Molecular Biology 1-4

Molecular Biology 1-4

put together by: Linda Fahlberg-Stojanovska

Disclaimer: I put these together for my kid for his smartphone.

However, I found most images had very small type and increased the font size. I am posting it because another teacher might find this useful.

The sources are given. If I have used anything illegally, write me and I will take it off.

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• Small Molecules and Polymers

• Proteins, Polysaccharides, Nucleic Acid

• More Bonds, Polarity

• Hydrophobic, Hydrophillic

• Osmosis, Tonicity, pH

• Enzymes

Contents

• simple molecules containing C, H, O and N react to form• reduced carbon-containing molecules,

which then react to form • organic compounds. The process is triggered by an energy source such as sunlight or

the heat released in a volcanic eruption.

Chemical evolution

simple molecules reduced carbon-containing organic compounds molecules

cannot find source3

Small MoleculesSmall Molecules: small molecular weight ,not a polymer

Examples: Metabolites and most drugs

Metabolite: is a small molecule that is

an intermediate or final product of metabolism.

•2 classes: Primary and Secondary

Primary metabolites: important for growth, development and reproduction. Ex: vitamins, energy-rich phosphates (ATP, GTP), membrane lipids, ...

Secondary metabolites: other small molecules often with a significant relationship with the environment.

Ex: antibiotics, alkaloids, toxins, dyes, ...

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Keywords

• Membrane lipids are lipids in the cell membrane. Examples are: phospholipids, glycolipids, and cholesterol.

• Alkaloids are a group of naturally occurring chemical compounds that contain mostly basic nitrogen atoms.

http://publications.nigms.nih.gov/insidethecell/chapter1.html

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http://www.bio.miami.edu/~cmallery/150/life/top_10_life.htm

• Monomers are the building blocks of polymers.– amino acids (build proteins)

– monosaccarides (build polysacharides)

– nucleotides (build nucleic acid)

• Polymers are “large molecules” or macromolecules

Monomers and Polymers

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Anabolic = synthesis reactionCondensation = H2O released

Dehydration reaction in the synthesis of a polymer

(catalysed by polymerase enzyme)

Polymers – Linking - ANABOLISM

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Catabolic = decomposition reactionHydrolysis = H2O absorbed

Splitting of polymer by adding water to covalent bond

(catalysed by hydrolase enzyme)

Polymers – Unlinking - CATABOLISM

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Macromolecules are large molecules:

Proteins, Nucleic acids, Polysacharides

These are polymers.

They are essential parts of organisms and participate in virtually every process within cells.

A polymer is a large molecule (macromolecule) composed of repeating structural units.

A macrocycle is a macromolecule with ring (chlorophyll).

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Macromolecules

• Proteins are composed of chains of amino acid / peptide bond …

• Proteins are linear polymers.

• Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism.

• Proteins also have structural or mechanical functions,

• such as actin and myosin in muscle and

• the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape.

• Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle.

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Proteins

peptide bond

Proteins

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http://en.wikipedia.org/wiki/Amino_acid

The anabolic

process =

condensation

of two amino

acids to form a

peptide bond(releases water)

Amino Acid Peptide Bonds

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Catabolic

Hydrolysis =

H2O absorbed

Anabolic

Condensation =

H2O released

Amino Acid Peptide Bonds

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• Polysaccharides are composed of chains of

monosaccharide /glycosidic bond …

• Polysaccharides can be linear or branched polymers.

• Polysaccharides: general formula of Cx(H2O)y

where x is usually a large number between 200 and 2500

• Examples:

• storage: starch and glycogen

• structural: cellulose and chitin.

Polysaccharides

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Polysaccharides

glycosidic bond

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disaccharide glycosidic bond

Disaccharide

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• Nucleic acids are composed of chains of

nucleotide/ phosphodiester bond …

• Nucleic acids include

• DNA (deoxyribonucleic acid) and

• RNA (ribonucleic acid).

• Nucleic acids are linear polymers.

• Together with proteins, nucleic acids function in

encoding, transmitting and expressing genetic

information.

Nucleic Acid

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Nucleic Acid

http://www.bio.miami.edu/dana/250/250S11_7.html

phosphodiester bond

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• Most biochemical reactions take place in the water environment.

• Molecules in the body are surrounded by water, and most

reactions occur in the presence of water.

Hydrogen Bonding

• The oxygen atom has a slightly negative charge.

• The hydrogen atoms have a slightly positive charge.

• This causes the molecules to “line up”

oxygen to hydrogen with a hydrogen

bond or H-bond.

Water and Hydrogen Bonding

http://www.biology.arizona.edu/biochemistry/tutorials/chemistry/page3.html19


http://runningstrong-biologylibrary.blogspot.com/2010_04_01_archive.html20

http://course1.winona.edu/sberg/241f09/Lec-note/Water.htm


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Chemical Polarity• Polarity underlies a number of physical properties including

surface tension, solubility, melting-point and boiling-point.

• Polar molecules interact through dipole–dipole intermolecular forces and hydrogen bonds.

• Molecular polarity depends on the difference in electronegativity between the atoms and the asymmetry of the molecule's structure.

• For example, a molecule of water is polar because of the unequal sharing of its electrons between oxygen and hydrogen in which the Oxygen has larger electronegativity than the Hydrogen, resulting in a "bent" structure.

• Methane is non-polar because the carbon shares the electrons with the hydrogen atoms almost uniformly.

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The following functional groups are polar moleculesOH ……………. hydroxylNH2 …………… amineCOOH ……...… carboxylSH …………….. sulfhydryl

Example:

The carboxyl group COOH is polar because of oxygen's high electronegative potential.

This gives the C=O bond a high dipole moment with the negative side at the oxygen atom.

Chemical Polarity within Molecule

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• A hydrophilic molecule is one that has a tendency to interact with or be dissolved by water and other polar substances.

• Hydrophillic molecules are polar.

• Hydrophillic molecules are capable of hydrogen bonding.

• Ex: Cl-, Na+, H+,…

• A hydrophobic molecule avoids water and is not water soluble.

• Hydrophobic molecules are non-polar.

• Ex: include alkanes, oils, fats

• Some molecules have parts that are hydrophillic and parts that are hydrophobic

• Hydrophillic parts are in contact (hydrogen bond) with water,

• Hydrophobic parts “move” where the water recedes.

Hydrophillic and Hydrophobic

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• Proteins are part hydrophillic and part hydrophobic.

• This affects their structure.

Hydrophillic and Hydrophobic

http://www.exobiologie.fr/wp-content/uploads/2008/12/image1-8.jpg

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Protein Folding in Cell Membrane

Hydrophyllic / Hydrophobic Interactions

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http://kvhs.nbed.nb.ca/gallant/biology/tertiary_structure.jpg

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Protein Folding in Cell Membrane

Hydrophyllic / Hydrophobic Interactions

Alpha Helix Structure

• What is a feature characteristic of an α-helix?

• The alpha helix (α-helix) is a right-handed coiled or

spiral conformation common in the secondary structure

of proteins.

• The alpha helix is stabilized by hydrogen bonds

between the carbonyl oxygen C=O of one amino acid

and the backbone nitrogen N-H of a second amino

acid located four positions away.

Alpha Helix Structure

Hydrogen

bonds in red

in α-helix

structure

Osmosis - 1

• Osmosis is the movement of solvent molecules through a semi-permeable membrane into a region of higher solute concentration, aiming to equalize the solute concentrations on the two sides.

• Osmosis provides the primary means by which water is transported into and out of cells.

• Although osmosis does not require input of energy, it does use kinetic energy and can be made to do work.

• Osmosis can be countered by increasing the pressure of the hypertonic solution, with respect to the hypotonic.

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Osmosis -2

• Osmosis is essential in biological systems, as biological

membranes are semipermeable.

• Semipermeable membranes are impermeable to

large and polar molecules, such as ions, proteins, and

polysaccharides.

• They are permeable to non-polar and/or hydrophobic

molecules like lipids as well as to small molecules like

oxygen, carbon dioxide, nitrogen, nitric oxide, etc.

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Permeability• A solvent is a liquid, solid, or gas that dissolves a solute.• A solute is disolved in a solvent.• Semi-permeable membrane is a membrane that is

permeable to the solvent, but not the solute.

semi-permeable = selectively permeable• Permeability depends on solubility, charge, or

chemistry, as well as solute size.• Water molecules travel through the plasma membrane,

vacuole or protoplast by diffusing across the phospholipid bilayer via aquaporins

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Permeability and Water

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Osmotic pressure -1

• Osmotic pressure is the pressure which needs to be applied to a solution to prevent the inward flow of water across a semipermeable membrane.

• Osmotic pressure is a colligative property, meaning that the osmotic pressure depends on the molar concentration of the solute but not on its identity.

• Example: osmotic pressure of ocean water is ≈ 27 atm.

• Diffusion is the movement of particles from a region of higher concentration to one of lower concentration (this is freeflow – there is no membrane).

• Solutes able to freely cross the membrane do not exert osmotic pressure because they will always be in equal concentrations on both sides of the membrane.

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Osmotic pressure -2

http://www.sparknotes.com/chemistry/solutions/colligative/section1.html

Example: Salt water is “lighter” so has greater osmotic pressure than pure water.

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Tonicity - 1

• Tonicity measures the difference in the osmotic pressures.

• When the osmotic pressure of the solution outside a cell is higher than the osmotic pressure inside the blood cells, the solution is hypertonic.

• Example: Normal salt content of a red blood cell is 9g/L• HypERtonic: salt content outside the RBC is >9g/L

(The osmotic pressure is greater outside, water will EXIT the RBC and cause shriveling.)

• Isotonic: salt content outside the RBC is 9g/L. (The osmotic pressure is equal on both sides.)

• HypOtonic: salt content outside the RBC is <9g/L• (The osmotic pressure is smaller outside, water will ENTER the RBC

and cause swelling.)36

Tonicity - 2

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• Water is a solvent.

• Water travels from the region of low concentration of

solute to the region of high concentration of solute in

order to equalize the concentrations .

Water molecules travel through the plasma membrane,

vacuole or protoplast by diffusing across the

phospholipid bilayer via aquaporins.

Permeability and Water

hypotonic environment hypertonic environment water

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Water self-ionization - 1

The self-ionization of water is the reversible chemical reaction in which a proton is transferred from one water molecule to another, in pure water or an aqueous solution to create the two ions: hydronium H3O+ and hydroxide OH−.

The self-ionization of water depends on temperature and pressure.

In autoprotolysis is the transfer of a proton between two identical molecules. Every solvent containing hydrogen can undergo autoprotolysis.

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The equilibrium constant of water is:

The constant of dissociation of water is:

where [H3O+] is the concentration of hydronium ion and

[OH−] is the concentration of hydroxide ion.

At 25 °C, Kw ≈1.0×10−14.

Water self-ionization - 2

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• Pure water molecules dissociate into equal amounts of H3O+ and OH−, so each of their concentrations are

equal to ≈ 1.0 × 10−7 mol/dm3.

• A solution in which the H3O+ and OH− concentrations

equal each other is considered a neutral solution.

• pH = - log [H+]

pH[neutral solution] = - log 10-7 = -(-7)log10 = 7

• Result: The pH of a neutral solution is 7.

Water self-ionization and pH

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pH

http://packerpedia.wiki.packer.edu/file/view/pH_Scale.jpg

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pH

http://packerpedia.wiki.packer.edu/file/view/pH_Scale.jpg

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Enzymes

• Enzymes are proteins that catalyze (i.e., increase the rates of) chemical reactions.

• Names of Enzymes - often end in “ASE” – hydrolase (digestive enzyme catalyzes hydrolysis)– toplomerase (regulation of unwinding of DNA)

• Almost all chemical reactions in a biological cell need enzymes in order to occur at rates sufficient for life.

• A substrate is a reactant that has been acted upon by a catalyst. In enzymatic reactions, the reactants are called substrates.

Enzymes

• In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products.

http://en.wikipedia.org/wiki/Enzyme#Cofactors_and_coenzymes

Enzyme Reactions – Gibbs Free Energy


Copyright @Pearson Education Inc, publishing as Benjamin Cummings

• Phosphorylation (e.g. making ATP) is an energy-storing endergonic reaction


http://faculty.clintoncc.suny.edu/faculty/michael.gregory/files/bio%20101/bio%20101%20lectures/energy/energy.htm

Enzymes

• Enzymes are selective for their substrates.• So, the set of enzymes made in a cell determines which

metabolic pathways occur in that cell.• Like all catalysts, enzymes work by lowering the

activation energy (Ea‡) for a reaction, thus dramatically

increasing the rate of the reaction.


Copyright @Pearson Education Inc, publishing as Benjamin Cummings

Enzyme Classification

• EC 1 Oxidoreductases: catalyze oxidation/reduction reactions

• EC 2 Transferases: transfer a functional group (e.g. a methyl or phosphate group)

• EC 3 Hydrolases: catalyze the hydrolysis of various bonds

• EC 4 Lyases: cleave various bonds by means other than hydrolysis and oxidation

• EC 5 Isomerases: catalyze isomerization changes within a single molecule

• EC 6 Ligases: join two molecules with covalent bonds.

Cofactors

• Some enzymes do not need any additional components to show full activity. However, others require non-protein molecules called cofactors to be bound in order to activate.

• Cofactors can be either inorganic (e.g., metal ions and iron-sulfur clusters) or organic compounds (e.g., flavin and heme).

• Organic cofactors can be either – prosthetic groups (tightly bound to an enzyme) or – coenzymes (released from the enzyme's active site during the

reaction).

Cofactors

• Cofactors

Coenzymes

• Coenzymes include NADH, NADPH and ATP adenosine triphosphate. These molecules transfer chemical groups between enzymes.

Enzyme Inhibitors

Michaelis–Menten Equation

• In biochemistry, Michaelis–Menten kinetics is one of the

simplest and best-known models of enzyme kinetics.

• In biology, kinetics is the rate of reactions.

• Michaelis–Menten kinetics describes the rate of enzymatic

reactions, by relating concentration [S] of a substrate S reaction rate v constant Km

Here, notice that the fraction has NO unit (everything is concentrations).

On the next page, notice that Km depends on both the curve and Vmax .

So Km is found by experiment (empirically) and given in tables.

Michaelis–Menten Equation

• If Vmax represents the maximum reaction velocity

achieved at saturating substrate concentrations…

Michaelis–Menten Constant

• Then, the Michaelis constant Km is the substrate

concentration at which the reaction rate is half of Vmax

• Biochemical reactions involving a single substrate are often assumed to follow Michaelis–Menten kinetics.