Biological Molecules

Many organic compounds are large molecules called MACROMOLECULES. Macromolecules are usually polymers – molecules made up of repeating subunits called monomers.

monomer monomermonomermonomer polymer

Making and Breaking Macromolecules

4 main types of chemical reactions involvedin building macromolecules (anabolism) andbreaking them down (catabolism).

1. Redox reactions – aka: oxidation – reduction reactions

- involve the transfer of electrons between molecules “LEO the lion” says “GER”

Electrons

Reduction

Gain

Lose

E

lect rons

Oxidation

O xidation

I sL ose electrons

R eduction

I s

G ain electrons

Oxidation reactionsLose e-

Remove HAdd oxygenRelease energy

Reduction reactions:Gain e-

Add HRemove OxygenRequire energy

Oxidation-Reduction Reaction(Redox Rxn)

LEO the lion says GER

Cu + 2Ag+ Cu2+ + 2Ag

2. condensation reaction – aka dehydration synthesis– enzyme aided reaction where a hydroxyl group from one molecule& a hydrogen from another moleculeare removed, producing H2O and anew (larger) molecule

← C H HO C→ C + C← C OH H C→

enzyme: takes OH out of 1 and H out of other

← C H C→ C O C← C H C→ ‘O’ joins 2 molecules

H2O comes out

-

3. cleavage – aka hydrolysis- the components of a water molecule (H+ and OH)

are added to a molecule to break it into 2 molecules

- Opposite of dehydration synthesis

H 2O

H OH C H C→ C O C C H C→ H & OH break O bond

C H HO C→ C + C C OH H C→ 2 separate molecules

Dissolved Ions and the pH Scale• many substances come apart (dissociate) into ions when

they dissolve in water

Water dissociates into:H2O ↔ H+ + OH- * reversible reaction

hydrogen ions hydroxide ions

• A higher [H+] = stronger acid

4. acid-base – aka neutralization reactions – transfer hydrogen ions (H+) between molecules.

pH ScaleSummary: If…..

[H+] < [OH-] base

[H+] = [OH-] neutral

[H+] > [OH-] acid

NOTE: pH scale is a logarithmic one. Each consecutive pH unit is separated by a factor of 10X.

Blood pH?7.4

A slight change in pH (± 0.1) can lead to coma,paralysis and DEATH

What helps to control fluctuations in pH?

BUFFERS – help to keep the pH in different parts of your body constant by absorbing or releasing H+ as needed

how?

buffers release H+ in basic solutions, but can accept H+ in an acidic solution

e.g. bicarbonate ion (HCO3-) buffering an acid:

H+ + HCO3- ↔ H2CO3 ↔ H2O + CO2

carbonic acid decomposes into

If blood too acidic ( H+), rxn moves left

CO2

H2O

H+H+

H2CO3 (aq)

H+

H+

carbonic acid

H+

surplus hydroge

n ion

If blood too basic ( H+), rxn moves right

HCO3-

(aq)

H+

bicarbonate ion

Carbohydrates lipids Proteins Water

MOST

LEAST

Types of Biological Molecules

1. Carbohydrates – contain C, H, O in 1:2:1 ratio

a) simple sugars – monosaccharides - formula is C6H12O6 or (CH2O) 6 - not usually in a chain but in a 6 carbon

ring called a hexose

i. glucose

O

C1

C2C3

C4

C6

C5

OH

OH

OHHO

– OH

H

H

H

H

H –

H

- locations of OH are important for dehydration synthesis or hydrolysis reactions

* simple sugars are chains in solids, rings in sol’n * 

Disc-OHDownDownUp Down

http://www.stolaf.edu/people/giannini/flashanimat/carbohydrates/glucose.swf

O

C1

C2C3

C4

C6

C5

OH

OH

– OH

OHHO

H

H

H –

H

H H

ii. galactose

isomers – are compounds with the same molecular formula but a different arrangement of atoms

e.g. galactose & fructose are glucose isomers

–

iii. fructose

C1

C6

C2

C4 C3

C5

– OH

OHO –

HO

OH

OH

H

– H

H-

HH

H

H

– found in fruits

Disc –OH UpDownUp Up

Disc –OH Up DownDown

Molecular Isomers: The same, yet different

Carvone

Optical isomers – mirror image

The devastating case of Thalidomide

b) disaccharides – high energy monosaccharides are bound into more stable chains for/during transportation

- Condensation (dehydration synthesis) reactions involved

O

C1

C2C3

C4

C6

C5

OH

OH

OHHO

– OH

H

H

H

H

H –H

glucose + glucose

O

C1

C2C3

C4

C6

C5

OH

OH

OHHO

– OH

H

H

H

H

H –H

α linkage is bottom-to-bottom condensation

O

C1

C2C3

C4

C6

C5

OH

OHHO

– OH

H

H

H

H

H –

H

O

C1

C2C3

C4

C6

C5

OH

OH

OH

– OH

H

H

H

H

H –H

O

Maltose + water

Condensation reaction

O

C1

C2C3

C4

C6

C5

OH

OH

OHHO

– OH

H

H

H

H

H –H

glucose +

O

C1

C2C3

C4

C6

C5

OH

OH

– OH

OHHO

H

H

H –H

H H

galactose

O

C1

C2C3

C4

C6

C5

OH

OHHO

– OH

H

H

H

H

H –H

Lactose + water

O

C1

C2C3

C4

C6

C5

OH

OH

– OH

OH

H

H

H –H

H HO

β linkage is top-to-bottom condensation

O

C1

C2C3

C4

C6

C5

OH

OH

OHHO

– OH

H

H

H

H

H –H

glucose +

C1

C6

C2

C4 C3

C5

– OH

OHO –

HO

OH

OH

H– H

H- H

H

H

H

fructose

O

C1

C2C3

C4

C6

C5

OH

OHHO

– OH

H

H

H

H

H –H

C1

C6

C2

C4 C3

C5

– OH

OHO –

OH

OH

H– H

H- H

H

H

HO

sucroseLinkage???α linkage

c) polysaccharides – are complex carbohydrates composed of hundreds-thousands of monosaccharide subunits

- e.g. starch – long chains of carbohydrates, plants store glucose as starch

glycogen – storage form of glucose in animals

cellulose – is a structural carbohydrate that forms cell walls aka fibre – holds feces together- constipated, eat more fibre

Carbohydrates – Complex (Polysaccharides)

What is the difference between starch and cellulose?

Starch

Cellulose

d) Chitin – sounds like “kite-in”- structural carbohydrate found in crustaceans like

crabs and shrimp, the exoskeleton of insects- Strong, similar structure to cellulose- Used in medical industry – biodegradable stitches

Types of Biological Molecules - LIPIDS

GlycerolGlycerol Fatty acidsFatty acids

11

22

33

– include: fats, oils, phospholipids, waxes -do not readily dissolve in H2O (largely hydrophobic)

a) Triglycerides – include fats and oils-Large molecules made up of 2 kinds of smaller molecules: glycerol and 3 fatty acid chains

Making and Breaking Lipids (fats)

Fats and oils are called triglycerides because of their structure

CondensationSynthesis

Hydrolysis

What functional groups are present on the glycerol and fatty acid molecules?

+ 3 H2O

Ester linkage

Two types of fatty acids:

saturated and unsaturated

• Unsaturated fats contain C to C double bonds- create “kinks”, keeps the fatty acid chains from packing close to one another – remain liquid at room temperature

• Saturated fats have no double bonds, more H atoms, solid at room temperature

• Hydrogenated fats – bad why?

b) phospholipids- composed of 2 fatty acid chains

and a glycerol + phosphate group- Make up cell membrane

c) sterols – have 4 fused carbon rings as a backbone, no fatty acid chains - functional groups attached to carbon rings- different

structure, different function- Include: cholesterol, steroids, (test., est., prog.) bile

salts

Double lipid bilayer – cell membrane

Proteins8 Main types:8 Main types:Transport proteins - move molecules across cell membraneEnzyme proteins - biological catalysts – speed up reactionsAntibody proteins - fight infectionsContractile proteins -can change shape rapidly – found in

muscle tissue, cilia, flagellaHormone proteins - some hormones are proteins (e.g insulin)Extra Storage Proteins -act as a storage supply of amino acids –

used for building new proteinsReceptor proteins - found on cell surface- bind hormonesStructural proteins -make up skin, hair, fingernails bird feather,

tendons, cartilage

Proteins are made up of….

Amino acids

Amino Acid Structure

Amino Group Carboxyl (acid) Group

Any one of the 20 different side-chains

…20 different R chains …… 20 different amino acids

• 8 are essential – must get them in your diet

• Red meat gives you all 8

• 12 nonessential amino acids - can be synthesized by your body

Protein synthesis – occurs in ribosomes

- long chains of amino acids are linked together by condensation reactions to create a polypeptide

- condensation reaction forms a peptide bond

Protein structure - the sequence of amino acids in a protein determines the

shape of the protein ( sequence = structure)

1. primary structure

– the order of amino acids determined by DNA

• H – bonds form btw the oxygen of the carboxyl group of one amino acid with the hydrogen of the amino group of a different amino acid creating a coiling pattern within the protein thread , called α (alpha) helix

2. secondary structure – forms spontaneously – as soon as polypeptide chain synthesized

- sheet-like can also be formed, called a β (beta) pleated sheet

• Alpha helix Beta (β) pleated sheet

hydrogen bonds

H bonds (dotted lines) in a polypeptide chain. Such bonds can give rise to a coiled chain or to a sheet like array of chains

3. tertiary structure – involves highly specific looping and folding of the polypeptide chain to form a globular shape (semi-solid)

- Results from interactions between the various side chains (R-groups)

4. quaternary structure – 2 or more polypeptide (amino acid) chains can interact to form a complex protein

- this interaction is the quaternary structure

Quaternary structure of human hemoglobin - made up of 4 polypeptide chains

hemegroup

Twisting and folding of the polypeptide chain

Protein denaturation

– if a protein loses its quaternary or tertiary shape (due to bond breakage), the protein loses it structure and possibly, its function

What can cause a protein to lose its shape?

Ignore the slides that follow (nucleic acids and nucleotides)

We’ll cover this in Unit 3

4. nucleic acids & nucleotides nucleotides - have: 5 C sugars – ribose

- deoxyribose - phosphate group

- a single or double C ring structure which contains nitrogen, called a nitrogen base

Pdeoxyribose or ribose

O

N

e.g. i) ATP (adenosine triphosphate) - needed to deliver energy from one reaction site to another

ii) coenzymes – assist enzymes by accepting H’s or electrons that are removed from a molecule by an enzyme

e.g. NAD+ (nicotinamide adenine dinucleotide) FAD (flavin adenine dinucleotide) iii) messengers – chemical messengers such as

cyclic adenosine monophosphate (cAMP) - trigger parts of cells to become active

nucleic acids – RNA (ribonucleic acid) – single strand - DNA (deoxyribonucleic acid) – double strand - are long, twisted chains of nucleotides (G, C, A, T) - they contain genetic codes for cellular function - the sugars of one group covalently bond in the

phosphate of another group to form a backbone with the N base free in RNA

- in DNA, 1 N base hydrogen bonds with the 2nd strand’s N base

- the importance of nucleic acid is that they allow living organisms to reproduce

- recall that there are 2 types: DNA & RNA, and each are polymers of nucleotides

– each nucleotide has: i) a pentose (5 C sugar) ii) phosphate group iii) a nitrogen base

i. pentose a) ribose (RNA)

OCH2OH

OH

OH OH

b) deoxyribose (DNA)

OCH2OH

OH

H OH

One fewer ‘O’

ii. phosphate group

- O – P – OH

OH

O

- O – P – O-

O-

O

or

iii. nitrogen bases

a) pyrimidines – have a 6 member ring of C & N e.g. cytosine (c), thymine (T), uracil (U)

In DNA only

RNA only (replaces T’s)

* RNA made of U,G,C,A *

b) purines – have a double 6 member C & N ring e.g. adenine (A) & guanine (G)

- a nucleoside is a pentose connected to a nitrogenous base:

ribose

O

N

- a nucleotide is a nucleoside + a phosphate group:

Pribose

O

N

A Arrangement of nucleotides in DNA

A B

1

1

1

1 Deoxyribose

2

2

2

2 Phosphate

3

3

3 Paired Bases

B Schematized double helix