lecture – 2 cont. functional groups. outline water structure - review important properties #4...
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Water Structure - Review Important properties
#4 Solvent properties Carbon
Structure Important properties Functional Groups
#4 – Solvent Properties
Water can disassociate into hydronium and hydroxide ions
2 H2O Hydroxideion (OH)
Hydroniumion (H3O
+)
+
#4 Solvent Properties: Acids & Bases
The dissociation of water molecules has a great effect on organisms
Changes in concentrations of H+ and OH– can drastically affect the chemistry of a cell
#4 Solvent Properties: Acids & Bases
Acid – donates a proton Increases the number of Hydronium Ions in
an aqueous solution Base –
Accepts a proton Reduces the number of Hydronium Ions in
an aqueous solution
#4 – Solvent Properties: The pH scale
pH is a measure of the relative concentration of protons. 0 < pH < 7 is an Acid ([H30+] > 10-7M) 7 < pH < 14 is a Base ([H30+] < 10-7M) pH 7 is neutral ([H30+] = [OH-] = 10-7M)
Figure 3.10pH Scale
Battery acid
Gastric juice, lemon juice
Vinegar, wine,cola
BeerTomato juice
Black coffee
Rainwater
Urine
SalivaPure waterHuman blood, tears
Seawater
Inside of small intestine
Milk of magnesia
Household ammonia
Householdbleach
Oven cleaner
Basicsolution
Neutralsolution
Acidicsolution
0
1
2
3
4
5
6
7
8
9
10
Neutral
[H+] = [OH]In
cre
asin
gly
Basic
[H+]
< [
OH
]
Incre
asin
gly
Acid
ic
[H+]
> [
OH
]
H+ H+
H+
H+H+
H+
H+
H+
OH
OH
H+
OH
H+
OH
OH
OHOH
H+H+
H+
H+
OHOH
OH
OH OHOH
OHH+
11
12
13
14
#4 – Solvent Properties: Buffers
Buffers are substances that minimize changes in concentrations of H+ and OH– in a solution. They resist a change in pH when a small
amount of acid or base is added to a solution.
Most buffers consist of an acid-base pair that reversibly combines with H+
Buffers work within a specific pH range.
#4 – Solvent Properties: Buffers Carbonic Acid – contributes to pH
stability in blood and other biological solutions.
H2CO3 is formed when CO2 reacts with water.
Carbon
The backbone of life Living organisms consist
mostly of carbon-based compounds.
Really good at forming large, complex, and diverse molecules.
Proteins, DNA, carbohydrates, and other molecules - all composed of carbon compounds.
Carbon
Electron configuration determines the kinds and number of bonds an atom will form with other atoms
Four valence electrons – Four covalent
Allows for the formation of large, complex molecules
Figure 4.3
Name andComment
MolecularFormula
(a) Methane
(b) Ethane
CH4
Ball-and-Stick Model
Space-FillingModel
(c) Ethene (ethylene)
C2H6
C2H4
StructuralFormula
Carbon bonds determine molecular shape
Diversity of carbon molecules Carbon chains form the skeletons of most organic
molecules Carbon chains vary in length and shapeFigure 4.5
(a) Length
Ethane 1-Butene
(c) Double bond position
2-ButenePropane
(b) Branching (d) Presence of rings
Butane 2-Methylpropane(isobutane)
Cyclohexane Benzene
Valence Electrons
The electron configuration of carbon gives it covalent compatibility with many different elements
The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules
Figure 4.4
Hydrogen(valence 1)
Oxygen(valence 2)
Nitrogen(valence 3)
Carbon(valence 4)
Isomers
Compounds with the same molecular formula but different structures and properties
Structural isomers have different covalent arrangements of their atoms (constitutional)
Cis-trans isomers have the same covalent bonds but differ in spatial arrangements
Enantiomers are isomers that are mirror images of each other (they are chiral)
Isomers – Three typesFigure 4.7 (a) Structural isomers
(b) Cis-trans isomers
(c) Enantiomers
cis isomer: The two Xsare on the same side.
trans isomer: The two Xsare on opposite sides.
CO2HCO2H
CH3
H NH2
L isomer
NH2
CH3
H
D isomer
Isomers - EnatomersFigure 4.8
Drug
Ibuprofen
Albuterol
Condition EffectiveEnantiomer
IneffectiveEnantiomer
Pain;inflammation
Asthma
S-Ibuprofen R-Ibuprofen
R-Albuterol S-Albuterol
http://www.youtube.com/watch?v=L5QbBYj_zVs
Functional Groups
The components of organic molecules that are most commonly involved in chemical reactions
The number and arrangement of functional groups give each molecule its unique properties
The importance of functional groups
CH3
OH
HO
O
CH3
CH3
OH
Estradiol
Testosterone
Female lion
Male lion
Figure 4.9a
STRUCTURE
EXAMPLE
Alcohols(Their specificnames usuallyend in -ol.)
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
(may be written HO—)
Ethanol
• Is polar as a resultof the electronsspending moretime near theelectronegativeoxygen atom.
• Can form hydrogenbonds with watermolecules, helpingdissolve organiccompounds suchas sugars.
Hydroxyl
Figure 4.9b
Carbonyl
STRUCTURE
EXAMPLE
Ketones if the carbonylgroup is within acarbon skeleton
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Aldehydes if the carbonylgroup is at the end of thecarbon skeleton
• A ketone and analdehyde may bestructural isomerswith different properties,as is the case foracetone and propanal.
Acetone
Propanal
• Ketone and aldehydegroups are also foundin sugars, giving riseto two major groupsof sugars: ketoses(containing ketonegroups) and aldoses(containing aldehydegroups).
Carboxyl
STRUCTURE
EXAMPLE
Carboxylic acids, or organicacids
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Acetic acid
Polar; can form H-bonds
Weak acids; reversible dissociation in H2O
• Found in cells in the ionizedform with a charge of 1– andcalled a carboxylate ion.
Nonionized Ionized
Figure 4.9c
Amino
Amines
Glycine
STRUCTURE
EXAMPLE • Acts as a base; canpick up an H+ from thesurrounding solution(water, in livingorganisms):
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
• Found in cells in theionized form with acharge of 1.
Nonionized Ionized
Figure 4.9d
Sulfhydryl
Thiols
(may bewritten HS—)
STRUCTURE
EXAMPLE • Two sulfhydryl groups canreact, forming a covalentbond. This “cross-linking”helps stabilize proteinstructure.
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
• Cross-linking of cysteinesin hair proteins maintainsthe curliness or straightnessof hair. Straight hair can be“permanently” curled byshaping it around curlersand then breaking andre-forming the cross-linkingbonds.
Cysteine
Figure 4.9e
Figure 4.9f
Phosphate
STRUCTURE
EXAMPLE
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Organic phosphates
Glycerol phosphate
• Contributes negativecharge to the moleculeof which it is a part(2– when at the end ofa molecule, as at left;1– when locatedinternally in a chain ofphosphates).
• Molecules containingphosphate groups havethe potential to reactwith water, releasingenergy.
Figure 4.9g
Methyl
STRUCTURE
EXAMPLE
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Methylated compounds
5-Methyl cytidine
• Addition of a methyl groupto DNA, or to moleculesbound to DNA, affects theexpression of genes.
• Arrangement of methylgroups in male and femalesex hormones affects theirshape and function.
Outline
Monomers & Polymers Four basic classes of biological
macromolecules Carbohydrates Lipids Proteins Nucleic Acids
Form follows function
Polymers
Polymer is a large molecule build from similar building blocks Legos!
Building blocks are monomers Carbohydrates, Proteins, Nucleic acids
are polymers
Polymer Synthesis
Usually, monomers are joined via a dehydration reaction.
Broken apart via hydrolysis.
Polymer Diversity
Thousands of different macromolecules
They vary Cell to cell Individuals Species…
Can build an immense variety of polymers with a small set of monomers legos
#1 Carbohydrates
Fuel & building blocks Monosaccharides
Single sugars One carbon ring
Polysaccharides Polymers built from many sugar building
blocks
#1 Carbohydrates: Simple Sugars
General Characteristics of Sugars Generally have some multiple of CH2O Have a carbonyl group (C=O) Multiple hydroxyl groups (-OH) Aldoses & Ketoses Trioses (C3H6O3), Pentoses (C5H10O5) &
Hexoses (C6H12O6)
(Fischer Projections)
Glyceraldehyde
Ribose
Glucose
#1 Carbohydrates: Simple Sugars
Aldoses vs. Ketoses Aldoses – Carbonyl group at the end of carbon
skeleton (aldehyde sugar) Ketoses – Carbonyl group within the carbon skeleton
(ketones)
Figure 5.3a
Aldose (Aldehyde Sugar)Ketose (Ketone Sugar)
Glyceraldehyde
Trioses: 3-carbon sugars (C3H6O3)
Dihydroxyacetone
#1 Carbohydrates: Simple Sugars
Most sugars exist as ring structures.Figure 5.4
(a) Linear and ring forms
(b) Abbreviated ring structure
12
3
4
5
6
6
5
4
32
1 1
23
4
5
6
123
456
Glucose
#1 Carbohydrates: Disaccharide
2 monosaccarides joined by a glycosidic linkageFigure 5.5
(a) Dehydration reaction in the synthesis of maltose
(b) Dehydration reaction in the synthesis of sucrose
Glucose Glucose
Glucose
Maltose
Fructose Sucrose
1–4glycosidic
linkage
1–2glycosidic
linkage
1 4
1 2
(important for making beer)
(Table sugar)
#1 Carbohydrates: Polysaccarides
Hundreds to 1000s of monosaccarides held together via glycosidic linkages.
#1 Carbohydrates: Polysaccarides
Storage and structural roles Storage - Carbohydrate “bank” - stored
sugars can later by released by hydrolysis for use in metabolism.
Structure – Strong structural components are built from polysaccharides.
Structure and function are determined by its sugar monomers and the positions of glycosidic linkages
#1 Carbohydrates: Polysaccarides; Storage - Starch
Starch – Plants version of storage polysaccharides Consists entirely of glucose monomers Plants store surplus starch as granules within
chloroplasts and other plastids
Most starches are built from 1-4 linkages – more complex starches can be linked differently
amylose
#1 Carbohydrates: Polysaccarides; Storage - Starch
Starches are stored in plasteds Animals have enzymes that can
hydrolyze starches Major sources:
Potatoes Grains
Wheat Maize Corn Rice
Chloroplast Starch granules
1 m
#1 Carbohydrates: Polysaccarides; Storage - Glycogen
Animals store glucose as a polysaccharide called glycogen. Made up of glucose
monomers – like Amylopectin but more extensively branched.
In vertebrates it is mostly stored in the liver and muscle cells.
Glycogen stores don’t last long.
MitochondriaGlycogen granules
0.5 m
#1 Carbohydrates: Polysaccarides; Structure
Cellulose is a major component of the tough wall of plant cells
Cellulose is a polymer of glucose. The glycosidic linkages differ from
starch. The difference is based on two ring
forms for glucose: alpha () and beta ()
Figure 5.7b
(b) Starch: 1–4 linkage of glucose monomers
(c) Cellulose: 1–4 linkage of glucose monomers
41
41
Cell wall
Microfibril
Cellulosemicrofibrils in aplant cell wall
Cellulosemolecules
Glucosemonomer
10 m
0.5 m
Figure 5.8
#1 Carbohydrates: Polysaccarides; Structure
Enzymes that digest starch by hydrolyzing linkages can’t hydrolyze linkages in cellulose
Cellulose in human food passes through the digestive tract as insoluble fiber
Some microbes use enzymes to digest cellulose
Many herbivores, from cows to termites, have symbiotic relationships with these microbes
#1 Carbohydrates: Polysaccarides; Structure
Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods
Chitin also provides structural support for the cell walls of many fungi
Figure 5.9a
Chitin forms the exoskeletonof arthropods.
#2 Lipids
Lipids - do not form polymers Lipids is having little or no affinity for
water Hydrophobic
Consist mostly of hydrocarbons (nonpolar covalent bonds)
Fats, phospholipids, and steroids
#2 Lipids - Fats
Constructed from two types of smaller molecules: glycerol and fatty acids
Glycerol -a three-carbon alcohol with a hydroxyl group attached to each carbon
A fatty acid consists of a carboxyl group attached to a long carbon skeleton
Figure 5.10
(a) One of three dehydration reactions in the synthesis of a fat
(b) Fat molecule (triacylglycerol)
Fatty acid(in this case, palmitic acid)
Glycerol
Ester linkage
#2 Lipids – Fats; Saturated vs Unsaturated
Saturated fatty acids (saturated fats) solid at room temperature Most animal fats are saturated
Unsaturated fatty acids (unsaturated fats, or oils) liquid at room temperature Plant fats and fish fats are usually
unsaturated
Figure 5.11
(a) Saturated fat (b) Unsaturated fat
Structuralformula of asaturated fatmolecule
Space-fillingmodel of stearicacid, a saturatedfatty acid
Structuralformula of anunsaturated fatmolecule
Space-filling modelof oleic acid, anunsaturated fattyacid
Cis double bondcauses bending.
#2 Lipids – Fats; Saturated vs Unsaturated
Saturated fats – Not so good for you The “tails” lack double bonds so they are
more flexible Flexibility allows them to clump together May contribute to cardiovascular disease
through plaque deposits
#2 Lipids – Fats; Trans fats
Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen
Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds
These trans fats may contribute more than saturated fats to cardiovascular disease
#2 Lipids – Fats; Unsaturated Fats
Certain unsaturated fatty acids are not synthesized in the human body. Essential fatty acids
Must be supplied in the diet Include omega-3 fatty acids Required for normal growth, thought
to provide protection against cardiovascular disease
#2 Lipids – Fats – what are they for?
The major function of fats is energy storage
Humans and other mammals store their fat in adipose cells
Adipose tissue also cushions vital organs and insulates the body
#2 Lipids – Phospholipids
Two fatty acids and a phosphate group are attached to glycerol.
The two fatty acid tails are hydrophobic; the phosphate group and its attachments form a hydrophilic head
Figure 5.12
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilichead
Hydrophobictails
(c) Phospholipid symbol(b) Space-filling model(a) Structural formula
Hyd
rop
hilic
head
Hyd
rop
hob
ic t
ails
#2 Lipids – Steroids; Cholesterol
An a component in animal cell membranes Plays a roll in cell/cell signaling and helps
maintain membrane integrity Essential in animals High levels in the blood may contribute to
cardiovascular disease
#3 Nucleic Acids
Two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)
DNA provides directions for its own replication
DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis
Figure 5.25-3
Synthesis ofmRNA
mRNA
DNA
NUCLEUSCYTOPLASM
mRNA
Ribosome
AminoacidsPolypeptide
Movement ofmRNA intocytoplasm
Synthesisof protein
1
2
3
#3 Nucleic Acids
Polymers called polynucleotides Made of monomers called nucleotides
Nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups
The portion of a nucleotide without the phosphate group is called a nucleoside
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