Section 1 Lectures 1-3

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

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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?

1. 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


2. High surface tension - i.e. light objects don’t fall through
3. 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


4. 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 (

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)

1) Ribosome makes unfolded polypeptide (primary structure)

2) 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