Lecture 3: Proteins

Question 1

Titration Curve

Answer 1

ex. 10 ml 0.5 M acetic acid (CH3COOH) titrated with 0.5 M NaOH
- Initially you make a 0.5M solution and the pH is around 2.5 (when non-dissociated)
- Then add 0.5M into a OH solution
- Initially, pH is rising very slowly (because when adding OH- atoms, the OH- combines with H+ to form water)
- Continue to add more, where you reach equivalence point (have 100% dissociation, all acid converted to conjugate base)
- What you notice right away is that the pH rises rather rapidly because theres no more protons around
- This can act as a buffer because it can buffer OH- ions, but only works in one direction

Question 2

Buffers

Answer 2

make the overall solution resistant to pH change, because they react with both added bases and acids.
- important for chemical reactions to take place in our body (ex. stability of proteins)
•How do they work?
you want to avoid the examples below where the pH rises/falls very rapidly
- But have to set up run where you’re at half equivalence to start with
Add equal parts of acetic acid (conjugate base of acidic acid) and OH-

Question 3

law of mass action

Answer 3

• illustrated by buffers
  • Addition of reactants accelerates the reaction. Likewise, removal of products accelerates the reaction (towards the right side).

Question 4

Buffering Range

Answer 4

where the titration curve slowing increases in pH

Question 5

Functional Groups

Answer 5

Hydroxyl
Phosphate
Sulfhydrl
Amino
Carbonyl
Carboxyl
 (review structural formula)

Question 6

Hydroxyl

Answer 6

In:
- alcohols and sugars
Properties: 
- very polar (more soluble bc of h bonds)
- acts as a weak acid and drops a proton

Question 7

Phosphate

Answer 7

In:
- organic phosphates
Properties:
- when several groups are linked together, breaking O-P bonds between them releases large amounts of energy
- important for energy and metabolism

Question 8

Sulfhydrl

Answer 8

In:
- Thiols
Properties:
- When present in proteins, can form disulphide (S-S) bonds that contribute to protein structure

Question 9

Amino

Answer 9

In:
- amines
Properties:
- Acts as a base- tends to attract a proton to form

Question 10

Carbonyl

Answer 10

In:
Aldehydes (terminal C), ketones (middle)
- sugars
Properties:
- react with certain compounds to produce larger molecules to form alcohols

Question 11

Carboxyl

Answer 11

In:
- carboxylic acids
Properties:
- acts as an acid- tends to lose a proton in solution to form CooO- (review structure)

Question 12

Large Molecules

Answer 12

• Macromolecules*
• Proteins, nucleic acids, and carbohydrates are macromolecules that can form huge polymers

• Most of you is made up of water (the blue)
As you grow, water content drops (as you die its around 67%)
Rest are large molecules, and ions and small molecules

• Large molecules
macromolecules: everything that forms polymers
Lipids are typically smaller in size, but never form polymers
So most important are proteins, nucleic acids and carbohydrates

Question 13

Macromolecules synethsis

Answer 13

• Macromolecules are made the same way in all living things, and are present in all organisms in roughly the same proportions.
• An advantage of this biochemical unity is that organisms acquire needed biochemicals by eating other organisms. Another advantage, aliens couldn’t digest us because their components would be different (perhaps different stereoisomer)

Question 14

Polymerization

Answer 14

bonding together of monomers in order to form a polymer

Question 15

Condensation Reaction

Answer 15

MONOMER IN, WATER OUT
building polymer
Water molecule is released
DNA, Protein, RNA, sugar synthesis all require energy input (polymerization or condensation)

Question 16

Hydrolosis

Answer 16

WATER IN, MONOMER OUT
Break down polymer using water
When we eat food (reactions are releasing energy)
Anabolic reactions (require energy), catabolic (release energy)

Question 17

CHEM VS. BIO- bonds

Answer 17

Chemistry: breaking bonds require energy (refers to exactly one covalent bond)

Biology: breaking bonds release energy (refers to entire chemical reaction, made up of several covalent bonds that are broken and formed)

Question 18

Proteins

Answer 18

- most abundant types of
molecules found in the body
- Varies in shape and size
- Made up of amino acids
- Collagen: found in tendons which connect bones to muscles (rope like)
- Deoxyribonuclease: cuts DNA

• Range in size from a few amino acids to thousands of them (titin = 33000 amino acids).
- Folding is crucial to the function of a protein and is influenced largely by the sequence of amino acids.

Question 19

Primary Structure

Answer 19

• determines how proteins fold (sequence)

Question 20

Ionized vs. Non-ionized form

of amino acid

Answer 20

review structure
Ionized : OH on the carboxyl group is just O^-
Non-ionized form: just OH on the carboxyl group

Question 21

R group on Amino Acid

Answer 21

• determines the identity of the amino acid*
• can be nonpolar (just C, H and sometimes N)
• can be polar (Hydroxyl groups, or C=O)
• can be charged side chains which form H bonds that are highly soluble in water

Question 22

Peptide Bond Formation

Answer 22

• amino group of amino acid (N) forms covalent bond with C (carboxyl group of amino acid)
• Peptide bond is fairly stable due to electron distribution (very rigid therefore, unable to rotate bond)
• electron sharing here makes peptide bond double bond like

Question 23

Polypeptide Chain

Answer 23

N terminus to C terminus
- Amino acids joined by peptide bonds
- Peptide bonded backbone
- Keep adding amino acids and you get PRIMARY STRUCTURE
- Protein always stats at amino group, ends at carbon group (N terminus ad C terminus)
Peptide bond separates different amino acids

Question 24

Possibilities of Proteins

Answer 24

Enormous numbers of different proteins are possible: 20 kinds of amino acids; 100 aa (very small) in one protein = 20^100 = 10^130 possible combinations. Means there is a huge space for proteins to evolve.

Question 25

Why do polypeptides flex?

Answer 25

• groups on either side of each peptide bond can rotate about their single bonds

Question 26

Secondary Structure (FOLDING of amino acids)

Answer 26

a) hydrogen bonds form between peptide chains
- at this point infolding, side chains are not involved (only back bone)

b) * Secondary structures of proteins results*
• Alpha helix (winks hair):
3.6 amino acids
- bond forms in same direction as helix (keeps structure fairly stable)
- R groups actually point away from helix, towards exterior to interact with neighbouring helix or parts of proteins
• Beta pleated sheets
Bonds in the plane of the pleated sheet:
- Stable
- R groups point upward and downward from plane
- Interact with other parts outside of plane

Question 27

Proline

Answer 27

Proline fits neither in a α helix nor in a β sheet.
•Why? (review picture)
- forms second covalent bond (to N)
- Normally would be R group
- Means that there is a ring structure (which the C bond cannot rotate anymore, making it rigid)
- Cannot be a H bond to contribute to structures
- Proline would cause a kink at the end of Alpha helix and the helix would end (or beta sheath)