Carbon Compounds

Section 2.3

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

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

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.

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

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

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

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

Soot amorphous form of carbon (no structure)

impure carbon particles resulting from incomplete combustion

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

Carbon Bonding Carbon can form straight chains, branched

chains, or ringso Leading to a great variety of organic

compounds

Isomers

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

Ex #1) Butane, C4H10

Ex #2) Butene, C4H8

Ex #3) 2-Butene, C4H8

Ex #4) methyl propene, C4H8

ISO

ME

RS

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

Structural Isomers Isomers in which the atoms are bonded

together in different orders. C4H10 (note continuous chain of C atoms)

butane

methylpropane

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

Hydrocarbons Only have carbon and hydrogen Simplest organic compounds From petroleum (crude oil)

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

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-

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.

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

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

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

Unsaturated Hydrocarbons

2. Alkynes: compounds that contain a triple bond

– Skeleton: CC– Molecular formula = CnH2n-2

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)

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

http://wps.prenhall.com/wps/media/objects/476/488316/index.html

Naming Alkynes Named just like the alkenes except the suffix –

yne is added

1-butyne

2-butyne

ethyne

propyne

Write the names of the organic compounds

methane

propyne

1-pentene

2-pentene

nonane

3-hexene

2-butyne

Give the structural formulas for the organic compounds

1. ethene2. heptane3. 3-

decyne4. butane5. 2-

octene

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.

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.

Hydroxyl Group

Structure

Compound Name Alcohols

Properties

Polar, attracts water (good

solvent)

Naming -ol

Carbonyl Group

Carbonyl (end):

Structure

Compound Name Aldehydes

Properties

Structural isomers with

different properties

Naming -al

Carbonyl (middle):

Structure

Compound Name Ketones

Properties

Structural isomers with

different properties

Naming -one

Carboxyl Group

Structure

Compound Name

Carboxylic acid

(organic acids)

Properties

Acidic properties

Naming -oic acid

Amino Group

Structure

Compound Name Amines

Properties

Basic properties

Naming -amine

Phosphate Group

Structure

Compound Name Phosphates

Properties

Makes the molecule and

anionTransfer energy

DNA

Methyl Group

Structure

Compound Name

Methylated compounds

Properties

May affect gene expression

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.

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

Biological Reactions WATER is the most important

inorganic compound in the body and it participates in two biological reactions:o Hydrolysis o Dehydration Synthesis

Hydrolysis Breaking down polymers by adding a

water molecule.

Hydrolysis Breaking down polymers by adding a

water molecule.C12H22O11 + H2O C6H12O6 +

C6H12O6

HydrolysisPolymers are broken down to monomers

Animation: Hydrolysis of sucrose

H

H2O

OH

H OH

OH H

Hydrolysis

Dehydration Synthesis Build up large molecules by releasing a

molecule of water.

Dehydration Synthesis Build up large molecules by releasing a

molecule of water.

C6H12O6 + C6H12O6 C12H22O11 + H2O

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

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

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.

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.

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)

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)

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

Carbohydrates Disaccharides are double sugars Two monosaccharides condense to form

disaccharideso Formed by dehydration synthesiso Molecular formula = C12H22O11

Carbohydrates: Bond that joins monosaccharides

(carbohydrates) = glycosidic bond

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

Enzyme Catalytic Cycle

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)

Carbohydrates Polysaccharides many sugars: General formula – (C6H10O5)n plus H2O (n = #

monomers) Formed by dehydration synthesis Long chains of glucose molecules

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

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

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

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

Fatty Acid

General Structure

Saturated (single bonds)

Unsaturated (double bonds)

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

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

Look at the structures of the fatty acids and explain the differences between saturated, unsaturated and polyunsaturated fats.

Lipids

Saturated and Unsaturated Fatty Acids:

Lipids (4:52)

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

Saturated vs. Unsaturated Fatty Acids

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

Lipids Lipids (fats, oils, and waxes) are formed by a

glycerol molecule bonding to fatty acid(s) o formed by dehydration synthesis

Dehydration Synthesis

Ester Linkage

Triglycerides

Three fatty acids attached to glycerol

Formation of a Triglyceride

Phospholipids Two fatty acids joined to a glycerol Makes up cell membrane - PHOSPHOLIPID BILAYER

Phospholipid

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

20 Amino Acids

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.

Proteins Bond that joins amino acids (protein) = PEPTIDE

BOND

Formation of a peptide bond

amino acid 1 amino acid 2 dipeptide water

Peptide bond

Formation of a peptide bond

Proteins

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

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

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

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.

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

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

Protein Structure

(Conformation)

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

Protein Structure (Conformation):

Enzymes and Substrates:

Enzyme + Substrate = ES complex EP complex = Enzyme + product(s)

Enzymes (Proteins)

Enzyme Catalytic Cycle

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

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)

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

Denaturing Proteins Protein that has lost its active conformation, or

shape Denaturing caused by:

o Temperatureo Solute (salt) Concentrationo pH

Enzyme concentration

amount of enzyme

reacti

on

rate

http://www.kscience.co.uk/animations/anim_2.htm

Substrate concentration

amount of substrate

reacti

on

rate

37°Ctemperature

reacti

on

rate

Temperature

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

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

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)

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

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

Nitrogenous Bases There are FOUR Nitrogen bases

Purines - 2 ring base• Adenine (A)• Guanine (G)

Pyrimidines - 1 ring base• Cytosine (C)• Thymine (DNA) (T), Uracil (RNA) (U)

Nitrogen Bases

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

Type of Bond Bond Between……

phosphodiester phosphate group and sugar

N-glycosidic sugar (glycosidic) and nitrogen base

hydrogen nitrogen bases

Nucleic Acids:

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:

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

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