Biochemistry

• polar covalent bonds occur when the difference in electronegativity is from 0.5 to 1.7. Electrons are shared unequally and are closer to the more electronegative atom giving the other a slightly positive charge.
• non-polar covalent bonds occur when the difference in electronegativity is less than 0.5. The Electrons are shared equally.
• forces between atoms within a molecule or ionic crystal are intramolecular forces.
• forces which act between neighbouring molecules are intermolecular forces and are relatively weak.
• ionic bonds occur when the difference in electronegativity is greater than 1.7. Electrons are transferred and the atoms become stable but charged and create a crystal structure.
• dipole-dipole forces occur only in polar molecules. The negative end of one molecule attracts the positive end of another molecule.
• hydrogen "bonding" occurs between polar molecules with a oxygen bonded to a fluorine, nitrogen or oxygen.
• London dispersion forces act in all molecules (even non-polar). Because Electrons are always vibrating there is a moment when an atom/molecule has a slight charge.
• primary folding is the chaining of 100s to 1000s of amino acids.
• secondary level of folding it divided in two: alpha helix and beta pleated sheet. These 3D structures are held together by hydrogen bonds between the amine group and carbonyl (ketone)
• tertiary level folding is the intermolecular forces between the r groups in the polypeptide chain. from strongest to weakest: disulfide bridge (between cysteine), Ionic forces, dipole-dipole forces (including hydrogen bonds) and hydrophobic interactions
• quaternary structure is the interaction between multiple polypeptides that make up a protein. this can be either permanent or temporary.
• peptide bonds are formed between amino acids by condensation reactions
• there are roughly 28000 proteins in the human body
• there are many jobs proteins do in the body: protein pumps and channels, structural protein, hormones, enzymes, antibodies, hemoglobin,
• glycosidic bonds hold the polysaccharides together and are formed by condensation reactions
• label these functional groups

  A) hydroxyl

  B) alcohol

  C) carboxyl

  D) carboxylic acid

  E) amine

  F) amine

  G) sulfhydryl

  H) thiol

  I) phosphate

  J) phosphate

  K) carbonyl

  L) aldehyde

  M) ketone

  
• ether functional group: R-O-R

  ester functional group: R-C double bonded O and O with R2
• amylose is made by plant cells for storage (like in seeds). It is made of alpha glucose. Has alpha 1-4 bonds. It is linear but does coil. We can break it down into glucose and is a major source of glucose for us.
• glycogen is made in animal cells for the long term energy storage and is made by alpha glucose alpha bonded between 1,4 and 1,6 glycosidic bonds. it is highly branched and coiled and can be broken down into glucose.
• cellulose is made by plant cells for structure and strength, it is a long chain of beta glucose molecules that can form hydrogen bonds between other strands. Glycosidic beta bonds between carbon 1 and 4. Humans are unable to break it down.
• Amylopectin is made by plant cells and is basically the same as amylose but is highly branched and coiled and makes bonds between 1 and 6 where it branches.
• disaccharides are two sugar units joined together by a glycosidic bond. Three examples are: maltose (two glucose, alpha 1 and 4), lactose (glucose and galactose, beta 1 and 4) and sucrose (glucose and fructose, alpha 1 and 2)
• enzymes are biological catalysts that speed up chemical reactions in the body
• factors that limit the rate of reactions are temperature, concentration and the size of molecules.
• enzymes speed up reaction rate by reducing the amount of activation energy
• enzymes are always globular proteins with very specific shapes. the surface depression is called the activation site. They are substrate specific and work for no other reactions
• The induced fit model is when the active site changes shape to fit the substrate (like a hug)
• The denaturation of proteins is the process by which the shape of a protein is permanently changed which results in the loss of function because enzymes depend on its shape.
• denaturation is caused by change in temperature, pH or ionic concentrations.
• temperature can denature a protein. Higher temperature leads to molecular vibrations which can overcome the weaker forces between side chains
• What is competitive inhibition?

  An inhibitor molecules with a similar structure to a substrate binds to the active site blocking it from the substrate.
• What is non-competitive inhibition?

  An inhibitor binds somewhere else on the enzyme and changes the shape of the active site.
• What is allosteric regulation?


  Regulation of enzyme activity by binding of a molecule at a site other than the active site. There is allosteric inhibition or activation.
• Define feedback inhibition?

  An enzyme is regulated by the product of an enzyme down the line in a membrane.
• exothermic reactions are reactions that release energy to the surroundings
• endothermic reactions are reactions that take in energy from the surroundings
• the first law of thermodynamics states that energy can be transferred from one form to another but cannot be created or destroyed
• the second law of thermodynamics states that the entropy of a closed system always increases. This is why organisms need a constant supply of energy.
• lipids and fats are mostly carbons and hydrogen therefore are non-polar (not soluble). They are for long term storage of energy, make up membranes, hormone signalling.