Chemistry, Bonds, Acids, Bases, Polymerization, Proteins
Atoms
Always have the same number of protons and neutrons, make up the nucleus.
What is the mass number and the atomic number? For mass # specify units.
Mass number = # protons + # neutrons, Unit is daltons (Da, D), kilodaltons (kD)
Atomic number = # protons
What are Isotopes?
Atoms with the same # of protons but a different number of neutrons. Often unstable (radioactive).
Molecules
Atoms linked together by covalent bonds.
Trends of elements in the same row or column, regarding electrons
Same row, all electrons in the same shell thus similar size
Same column, same # of valence electrons thus similar chemical properties
Covalent Bond
Made of 2 electrons (1 from each atom), they are shared between the atoms
Difference Between Molecular Formula and Structural Formula
Electronegativity, What if atoms have the same # of shells?
How strongly electrons are attracted to the nucleus.
For elements with the same # of shells, those with more protons are more EN.
How are non-polar Covalent bonds drawn?
Electrons are shown to be superimposed on the bond to indicate they are halfway between the 2 atoms, shared equally.
Polar Covalent Bonds
Electrons are not shared equally, the atoms with a higher EN have a stronger pull and create partial charges. (Dipoles)
What 4 properties does water’s polarity cause?
Two forces cause water to make a meniscus
Adhesion: water molecules adhere to the glass to resist the downward pull of cohesion
Cohesion: water molecules at the surface experience a net downward pull from the H-Bonds in the water molecules below
High surface tension - i.e. light objects don’t fall through
In ice, molecules form a crystal lattice, but in liquid water there is no crystal lattice.
This is why liquid water is more dense, and ice floats in water
Water moderates temperature since H-bond formation or disruption, buffers heat energy
Ionic Bond
The valence electrons of one atom is transferred completely to another, forming two ions, bonded/attracted by electrostatic attraction
Salts (Ionic)
Ionic compound composed of a cation and anion, resulting from an acid-base reaction.
Commonly formed between elements at the edges of the periodic table since the EN difference is large.
Why does water facilitate reactions?
Water is a good solvent because polar molecules and ions dissolve easily in water due to its polarity.
Hydrophilic - Explain NaCl in Water
A substance that has a strong affinity for water, typically a polar molecule or ion.
For NaCl in water; Na+ is attracted to the negative O dipole, and the Cl- is attracted to the positive H dipole.
Hydrophobic - Why are molecules forced together?
Non-polar molecules that are introduced to water and do not dissolve.
They are forced together as it minimizes the disruption of the hydrogen bonding in the water. Van Der Waals forces also attract the non-polar molecules to each other.
Bond Energy
The amount of energy needed to separate two bonded/interacting atoms under physiological conditions.
Hydrogen Bonds
Occur btw H and N, O, F. Attraction of opposite charges since there is a high EN difference.
Rank Covalent, Hydrogen, and Ionic Bonds, and Hydrophobic, and van der Waals interactions, in order of INCREASING strength. (In biological/physiological conditions)
Van Der Waals, Hydrophobic, Ionic = Hydrogen, Covalent
Explain the weakness of ionic bonds in biological settings.
Ionic bonds are within proteins and are relatively weak, ionic bonds in salt crystals are MUCH stronger.
Mole
Amount of a substance in grams whose weight is equal to its molecular weight. Ex. silver has an atomic weight of 107.8682 amu, so one mole of silver has a mass of 107.8682 grams.
Molar/Molarity
A 1M (molar) solution is one mole of a compound dissolved in water to make 1L.
Acids, give example
Release/donate H+ ions in solution.
Strong acids dissociate completely. (reaction is complete)
Ex. the carboxyl group (-COOH) functions as a weak acid because it dissociates partially and reversibly. The O is more EN and releases H+ to grab an electron pair.
Bases, give example
Accept H+ ions in solution, thus releasing OH-.
Ex. the amino group (-NH2) functions as a weak base because it partially and reversibly accepts H+. N is less EN so its free electron pair can accept H+.
pH
pH is defined as the negative logarithm of the H+ concentration in moles/liter.
High pH = basic
Low pH = acidic
What are buffers? Relate to law of mass action
Make the overall solution resistant to pH change because they react with both added bases and acids.
Illustrate the law of mass action: Adding reactants accelerates the reaction forward, and removing products accelerates the reaction “backwards”.
What can be a buffer/how do they work?
Need equal amounts of a weak acid and its conjugate base to reach the half-equivalence point (just means 50% of each at this point)
Now, adding H+ or OH- will not change much as it pushes the reaction left or right
Ex. Adding more H+ reacts withe acetate (CH3COO-) to form morn acetic acid, which removes the H+ in solution
Then, adding OH- will react with H+ to form water, and the acid can dissociate adding more H+ back to solution, to balance everything out
What is the equivalence point, and what happens after?
Equivalence point: means that you have 100% of the base and all the acid is dissociated
After this, only OH- ions alter the pH so the curve usually increases rapidly
Why are buffers important for our body? (How are they used)
Rapid pH change is bad for our body.
For ex., in our blood we want the intracellular solution of our cells to keep the pH constant and we use buffers to do so.
Carbon Backbone
Carbons linked in a linear molecule that is the basis for all molecules in our body.
Hydroxyl Formula and Properties
Highly polar
Makes compounds more soluble through H-bonding with water
Can act as a weak acid and drop a proton
Phosphate Formula and Properties
Breaking O-P bonds between multiple phosphate groups linked together releases large amounts of energy
Sulfhydryl Formula and Properties
When present in proteins, can form disulfide (S-S) bonds, contributing to protein structure
Amino/Amines Formula and Properties
Acts as a base
Tends to attract a proton to form: -RNH3+ complex
Carbonyl (<- Functional Group) Formula and Properties (Name 2 molecule families)
Aldehydes and Ketones
React with certain compounds to produce larger molecules with the form:
Carboxyl (Acid) Formula and Properties
Acts as an acid
Tends to lose a proton in solution to form:
Macromolecules
Proteins, nucleic acids (DNA & RNA), and carbohydrates
They all can form large polymers
Biochemical Unity and Advantages
The idea that:
Macromolecules are made the same way and present in all organisms
Exist in roughly the same proportions in all organisms
Advantageous as it allows organisms to get biochemicals by eating other organisms.
Polymerization and Examples
Occurs through a condensation reaction (monomer in water out), anabolic (requires energy)
Releases one water molecule with each monomer added, forming a covalent bond
Ex. DNA replication, protein synthesis, making of starch
Depolymerization and Examples
Occurs through a hydrolysis reaction (water in monomer out), catabolic (releases energy)
With the help of one water molecule, the polymer releases one monomer
Ex. digestion of food molecules for energy generation
Bond Formation and Breaking (Biology)
In chemistry we think breaking bonds needs energy, forming them releases energy.
In biology we observe the ENTIRE reaction so we think that:
ATP hydrolysis releases energy
Covalent bond formation requires energy
***BOTH ARE TRUE
Proteins
Do all the work in a cell (Ex. replicate DNA)
Polymers made of amino acids (each monomer is 1 amino acid)
Protein Folding
Crucial to the protein’s function
Result of the sequence of amino acids
What do amino acids look like? (non-ionized and ionized)
Both are made of an amino group, side chain, and carboxyl group.
The ionized form has 3 H on the Nitrogen with a positive formal charge, and the OH group donates a proton, which occurs at a pH of 7.
The non-ionized has 2 H on the Nitrogen.
The backbone is everything other than the side chain.
There are 20 amino acids
Non-Polar Side Chains
Only have carbon and hydrogen atoms in their side chains
Occasionally a N or S atom
Chain is not charged
No EN atoms to forms H-bonds, thus hydrophobic
Polar Side Chains
Can have a hydroxyl group, or the groups with partial charges
H-bonds can be formed, thus hydrophilic
Electrically Charged Side Chains
Has an atom with a formal charge
Can form ionic bonds in the interior of proteins
Forms H-bonds, thus very hydrophilic
Can have acidic (-FC) or basic properties (+FC)
Peptide Bond Formation
C on the carboxyl end of the first joins with the N on the ionized amino group of the added amino acid
One water molecule is produced with each bond
The electron sharing makes the peptide bond double-bond like
Bond cannot rotate, would make a straight chain protein
Polypeptide Chain
Chain of amino acids joined by peptide bonds (protein)
Always start with amino group or “N-terminus” and end with a carboxyl group “C-Terminus”
Side chains dictate folding and function
All start with methionine
How are proteins created and fold? (1st and 2nd structure)
Ribosome makes unfolded polypeptide (primary structure)
H-bonds form between peptide chains with C=O oxygen and N-H nitrogen (secondary structure), alpha helix or beta pleated sheet
Alpha Helix
A very stable straight rod
Occurs due to a H-O bond of every fourth amino acid
One “turn” of the helix is 3.6 amino acids
Side chains not yet involved, they point outwards, away from helix
Beta Pleated Sheet
H-Bonds are formed across in the plane of the paper
Very stable
Arrowheads on its ribbon diagram are the carboxyl end (C-terminus)
Side chains point away from the plane, up or down
Proline (Pro) (P)
Never occurs in an alpha helix or beta pleated sheet
The side chain forms a ring structure by bonding to its “own” N
No H-bond can form between N and H, so no secondary structures can form
The N-C bond is in a ring so it cannot rotate and it causes a kink in the peptide