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