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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Contents
Small Molecules and Polymers

Proteins, Polysaccharides, Nucleic Acid

More Bonds, Polarity Hydrophobic, Hydrophillic Osmosis, Tonicity, pH Enzymes

Chemical evolution
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.

simple molecules

reduced carbon-containing molecules

organic compounds

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cannot find source

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

Monomers and Polymers

Monomers are the building blocks of polymers.
amino acids (build proteins) monosaccarides (build polysacharides) nucleotides (build nucleic acid)

Polymers are large molecules or macromolecules

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

Polymers Linking - ANABOLISM

Anabolic = synthesis reaction
Condensation = H2O released Dehydration reaction in the synthesis of a polymer

(catalysed by polymerase enzyme)

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

Polymers Unlinking - CATABOLISM

Catabolic = decomposition reaction
Hydrolysis = H2O absorbed
Splitting of polymer by adding water to covalent bond

(catalysed by hydrolase enzyme)

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

Macromolecules
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).

Proteins
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
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Amino Acid Peptide Bonds

The anabolic process = condensation of two amino acids to form a peptide bond
(releases water)

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

Amino Acid Peptide Bonds

Anabolic

Condensation = H2O released

Catabolic Hydrolysis = H2O absorbed

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Polysaccharides
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.

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Polysaccharides

glycosidic bond
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Disaccharide

disaccharide glycosidic bond

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Nucleic Acid
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.
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Nucleic Acid

phosphodiester bond

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

Water and Hydrogen Bonding

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.

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

Water and Hydrogen Bonding

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

Water and Hydrogen Bonding

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

Chemical Polarity
Polarity underlies a number of physical properties including surface tension, solubility, melting-point and boiling-point. Polar molecules interact through dipoledipole 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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Chemical Polarity within Molecule

The following functional groups are polar molecules
OH . NH2 COOH ... SH .. 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. hydroxyl amine carboxyl sulfhydryl

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Hydrophillic and Hydrophobic

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.
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Hydrophillic and Hydrophobic

Proteins are part hydrophillic and part hydrophobic. This affects their structure.

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

Protein Folding in Cell Membrane Hydrophyllic / Hydrophobic Interactions

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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

Alpha Helix Structure

What is a feature characteristic of an -helix?
The alpha helix (-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 -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. 34

Osmotic pressure -2

Example: Salt water is lighter so has greater osmotic pressure than pure water.
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http://www.sparknotes.com/chemistry/solutions/colligative/section1.html

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.)

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Tonicity - 2

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Permeability and Water

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

hypotonic environment

hypertonic environment

Water molecules travel through the plasma membrane, vacuole or protoplast by diffusing across the phospholipid bilayer via aquaporins.
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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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Water self-ionization - 2
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 1.01014.
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Water self-ionization and pH

Pure water molecules dissociate into equal amounts of H3O+ and OH, so each of their concentrations are equal to 1.0 107 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.
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pH

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

pH

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

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

Enzyme Reactions Gibbs Free Energy

Copyright @Pearson Education Inc, publishing as Benjamin Cummings

Enzyme Reactions Gibbs Free Energy

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.

Enzyme Reactions Gibbs Free Energy

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

MichaelisMenten Equation
In biochemistry, MichaelisMenten kinetics is one of the simplest and best-known models of enzyme kinetics. In biology, kinetics is the rate of reactions. MichaelisMenten kinetics describes the rate of enzymatic reactions, by relating concentration [S] of a substrate S reaction rate v MichaelisMenten Equation 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.

MichaelisMenten Constant
If Vmax represents the maximum reaction velocity achieved at saturating substrate concentrations
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 MichaelisMenten kinetics.