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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