bio 11 lecture- chemistry ii chemical reactions, ions, ph, functional groups, organic molecules
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Bio 11 Lecture- Chemistry II
Chemical reactions, Ions, pH, functional groups, organic molecules
Lecture outline
• Chemical Bonds review5. Ions6. pH7. Functional groups8. Organic molecules4. Chemical Reactions9. Carbohydrates
What part(s) of an element’s atoms determines its mass?
• A. Protons• B. Neutrons• C. Electrons• D. Protons + Neutrons• E. Electrons/Protons
What part(s) of an element’s atoms define the element?
• A. Protons• B. Neutrons• C. Electrons• D. Protons + Neutrons• E. Electrons/Protons
What part(s) of an element’s atoms differentiate its isotopes?
• A. Protons• B. Neutrons• C. Electrons• D. Protons + Neutrons• E. Electrons/Protons
What part of atoms determine how they bond with other atoms?
• A. Protons• B. Neutrons• C. Electrons• D. Protons + Neutrons• E. Electrons/Protons
Basic atomic structure- protons, neutrons, and electrons
The periodic table logically arranges and describes all matter
Molecules, compounds, chemical reactions, and bonding
Elements combine in chemical reactions to form compounds
• Molecules- 2 or more atoms combined in a specific way• Compounds- different elements in a molecule, in exact,
whole-number ratios, joined by a chemical bond• 2 major means of intramolecular chemical bonding:
Covalent (incl. polar and nonpolar) and Ionic
Valence electrons determine bonding
Atoms seek complete valence electron shells (the octet rule)
In Ionic bonding, atoms strip valence electrons from partners, forming ions
Atoms are stable when their outer shells are filled with electrons
• Shell 1: Holds 2 electrons• Shell 2: Holds 8• Shell 3: Holds 8• Hydrogen- 1p, 1e, seeks a
second electron in its outermost shell
• Carbon seeks 4• The electrons in the
outermost shell are called valence electrons
Noble gases have a stable electron structure
• Their outer orbitals have a full complement of electrons
• Noble gases are very unreactive
In ionic bonding, an atom takes an electron from another atom, forming 2
ions
LE 2-7
Transfer ofelectron
NaSodium atom
ClChlorine atom
Na
Sodium ionCl
Chloride ion
Sodium chloride (NaCl)
5. Ions
• Ions- Charged atoms or molecules
• Anion- negative ion• Cation- positive ion• Ionization- reaction
producing ions• Salt- a neutral
compound comprised of ions
LE 2-7a-2
Na
Sodium ionCl
Chloride ion
Sodium chloride (NaCl)
LE 2-7b
Na
Cl
Water dissolves many ionic compounds (“like dissolves like”)
Individual soluble ions are not physically bound to each other
In covalent bonding, pairs of valence electrons are shared, and molecules are formed
LE 2-17a
2 H2 O2 2 H2O
LE 2-6b
Nitrogen (N)Atomic number = 7
Oxygen (O)Atomic number = 8
In neutral molecules, carbon always forms 4 bonds
Structuralformula
Ball-and-stickmodel
Space-fillingmodel
Methane
The 4 single bonds of carbon point to the corners of a tetrahedron.
LE 3-1b
Ethane PropaneCarbon skeletons vary in length.
LE 3-1c
Butane Isobutane
Skeletons may be unbranched or branched.
Butane and Isobutane are _______________of each other.
LE 3-1d
1-Butene 2-Butene
Skeletons may have double bonds, which can vary in location.
LE 3-1e
Skeletons may be arranged in rings.
Cyclohexane Benzene
Organic Chemistry
• The chemistry of carbon• Hydrocarbons are the
most basic example– Combustible– Can form rings
The variety of carbon compounds is limitless
inorganic - lack carbon atomsorganic - with carbon (plus hydrogen)biochemical - organic molecule in life
• carbohydrates • proteins• lipids • nucleic acids
Covalent bonds hold together the macromolecules of life
• Living things create macromolecular products for structure:
• 6CO2(g)+ 6H2O(l) + hν C6H12O6(s) + 6O2(g)
• Macromolecules as reactants are broken down for energy:
C6H12O6(s) + 6O2(g) 6CO2(g)+ 6H2O(l)
All the reactions of a living thing are called its metabolism
Electronegativity determines properties of covalently bonded
molecules
Electronegativity = “electron greediness”
• Atoms in covalently bonded molecules do not always share electrons equally
• This creates polar molecules• Polar regions of water
molecules interact to form hydrogen bonds
• Hydrogen bonds: weak/temporary intermolecular forces
Some electronegativity values
• Hydrogen: 2.20• Oxygen: 3.44• Carbon: 2.55• Chlorine: 3.16• Sodium: 0.93
• Difference between:• H and O: 1.22• H and C: 0.35
Hydrogen bonding in water determine many of water’s unique properties
• H-bonds can form a lattice (ice)
• H-bonds require much energy to break
• H-bonds give water surface tension
Hydrogen bond
Water dissolves many ionic compounds (“like dissolves like”)
Intermolecular Hydrogen bonds give water its surface tension
Intermolecular Hydrogen bonds require much heat in order to be broken
Water also forms ions sometimes
H2O ↔ H+ + OH-
• Spontaneously happens to water molecules
• 1/ 107 water molecules are ionized in distilled water
• In dH2O, [H+ ]= [OH-]
salt - neutral molecule releases ionsacid releases hydrogen H+, burnsbase releases hydroxide OH–, slimy
pH is a measure of acidity/basicity• pH = -log [H+] (logarithmic scale)• pH 1 6.9: acid• pH 7.114: base• pH 7 neutral• buffers - absorb excess H+ or OH–• - stomach 2, urine 5-7.8, blood 7.4 • Acids donate [H+] to water• Bases remove [H+] from water (or donate [OH-] to
water)• Proteins are very sensitive to small changes in pH
LE 2-15
Acidic solution
OH
H
HH
HOH
H H
H
OH
OH
OH
OH
OH
H
H
H
H
HH
I ncr
e asi
ngl y
ACI
DI C
(Hi g
her c
once
ntra
ti on
of H
)Neutral solution
OH
OH
OH
OH
OH
OH
H
H
Basic solution
NEUTRALH
pH scale
Lemon juice, gastric juice
Grapefruit juice, soft drink
Tomato juice
Human urine
Pure waterHuman blood
Seawater
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner
Incr
easi
ngl y
BAS
I C( L
owe r
con
cent
ratio
n of
H )
7. FUNCTIONAL GROUPShydroxide group – OH
amino group – NH2carboxyl group – COOHphosphate group – PO4methyl group – CH3
The physical/ chemical
properties of carbon
skeletons can be modified by functional
groups
2.20 – Part 2
Figure 2.20 – Part 2
figure 02-20b.jpg
Functional groups can radically change the function of a molecule
Estradiol
TestosteroneMale lion
Female lion
• The six functional groups that are most important in the chemistry of life:– Hydroxyl group (alcohols)*– Carbonyl group– Carboxyl group (carboxylic acids)*– Amino group*– Sulfhydryl group– Phosphate group*– Methyl group
LE 4-10aa
STRUCTURE
(may be written HO—)
NAME OF COMPOUNDS
Alcohols (their specific namesusually end in -ol)
Ethanol, the alcohol present inalcoholic beverages
FUNCTIONAL PROPERTIES
Is polar as a result of theelectronegative oxygen atomdrawing electrons toward itself.
Attracts water molecules, helpingdissolve organic compounds suchas sugars (see Figure 5.3).
LE 4-10ab
STRUCTURE
NAME OF COMPOUNDS
Ketones if the carbonyl group iswithin a carbon skeleton
EXAMPLE
Acetone, the simplest ketone
A ketone and an aldehyde maybe structural isomers withdifferent properties, as is the casefor acetone and propanal.
Aldehydes if the carbonyl group isat the end of the carbon skeleton
Acetone, the simplest ketone
Propanal, an aldehyde
FUNCTIONAL PROPERTIES
LE 4-10ac
STRUCTURE
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
EXAMPLE
Has acidic properties because it isa source of hydrogen ions.
Acetic acid, which gives vinegarits sour taste
FUNCTIONAL PROPERTIES
The covalent bond betweenoxygen and hydrogen is so polarthat hydrogen ions (H+) tend todissociate reversibly; for example,
Acetic acid Acetate ion
In cells, found in the ionic form,which is called a carboxylate group.
LE 4-10ba
STRUCTURE
NAME OF COMPOUNDS
Amine
EXAMPLE
Because it also has a carboxylgroup, glycine is both an amine anda carboxylic acid; compounds withboth groups are called amino acids.
FUNCTIONAL PROPERTIES
Acts as a base; can pick up aproton from the surroundingsolution:
(nonionized)
Ionized, with a charge of 1+,under cellular conditions
Glycine
(ionized)
LE 4-10bb
STRUCTURE
(may be written HS—)
NAME OF COMPOUNDS
Thiols
EXAMPLE
Ethanethiol
FUNCTIONAL PROPERTIES
Two sulfhydryl groups caninteract to help stabilize proteinstructure (see Figure 5.20).
LE 4-10bc
STRUCTURE
NAME OF COMPOUNDS
Organic phosphates
EXAMPLE
Glycerol phosphate
FUNCTIONAL PROPERTIES
Makes the molecule of which itis a part an anion (negativelycharged ion).
Can transfer energy between organic molecules.
Organic molecules are good energy sources
Energy is required to form covalent bonds; energy is released when bonds are broken
Most molecules in living things fall into four categories
• Carbohydrates• Lipids• Proteins• Nucleic acids
These all exhibit modular construction
Modular housing
Made of interchangeable parts
Freight trains have modular assembly
Modular assembly allows a wide variety of products from a few pieces
Most biopolymers of life are formed by dehydration synthesis
Hydrolysis is the reverse
reaction (Catabolic)
4. CHEMICAL REACTIONS • metabolism
- all chemical reactions in body- reactants ‹ products
synthesis - build larger molecule CH3-OH + H-CH3 ‹ CH3-CH3 + H2O hydrolysis - break down molecule CH3-CH3 + H2O ‹ CH3-OH + H-CH3 exchange reaction
- example: AB + CD ‹ AD + CB
Carbohydrates• “Carbon” + “Hydro”• Formula (CH2O)n
• Different from hydrocarbons
• Soluble in water• Includes: table
sugar, honey, starch, glycogen, cellulose, high fructose corn syrup
• Glucose is the monomer
Glucose can cyclize to form a ring structure
Atoms in bonds are free to rotate around the bonds
Glucose + Glucose = Maltose (A Sugar dimer)
Chain can be extended to thousands
9. Carbohydrates• functions - principle source of energy
(4 kcal/g)- structure & energy storage
in plants atoms - C H Ostructure - ring or chain of
5-6 C’s monosaccharide
- single sugars (example: glucose)
disaccharide - double sugars (example:
sucrose) polysaccharide - polymer or chain of 100’s
sugars- starch & cellulose (mostly
plants)- glycogen (animals, esp.
liver)
Proteins are polymers made of 20 different kinds of amino acid monomers
Table 3.2 – Part 2
Table 3.2 – Part 2
table 03-02bc.jpg
Table 3.2 – Part 3
Table 3.2 – Part 3
table 03-02d.jpg
Proteins: Polymers of Amino Acids
• Amino acids are covalently bonded together by peptide linkages. Review Figure 3.4
3.4
Modular assembly of amino acids through dehydration synthesis
figure 03-04.jpg
Proteins have an incredible variety of structures
Proteins have an incredible variety of functions
Hair, skin, fingernails, muscles, eye pigments, are all made of protein
11. Proteinsfunctions - energy (4 kcal/g)- structure in animals (meat)- enzymes (speed up & reg chem
rxs) atoms - C H O Namino acid- central C, hydrogen –H- amino group –NH2- carboxyl group –COOH• - R-group (20 different)• polypeptide - polymer of amino
acids• protein - 1 or more polypeptides
• 4 levels of structure - necessary • for protein function,
esp. enzymes•• I° primary structure - sequence of • amino acids in
polypeptide chain•• II° secondary structure• - coiling or folding of chain• - hydrogen bonds between
regions•• III° tertiary structure• - folding of coiled-folded chain•• IV° quaternary structure• - linkage to other polypeptides
Lipids
• Non-polar• High-energy molecules• For energy storage• Forms cell membranes• Hormones• Members of family
include oils, fats, waxes, and cholesterol (steroids)
Lipids are non-polar
• Therefore, they are hydrophobic
Triglycerides are a primary lipid structure
Dehydration synthesis links fatty acids to glycerol
Fatty acids can be saturated and unsaturated (cis and “trans”)
10. Lipids• functions • - energy storage (9 kcal/g)• - also animal structure (blubber)• • atoms - C H O• • structure - glycerol + 3 fatty acids• • oil - liquid, unsaturated (missing H’s)• • fat - solid, saturated (maximum H’s)• - promotes heart disease• • others • - steroids, phospholipids, waxes
Nucleic acids
• Informational molecules in cells
• Include DNA, RNA, and ATP/ADP
• Have other functions
Nulceotides are the subunits of nucleic acids
• Consist of a sugar, a phosphate, and a nitrogen-containing base
• Sugar can be deoxygenated
12. Nucleic Acids• function - not energy• - genetics (genes &
chromosomes)• • atoms - C H O N P S• • structure - chain of 100’s
nucleotides• • examples - DNA, RNA, ATP• •
Review
• Atomic structure- protons, neutrons electrons• Valence electrons• Carbon • Functional groups• Carbohydrate structure• Protein structure• Lipid structure
Things left unsaid• Isotopes of all elements exist (some of these are
radioactive)• Electronegativity determines polarity of covalent
bonds, and thus solubility• Water has important physical properties essential
to life on earth• Isomers have the same molecular formula but
not the same shape in space• Nucleic acids are comprised of nucleotide
monomers
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