Cellulose
• Gives plants strength and rigidity• Major component of wood and paper
• Component of cell wall
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o Starch and glycogen are polysaccharides• That store sugar for later use
o Cellulose is a polysaccharide found in plant cell walls – provides structure
Starch granules in potato tuber cells
Glycogen granules in muscle tissue
Cellulose fibrils in a plant cell wall
Glucose monomer
Cellulose molecules
STARCH
GLYCOGEN
CELLULOSE
O O
OOOOOO
O O O
O
OO
OO
OO
OOOO
OO
OOO
OO
OOOO O
OOOOOO
OOOOOO
O
OH
OH
Figure 3.7
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Lipids: Fats, Oils, and Waxes
Elements – carbon, hydrogen, and oxygen (NOT a 2:1 H:O ratio)
Do not dissolve in water Lipids contain a large number of C-H bonds which store
more energy than C-O bonds in carbohydrates Monomers: glycerol and fatty acid
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Lipids Fatty Acids:
o Fatty acids are unbranched C-chains (12-28 C) with a carboxyl group (acid) at one end
• The carboxyl end is POLAR and attracted to water – HYDROPHILIC
• The hydrocarbon end is NONPOLAR and does not interact with water – HYDROPHOBIC
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Fatty Acid
General Structure
Saturated (single bonds)
Unsaturated (double bonds)
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Functions of Lipids in living organisms
Lipids can be used to store energy – long term E storage Lipids are important parts of biological membranes Lipids are waterproof coverings – nonpolar Heat insulation and protection around internal organs Steroids and hormones are lipids that send messages to
cells (eg. estrogen, progesterone, testosterone) o anabolic steroids - synthetic
Cholesterol, an important steroid, is an important component of the animal cell wall
Steroid – 4 fused rings
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Wax Long fatty acid chain joined to an
alcohol chain Highly waterproof
o Plant parts (leaves, fruit) form a protective coating on the outer surface (reduce transpiration)
In animals ear wax
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Look at the structures of the fatty acids and explain the differences between saturated, unsaturated and polyunsaturated fats.
Lipids
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Saturated & Unsaturated Fatty Acids
Saturated Fatty Acids
• Carbon atoms with 4 atoms covalently bonded
• All single bonds
• High melting points• Solid @ room temperature• Ex.) animal fat, shortening
Unsaturated Fatty Acids
• Carbon not bonded to the maximum # of atoms
• There are double bond(s)• polyunsaturated
• Liquid @ room temperature• Primarily in plants• Energy storage in animals
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Saturated vs. Unsaturated Fatty Acids
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Trans fats A diet rich in saturated fats
may contribute to cardiovascular disease through plaque deposits
Hydrogenation – process of converting unsaturated fats to saturated fats by adding hydrogen
Hydrogenating vegetable oils also creates unsaturated fats with trans double bondso These trans fats may
contribute more than saturated fats to cardiovascular disease
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Lipids Lipids (fats, oils, and waxes) are formed by a
glycerol molecule bonding to fatty acid(s) o formed by dehydration synthesis
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Dehydration Synthesis
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Ester Linkage
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Triglycerides
Three fatty acids attached to glycerol
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Formation of a Triglyceride
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Phospholipids Two fatty acids joined to a glycerol Makes up cell membrane - PHOSPHOLIPID BILAYER
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Phospholipid
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Proteins Elements: Carbon, Hydrogen, Oxygen, Nitrogen Monomer: AMINO ACID (20 different kinds) Each amino acid has a central carbon atom bonded
to 4 other atoms or functional groups
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20 Amino Acids
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Essential and Nonessential Amino Acids
Essential Amino Acids: Cannot be synthesized in the animal body and should be obtained from diet
Nonessential Amino Acids: Can be synthesized in the animal bodyo Some may be conditionally essential in newborns or during
illness
o Amino acids absorbed from food are used to synthesize structural proteins, functional proteins, protein hormones, carrier proteins, and proteins essential for growth, development and tissue repair.
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Proteins Bond that joins amino acids (protein) = PEPTIDE
BOND
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Formation of a peptide bond
amino acid 1 amino acid 2 dipeptide water
Peptide bond
Formation of a peptide bond
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Functions of Proteins1. Structural component of cell2. Transport substances into or out of cells3. Regulate cell processes4. Control the rate of reactions - enzymes5. Skin, hair, muscles, parts of skeleton (structural
proteins – collagen and elastin in tissue)6. Help to fight disease – antibodies7. Hemoglobin – transport O2
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Types of Proteins:Type Example(s) Description
EnzymesLigasePepsinLactase
Speed up reactions (catalyst)Have a specificity for one
substance
Antibodies(Immunoglobulin
s)
IgMIgAIgGIgD
Highly specificBind to foreign antigens
First line of defense against disease-causing organisms
HormonesInsulin
ThyroxinEpinephrine
Produced at one site – function at another
Small amount to bring about a response
Structural Proteins
KeratinCollagen
Actin & MyosinBuild body and cell parts
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Structural Proteins:
Structural Protein
Description/Function
Tubulin Found in microtubules – cell skeleton
Actin & Myosin In muscle for contraction
Keratin In hair and nails
Collagen Elasticity of skin
Histones Proteins in chromosomes for support
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ProteinsProtein Structure: Proteins can only function properly if they have the proper shape
Levels of Protein Structure: Primary Structure: the sequence of amino
acids. Secondary Structure: the folding or
coiling of the polypeptide chain. Tertiary Structure: the complete 3D
arrangement of polypeptide chain. Quaternary Structure: the arrangement of
the different polypeptide in a protein.
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GrooveGroove
A protein’s specific shape determines its function
o A protein consists of one or more polypeptide chains folded into a unique shape that determines the protein’s function
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Protein Structure (Conformation):
Primary StructureThe way the amino acids are lined upDictated by your genes
Secondary Structure
Alpha Helix - coil/spiralBeta Pleated - formed due to hydrogen bonding between functional groups
Tertiary StructureDetermines protein’s function – Active ConformationBonds between R groups: Ionic, Hydrogen, Hydrophobic, Disulfide
Quaternary Structure
Only get this if there is more than 1 polypeptide chainEx.) Collagen (makes skin elastic) – 3 chains; Hemoglobin 2 & 2
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Protein Structure
(Conformation)
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Primary Structure Levels of Protein Structure
Primary structure GlyThrGlyGlu
SerLysCys
ProLeuMet
ValLys
ValLeuAspAlaValArgGlySer
Pro
AlaIle
AsnValAla
ValHisVal
Amino acids
PheArg
Secondary structure
CN
O CC
N HO C
C
H
Hydrogenbond
O CN H
CCONH
O C
CN H
CNO C
CN H
O CC
N HCO
C
H
N HCO
H C RHN
Alpha helix
C NH
C CHHO
NR CC
ONH
OC CN
H
CCO
NH
OC CN
H
CO
C NH
OC C N
H
CO
OC
CNH
CCO
NH
C CO
NH
CCO
NH
C CO
NH
CCO
NH
C CO
NH
CCO
HN
C
Pleated sheet
Amino acids
Secondary structure
Tertiary structure
Polypeptide(single subunitof transthyretin)
Tertiary Structure
Quaternary structure
Transthyretin, withfour identical
polypeptide subunits
Quaternary Structure
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Protein Structure (Conformation):
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Enzymes and Substrates:
Enzyme + Substrate = ES complex EP complex = Enzyme + product(s)
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Enzyme Catalytic Cycle
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Got Lactase?o Many people in the world suffer from lactose
intolerance• Lacking an enzyme (lactase) that
digests lactose, a sugar found in milk• “ase” = enzyme• “ose” = sugar
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Each enzyme is the specific helper to a specific reaction
o each enzyme needs to be the right shape for the jobo enzymes are named for the reaction
they help• sucrase breaks down sucrose• proteases breakdown proteins• lipases breakdown lipids• DNA polymerase builds DNA• Catalase breaks down hydrogen peroxide
Enzymes
Enzymes - a fun intro (4:46)
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Most enzymes work the best at certain pH and temperature.
Denaturation: a change in the shape of the enzyme.o Cause the enzyme to ineffective because the active site
and the substrate no longer fit together.o Changes in pH and increases in temperature can denature
enzymes.
Regulation of Enzyme Activity
Animation
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Denaturing Proteins Protein that has lost its active conformation, or
shape Denaturing caused by:
o Temperatureo Solute (salt) Concentrationo pH
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Enzyme concentration
amount of enzyme
reacti
on
rate
http://www.kscience.co.uk/animations/anim_2.htm
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Substrate concentration
amount of substrate
reacti
on
rate
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37°Ctemperature
reacti
on
rate
Temperature
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Temperature on Enzymes
Temperature effect on rates of enzyme activityo Optimum temperature
• greatest number of collisions between enzyme & substrate
• human enzymes = 35°- 40°C (body temp = 37°C)
o Raise temperature• denature protein = unfold = lose shape
o Lower temperature • molecules move slower • decrease collisions
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7pH
reacti
on
rate
20 1 3 4 5 6 8 9 10
stomachpepsin
intestinestrypsin
11 12 13 14
pH levels
Pepsin breaks down proteins in stomach
Trypsin is produced in the pancreas and breaks down proteins in the small intestine
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pH effects on rates of enzyme activity
o pH changes protein shapeo most human enzymes = pH 6-8
• depends on where in body• pepsin (stomach) = pH 3• trypsin (small intestines) = pH 8
Some enzymes can be turned on and off by regulator molecules that bind to the enzyme causing the active site to change shape.
Enzyme function and inhibition (1:07)
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Nucleic Acids Large, complex organic compounds that store
information in cells, using a system of four compounds to store hereditary information, arranged in a certain order as a code for genetic instructions of the cell.
Elements: Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus Monomer: Nucleotide1. Phosphate group (Phosphoric Acid)2. 5-carbon (pentose) sugar (Deoxyribose or Ribose)3. Nitrogenous Base
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Polymer: polynucleotide Polynucleotides are formed when the
phosphate group of one nucleotide binds to the sugar of another nucleotide.
Function: Provides instructions to the cell on how to
make proteins - Dictates the amino acid sequence which controls protein synthesis
Stores and transmits genetic information - allows genetic information to be passed on from one generation to the next.
Specificity determined by the fact that only certain bases bond with each othero Said to be complementary
• A –T• C-G
Nucleic Acids
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Nitrogenous Bases There are FOUR Nitrogen bases
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Purines - 2 ring base• Adenine (A)• Guanine (G)
Pyrimidines - 1 ring base• Cytosine (C)• Thymine (DNA) (T), Uracil (RNA) (U)
Nitrogen Bases
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Nucleic Acids Nucleotides combine, in DNA to form a double
helix, and in RNA a single helix The sides of the ladder are made up of the phosphate group and the sugar and the rungs of the ladder are nitrogen bases Examples of Nucleic Acids:
1. Deoxyribonucleic Acid (DNA)
2. Ribonucleic Acid (RNA)
Nucleic Acids and Dehydration Synthesis
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Type of Bond Bond Between……
phosphodiester phosphate group and sugar
N-glycosidic sugar (glycosidic) and nitrogen base
hydrogen nitrogen bases
Nucleic Acids:
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Dictate the amino acid sequence – controls protein synthesis
Stores and transmits genetic information Specificity determined by the fact that only certain
bases bond with each othero Said to be complementary
• A –T• C-G
Functions of Nucleic Acids:
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Making a Polymer
The glue contains long strands of molecules like spaghetti.
If the long molecules slide past each other easily, then the substance acts like a liquid because the molecules flow.
If the molecules stick together at a few places along the strand, then the substance behaves like a rubbery.
Borax is the compound that is responsible for hooking the glue’s molecules together to form the putty-like material
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Making a Polymer
1. Measure 20 ml of solution a into a small beaker
2. Use a graduated cylinder to measure 10 ml of solution B, add it to the beaker.
• Add food coloring if you want
3. Stir with a glass rod and knead with fingers
4. Put it into a plastic cup and cap. Label with your name and pick up at the end of the day