BIOC 300A, I Flashcards
What key property of water emerges from its high melting & boiling points and heat of vaporization?
Cohesiveness between water molecules in solution.
Which is the strongest type of chemical bond?
Covalent.
What functional group promotes solubility in water?
-OH (hydroxyl).
What is the consequence of H-bonding between water molecules?
Each molecule of water forms 4 H-bonds to other water molecules, creating water’s characteristic lattice structure.
Under what circumstances can H-bonding occur?
When a H atom attached to an electronegative atom approaches another electronegative particle.
Define van der Waals forces.
Very weak attractions created by transient dipole moments between uncharged molecules.
How do weak intermolecular attractive forces contribute to bonding?
Abundance - many weak bonds together can form one stronger bond.
What is the significance of weak nonpolar molecular interactions in biology?
The ability to easily form and break bonds allows for fluid, dynamic biological processes and contributes to the constant ebb & flow of macromolecules.
Define metabolite.
Low-molecular-weight molecules (such as glucose & glycerol) that are chemically transformed in biological processes.
Define protein.
A biological macromolecule made of a linear array of amino acids joined by peptide bonds.
What is the basic structure of all life processes?
The interplay between macromolecules and metabolites, with members of both classes common to all living things.
What is the basic structure of DNA?
A linear polymer consisting of a fixed sugar-phosphate backbone with attached bases (A, T, G, C) oriented to give the whole strand directionality with a distinct head and tail end.
What is indicated by similar 3D structures between proteins in different organisms?
They likely perform similar functions.
Define hydrophobic interaction.
The tendency of nonpolar molecules in water to interact with one another; interactions are driven by an increase in the entropy of water when water molecules in contact with nonpolar molecules are released into bulk water.
What are the 4 fundamental noncovalent bond types?
Ionic interactions, hydrogen bonds, van der Waals forces, and hydrophobic interactions.
What 2 features of water make it an especially versatile solvent?
The asymmetric distribution of charge between H and O makes it polar, and H-bonding between water molecules makes water highly cohesive.
Define dielectric constant.
A quantity measuring the ability of a substance to store electrical energy in an electric field, giving a rough measure of a solvent’s polarity; a higher constant means greater polarity.
What is the significance of water’s high dielectric constant?
A high dielectric constant means greater polarity, so ionic compounds are more likely to dissolve in water than in less polar solvents as it is more energetically favourable for its component ions to associate with water molecules than with each other.
What makes for the strongest hydrogen bonds?
A straight, linear configuration of all atoms involved.
How does water break ionic compounds apart?
Water’s high dielectric constant means it can store a large amount of electrical energy in its electrical field, which it can use to cancel out some of the electric bond strength between ionic molecules and make ionic compounds less likely to stick together.
What is the difference between H-bond acceptors and H-bond donors?
The H-bond donor is the molecule containing the H and is thus more tightly linked to the H atom; the acceptor is the electronegative atom that becomes less tightly linked to the H atom on the donor.
How do H-bonding and ionic interactions affect surface complementarity?
When complementary surfaces meet, H-bond donors align with H-bond acceptors, and nonpolar surfaces come together via the hydrophobic effect to maximize van der Waals interactions between each other and to minimize the surface area exposed to the aqueous environment.
In the hydrophobic effect, why is it favourable for some water molecules to be released from their shells when two nonpolar molecules come together in solution?
Molecules in the water shells are highly ordered, so release of some results in an increase in entropy, which is energetically favourable (2nd Law of Thermodynamics).
In the hydrophobic effect, why do water molecules form ordered shells around nonpolar molecules?
Nonpolar molecules can’t participate in H-bonding or ionic interactions, so it is easier for water molecules to bond with each other.
Define entropy.
The degree of randomness or disorder in a system.
What is the 1st Law of Thermodynamics?
The total energy of a system and its surroundings is always constant.
What is the 2nd Law of Thermodynamics?
The total entropy of a system and its surroundings is always increasing.
According to the 2nd Law of Thermodynamics, what must happen when biological processes create order within a system?
The decrease in the entropy of the system must be balanced by an increase in the entropy of the surroundings (usually by the release of heat).
According to the 1st Law of Thermodynamics, what must happen when energy is released during bond formation?
The energy released must be used to break other bonds, released as heat or light, or stored in some other form.
How are entropy, enthalpy, and temperature related?
Any change in entropy of the surroundings is proportional to the amount of heat transferred from the system and inversely proportional to the temperature of the surroundings.
Why is change in entropy/enthalpy inversely proportional to temperature?
If heat is released into matter that is already hot, the change will be small; if the matter is relatively cold, the change will be greater.
Define buffer.
An aqueous solution consisting of a weak acid and its conjugate base (or vise versa) that resists changes in pH when strong acids or bases are added.
Which amino acid is Ala?
Alanine.
Which amino acid is Arg?
Arginine.
Which amino acid is Asn?
Asparagine.
Which amino acid is Asp?
Aspartic acid.
Which amino acid is Cys?
Cysteine.
Which amino acid is Gln?
Glutamine.
Which amino acid is Glu?
Glutamic acid.
Which amino acid is Gly?
Glycine.
Which amino acid is His?
Histidine.
Which amino acid is Ile?
Isoleucine.
Which amino acid is Leu?
Leucine.
Which amino acid is Lys?
Lysine.
Which amino acid is Met?
Methionine.
Which amino acid is Phe?
Phenylaline.
Which amino acid is Pro?
Proline.
Which amino acid is Ser?
Serine.
Which amino acid is Thr?
Threonine.
Which amino acid is Trp?
Tryptophan.
Which amino acid is Tyr?
Tyrosine.
Which amino acid is Val?
Valine.
What is the abbreviation for alanine?
Ala.
What is the abbreviation for arginine?
Arg.
What is the abbreviation for asparagine?
Asn.
What is the abbreviation for aspartic acid?
Asp.
What is the abbreviation for cysteine?
Cys.
What is the abbreviation for glutamine?
Gln.
What is the abbreviation for glutamic acid?
Glu.
What is the abbreviation for glycine?
Gly.
What is the abbreviation for histidine?
His.
What is the abbreviation for isoleucine?
Leu.
What is the abbreviation for lysine?
Lys.
What is the abbreviation for methionine?
Met.
What is the abbreviation for phenylaline?
Phe.
What is the abbreviation for proline?
Pro.
What is the abbreviation for serine?
Ser.
What is the abbreviation for threonine?
Thr.
What is the abbreviation for tryptophan?
Trp.
What is the abbreviation for tyrosine?
Tyr.
What is the abbreviation for valine?
Val.
What is the typical pKa of a terminal α-carboxyl group?
3.1
What is the typical pKa of a terminal α-amino group?
8.0
What is the typical pKa of the histidine side chain?
6.0
What is the typical pKa of the aspartic acid and glutamic acid side chains?
4.1
What is the typical pKa of the cysteine side chain?
8.3
What is the typical pKa of the tyrosine side chain?
10.9
What is the difference between tyrosine and phenylalanine?
Tyrosine has an -OH group attached to the aromatic ring.
What is the difference between alanine and phenylalanine?
Where alanine has a methyl group, phenylalanine has a benzene ring substituted for one of the methyl group’s H atoms.
What is the typical pKa of the lysine side chain?
10.8
What is the typical pKa of the arginine side chain?
12.5
Which amino acids are basic?
Lysine, arginine, and histidine.
Which amino acids are acidic?
Glutamic acid and aspartic acid.
What is the side chain of glycine?
H.
What is the side chain of alanine?
A methyl group.
What is unique about the structure of proline?
The side chain is bonded to both the α-C and the α-N, forming a 5-membered ring.
Which amino acid includes a thioether group?
Methionine.
Why does proline significantly affect protein structure?
Its cyclic structure makes it more conformationally restricted than other amino acids, and the reduction of the embedded N to a secondary amine means it can’t act as a H-bond donor.
Which amino acids are hydrophobic (nonpolar)?
Glycine, alanine, valine, leucine, isoleucine, phenylalanine, tryptophan, proline, and methionine.
Which amino acids are hydrophilic (polar), but uncharged?
Serine, threonine, tyrosine, asparagine, glutamine, and cysteine.
Which amino acid includes a thiol group?
Cysteine.
What is the significance of the thiol group in cysteine?
Cysteine residues can form disulfide bonds, which are especially strong but easily reversible, making cysteine a good residue for enzymatic active sites and other reactive structures.
What is the difference between serine and cysteine?
They are structurally similar, but cysteine has a thiol (-SH) where serine has a hydroxyl (-OH) group.
What structure is unique to tryptophan among the amino acids?
An indole group (2 fused rings, 1 containing an NH group).
What is the significance of the indole group in tryptophan?
The NH group makes tryptophan less purely hydrophobic than the other non-polar amino acids.
What is the difference between valine and leucine?
Both have terminal isopropyl groups, but leucine has an additional CH2 between the α-C and the isopropyl group.
What is the difference between leucine and isoleucine?
They are isomers of one another: leucine’s side chain forks at the end, while isoleucine’s has a methyl group jutting off its first CH group.
Where is the S in methionine?
Just before the terminal methyl group (after two CH2 groups).
What is the difference between serine and alanine?
Serine has an -OH group where one of alanine’s methyl H atoms would be.
What is the difference between serine and threonine?
Serine’s side chain is -CH2-OH, but threonine has an additional methyl group in place of one of the H atoms.
What is the difference between tyrosine and alanine?
Tyrosine has a phenol group where one of alanine’s methyl H atoms would be.
What is the difference between asparagine and alanine?
Asparagine has a carboxamide group where one of alanine’s methyl H atoms would be.
What is the difference between asparagine and glutamine?
Both have terminal carboxamide groups, but glutamine has 2 CH2 groups leading up to it while asparagine has only 1.
What is the difference between cysteine and alanine?
Cysteine has an SH (thiol) group attached where one of alanine’s methyl H atoms would be.
What is the difference between cysteine and methionine?
Both have S in their side chains, but methionine has an S atom between two methyl groups while cysteine has a terminal SH group attached to one methyl group.
Which is more reactive: -SH or -OH?
-SH.
What is the significance of histidine’s pKa (6)?
It can be positively charged or uncharged near neutral pH, so it is extremely sensitive to small changes in physiological pH.
Which amino acids have readily ionizable side chains?
Tyrosine (phenol), cysteine (thiol), arginine (guanidinium), lysine (primary amine), histidine (imidazole), aspartic acid and glutamic acid (carboxyl).
Define cystine.
A unit of 2 cysteine residues cross-linked by a disulfide bond.
Why are valine, threonine, and isoleucine unfavourable residues for an alpha helix?
Branching at the β-carbon creates steric clashes, destabilizing the helix.
How do serine, aspartic acid, and asparagine disrupt alpha helices?
Their side chains contain H-bond donators or acceptors too close to the main chain, where they compete for main-chain NH and CO groups.
How does proline disrupt alpha helices?
It lacks an NH group (so it can’t participate in additional H-bonds), and its ring structure prevents it from assuming the right bond angle to fit into a helix.
In an alpha helix, how many amino acid residues are present per turn?
3.6
In an alpha helix, which amino acids will be closest to one another spatially?
Residues spaced 3-4 units apart in the amino acid sequence.
Within a turn of an alpha helix, which amino acids will be furthest apart?
Residues spaced 2 apart in the amino acid sequence (they will be on opposite sides of the helix).
Why are right-handed alpha helices energetically more favourable than left-handed helices?
There is less steric clash between the side chains and the backbone in a right-handed helix.
What does the small outlying region of the Ramachandran plot represent?
Left-handed alpha helices.
Which is more structurally diverse: alpha helices or beta sheets?
Beta sheets.
How are antiparallel beta sheets constructed?
2 beta strands oriented in opposite directions come together, linking amino acids by H-bonds between the NH group of one and the CO group of the other.
How are parallel beta sheets constructed?
2 beta strands oriented in the same direction link up by H-bonding so that each amino acid of one sheet is bonded to 2 different amino acids in the other.
What is a hairpin/reverse turn?
A secondary protein structure made of 4 amino acids: CO and NH of residue 1 H-bond to NH and CO of residue 4, respectively, allowing the whole polypeptide chain to reverse direction.
Where are turns and loops found in protein structures?
On protein surfaces (so they are often involved in interactions between proteins and other molecules).
