Lecture 3: Proteins Flashcards
Titration Curve
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
Buffers
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-
law of mass action
- illustrated by buffers
• Addition of reactants accelerates the reaction. Likewise, removal of products accelerates the reaction (towards the right side).
Buffering Range
where the titration curve slowing increases in pH
Functional Groups
Hydroxyl Phosphate Sulfhydrl Amino Carbonyl Carboxyl (review structural formula)
Hydroxyl
In: - alcohols and sugars Properties: - very polar (more soluble bc of h bonds) - acts as a weak acid and drops a proton
Phosphate
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
Sulfhydrl
In:
- Thiols
Properties:
- When present in proteins, can form disulphide (S-S) bonds that contribute to protein structure
Amino
In:
- amines
Properties:
- Acts as a base- tends to attract a proton to form
Carbonyl
In: Aldehydes (terminal C), ketones (middle) - sugars Properties: - react with certain compounds to produce larger molecules to form alcohols
Carboxyl
In:
- carboxylic acids
Properties:
- acts as an acid- tends to lose a proton in solution to form CooO- (review structure)
Large Molecules
- 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
Macromolecules synethsis
- 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)
Polymerization
bonding together of monomers in order to form a polymer
Condensation Reaction
MONOMER IN, WATER OUT
building polymer
Water molecule is released
DNA, Protein, RNA, sugar synthesis all require energy input (polymerization or condensation)
Hydrolosis
WATER IN, MONOMER OUT
Break down polymer using water
When we eat food (reactions are releasing energy)
Anabolic reactions (require energy), catabolic (release energy)
CHEM VS. BIO- bonds
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)
Proteins
- 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.
Primary Structure
• determines how proteins fold (sequence)
Ionized vs. Non-ionized form
of amino acid
review structure
Ionized : OH on the carboxyl group is just O^-
Non-ionized form: just OH on the carboxyl group
R group on Amino Acid
- 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
Peptide Bond Formation
- 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
Polypeptide Chain
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
Possibilities of Proteins
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.
Why do polypeptides flex?
- groups on either side of each peptide bond can rotate about their single bonds
Secondary Structure (FOLDING of amino acids)
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
Proline
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)
