18
Biomolecules 2/2/07 A. Synthesis & Hydrolysis reaction Vocab: monomer mono = one meros = piece/part polymer poly = many meros = piece/part Synthesis = to make/build Hydrolysis Hydro = water lyse = to break 1. Synthesis reaction (Condensation reaction, Dehydration synthesis) - In such a reaction a H atom is removed from the end of one building-block molecule and a hydroxyl (OH) group from the end of a second molecule. The two molecules are now joined together (polymerization) i.e., H-A-OH + H-B-OH H-A-B-OH + HOH C 6 H 12 O 6 + C 6 H 12 O 6 C 12 H 22 O 11 + H 2 O - Analogy: shifting of boxcars on a train, where H(engine) + A (a boxcar) + B ( another boxcar) + OH (caboose) 2. Hydrolysis reaction - Synthesis reactions are reversible; the complex organic molecules can be hydrolyzed into simpler building-block molecules H-A-OH + H-B-OH H-A-B-OH + HOH Notes Monomers are linked to other monomers by covalent bonds to form polymers.

2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

  • Upload
    dinhdan

  • View
    226

  • Download
    1

Embed Size (px)

Citation preview

Page 1: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules 2/2/07

A. Synthesis & Hydrolysis reaction Vocab:

• monomer mono = one meros = piece/part

• polymer poly = many meros = piece/part

• Synthesis = to make/build

• Hydrolysis Hydro = water lyse = to break

1. Synthesis reaction (Condensation reaction, Dehydration synthesis)

- In such a reaction a H atom is removed from the

end of one building-block molecule and a hydroxyl (OH) group from the end of a second molecule. The two molecules are now joined together (polymerization) i.e.,

H-A-OH + H-B-OH H-A-B-OH + HOH C6H12O6 + C6H12O6 C12H22O11 + H2O

- Analogy: shifting of boxcars on a train, where H(engine) + A (a boxcar) + B ( another boxcar) + OH (caboose)

2. Hydrolysis reaction

- Synthesis reactions are reversible; the complex organic molecules can be hydrolyzed into simpler building-block molecules

H-A-OH + H-B-OH H-A-B-OH + HOH

Notes

Monomers are linked to other monomers by covalent bonds to form polymers.

Page 2: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 2 Biomolecules

B. Carbohydrates

• sugars, starch, and cellulose being typical representatives

• Energy source • Compounds composed of carbon, hydrogen, and

oxygen, (C, O, H) - with the general molecular formula of Cx(H2O)y

- in simple sugars x=y - in complex sugars y=x-(n-1) where n=number of

monomer units

1. Monomer: Monosaccharides (Simple sugars) - are the simplest sugars (generically referred to as

“glucose”) - serve as building blocks for more complex

sugars

- named and classified on the basis of the length of their carbon chain

e.g., 5-C sugars are pentoses, 6-C sugars are hexoses - these sugars may have other names, but generally

end in —oses.

Three most common sugars utilized by cells for energy and structural purposes are the hexoses;

glucose, fructose, and galactose (aka glactose).

Healthy Eating Daily intake ratio of: Carbohydrate (sugars) = 70-65% (<60%) [fibre 20-30g] GI less than 55; GL less than 10. Lipids (fats) = 20% (25-40% ) and (<10% from saturated fats, 5%) (ave. intake in US = 37%) Protein = 12-15% (0.8 g per kg ave., 1.2-1.6 per kg active, max 1.8) Water = 1 L per 1,000 kcal of food eaten plus... A tenet of a good diet is to vary your diet, eat bright coloured fruits and vegetables, more raw F & V, and at least 5 servings of F & V a day. Eat well and exercise. Calories To calculate your caloric needs, Activity Level - Calories (kcal/kg)

Inactive 27 Lightly active 30-34 Moderately active 36-45 Very active 47-56 Intensely active 56-68+

Your body weight (kg) x level of activity e.g., 70 kg x 50 (very active) = 3,500 kcal per day % kcal from carbs 3500 x 65% = 2275 kcal carbs have 4 kcal/g, 2275 kcal / 4 = 568 g of carbs a day (or about 6 - 8 g of carbs per kg of body weight a day)

Page 3: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 3 Biomolecules

Source: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Carbohydrates.html

NB. Glucose, fructose, and galactose have the same chemical composition, but different chemical properties; they are isomers. (Galactose differs in only single hydroxyl group so it is an epimer, an isomer that differs only in the configuration at a single atom.)

- glucose is formed in green plants by photosynthesis i.e.,

6CO2 + 6H2O + Light energy C6H12O6 + 6O2

- It is the pentose sugars (ribose and deoxyribose) which are of critical importance as structural elements in the formation of nucleic acids, i.e., DNA and RNA

• Monosaccharides are the "small building blocks"

used to form large molecules.

2. Disaccharides (still a relatively simple sugar) - consist of two such molecules linked (via a

synthesis reaction) together:

Mono + Mono = Di + Water glucose + glucose = maltose + water glucose + fructose = sucrose + water glucose + galactose = lactose + water

- the above reactions are reversible (hydrolysis)

- sugar molecules are transported within the body as “transport disaccharides”

- In Lactose the bond formed between the two monosaccharides is called a beta glycosidic bond (figure). The alpha glycosidic bond, found in sucrose and maltose, differs from the beta glycosidic bond only in the angle of formation between the two sugars. Unfortunately, unlike alpha glycosidic bond, beta-glycosidic bonds are unable to be digested by some people. Therefore, many people are lactose intolerant and suffer from intestinal cramping and bloating due to the incomplete digestion of the substance.

Page 4: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 4 Biomolecules

3. Polysaccharides (complex sugars)

- are long-chain molecules made up of repeated monosaccharides

- Starch and cellulose are common plant examples - Glycogen is typical of animals

a. Cellulose is the most prevalent polysaccharide on

Earth, with at least 50% of all of the carbon in plants in this form. (structural support) - e.g., purest state: cotton & linen - structure is unbranched

b. Starch is a plant reserve carbohydrate (storage form

of glucose) - structure is branched

c. Glycogen is stored in the liver and muscle cells, like starch, is a reserve carbohydrate which can be drawn upon when energy needs demand. - structure is highly branched

C. Lipids

• Include neutral fats, oils, waxes, and steroids (etc.) • Fcn:

(1) as structural component of membranes. (2) as storage forms of metabolic fuel e.g. fats. (3) as transport forms of metabolic fuel e.g. fatty

acids.

Glycemic Index (GI) Refers to how quickly a complex sugar can become a simple sugar this can elevate insulin levels rapidly which is not good for diabetics, or your immune system

- Banana, under-ripe 42 - Banana, ripe 54 - Banana, over-ripe 64 - Glucose 100 - Sucrose 65 - Lactose 49 - Fructose 25

- White bread 71

- Processed foods tend to have a

higher GI, while fruits and vegetables (especially uncooked), whole grains have a lower GI.

- Odder yet GI often varies from

country to country, US cereals tend to have a higher GI than Canadian cereals of the same brand.

- Australia requires food to be

labeled for its GI - http://www.glycemicindex.com/

Carbohydrates that contain more than two simple sugars are called oligosaccharides or polysaccharides, depending upon the length of the structure. Oligosaccharides usually have between three and ten sugar units while polysaccharides can have more than three thousand units. These large structures are responsible for the storage of glucose and other sugars in plants and animals.

Page 5: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 5 Biomolecules

(4) as protection against shock and insulation agents in cells/tissues.

• Organic compounds; C, O, H • All are insoluble in water (hydrophobic), - but are soluble in oil and non-polar substances

WHY? - The C-H bond of fats is nonpolar and cannot form H

bonds. Because of the large number of C-H bonds that they contain, fat molecules are hydrophobically excluded by water, since water molecules seek to form H bonds with other water molecules. The result is that fat molecules cluster together and are therefore insoluble in water.

• Many more C-H bonds than carbohydrates, as such able

to store more Energy • Fats are composite molecules, each made up of two

sub-units: e.g.,

Neutral fat / triglyceride = 1 glycerol + 3 fatty acids

i. Glycerol (head) - a 3-carbon alcohol, each of whose carbons bears a

hydroxyl group - the 3 Cs form the backbone of the fat molecule, to

which 3 fatty acids are joined

Head Tails

Glycemic Load You might have second thoughts about eating a carrot with a GI of 92, vs. a carrot muffin with a GI of 62. Common sense tells you that a carrot ought to be good for you. That’s where Glycemic Load (GL) comes in: it takes into consideration a food’s Glycemic Index as well as the amount of carbohydrates per serving. A carrot has only four grams of carbohydrate, per 80 g servings. To get 50 grams, you’d have to eat about a 3/4 of a Kg of them, that carrot muffin has 28g per 60 g serving, so just two muffins will do it. GL for a carrot is 4, for the muffin 17. GI of 55 is low; GL of 10 is low. A GI is 70 or more is high, a GI is 56 to 69 inclusive is medium, and a GI of 55 or less is low. A GL of 20 or more is high, a GL of 11 to 19 inclusive is medium, and a GL of 10 or less is low.

Page 6: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 6 Biomolecules

Saturated fats Unsaturated fats

Source Animal, tropical oils

Vegetable, fish oils

Examples

Beef fat, butter, palm, coconut

Canola (Canadian Oil), olive, peanut

State

Solid or semi-solid

Oil

Defined

(diagram)

Saturated with, i.e., contains only C-H bonds (excluding functional group carboxyl)

Not saturated with just C-H, also has at least 1 C=C (monounsaturated), or many C=C (polyunsaturated)

ii. Fatty acids (tails)

- important building blocks of lipids

- long hydrocarbon chain ending in a carboxyl group

(COOH) - Includes both saturated and unsaturated fats

Fatty acids are the building blocks of fats. Some fatty acids are "essential" because we need them to live, yet we cannot manufacture our own, so we must ingest them through the foods we eat. The word "essential" is used to mean "must be ingested". Other fatty acids are manufactured by the body, thus although we need them, they are not labeled as "essential". The polyunsaturated fatty acids -- chemically speaking, those that are not "saturated" and thus have more than 1 double bond -- are divided into families depending on where their end-most double bond is located. There are two main subtypes of fatty acids: the omega-3 and omega-6 fatty acids. The Omega-3's are those with their endmost double bond 3 carbons from their methyl end. The Omega-6's are those with their endmost double bond 6 carbons from their methyl end. Linoleic acid (an omega-6) and alpha-linolenic acid (an omega-3) are the only true "essential" fatty acids, because although a slow process, given enough alpha-linolenic acid, the body can synthesize eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) -- both important fatty acids of the omega-3 family. But, in order to effectively increase the body's stores, they too must be consumed.

Page 7: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 7 Biomolecules

Energy

More C-H, therefore more E per gram (~ 9Kcal)

Fewer C-H, because of C=C, therefore less E

Health

Excess associated with Heart Disease, e.g., Arteriosclerosis

Essential fatty acids, essential for good health. Can be Hydrogenated (trans fatty acids), associated with Cancer, Type 2 diabetes, and Heart Disease.

• Energy Storage - fats are very efficient because of the high concentration of C-H bonds - most fats contain over 40 C atoms - the ratio of C-H bonds to C atoms is more than twice that of carbohydrates

Fats yield Carbohydrates yield 9 kcal of chemical energy per gram 4 kcal of chemical energy per gram

- the more highly saturated the fat, the more energy, the

more calories - animal fats are more saturated - BUT large amounts of saturated fats upset the normal

balance of fatty acids in the body, which may lead to heart disease - humans are not carnivores, but omnivores - traditionally most of dietary needs have been met by

plants, not meat - the total amount of carbohydrates consumed is handled

in three ways: 1) held as glucose for immediate use 2) converted to transport disaccharides, for shipping 3) converted to glycogen and then fats for future use

- the reason people gain weight as they grow older is that

the amount of carbohydrates decreases, but food intake does not. More carbohydrates are then available to be converted to fat

Page 8: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 8 Biomolecules

• Polymers

1. Triglycerides - aka Neutral fats

- animal fat

2. Phosopholipids - The basic foundation of the cell membranes is a lipid

bilayer, formed of a double layer of phospholipids

- is amphiphatic, both hydrophobic and hydrophilic

- in which the nonpolar hydrophobic tails of the phospholipids molecule point inward, forming a non polar zone in the interior of the bilayer .

- Lipid bilayer membranes are permeable to oxygen, to

lipids, and to small uncharged molecules, and water; - they are not permeable to large molecules if they are

polar, or to anything that is charged, such as ions and proteins.

- the flow of such material into and out of the cell is

controlled through special protein gateways embedded

Water is permeable because of aquaporins, the molecular [protein] aqueducts that transport water in and out of cell membranes. Yes, proteins are charged…review your notes on buffers and proteins.

Source:http://ww

w.brooklyn.cuny.edu/bc/ahp/SD

PS/SD.PS.LG

2.html

Page 9: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 9 Biomolecules

within the bilayer (facilitated / active transport) or by bulk transport (endocytosis and exocytosis)

(NB. We will discuss this further when talk about “the fluid mosaic model” – a two-dimensional fluid of freely diffusing lipids, dotted or embedded with a mosaic of proteins.)

- Lungs are a collection of a huge number of small bubbles called alveoli, which provide about 100 square metres of surface area for exchange of gases. To allow exchange of gases the walls of the alveoli must be very very thin, and as such the walls are not strong enough to maintain their bubble shape against the strong force of surface tension created by water, (about 0.07 N/m), causing the bubble to collapse.

- The body overcomes the problem by reducing the

surface tension of water by secreting the - - phosopholipid (called di-palmitoylphosphatidyl

choline (DPPC)) to act as a detergent or surfactant.

- Surface tension arises from the hydrogen bonding between water molecules, which holds the water molecules together e.g. in a water droplet like a large crowd holding arms together. The DPPC fits in between the water molecules so disrupting the cohesive hydrogen bonds reducing the surface tension like policemen going into a crowd and breaking up the arm holding. In the presence of DPPC the surface tension is reduced to a very low level of 0.01 N/m.

Glycolipids (gl) - are carbohydrate-attached lipids.

Their role is to provide energy and also serve as markers for cellular recognition.

- also to attach cells to form tissues Glycoproteins (gp)

- a group of extracellular protein-carbohydrate compounds, e.g.,

- mucins (mucous) o surfactant: serves to

maintain the stability tissue by reducing the surface tension of fluids that coat the lung/stomach…

- are important for immune cell recognition

o antibodies (immunoglobins) o major histocompatibility

complex (or MHC) Lipoproteins (lp)

- a combination of fat (cholesterol) and protein that transports lipids, such as cholesterol,in the blood. - HDL (high density lipoprotein),

the good cholesterols - LDL (ow density lipoprotein), the

bad cholesterols

Carrier Protein (cp) - an integral protein that acts as a

gateway for water, Na+ and the like o e.g., aquaporins, Na+ / K+

pump, glucose carrier - an integral membrane proteins that

bind to a "substrate" and transport it across the membrane

- aka Carrier Molecule

Page 10: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 10 Biomolecules

- Notice that there are molecules of cholesterol

(lipoproteins) embedded in the membrane. Cholesterol is a necessary component of biological membranes. Cholesterol breaks up the Van der Waals interactions and close packing of the phospholipid tails. This disruption makes the membrane more fluid.

3. Steroids

- A substantially different group of lipids from those already considered examples are cholesterol, oestrogens, androgens, progesterone, bile salts and are characterised by having ring structures.

- composed of four carbon chains, resembling “chicken wire”

- structurally they are different from other lipids, but are "soluble in nonpolar organic solvents" (i.e., “oils’)

Cholesterol is: - an important structural component of cell membranes

- precursor of steroids in animals, especially of male and

female sex hormones - manufactured by plants but vital to animals because of

their involvement in the chemistry of vision, and vitamins such as A, D, E, and K; e.g., carotene

4. Prostaglandins

- are a group of 20 lipids that are modified fatty acids (phospholipids), with two nonpolar “tails” attached to a five carbon ring.

More About Prostaglandins There are many different types of prostaglandins, all of which affect muscle tension. However, not all prostaglandins affect muscles in the same way. Some, such as the series two prostaglandins (specifically the E2 and F2 Alpha), trigger powerful smooth muscle contractions. Because of this physiological effect, an overabundance of series two prostaglandins is strongly linked to menstrual cramps and pain. These prostaglandins have also been linked to high blood pressure because they act to narrow the diameter of blood vessels. They can also trigger irritable bowel syndrome since they cause cramping of the intestinal muscles. Not all prostaglandins, however, cause muscle contraction. Others, such as the series-one and series three, actually promote muscle relaxation and can help relieve menstrual cramps. Prostaglandins are derived from fatty acids in the diet. The series two prostaglandins that trigger muscle contractions are derived from animal fat meat, dairy products, and eggs. The beneficial muscle relaxant series one and series three prostaglandins are derived from vegetable and fish sources of fatty acids. These fatty acids, called linoleic acid and linolenic acid, are found predominately in raw seeds and nuts, such as flax seed or pumpkin seed, and in certain fish, such as trout, mackerel, and salmon. Thus, how we eat can actually determine which hormonal pathway we travel, leading to either muscle tension or muscle relaxation. This is a very good example of how our food selection can determine our state of health. Like progesterone, excessive prostaglandin production is seen only during ovulatory menstrual cycles. Prostaglandin production increases during the second half of the cycle, peaking toward the end of the cycle with the onset of menstruation.

Source: Susan M. Lark M.D., http://www.healthy.net

Good & Bad Low Density Lipoproteins: LDL’s transport cholesterols from the liver to cell membranes, excess can cause arteriosclerosis (hardening of the arteries). High Density Lipoproteins: HDL’s scavenge excess cholesterols, to prevent hardening of the arteries. Note there are many types of LDL and HDL’s, some are better at their job than others. Bigger, fluffier HDL’s scavenge much more cholesterol…a simple blood test for LDL and HDL levels would not tell you what kind you have…

Page 11: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 11 Biomolecules

- occur in vertebrate tissue, where they appear to act as local chemical messengers

- some stimulate smooth muscle (e.g., uterus) to contract or expand the diameter of small blood vessels

- In women - (Type E2 and F2 alpha) stimulate uterine

contractions when a woman goes into labour, and which are recognized as cramps during the menstrual period,

- a surge in lutenizing hormone (LH) promotes the intrafollicular production of prostaglandins A and E, which are associated with rupture of the follicle; ovulation

- is also key in the demise of the corpus luteum (and subsequent decrease in progesterone levels)

- In males

- (Type E1) is a vasodilating agent which acts by relaxing the smooth muscles of the corpus cavernosum and by increasing the diameter of cavernous arteries; this leads to erection.

- male seminal fluid is rich in prostaglandins that increases sperm motility and viability, decrease mucous viscosity at cervix, and stimulate female uterine contractions to move the semen up into the uterus (may be acting as a pheromone)

- involved in varied aspects of reproduction (much of

which is still unclear), and in the inflammatory response to infection

- it is because aspirin inhibits prostaglandins

production that it reduces pain, inflammation, and fever

Uterine cramping is one of the most common uncomfortable sensations women may have during menstruation. There are two kinds of cramping. Spasmodic cramping is probably caused by prostaglandins, chemicals that affect muscle tension. Some prostaglandins cause relaxation, and some cause constriction. A diet high in linoleic and liblenic acids, found in vegetables and fish, increases the prostaglandins for aiding muscle relaxation

Source: http://www.fwhc.org/health/moon.htm

Page 12: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 12 Biomolecules

D. Protein • Structural and enzymatic function • composed of C, H, O, N, and sometimes P and S • are associated with every structure in the cell and are

involved in almost every cellular activity • predominant kind of molecule found in cell -~50% of the dry weight of living matter is protein • generally quite large

• despite their diverse function, all have the same basic

structure: a long polymer chain of amino acid subunits linked end to end

• Components of :

1. Amino acids - the building blocks of proteins - while there are many a.a. in nature, only 20 are used

in proteins

a. General Structure: - amino group (NH2); a carboxyl “Acid” group

(COOH); and a H atom, all bonded to a central C atom

C

H

R

C

O

OH

H N2

- the identity and unique chemical properties of

each a.a. are determined by the R group

2. Polypetides (the “glue” that binds a.a.) -The a.a. are bonded to form a protein by synthesis

between the amino group of one amino acid and the carboxyl group of another.

- The resulting bond is a peptide bond (a covalent bond) and the chains produced are polypeptide chains.

- Dipeptide = a.a. — a.a.

Essential Amino acids (human), must be eaten/ingested. Most animal products, such as meat and dairy products, contain all of the essential amino acids and have been designated as containing complete proteins. Most proteins from vegetables also contain all 9 essential amino acids, but 1 or 2 may be low in a particular food compared with a protein from most animal sources. Beans, however, are rich sources of all essential amino acids:

• tryptophan, • methionine, • valine, • threonine, • phenyalanine, • leucine, • lycine

R “Radical” Groups It is these Side Groups which make each amino acid different from the others. Of the 20 used to make proteins, there are three groups. The three groups are IONIC, POLAR and NON-POLAR . These names refer to the way the side groups interact with the environment. Polar amino acids like to adjust themselves in a certain direction. Non-polar amino acids don't really care what's going on around them. And Ionic amino acids, act much like ionic compounds.

• Tryptophan (nonpolar) • Threonine (polar) • Lycine (ionic)

Page 13: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 13 Biomolecules

R R R

peptide bond

a.a.

amino group

carboxyl group

- Simple Proteins: - consist simply of a.a., e.g., Lactoglobin, C1864

H3012 O576 N468 S21 - Conjugated Proteins:

- a.a. plus some other component, e.g., iron in Haemoglobin, C3032 H4816 O872 N780 S8 Fe4

• Structures:

1. Primary Structure (1°) Shape: Linear

- a linear sequence of a.a. that makes up a particular polypeptide chain

- the R group plays no role in the peptide backbone of

proteins, as such a protein can be composed of any sequence of a.a. - a protein of 100 a.a. linked together in a chain

might have 20100 different a.a. sequence - it is this key property of diversity that allows for

such a wide range of proteins

2. Secondary Structure (2°) Shape: Helix (alpha-helix and beta-pleated sheet)

- each a.a. of a chain interacts with its neighbours, forming H-bonds - because of these interactions, polypeptide chains

Page 14: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 14 Biomolecules

tend to fold spontaneously into sheets or wrap into coils - this change in shape is called its secondary

structure

3. Tertiary Structure (3°)

Shape: Globular (“cupped hand shaped”) - a.a. in a chain also interact with water, forming a

folded helix, - disulphide (SS) bonds often stabilise the fold.

- aka disulphide bridge - a covalent bond formed in RER

- the nonpolar side of the chain tends to fold so that

(hydrophobic groups) are shielded from the surrounding water - the polar side (hydrophilic) will tend to expose

itself to the surrounding water - all this minimizes disruption of H-bonds

- this folding leads to a complicated globular

shape, indicative of tertiary structure

4. Quaternary Structures (4°) - results when two or more Polypetides unite to

form a multimeric protein - proteins with more than one polypeptide chain

are said to be oligomeric

source: http://ww

w.accessexcellence.org/A

B/G

G/

Priamary (linear)

Secondary

Tertiary & Quaternary

Page 15: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 15 Biomolecules

- e.g., haemoglobin - a tetramer, containing 2

alpha + 2 beta sub-units.

Aside: - What is the advantage of association rather than

staying as monomers? In some proteins the subunit alone is not active - so biological activity depends on intact oligomeric structure. So in this case oligomeric structure provides increased stability such that in the absence of oligomeric structure, the single subunits are unstable. - However, in other oligomeric proteins the

single subunit is biologically active, and appears to act independently of the oligomeric structure. So stability is not the only factor involved.

- Another advantage of multiple subunits is greater

flexibility of activity e.g. hemoglobin (Hb) and many enzymes show cooperativity. In the case of tetrameric Hb one subunit binds oxygen then stimulates neighbour subunits to bind oxygen more readily and so on through the 4 subunits so the subunits cooperate to ensure rapid and effective binding of oxygen. - If there were no cooperativity then it is likely

that competition between the subunits for binding oxygen would be overall less efficient. Cooperativity is mediated through intersubunit contacts.

- Also subunits provide an advantage in regulation

of protein activity. In proteins and enzymes containing identical subunits it is found that the subunits contain special sites called allosteric sites located away from the active site of the

Page 16: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 16 Biomolecules

enzyme or protein. - Allosteric sites bind small molecules such as

sugars, nucleotides etc., and these cause intersubunit changes in shape that regulate the activity at the active site so giving a fine control over the biological activity. Not all enzymes or proteins have allosteric sites, many do not e.g., lactate dehydrogenase (LDH) is a tetramer, and has no known mechanisms of regulation.

- Lastly there is a genetic advantage in having

oligomeric structure. - The four protein sub-units of a tetramer will

be coded by four different genes. - If an error occurs in DNA transcription or

RNA translation producing faulty copies of one of the sub-units, then provided some correct copies have been produced elsewhere of the other three other submits, there is not a total loss of protein activity only a partial loss, which may be enough for survival. - If one gene produced one polypeptide

chain, and a mutation produced an error in the DNA then all copies of the subsequent protein would be faulty. If the protein is vital then the mutation may be fatal. So oligomeric structures may be important in survival.

- Caveat: The text describes the shape as being 3

dimensional, but then all these shapes are 3 dimensional…

• Denaturation

- the structure of a protein is not haphazard

- any force that disrupts the delicate balance (e.g., of weak bonds and interactions) will denature the protein, resulting in altered structure and hence in malfunction

- Two such forces:

1. Extremes in pH, which affect charges on different parts of the molecule

2. Extremes of temperature, which disrupts H bonds

Allosteric - enzymes, in which a compound

combine with a site on the protein other than the active site

o the allosteric site - Changes that enhance activity are

referred to as allosteric activation, o the binding of oxygen

molecules to haemoglobin o The binding of oxygen to

one subunit induces a conformational change in that subunit that interacts with the remaining active sites to enhance their oxygen affinity.

- while the opposite is called allosteric inhibition.

o when 2,3-BPG (2,3-bisphosphoglycerate) binds to a regulatory site on hemoglobin, the affinity for oxygen of all subunits decreases.

Page 17: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 17 Biomolecules

• Proteins therefore operate within a limited range of pH and temperature

Page 18: 2/2/07 A. Synthesis & Hydrolysis reaction Notesterrimosher.weebly.com/uploads/4/8/5/7/4857713/4_biomolecules.pdf2/2/07 A. Synthesis & Hydrolysis reaction Vocab: • monomer ... Notes

Biomolecules

Cell Biology 18 Biomolecules

Form & Function of a Variety of Proteins: Function Form Example Use Structure

fibres

collagen; keratin; fibrin

cartilage; hair & nails; blood clot

Metabolism enzymes protease break down proteins

sodium-potassium pump; anion pump

excitable membranes; transport of Cl- ions

Membrane transport channels

aquaporins water transport through cell membranes

Cell recognition cell surface antigens MHC proteins; ABO blood group

“self” recognition; identifies red blood cells

Osmotic concentration albumin serum albumin

maintains osmotic concentration of blood

Regulation of gene action repressors lac repressors regulates transcription

Regulation of body function hormones insulin; vasopressin;

oxytocin

controls blood glucose levels; increases water retention by kidneys; regulates milk production

Transport throughout the body

globins hemoglobin; myoglobin; cytochromes

carries O2 and CO2 in blood; carries O2 and CO2 in muscle; electron transport

Contraction muscle actin; myosin contraction of muscle fibres

Defense immunoglobins; toxins

antibodies; snake venom

mark foreign proteins for elimination; blocks nerve function

Aside: Plasma protein refers to any protein found in the blood plasma, e.g, hemoglobin, albumin,

immunoglobins, various peptide hormones etc.