The Molecules of Cells

Chapter 3

Overview

• Introduction to Organic Compounds

• Categories of Reactions

• Molecules of Life– Carbohydrates

– Lipids

– Proteins

– Nucleotides

What Are Organic Compounds?

Unique to living systems

Contain C & at least one H atom

Each has a functional group:– Specific atoms/groups of atoms covalently

bonded to C– Have specific physical & chemical properties

Why Carbon?

Versatile bonding

Can covalently bond with up to 4 atoms

Forms stable bonds

Helps form backbone for other elements to bond with

How Do Cells Build Organic Compounds?

Monomer:

Individual subunit of larger molecules needed to maintain cell structure & function

e.g. amino acids

Polymer:

Combination of 3 to millions of subunits

e.g. proteins

Hydrocarbons

H covalently bonded to C

e.g. gasoline, other fossil fuels

All 2 million+ are non-polar

Some of Earth’s most important energy sources

(electric & heat energy)

Functional Groups

Specific atoms or groups of atoms covalently bonded to carbon atoms in organic

compounds

More reactive than hydrocarbon groups

Can affect how structurally similar molecules work

e.g. estrogens & testosterone(different positions of functional groups determines

sexual traits)

Types of Functional Groups

Hydroxyl

– Alcohols, sugars, amino acids

– Water-soluble

Methyl

– Fatty acid chains– Insoluble in water

—OHC

H

H

H

Types of Functional Groups continued

Carbonyl

– Sugars, amino acids, nucleotides– Water-soluble– Aldehyde if at end of carbon backbone– Ketone if within carbon backbone

—CHO

C

O

C

O

H

CO(aldehyde) (ketone)

Types of Functional Groups continued

Carboxyl

– Amino acids, fatty acids– Water-soluble– Highly polar– Acts as acid by giving up H+

C

O

OH C

O

O-

—COOH —COO-

(ionized)(non-ionized)

Types of Functional Groups continued

Amino

– Amino acids, some nucleotide bases– Water-soluble– Acts as weak base by accepting H+

—NH2 —NH3+

N

H

H+

H

N

H

H

(non-ionized) (ionized)

Types of Functional Groups continued

Phosphate

– Nucleotides (e.g. ATP), DNA, RNA, some proteins, phospholipids

– Water-soluble– Acidic

P

O

O-

O-

O — P

Sulfhydryl

– Cysteine (an amino acid)– Helps stabilize protein structure via disulfide

bridges

Types of Functional Groups continued

—SH —S—S—(disulfide bridge)

Categories of Reactions

(1) Functional Group Transfera.k.a. exchange reaction

AB + CD → AD + BC

1 molecule gives up group to another

Making & breaking of bonds

e.g. ATP gives phosphate group to glucose in cellular respiration

a.k.a. redox reaction

One molecule loses e-s

Another gains them

e.g. cellular respiration, where glucose is oxidized (loses e-s) to CO2 & O is reduced (gains e-s) to

H2O

(2) Electron Transfer

(3) Rearrangement

Internal bonds reform to turn one organic compound into another

= structural isomer of original

(same molecular formula, different order of bonding)

a.k.a. synthesis reaction

A + B → AB

2 molecules covalently bond to form a larger molecule

(1 water molecule produced for each joining)

Making of bonds (= anabolic)

e.g. Na & Cl forming NaCl, amino acids forming a protein

(4) Condensation

a.k.a. decomposition reaction

AB → A + B

Molecule is split into 2 smaller ones

Breaking of bonds (= catabolic)

e.g. glycogen being broken down into glucose, carbs being broken down into simpler sugars

(5) Cleavage

e.g. hydrolysis

Cleavage reaction

Molecule split by enzyme action

OH & H from H2O attached to exposed sites

e.g. hydrolysis of sucrose into glucose

& fructose

Factors Influencing Reaction Rates

Temperature– ↑ temp, ↑ rxn rate– ↑ kinetic energy, ↑ collisions

Concentration of reactants– ↑ concentration, ↑ frequency of collisions

For reactions to occur, atoms & molecules must collide with enough force to overcome repulsion

between e-s

Particle size– Smaller move faster so collide more

frequently

Catalyst– Substance that speeds up chemical rxns– Does not become chemically changed or part

of product

Molecules of Life

• Carbohydrates

• Lipids

• Proteins

• Nucleotides

(1) Carbohydrates

Sugars & starches

Make up 1-20% of cell mass

Contain C, H, O

Important source of energy

Also serve some structural purposee.g. ribose & deoxyribose in RNA &

DNA

Classified by size & solubility

(a) Monosaccharides

“1 sugar”

Building blocks of other carbs

Most water-soluble sugars

2 or more –OH groups bonded to C backbone

1 aldehyde or ketone (carbonyl) group

Most have a 5-C or 6-C ring

—CHO CO

Monosaccharide Structure

glucose fructose galactose

deoxyriboseribose

(b) Disaccharides

Double sugar

Consist of 2 monosaccharides

Must be broken down to be absorbed

(c) Oligosaccharides

“Few” or short-chain sugars

Includes disaccharides

Often found as side-chains on lipids & proteins

(d) Polysaccharides

“Many sugars”

Chains of glucose

Least water-soluble of carbsMore complex = less soluble

Good energy storage product

Must be broken down to be absorbed

Polysaccharide Structure: Starch

Spiral structure

OH groups stick out from coils

Storage carbohydrate of plants

Filamentous (branched) chains

Storage carbohydrate of animal tissuesEquivalent to starch in plants

Stored in muscle & liver cells

Polysaccharide Structure: Glycogen

Polysaccharide Structure: Cellulose

Every other sugar is “upside-down”Sheets form by H-bonding between chains

Structural carbohydrate of plantsMakes up cell walls

Modified polysaccharideNitrogen groups attached to glucoses

Strengthens cuticle of arthropods & cell walls of fungi

=structural carbohydrate of animals & fungi

Polysaccharide Structure: Chitin

Simple Carbohydrates

a.k.a. simple sugars

Monosaccharides & disaccharides

Taste sweet

Few essential nutrients & high in calories

e.g. candy, milk products, fruit

Complex Carbohydrates

a.k.a. starches & fibres

Oligosaccharides & polysaccharides

Taste pleasant but not sweet

e.g. whole grains, legumes, starchy vegetables (potatoes, etc.)

Fibre

= cellulose

↑ fibre in diet = ↓ risk of cancer, diabetes, hypertension, etc.

Processing plant foods decreases the amount of fibre & vitamins

In excess, carbs can lead to:• Increased blood sugar

• Excess sugar being stored as fat• Increased risk of heart disease, etc.

Diet rich in whole grains, fruits, & vegetables may reduce risk of heart disease & some cancers

(2) Lipids

Fats & oils

Contain C, H, OLess O than carbs

Some also have P

Non-polarInsoluble in water

(a) Fatty Acids

Carboxyl group attached to backbone of up to 36 atoms

Each C is covalently bonded to 1-3 H atoms

(i) Saturated fatty acids

C backbones completely filled with attached H atoms

Single covalent bonds only

Animal fats:Usually solid at room temperature

Associated with heart disease,

clogged arteries, etc. = bad fatse.g. palmitic acid, stearic acid

(ii) Unsaturated fatty acids

Not all Cs have H attached

≥1 double covalent bondCauses kinks in tails

Plant fats:Usually liquid at room temperature

Mono- vs. polyunsaturated fats

Mono-unsaturatede.g. oleic acid

– Only 1 double bond– Thought to lower cholesterol

Polyunsaturatede.g. linoleic acid

– More than 1 double bond

Partial hydrogenation of vegetable oils

Artificial saturation

Turns liquid oils into solids (e.g. margarine)

Oil is heated; H2 gas & nickel catalyst added

Breaks C double bonds & attaches H

Partial hydrogenation & trans-fatty acids

Partial hydrogenation = bad!Fat is now saturated

Trans-fats created by heat (e.g. deep frying) & hydrogenation

Double bonds fold in unnatural direction

Enzymes that process fat are unable to process trans-fatty acids in a normal way

Domino effect: Because trying to process trans-fatty acids, don’t

process essential fatty acids properly

Essential fatty acids

Body can manufacture some

(palmitic acid, oleic acid, etc.)

Others must be ingested via foods

(omega-3 & omega-6 fatty acids)

(b) Neutral Fats

3 fatty acid tails attached to glycerol backbone

= triglycerides

Large & found throughout entire body

“Body fat” used for insulation, protection, energy production

Yield > double the energy of complex carbs

e.g. butter, lard, veg. oils

(c) Phospholipids

Glycerol backbone with phosphorus group & 2

fatty acid tails– Tails are non-polar

– Head is polar

Make up double-layered cell membranes

Help regulate what crosses boundary of cell

(d) Waxes

Long-chained fatty acids bonded to long-chain alcohols or

carbon rings

Repel water

Protect

Lubricate

Add pliability to hair, skin, etc.

(e) Sterols

Backbone of 4 C-rings

Differ in functional groups

In all eukaryotic cell membranes

Steroids are essential for human life(homeostasis, vitamin D, sex & metabolic hormones)

Cholesterol

Found only in animal foods

Made in liver

Can’t dissolve in blood

Is carried to & from cells by lipoproteins (LDL & HDL)

Note: cholesterol itself is not bad

LDL (low-density lipoprotein)

Carries cholesterol through blood to body cells

Can form fatty deposits (plaques) in artery walls

– Eventually blocks blood flow– Leads to heart attack, stroke, etc.

HDL (high-density lipoprotein)

Carries cholesterol through blood to liver(will eventually be processed & excreted)

High levels appear to protect against heart attack

(may remove excess cholesterol from plaques, which slows build-up)

(3) Proteins

Make up 10-30% of cell mass

Contain C, H, O, N & sometimes S & P

Form basic structural material & aid in cell function

Long chains of amino acids (from 50 to 10,000+) joined by peptide bonds

Sequence of amino acid chain dictates which protein is made

(a) Amino Acids

Can act as bases or acids

20 amino acids– Identical except for R group

– Chemically unique

R

Amino group (NH3+), carboxyl group (COO-), H atom, & R group

Types of R-groups: Acidic

In neutral solutions, R-group can lose proton to become negatively-charged

If interaction with basic R-group, forms salt bridge: helps stabilize a protein

In neutral solutions, R-group can gain proton to become positively-charged

If interaction with acidic R-group, forms salt bridge: helps stabilize a protein

Types of R-groups: Basic

R-group is an aromatic (benzene) ring

Generally hydrophobic & non-reactive

Types of R-group: Aromatic

R-group contains S

Helps stabilize globular protein structure

Types of R-group: Sulfur

R-groups can form H-bonds

Types of R-group: Uncharged Hydrophilic

R-groups do not form H-bonds

Rarely reactive

Usually buried deep within a protein

Types of R-group: Inactive Hydrophobic

R-group & amino group are directly connected

Usually located at the turn of a polypeptide chain in 3D protein structure

Types of R-groups: Special

Essential & non-essential amino acids

Non-essential:– Can be synthesized from other substances in the body

Essential:– Can not be synthesized in the body– Must come from food– If not adequate intake, can’t make proteins

• Unable to sustain body structurally & functionally = illness & eventually death

Histidine

Isoleucine

Leucine

Lysine

Methionine(cysteine partially meets needs because has S)

Phenylalanine(tyrosine partially meets needs)

Threonine

Tryptophan

Valine

9 essential amino acids9 essential amino acids

Most animal sources:“Complete protein”: all of essential aas

Vegetables:

Missing or low in certain aas

If combine different vegetables, can get all essential aas

Lysine & tryptophan hard to get from plants so vegetarians need to ensure adequate intake

From Amino Acids to Proteins

Amino acids form proteins by dehydration reactions

Peptide bonds form between amino acids

2 amino acids bonded together

= dipeptide

Many amino acids linked

= polypeptide

Types of Proteins

Structural = hair, tendons, ligaments

Contractile = muscles

Defensive = antibodies

Signal

Transport = e.g. hemoglobin

Storage

Plus many more!

(b) Levels of Protein Structure

1° structure

Linear polypeptide chain

(unique sequence of amino acids)

Determined by inherited genetic info

2 ° structure

Proteins tend to twist or bend

H-bonds form between NH & CO groups

α-helix (coiled)or

β-pleated sheet

Tertiary structure

Proteins continue to fold upon themselves

Quaternary structure

Two or more polypeptide chains bonding & folding

together

(c) Other Types of Protein Structure

Glycoprotein:Oligosaccharide + polypeptide

Lipoprotein:Lipid + protein

Both types important in cellular processes

The Importance of Structure

Protein structure determines biological function

3D structure allows recognition & binding with specific molecular

targets”

(d) Fibrous Proteins

Mostly 2° structure; some have quaternary structure

Insoluble in water

Structural functions:

chief building materials of body

e.g. collagen, elastin, keratin

Tertiary or quaternary structure

Water-soluble

Chemically active

Used in all biological processes

e.g. antibodies, enzymes, protein-based hormones

Globular Proteins

(e) Enzymes

Biological catalysts that keep metabolic & biochemical reactions happening

Decrease the amount of activation energy required for chemical rxn to proceed

May be pure protein or may have cofactor (e.g. vitamin, metal ion)

Chemically specific– Named for type of reaction they catalyze

– Usually end in “ase”

Some must be activated before use

Others are inactivated directly after use

All have an active site:Allows binding of substrate so that rxns can

proceed

Why Is Protein Structure Important?

Structure dictates function

Proteins can only function if configured in specific way

Denaturation of Proteins

Breaking of H-bonds that results in shape change

Caused by temperature, pH, foreign substances, etc.

Can’t perform physiological functions

Active site is destroyed when bonds are broken

e.g. high fevers

• Denature proteins in body

• Proteins can no longer function

• Can result in serious damage/death

Denaturation is usually irreversiblee.g. albumin in cooked egg can’t regain

original shape

Note: not all changes are bad—can sometimes result in variation in traits

one

way

(4) Nucleotides

Contain C, H, O, N, P:N base, sugar, & phosphate

5 N bases:adenine, thymine, guanine, cytosine, uracil

Important in energy production, metabolism, cell signalling

Nitrogen-Containing Bases

Purines (double-ringed)

Pyrimidines (single-ringed)

Adenine Guanine

UracilThymine Cytosine

(a) DNA

Genetic material contained in cell nucleus(replicates itself before cell division so info in

cells is identical)

Contains deoxyribose sugar

Each species has unique base sequences somewhere in their DNA molecules

The History of DNA

Pre-1920s scientists knew that:– Genes are responsible for variation in traits

among individuals of a species– Genes are located within chromosomes

– Chromosomes are made of DNA & proteins

BUT most researchers thought genes were made of proteins that held heritable traits

– Diverse traits from diverse molecules?

Frederick Griffith (1928): – Tried to develop vaccine against Streptococcus

pneumoniae– Did not succeed BUT managed to transfer genetic

material from one bacterial strain to another

Oswald Avery (1940s): – DNA-digesting enzymes (NOT protein-digesting)

prevented bacterial cells from becoming pathogenic

Thus, genes are made of DNA

Still …

How does DNA store genetic info?

The answer lies in the structure of DNA

Polymer of nucleotides:

– Phosphate

– Deoxyribose sugar

– Nitrogen-containing base (A, C, G, T)

All nucleotides are identical except for base

DNA Structure

What does DNA actually look like?

Clues in Chargaff’s ratios:

In any species

#A = #T

#G = #C

Differs between species

e.g. humans 30% A/T & 20% G/C

E.coli 26% A/T & 24% G/C

Also clues in X-ray shadows:

X-ray diffraction of DNA crystals

No direct picture of DNA structure but could tell:

(a) long & thin

(b) helical

(c) repeating subunits

Watson & Crick Model

DNA resembles ladder

Bases on each strand pair to make rungsG pairs with C

A pairs with T

Explains Chargaff’s ratios

Also …

Ladder is twisted = double helix

Explains x-ray shadows

Watson & Crick Model

DNA is a double helix of nucleotides

Sugar-phosphate backbone

Nucleotides held together at N bases by H bonds

Sequence of bases in DNA codes for genetic info

Different sequences = different information

How does DNA store genetic info?

(b) RNA

Carries out protein synthesis

Similar to DNA except:

– Single strand of nucleotides

– Ribose instead of deoxyribose

– Uracil replaces thymine

(c) ATP

Stores & releases chemical energy for all life processes

Adenosine, ribose, 3 phosphate groups

Enzymes transfer terminal PO4- group from ATP to

other compounds so can use energy released from bonds breaking

P

Brief Overview of How ATP Works

P P

PP

Energy via glucose

ADENOSINE

ADENOSINEenergyP

So essentially:

P energyATP ADP +

+

+