Chapter 1 Flashcards
What is a side chain?
A side chain, or R group, is the part of the amino acid that defines and specifies the various amino acids.
What is an amino acid?
An amino acid is a molecule that contains an amino group (-NH2) and a carboxyl group (-COOH).
What are the proteinogenic amino acids?
Proteinogenic amino acids are the 20 alpha amino acids encoded by the human genetic code. These are the only amino acids with which you need to have a memorized familiarity.
All amino acids are chiral except, _____
glycine
Are chiral amino acids L or D?
L
What does it mean to be amphoteric?
An amphoteric substance is something that can react like an acid or a base.
Amino acids are amphoteric because the carboxyl group can donate protons and the amino group can accept protons.
At low ph, ionizable groups tend to be _______
protonated
At high ph, ionizable groups tend to be
deporotonated
If the pH is lower than the pKa of a group, then the group will be __________
protonated
If the pH is higher than the pKa of a group, then the group will be__________
deprotonated
What is a zwitterion?
A zwitterion is a molecule with both a positive and a negative charge simultaneously. This is seen in amino acids at neutral and body pH’s.
What will the titration curve of an amino acid look like?
The titration curve of an amino acid will look like the combination of two monoprotic titration curves (or three if the side chain has an ionizable group)
What is the isoelectric point (pI)?
Isoelectric point or pI is the pH at which the amino acid is completely neutral as a result of all positive and negative charges balancing out.
How does one calculate isoelectric point?
One must take the pKa’s of the functional groups that provide the protein with a +1 and a -1 charge respectively. Then, one simply averages them. For amino acids with no ionizable side chain, this is simply the average of the pKa of the carboxyl group and the pKa of the amino group.
Note, for amino acids with ionizable side chains, it is important to correctly select the 2 pKa’s that correspond to -1 and +1 charge out of the three available pKa’s.
Amino acids with acidic side chains have _____ pI’s?
low
Amino acids with basic side chains have _____ pI’s?
high
What is a peptide?
A peptide is a chain of amino acids.
What is a residue?
A residue is just another name for amino acid. It is usually used when referring to amino acids in a peptide.
What is an oligopeptide?
An oligopeptide is a relatively small peptide of up to only 20 residues.
What is a polypeptide?
A polypeptide is any chain of amino acids that is longer than 20 amino acids.
What is a peptide bond?
Peptide bond is just a specific name for the amide bond that holds amino acids together.
Peptide Bond Formation occurs via ____________
Remember, dehydration reactions displace a water from the molecules reacting.
condensation aka dehydration
What is meant by the term N-terminus?
An N-terminus is the free amino group at the very beginning of a peptide.
What is meant by the term C-terminus?
A C-terminus is the free carboxyl group at the very end of a peptide.
In what direction are peptides drawn?
Left to right from N-terminus to C-terminus.
Describe the strength of the peptide bond.
The peptide bond is resonance stabilized (partial double bond from N lone pair) , and is thus very strong. More often than not, we need to use special enzymes to break these bonds down.
What are the four levels of structure seen in proteins?
- Primary Structure
- Secondary Structure
- Tertiary Structure
- Quaternary Structure
What is primary structure and what is its characteristic bond?
Primary structure refers to the actual sequence of amino acids in the protein. These amino acids are held together by peptide bonds.
What is secondary structure and what is its characteristic bond?
Secondary structure refers to the formation of repeating patterns of pleated sheets and alpha helices. These patterns are held together by hydrogen bonds between the carboxyl and amino group backbone of the amino acids.
What is tertiary structure and what is its characteristic bond?
Tertiary structure refers to the three dimensional folding of the polypeptide chain into its final form. These forms are held together by hydrogen bonds between side chains, salt bridges between positively and negatively charged side chains, and disulfide bonds between cysteine residues.
What is quaternary structure?
Quaternary structure refers to the overall structure obtained when two or more separate polypeptides in tertiary structure combine.
What is sequencing?
Sequencing is a laboratory technique that allows one to determine the primary structure of a protein. This is most easily done by using the DNA that coded for the protein, although the protein itself can be used if necessary.
As you can see below, you can figure out the sequence by trying to replicate the DNA while adding ddnucleotides, which halt replication. For example, if only one nucleotide is produced from the DNA in the ddATP beaker, then I know the first nucleotide in the DNA is A. This can be repeated to get the whole sequence of DNA, which can then be translated into the amino acids present.
What is an alpha helix?
An alpha helix is a rodlike structure in which the peptide chain coils clockwise around a central axis. 3.6 residues per turn, H bonds every ten atoms
What is a beta pleated sheet?
A beta pleated sheet is a structure in which peptide chains lie alongside one another, forming rows.
Describe the special role played by proline in secondary structure
Proline’s rigid ring structure makes it unsuitable for inclusion in the middle of alpha helices and beta pleated sheets. When introduced into the middle of these structures, proline produces kinks in the secondary structure. However, proline’s rigidity makes it useful at the start of alpha helices and in the turns taken by beta pleated sheets. These are the two locations one is likely to find proline.
What are the two main structural classes of proteins?
- Fibrous Proteins
- Globular proteins
What is a fibrous protein?
A fibrous protein is a protein that resembles long sheets or strands.
What is a globular protein?
A globular protein is a protein that is spherical and round
During the formation of tertiary structure, hydrophobic amino acids are pushed ___________
into the core
What is Cystine?
Cystine is the name used to refer to the disulfide bond made between two cysteine’s in a protein.
The formation of a disulfide bond is a ________ reaction
oxiduction
What is denaturation?
Denaturation is the process by which a protein loses its tertiary structure. This is usually accomplished through disruption of the bonds that hold tertiary structure together.
What is a solvation layer?
A solvation layer is a layer formed around a molecule by nearby solvent molecules. These result as a consequence of electrostatic interactions.
Why is the pushing of nonpolar amino acids into the core of a protein spontaneous?
When there are nonpolar amino acids on the outside of the protein, water cannot hydrogen bind with the protein, which means it can only hydrogen bind with itself. This reduces water’s options, which lowers its entropy, which makes this process unfavorable.
On the other hand, if water can hydrogen bind with the outside of the protein (polar AA’s on the exterior), that gives water more options and lowers the entropy of the system, which is favorable.
What is a subunit?
A sub unit refers to one of the functional tertiary peptides comprising the overall quaternary peptide.
What roles can the formation of quaternary structure serve?
- Quaternary structure can stabilize a protein
- Quaternary structure can reduce the amount of DNA needed to encode a protein complex
- Quaternary structure can bring catalytic sites together, which allows intermediates to be shuttled directly to the next step.
- Quaternary structure can induce cooperativity, also known as allosteric effects.
What is a conjugated protein?
A conjugated protein is a protein that derives part of its function from the presence of proesthetic groups.
What is a prosthetic group?
A prosthetic group is a covalently attached molecule that allows a protein to function. Prosthetic groups can be organic molecules such as vitamins or metal ions, like iron.
What is a lipoproptein?
A lipoprotein is a protein with a lipid based prosthetic group.
What is a glycoprotein?
A glycoprotein is a protein with a carbohydrate based prosthetic group.
What is a nucleoprotein?
A nucleoprotein is a protein with a nucleotide based prosthetic group.
What are common ways to denature a protein?
- Heat. As temp increases, hydrogen bonds and salt bridges destabilize.
- Solutes such as urea and beta mercaptoethanol can disrupt disulfide bridges, causing denaturation.
- Detergents can solubilize proteins, which disrupts noncovalent bonds and therefore promotes denaturation.
