Proteins

and Enzymes

Topics:
• Amino Acids – Structure, Classification, Ionization
• Proteins - peptide bonds, peptide sequencing, function, levels of structure
• Enzymes – function, classification, kinetics, inhibition

Amino Acids
- building blocks of proteins; 20 natural occurring
- can be nonessential (produced in the body) or essential (need to be in diet)
Essential amino acids (10): Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan,
Threonine. Histidine, Lysine, Arginine
- can be classified as nonpolar (hydrophobic – afraid of water) and polar (hydrophilic – water loving)









Gly – G Ser - S
Ala – A Thr - T
Val – V Cys - C
Leu – L Asn -N
Ile – I Gln - Q
Met – M Asp - D
Pro – P Glu - E
Trp – W His - H
Phe – F Lys - K
Tyr – Y Arg - R




Ionization of Amino Acids (charges are affected by pH)
- What might be affected:
Carboxyl group (COOH) ( - at neutral pH, + at low pH)
Amino group (+ at neutral pH, - at high pH)
Some side chains (S, OH
- The total charges of the amino acid will be added, and when the sum is zero, this is called the
ISOELECTRIC POINT (pI)
- To get the structure of the amino acid wherein it has zero charge, use recently deprotonated structure
and then use the structure to be next deprotonated
 %&'()%&'*
- Equation: 𝑝𝐼 =
*

Titration table





















Example






















 Proteins: Peptide bonds
- Polypeptides; made up of amino acids Amide bond between α - carbonyl of
- Amino acids are linked to each other by peptide bonds one amino acid and α-amino group of
- The leftmost amino acid will be called the N – terminus another amino acid
While the rightmost will be called C – terminus
- In naming peptide bods, the amino acid with C-terminus will be parent, the one with N – terminus is
the substitute (drop –ine to –yl)
- Important Features of peptide bond
1. Has double character and is planar – due to resonance
2. Trans configuration
3. Restricted rotation, but can occur
- Isoelectric point can also be computed


Function of Proteins
1. Antibody – can bind to specific protein particles
2. Enzyme – catalysts
3. Messenger – transmit signals (e.g. Hormones)
4. Structural component – provide structure and support for cells, allows body to move
5. Transport/ storage – bind and carry atoms within cells and throughout body


Levels of Protein Structure
1. Primary – sequence of amino acids in the polypeptide chain; Stabilizing agent – peptide bonds
Primary structure determination
a. Determine composition through chromatography
b. Know your reagents (specific)
c. Fragmentation through reagents and enzymes
Step 1: separation of chains (destroy quaternary structure)
§ extreme pH, 8M urea, 6M guanide, HCl, high salt concentration
Step 2: Cleavage of disulfide bridges
§ Performic acid oxidation
§ Sulfyhydryl reducing agents to reduce
§ After reducing, to prevent recombination, follow with an Alkylating agent
Step 3: Determine amino acid component
§ Chromatogram
§ Complete hydrolyisis w/ 6M HCl, then analysis
Step 4: Identify N- and C- terminal residues
§ N-terminal – Dansyl Chloride, Edman degredation, Sanger’s reagent
§ C-terminal – Hydrazine (Chemical), Carboxypeptidase (enzyme)
Step 5 & 6: Fragmentation of chains
§ Enzymatic fragmentation: Trypsin, Chymotrypsin, Pepsin
§ Chemical: Cyanogen Bromide
Trypsin C (after) Lys, Arg
Chymotrypsin C Phe, Tyr, Trp
Pepsin N (Before) Phe, Tyr, Trp
Cyanogen bromide C Met



2. Secondary – mainly formed by hydrogen bonds, backbone of protein
- Local conformations of its polypeptide backbone
- Can either be alpha helix or beta-pleated sheet
o Alpha helix – can be right handed or left handed
§ 3.6 amino acid residues per turn
§ Hydrogen bond stabilizes – 4 residues away
§ Side chains are protruded outward
§ Several factors can disrupt
a. Proline – creates a bend bec. Of restricted rotation
b. Strong electrostatic repulsion
c. Steric crowding – caused by proximity of bulky side chains
o Beta pleated sheet – can be parallel or anti-parallel N – C
§ Peptide zigzag C – N
N – C
§ H bond can be inter or intra
N – C
§ Residues can be up or down
- Can either be Fibrous – long and narrow, insoluble in water, chemically stronger
a. Alpha keratin – present in hair
o Dominant structure: alpha helix (RIGHT HANDED), contains 2 polypeptide chain (when coiled
together: LEFT HANDED)
o Rich in hydrophobic residues – 7 amino acids (heptad)
b. Fibroin – present in cocoon, spider web
o Dominant structure: beta pleated sheet
o 2 alternating sequence – Gly – Ala
c. Collagen – Structural component
o Dominant structure: alpha helix (LEFT HANDED), contains 3 polypeptide chain (when coiled
together: RIGHT HANDED)
o Gly – X (proline) –Y (hydroproline)
3. Tertiary structure – native conformation, overall 3D shape of an entire protein molecule
- Dictate biological function of protein
- Hydrophobic amino acids tend to be inside (bec they’re afraid of water) while hydrophilic AA tend to
be outside
- Stabilized by hydrogen bonds and disulfide bridges
- Can be globular proteins
a. Myoglobin – single polypeptide chain, 153 amino acids
o Contains prosthetic group – part of protein but not made up of amino acids
*heme group (prosthetic) – single binding site of O2
o 8 regions of alpha helix
o 2 important histidine – connected to Fe (II) – connected to O2

b. Hemoglobin – tetramer of two alpha helix chains (141 AA each) and two beta pleated sheets (153 AA
each)
o each chain has a heme group ( 4 in total) so it can bind to 4 O2
o Positive cooperativity – enhances binding of O2 to other heme groups
§ Shape of graph is hyperbolic graph
o Job is to transport oxygen
4. Quaternary structure – association of polypeptide monomers into subunit group
- Held together by H bonds and electrostatic forces

Summary of
levels of
structure

Denaturation of Proteins
- Unfolding, loss of structural order (secondary, tertiary, quaternary) that gives a protein its biological
activity
- Can be done by heat treatment and acid/base treatment


Enzymes
- Biological catalysts that speed up chemical reactions without being used up in the process
May raise 1020 reaction rate
- Most are globular proteins – exception: Ribozymes
- Generally, highly specific
- Milder reaction conditioning – temp below 100 degrees C, atmospheric pressure, neutral pH
- Some require cofactors and coenzymes
o Cofactors – additional chemical groups to activate enzyme (inorganic ions)
o Coenzymes – complex organic molecules and metallorganic molecules
§ Transient carriers of specific function groups
§ Tightly bound (covalent) to the protein (prosthetic group)
o Apoenzyme – needs cofactor to be active (pure protein)
o Holoenzyme – activated apoenzyme
o Proenzyme – inactive precursor of an enzyme
Enzyme classification accdg to function

Naming of enzymes
- When first discovered, named after where it was found (e.g. Pepsin – pep: digestion)
- Then was named after activity (i.e. name of substrate + suffix -ase)
e.g. Urease (hydrolysis of urea)
- Systematic name – 4-digit combination (EC _ _ _ _) – 1st digit is important (6 major classifications)

Enzyme specificity
1. Bond (relative) – particular bond present in substrate
2. Group (moderate) – specificity to groups surrounding certain bond
3. Substrate (absolute) – specificity to one substrate and one reaction
*Active site – particular part of enzyme where substrates bond to
4. Optical (Stereospecificity) – optical configuration of its substrate
5. Geometrical – less specificity; molecular geometry of substrate
6. Cofactor specificity – proper combination of coenzyme and enzyme

Models for binding of enzyme and substrate
1. Lock and key model – enzyme has a rigid 3D structure where substrate binds to that portion w/ a
complementary shape
2. Induced-fit model – flexible 3D structure, substrate induces a change in shape – complementary
Upon binding of substrate – formation of enzyme-substrate complex













Energy in enzyme-catalyzed reactions
- Standard free energy change – energy difference
between reactant and product
- Activation energy – energy needed for reaction
*for catalyzed reactions – less energy needed
- Zero order – independent of substrate
concentration
- First order – rate of reaction is determined by
substrate concentration






Enzyme kinetics
E – enzyme
- Principle: S – substrate
ES –Enzyme substrate complex
P - Product

- The velocity of an enzyme catalyzed reaction depends on the rate of conversion of ES to E and P
- Michaelis - Menten equation derivation:
Vo = kcat [ES] Vo = velocity
&+', - ,.,'/ [1]
Vo = Kcat – catalytic constant, rate limiting step
34)[1] Km – substrate concentration at half vmax

o When [S] (substrate concentration) is increased, enzyme is saturated, only addition of enzyme
can increase velocity: Vmax = kcat [E] total
o Vmax is the constant velocity that is asymptotically approached
o Then it can be rewritten as:
Vo = initial velocity (moles/time)
[S] = substrate conc (molar)
vmax = maximum velocity
Km = substrate concentration at
half vmax
74'8 [1] 74'8
- If [S] = Km, 𝑣𝑜 = =
1 )[1] *
74'8
- If [S] >>> Km (negligible), 𝑣𝑜 =
*
74'8 [9]
- If [S] <<<KM, 𝑣𝑜 =
34




Graph of equation







 - Need to convert hyperbolic graph to linear graph by using double reciprocal on the equation to reach
vmax: Lineweaver-Burke plot

1 𝑘𝑚 1 1
= × +
𝑣𝑜 𝑣𝑚𝑎𝑥 [𝑆] 𝑣𝑚𝑎𝑥
- X intercept - -1/km
- Y intercept – 1/vmax
- Slope – km/vmax










Factors that can affect catalytic activity of enzymes
1. Temperature – heat can catalyze reaction until optimal temp
- Show little activity at low temp
- Temperature larger than optimal temp - denaturation
2. pH – most active at optimum pH
- lose activity at low or high pH as tertiary structure is disrupted
3. Substrate conc – as it increases, rate of reaction increases until enzyme eventually becomes saturated
4. Enzyme conc – if [E] is increased, there will be no change in reaction bec. Substrates are limited
5. Enzyme inhibitors – interfere with actions of an enzyme and slows the rate of reaction
- 2 general types: reversible and irreversible
o Irreversible (permanent deactivation)
o Reversible inhibitors (Inhibitor can bind to E or ES)
a. Competitive – inhibitor competes w/ substrate bec of similar structure (I binds to E)
§ Directly bind to active site of enzyme
§ To overcome, increase Enzyme concentration
b. Noncompetitive – S and I bind to different sites on the enzyme
§ Pure noncompetitive (I to E) – no effect on the binding of S and E
§ Mixed noncompetitive (I to E or I to ES) – affect substrate binding as well as catalytic
activity
c. Uncompetitive (I to ES) – binds at a site other than the active site

km vmax
Competitive decreases same
Pure noncompetitive same decreases
Mixed noncompetitive Increase or decrease (im Decreases
not sure) *slope changes
Uncompetitive decreases decreases
*slope does not change















Different Regulations (turning on & off)
1. Allosteric regulation
*Allosteric enzymes – more than one site (Active and allosteric)
- active site will undergo conformational change once effector molecule will to allosteric site
2. Feedback inhibition – is inhibited by an end product
- In metabolic pathways, main product will be the inhibitor to stop production
3. Proenzymes (zymogen) – inactive form of enzyme which can be activated by removing a small part on
their chain
- Mostly digestive enzymes and blood clotting enzymes – they undergo proteolysis
4. Protein modification – process wherein a new chemical group is covalently added to/ removed from
the protein

























 Carbohydrates

Carbohydrates: Hydrates of carbon

- Play metabolic roles, generates energy needed to sustain life
- Can be classified as: Monosaccharides, Oligosaccharides and Polysaccharides

Monosaccharides
- Contain a single polyhydroxyaldehyde or ketone unit
- Can be classified according to the number of carbon atoms they contain
- Can also be classified according to functional group attached (Aldo or keto)
- Physical properties:
o Sweet taste
o Solids at room temp
o Extremely soluble in room temp
- Family trees of aldoses and ketoses in Fischer projection




Aldoses



































Ketoses













Conversion of Fishcer projection to Haworth Projection

- For five membered ring, furanose
- For six membered ring, pyranose
- Has two forms, alpha and beta (more stable) – based on position of OH in anomeric carbon
- All OH in the right of fischer projection – down
- All OH in the left of fischer projection – up




Haworth projection of common sugars:

β -D- Glucopyranose β- D- Galactopyranose β - Fructofuranose

Chair conformation of some common sugars:
- Most stable; β -D- Glucopyranose is the baste structure because all bulky groups are in equatorial

Reaction of Monosaccharides
1. Concentrated mineral acids – undergo dehydration to give furfural & dihydroxymethylfurfural

2. Sugar derivatives
o Sugar acids – OXIDATION; aldoses (reducing sugars) keto- enol tautomerization
§ Aldonic (Gluconic)- C1 is oxidized, aldehydes to carboxylic acid; Benedict’s, Tollens (Ag)
and Barfoeds (Cu as oxidizing agent)
§ Uronic (Glucoronic) – oxidation of C6 to become primary alcohol
§ Aldaric (Glucaric) – C1 and C6 are oxidized – Mucic, Nitric acid

















o Sugar alcohols – reduction of carbonyl group
§ C=O of aldoses or ketoses can be reduced to C-OH by NaBH4 or H2 /Ni
§ Name the sugar alcohol by adding -itol to the root name of the sugar










o Deoxy sugars – removal of oxygen









o Sugar esters
o Amino sugars – contain amino acid group
§ Acetylamine sugras – acetyl group is bonded to amino group by an amide bond










 o Acetals, ketals and glycosides – formed when reacted with alcohol in the presence of an acid
catalysts
§ GLYCOSIDIC BOND – formed by elimination of water molecule between a hydroxyl
group on a monosaccharide and a hydroxyl group on another compound
























Oligosaccharides (2 or more monosaccharides)

Disaccharides
- Simplest form of oligosaccharides, two monosaccharides linked together by a glycosidic bond
- Soluble in water but too big to pass cell membrane – broken down to monosaccharides
- Common disaccharides:














 o Maltose – malt sugar
o Lactose – milk sugar
o Sucrose – table sugar, non-reducing

Polysaccharides
- Complex, contains hundreds/thousands of carb units
- Allows storage of large quantities of glucose, nonreducing Two monomer types, unbranched
- Can be homopolysaccharide or heteropolysaccharide Multiple monomer types, branched

Unbranched
Branched


- can be storage (α-glucose units) or structural (β-glucose units)
- Common Polysaccharides
o Starch – storage polymer consisting of D-glucose units from plants
§ Amylose – long unbranched chain of glucose, connected by α(1-4) glycosidic bond;
10-20% of starch, forms helices that can trap iodine
§ Amylopectin – long, branched chains of glucose connected by α(1-6) branches every 24
to 30 glucose units; 80-90% of starch in this form
o Glycogen – storage polymer, structurally similar to amylopectin containing α(1-4) glycosidic
bonds and α(1-6) branch points; more branched than amylopectin (every 8-12 glu units)
o Cellulose - β (1-4) glycosidic bonds – forming extended chains for rigid structure; material of the
plant cell wall (wood is 50% cellulose)
§ Every other glucose is flipped over – promoting intra chain and inter chain H bonds
§ Insoluble in water
o Chitin – exoskeleton of crustaceans, N-acetylglucoamine, β (1-4) glycosidic bonds
§ Chitosan (Derivative) – glucosamine as building blocks

Glycosaminoglycans (GAGs)
- Linear chains of repeating disaccharides (heteropoly)
- One will be amino sugar and the other is acidic sugar
- Negatively charged (sulfate or carboxyl)
o Heparin – natural anti-coagulant
§ composed of GlcNAc and glucuronic acid (GlcA) disaccharide units







o Hyaluronan – lubricant of eye
§ Composed of glucoronate and acetyl-glucoronate






o Chondroitin sulfate – connective
§ Composed of D- glucoronate and N-acetylgalactosamine






o Keratan sulfate – nails, cornea
§ Composed of D- galactose and N-Acetyl-D-glucosamine-6-sulfate






Glycoproteins and Proteoglycans

Glycoprotein
- Carbohydrates are covalently linked to protein (larger)
- Important in ABO blood types







Proteoglycans
- Protein + carbohydrates (larger) – made of glycosaminoglycans (GAGs)
- Found in connective tissues and surfaces of many cell types (bottle brush structure)













 Lipids

Lipids
- Esters of long chain fatty acids and alcohols
- Nonpolar and soluble in organic solvents
- Most are amphipathic (has a polar and nonpolar head)

Function of Lipids
1. Major source of energy – produce twice as sugars, energy is released by oxidative breakdown of fat
2. Food reserves – neutral fats; in plants – stored in seeds
3. Protein and insulation – in animals – stored in Adipose tissues
4. Cell membrane
5. Hormones – cholesterol is used in synthesis of hormones
- Prostaglandins are hormone – like compounds derived from fatty acids
6. Vitamins – lipid soluble vitamins (A,D,E,K) play major role in regulation of some bio process
7. Vitamin absorption – dietary fat serves as a carrier of the lipid soluble vitamins

Fatty acids
- Make up some of the Lipids (Except terpenes)
- Unlike proteins and carbohydrates where they are made up of amino acids and monosaccharides,
lipids have very diverse components
- Components: a hydrophilic carboxyl group (polar) is attached to one end of the hydrocarbon chain
(polar) w/c typically contains 12 to 20 carbons

- Can be classified as: Saturated or unsaturated


-solid in room temp -liquid in room temp (oils)
-no double bonds cannot stack like the

have higher melting saturated ones
points because of -contain double bonds –
straight shape can be cis (same side,
natural occurring) or trans
(opposite, manufactured
-has no straight shape



 Chemical Names and Descriptions of some Common Fatty Acids
Carbon Double
Common Name Atoms Bonds
Scientific Name Sources

Butyric acid 4 0 butanoic acid butterfat

Capric Acid 10 0 decanoic acid coconut oil
Lauric Acid 12 0 dodecanoic acid coconut oil
Myristic Acid 14 0 tetradecanoic acid palm kernel oil
Palmitic Acid 16 0 hexadecanoic acid palm oil
Palmitoleic Acid 16 1 9-hexadecenoic acid animal fats
Stearic Acid 18 0 octadecanoic acid animal fats
Oleic Acid 18 1 9-octadecenoic acid olive oil
Linoleic Acid 18 2 9,12-octadecadienoic acid grape seed oil
Alpha-Linolenic Acid flaxseed (linseed)
18 3 9,12,15-octadecatrienoic acid
(ALA) oil
Gamma-Linolenic Acid
18 3 6,9,12-octadecatrienoic acid borage oil
(GLA)
peanut oil,
Arachidic Acid 20 0 eicosanoic acid
fish oil
Arachidonic Acid (AA) 20 4 5,8,11,14-eicosatetraenoic acid liver fats
Behenic acid 22 0 docosanoic acid rapeseed oil
Erucic acid 22 1 13-docosenoic acid rapeseed oil
4,7,10,13,16,19-docosahexaenoic
DHA 22 6 fish oil
acid
small amounts
Lignoceric acid 24 0 tetracosanoic acid
in most fats

- can be essential (not synthesized by the body; needed in diet) e.g. Linolenic, Linoleic and arachidonic
or nonessential (synthesized by the body)
- can also be divided by location of double bonds:
omega-3 (double bond is located 3 carbons away from the end)
omega-6 (double bond is located 6 carbons away from the end)

Naming Fatty acids
1. Delta system (Δ) – # of carbons: number of double bonds
14:0 (Lauric Acid) 16:1:Δ9 (Palmitoleic acid)

2. Omega system – applicable only to polyunsaturated fatty acids; count from other end
16:1:Δ9 – omega-6




 Additional fact: Trans fat
-prevents rancidity by oxidizing double bonds (partial
hydrogenation for the cis double bond to become
trans)

-considered “bad cholesterol”



Classification of Lipids
- can be accdg to function – storage, membrane lipids, steroid, nonsteroid
- can be accdg to component – phospholipid, glycoside
- can be accdg to solubility – saponifiable and nonsaponifiable (Terpenes)
- can be accdg to structure – open chain or cyclic

1. Triglycerides – consists of one glycerol molecule bonded w/ 3 fatty acid molecules
- The bonds are covalent, called Ester bonds, formed during condensation
- Function: energy storage, thermal insulation, regulator of buoyant density
- Can be simple (same fatty acid components) or mixed (different fatty acid components)
*On naming simple TAGs: Palmitic acid + prefix tri- + suffix –in = Tripalmitin
On naming mixed TAGs: Myristic, Palmitic, Oleic + suffix –oyl + glycerol =
1-myristoyl-2-palmitoyl-3-oleoyl-glycerol
- Can be fats or oils
*Saponification
-formation of soap –
-solid in room temp -liquid in room temp
-mainly present in -mainly present in plants sodium/potassium salt of fatty acids,
animals and fish obtained when fats/oils are
-saturated, high melting -unsaturated, low hydrolyzed
points melting points - usage of alkaline hydrolysis (NaOH,
KOH)













2. Waxes – esters (1) formed from long-chain fatty acids (C14-C36) and long alcohols (C16-C30)
- Water insoluble because weak hydrophilic head
- Naming wax – Alcohol + Fatty acid
e.g. Stearyl Palmitate


Sterol (18C)
Palmitic Acid
3. Phospholipids – make up membrane, amphipathic
- Can be classified accdg to backbone (either glycerol or sphingosine)
a. Glycerophospholipids – the terminal OH of the glycerol is esterified with phosphoric acid instead of
fatty acids – which leads to the formation of phosphatidic acid (parent structure)
§ Only differ in the component attached to phosphoric acid

§ Common glycerophospholipids:
Lecithin – phosphoric acid is attached to the alcohol Choline
Cephalin – phosphoric acid is attached to the alcohol Ethanolamine

§Cleaving by enzyme Phospholipase
Phospholipase A1 – cleaves at first ester bond (C1)
Phospholipase A2 – cleaves at second ester bond (C2)
Phospholipase C – cleaves at third ester bond (between 3rd carbon of glycerol and
phosphoric acid)
Phospholipase D – cleaves between phosphoric acid and choline

b. Sphingophospholipids – has sphingosine as the backbone (not glycerol)
§ Sphingosine – 18 C amino alcohol – fatty acid will be attached to 1 amino group (C2)
§ The only difference will be the group attached to 1st carbon – either P or carb
§ Ceramide – parent chain of all sphingolipids









 § Abundant sphingophospholipid: Sphingomyelin – makes up myelin sheat
• At the 1st carbon, phosphoric acid + choline is attached

4. Glycolipids – fatty acids w/ carbohydrates (can be mono, oligo or poly) and nitrogen but w/o
phosphoric acid
- Important constituent of brain and other tissues
a. Glyceroglycolipids – glycerol backbone

a.1 Galactolipids – predominate in plant cells, can either a.2. Sulfolipids – also in plant cells, sulfonated
have 1 or 2 galactose glucose residue is joined to diacylglycerol in
glycosidic linkage











b. Glycosphingolipids – sphingosine backbone
o Cerebroside – ceramide w/ a single sugar

o Globoside – contain either di, tri and oligo (D-Glc, GalNAc, D-Gal)
o Ganglioside – complex, N-Acetylneuraminic acid is present
§ Important in ABO blood groups



5. Ether lipids – instead of an ester bond, ether link at C1
o Plasmalogens – C1 C2 double bonded

o Platelet activating factor

6. Terpenes - formed from combination of isoprene (5C) units – 2-methyl-1,3,-butadiene
- Classified according to number of isoprene units
Monoterpene (2 Isoprene u) – 10 Carbons
Sequiterpene (3 isoprene u) – 15 carbons
Diterpene (4 isoprene u) – 20 C
a. Steroids – derivatives of cyclopentanoperhydrophenanthrene
o Cholesterol – steroid most commonly found in humans
(but not plants)
§ Nonpolar rings and hydrocarbon chain – hydrophobic
While OH is hydrophilic
§ Fused rings are planar, rigid, amphipathic, but most likely nonpolar
§ Cholesterol will mostly exist as esters

Cholesterol

b. Steroid hormones – converted cholesterol, molecules that regulate the function of organs and
tissues
§ Function: metabolic regulation (Cortisol), electrocyte balance, reproductive function
(testosterone, estrogen), Message
c. Bile salts/acids- released from gallbladder, aid digestion by forming emulsions w/ dietary lipids
(Acted upon by lipases); detergents

 7. Lipid Soluble vitamins – not consumed at once – stored in adipose, Structurally similar to isoprene
o Vit A – retinal (aldehyde; pigment of retina), retinol (hormone)
o Vit D – from cholesterol (7 dehydrocholesterol)
o Vit E – tocopherol – has antioxidant properties
o Vit K – K1 – from plants, phylloquinone
K2 – from bacteria, menaquinone
















8. Eicosanoids – derived from arachidonic acid (20:4Δ5,8,11,14), act at very low concentrations
- Paracrine hormones
o Prostaglandin – smooth muscle contractions, sleep wake cycles, elevation of temp – fever
§ Nonsteroidal Anti-inflammatory drugs – inhibits formation of prostaglandin
o Thromboxine – produced by platelets – blood clotting
o Leukotrienes – asthma



Biological Membrane: Phospholipid Bilayer

Fluid- mosaic model
- Constantly moving
-plant membranes are more fluid
because of many unsaturated fatty acids)
-animal membranes (less fluid bec
cholesterol is present – more rigid)
-Prokaryotes (most fluid of all)
- Fluidity of bilayer is temperature dependent
(Colder – more rigid)
- Presence of proteins in the dominantly lipid bilayer
Molecular components:
o Polar Lipids – glycerophospholipid, cholesterol
o Carbohydrates (glycoproteins and glycolipids)


 o Proteins
§ Transmembrane – span the entire membrane from one side to another
§ Integral – solely inside the bilayer, permanently attached; can be separated by
detergents
§ Peripheral – only on the exterior, temporary – attaching to integral membrane
















- Bilayers are selectively permeable
o Hydrophobic and small uncharged polar – can freely pass
o Large uncharged polar and Ions – need assistance
- Movement
o Passive – along concentration gradient
§ Simple diffusion – no assistance
§ Facilitated diffusion– needs protein
o Active – against concentration gradient
§ Primary – energy directly from
§ Secondary – energy supplied by ion concentration gradient driven by H+ gradient

 Nucleic Acids

• Allows organisms to transfer genetic information from one generation to the next
• Has two kinds:
1. Deoxyribonucleic Acid (DNA)
2. Ribonucleic Acid (RNA)
• Made up (polymer) of Nucleotides; polynucleotides

Close up: Nucleotides as Building blocks of Nucleic Acids
a. Properties: Strong acids, primary ionization of phosphate group occurs w/ pka of 1.0, bases are capable
of conversion between tautomerism forms (keto – enol)
b. Made up of 3 components:

1. Sugar (pentoses) – either Deoxyribose (for DNA) or Ribose (RNA)

2. Phosphate group
3. Nitrogenous bases – divided into two kinds, the Pyrimidines and Purines
a. Pyrimidines – aromatic organic compound with 2 nitrogens at C1 and C3 of a six membered
ring; 3 kinds – Uracil (RNA), Thymine (DNA), Cytosine (DNA and RNA)

Tip: Uracil and
Thymine both have
oxygen on C4, only
difference is the
methyl group of
thymine in C5

 b. Purines – consist of a pyrimidine ring and imadazole ring; 2 kinds – Adenine and Guanine (both
found in DNA and RNA)

Tip: to differentiate,
remember that Adenine
has an NH2 group
attached to C6 while
Guanine has Oxygen on
C6 and NH2 on C2

Ø Properties of nitrogenous bases (both pyrimidine and purine)
i. Planar, aromatic, plain pyrimidine and purine have low solubility but cytosine, uracil,
thymine, adenine and guanine have more solubility
ii. Can absorb UV light bec. aromatic

*On naming Nucleotides:
- refer to naming Nucleosides below, and add the number of phosphate groups present (e.g.
Guanosine 5’ – monophosphate: meaning there is one phosphate group attached to C5 of sugar)

Additional info on nucleotides: Nucleosides – sugar bonded to nitrogenous base (w/o phosphate
group); positions of rings can be syn or anti, w/ anti being majority

*On naming nucleosides:
Pyrimidine – add –idine (e.g. cystidine, uridine, thymidine)
Purine – add –osine (e.g. anedosine, guanosine)
w/ ribose sugar – no prefix (e.g. Uridine, Guanosine)
w/ deoxyribose sugar – add prefix “deoxy” (e.g. Deoxythymidine, deoxyadenosine)
Close up: 2 kinds of Nucleic Acids
 1. Deoxyribonucleic acid (DNA) – more stable, carries genetic code, double stranded
- Pyrimidines: Cytosine and Thymine
- Purines: Adenine and Guanine
2. Ribonucleic acid (RNA) – important for synthesis of proteins; component of ribosomes, single
strand
- Pyrimidines: Cytosine and Uracil
- Purines: Adenine and Guanine

DNA Double Helix
History
1. Erwin Chargaff – discovered complementary base pairing: Adenine will always pair with
Thymine (A – T; 2 hydrogen bonds), Guanine will always pair with Cytosine (G – C; 3 hyd bonds)
- Chargaff’s rule: concentration of pyrimidine and purine is equal
2. Rosalind Franklin – X-ray of diffraction pattern
3. Watson-Crick model – found that DNA has 2 strands
- Properties of double strand:
o Right handed double helix
o Anti parallel - 1st strand: 5’ – 3’, 2nd strand: 3’ – 5’
o 1 turn – made of 10 base pairs (3.4 nm)
o 3 forms:
A – DNA – right handed, more compact, diameter is broader
B – DNA – physiological DNA (normal)
Z – DNA – left handed, taller, less packed




Levels of DNA structure
1. Primary – sequence of nucleotides; Secondary – double helix, 3D conformation of
connected by phosphodiester bonds polynucleotide backbone




















Tertiary – 3D arrangement of all atoms of a nucleic acid
- Supercoiling occurs – further coiling and twisting of DNA helix; occurs bec of topoisomerase in
eukaryotes

Quaternary – interaction of all atoms of a nucleic acid
- Compact so it can fit inside nucleus, bec of interaction with Histone (rich in basic amino acids)
- Double helix to Chromatin to Chromosome to Mitotic Chromosome


 Denaturation of DNA

- Disruption of Primary structure through increasing heat, but when gradually cooled afterwards,
it renatures
- As strands separate, absorbance at 260 nm increases: Hyperchromicity – increases amount of
light absorbed bec bases become unstacked
- Midpoint of transition (melting) curve = Tm
- The higher the % G – C, the higher the Tm , meaning there are more H bonds

Types of RNA
1. Messenger RNA (mRNA) – goes to nucleus to get DNA, then goes to Ribosome
- Carries the genetic code, its end is capped with guanosine triphosphate for recognition
2. Ribosomal RNA (rRNA) – 80% of total RNA, combine w/ proteins in cytoplasm to form
ribosomes
- Found in ribosomes, 2/3 RNA and 1/3 protein
3. Transfer RNA (tRNA) – smallest, single stranded, 73 – 94 nucleotide residues
- Has amino acids attached at the 3’ end
- Anticodon – interacts with mRNA’s codon

 Close up: Central Dogma

1. Replication – DNA is copied semi-conservative (one strand is old - template, the other is new)

a. Unwinding – with enzyme DNA helicase, unzips DNA molecule
- Single stranded DNA binding protein – separates strands of DNA after unwinding
b. Complementary base pairing – RNA primase adds RNA primer
- Elongated by DNA polymerase III
- DNA polymerase I degrades RNA primer
- Leading strand (continuous, direction same with helicase) and
Lagging strand (direction against helicase, forms okazaki fragments)
c. Joining – enzyme DNA ligase joins the strands

2. Transcription – a gene passes its coded information to an mRNA – 3’ to 5’
- Pre mRNA- codes for just one protein, with intron and exon (coding sequence)

a. Initiation – RNA polymerase binds to the promoter region ( tells where to start)
b. Elongation
c. Termination – reaches termination site

 3. Translation – RNA is converted to protein with the help of ribosomal RNA and transfer RNA
- tRNA carries amino acids (amino acids are building blocks of protein)
- Anticodon of tRNA reacts with codon of mRNA

Close up: Genetic Code
- Must First know:
1) sequence of nucleotides in the first strand (5’ – 3’)
2) complementary base pairs (A – T; C – G) of the first strand to form second strand (3’ – 5’)
Example:
1st strand (5’ - 3’): A T G C A A C T A G G C T A G
2nd strand (3’ -5’) : T A C G T T G A T C C G A T C
- Next step: transcription – from DNA to mRNA (use 3’ – 5’ of DNA)
Example: (sequence from ex above)
(3’ -5’) : T A C G T T G A T C C G A T C
mRNA: A U G C A A C U A G G C U A G
- Last step – translation – from bases to amino acid sequence (use table at the next page)
Example: (sequence from ex above)
mRNA: A U G / C A A / C U A / G G C / U A G
Amino acid sequence: methionine – glutamine – leucine – glycine - stop

Summary of steps

 Table for translation of mRNA codons to amino acid sequence