Term
| T/F: Peptide bonds are the only covalent bonds that can link together two amino acids in proteins. |
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Definition
| False. Disulfide bonds between cysteine side chains are also covalent. |
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Term
| T/F: Nonpolar amino acids tend to be found in the interior of proteins. |
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Definition
| True. Nonpolar A.A.s have hydrophobic side chains; thus, they usually cluster on the inside to avoid the water-rich cytosol. |
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Term
| T/F: Amino acid sequence similarities in essential proteins such as cytochrome c suggest evolutionary relationships between species. |
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Definition
| True. You can find cyt c in mitochondria. |
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Term
What happens to a protein molecule when you heat it? What does that mean? |
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Definition
It denatures. That is, the non-covalent bonds holding it together break. |
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Term
| What's primary protein structure? |
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Definition
| The sequence of peptide-bond linked amino acids. |
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Term
| What's a protein's secondary structure? |
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Definition
| The interaction of amino acid chains to form alpha-helices (where a series of N-H groups form hydrogen bonds with respective C=O groups four residues earlier) and beta-sheets/strands (where an H-bond forms in the polypeptide backbone to form pleated sheets). |
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Term
| What's a protein's tertiary structure? |
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Definition
| The 3D structure of a protein, that arises through noncovalent interactions. |
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Term
| What two bonds/interactions are most responsible for tertiary structure of a protein? |
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Definition
disulfide bonds between cysteine residues hydrophobic interactions (to sequester the hydrophobic side chains of residues in the center of a protein) |
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Term
| What is quaternary structure of a protein? |
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Definition
| How more than one protein subunit is arranged in a multi-unit complex (e.g., Hb) |
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Term
Which class(es) of amino acids is/are most important for the below interaction? Forming ionic bonds with negatively-charged DNA? |
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Definition
| BASIC (they're positively charged, so yeah-doy) |
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Term
Which class(es) of amino acids is/are most important for the below interaction? Forming hydrogen bonds to aid solubility in water? |
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Definition
| Uncharged polar (polar is soluble in water) |
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Term
Which class(es) of amino acids is/are most important for the below interaction? Binding to another water-soluble protein? |
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Definition
Uncharged polar Basic Acidic |
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Term
Which class(es) of amino acids is/are most important for the below interaction? Localizing an "integral membrane" protein that spans a lipid bilayer |
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Definition
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Term
Which class(es) of amino acids is/are most important for the below interaction? Packing the interior core of a globular protein |
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Definition
| nonpolar (hydrophobic side chains) |
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Term
The α helix and β sheet are found in many different proteins because they are formed by: - hydrogen bonding between the amino acid side chains most commonly found in proteins.
- ionic interactions between charged amino acid side chains.
- hydrophobic interactions between the many nonpolar amino acids.
- hydrogen bonding between atoms of the polypeptide backbone.
- noncovalent interactions between amino acid side chains and the polypeptide backbone.
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Definition
| hydrogen bonding between atoms of the polypeptide backbone. |
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Term
Disulfide bonds: - are formed by the cross-linking of methionine residues.
- are formed mainly in proteins that are retained within the cytosol.
- can be broken by oxidation through agents such as mercaptoethanol.
- stabilize a protein’s final conformation.
- rarely form in extracellular proteins.
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Definition
stabilize a protein’s final conformation. (remember, disulfide bonds are formed by cysteine residues -- methionine has a methyl group at the end of its side chain) |
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Term
Which of the following statements is FALSE?
- The three dimensional structure of a protein dictates its function by determining its binding specificity for other molecules.
- Many proteins have more than one binding site.
- Changes in the amino acid sequence of a protein can decrease binding to a ligand, even if the altered amino acid does not lie in the binding site for the ligand.
- Binding between protein and ligand generally involves noncovalent bonds.
- Proteins always bind their ligands as tightly as possible.
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Definition
Proteins always bind their ligands as tightly as possible. (if they actually did, they wouldn't be able to so efficiently release the products they form) |
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Term
Enzymes have active sites which have the greatest complementarity to the:
- substrate.
- transition state.
- product.
- both substrate and product.
- none of the above.
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Definition
transition state (this is the basis of the induced-fit model: enzymes are at the lowest energy when they have changed shape to bind with the substrate.) |
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Term
All of the following are correct statements about enzyme regulation EXCEPT:
- Enzymes can be inhibited by the products they produce.
- The activity of an enzyme is covalently affected by allosteric regulators.
- Enzymes can be inactivated by the addition of a functional group.
- Coenzyme and substrate availability can regulate enzyme reaction rate.
- Some enzymes are made as inactive precursors.
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Definition
The activity of an enzyme is covalently affected by allosteric regulators. (the reason it's false is because of the word covalently. Allosteric regulators bind to an enzyme through noncovalent interactions.) |
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Term
The active site of an enzyme contains amino acids that participate in acid-base as well as covalent catalysis. Which of the following amino acids would you not expect to find as part of the active site of an enzyme?
- lysine
- cysteine
- leucine
- aspartic acid
- arginine
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Definition
leucine (natch: it's nonpolar aliphatic, so it's got a hydrophobic side chain. Thus, it's not going to do much acid/base chemistry.) |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. alanine |
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Definition
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. glycine |
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Definition
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. leucine |
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Definition
-CHCH3-CH-CH nonpolar no R pKa Leu |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Isoleucine |
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Definition
-CH2-CH(CH3)2 nonpolar no R pKa Ile |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Valine |
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Definition
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Methionine |
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Definition
-CH2-CH2-S-CH3 nonpolar n/a Met |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Serine |
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Definition
-CH2OH polar uncharged n/a Ser |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Threonine |
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Definition
-CH(OH)-CH3 polar uncharged n/a Thr |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Cysteine |
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Definition
-CH2SH polar uncharged 8.18 Cys |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Asparagine |
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Definition
-CH2-CONH2 polar uncharged n/a Asn |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Glutamine |
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Definition
-CH2-CH2-CONH2 polar uncharged n/a Gln |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Tyrosine |
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Definition
-CH2-Ar-OH polar uncharged 10.46 Tyr |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Phenylalanine |
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Definition
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Tryptophan |
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Definition
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Proline |
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Definition
[image]nonpolar (IMINO) n/a Pro |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Histidine |
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Definition
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Arginine |
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Definition
-(CH2)3NH-C(NH)NH2 basic 12.48 Arg |
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Lysine |
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Definition
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Aspartic Acid |
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Definition
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Term
Amino Acid Quiz Give the side chain structure, the class, the pKa of the side chain (if applicable), and the abbreviation. Glutamic acid |
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Definition
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Term
Amino Acid Quiz There are seven amino acids with side chains that have pKas. What are they (and what are the pKas)? |
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Definition
Acidic aspartic acid = 3.90 (≈4) glutamic acid = 4.07 (≈4) cysteine = 8.18 (≈8) Basic histidine = 6.04 (≈6) arginine = 12.48 (≈12.5) lysine = 10.54 (≈10.5) Other tyrosine = 10.46 (≈10.5) |
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Term
Amino Acid Quiz Gun to the head: give a general range of pKaα-carboxylic acid and pKaα-amino across all amino acids. |
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Definition
In general: pKaα-carboxylic acid ≈ 2 pKaα-amino ≈ 9 - 10 |
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Term
Amino Acid Quiz What is an "essential amino acid"? |
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Definition
An amino acid that the human body cannot synthesize. Definitely essential: Phe, His, Ile, Lys, Leu, Met, Thr, Val, Trp Conditionally essential: Cys, Glu, Gly, Arg, Tyr |
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Term
Amino Acid Quiz Name all the nonpolar amino acids. |
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Definition
There are 10. Gly, Ala, Leu, Ile, Val, Met, Phe, Trp, Cys, Pro |
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Term
Amino Acid Quiz Name all the polar uncharged amino acids. |
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Definition
There are 5. Asn, Gln, Ser, Thr, Tyr |
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Term
Amino Acid Quiz Name the acidic amino acids. |
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Definition
Just two of these. Asp, Glu |
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Term
Amino Acid Quiz Name the basic amino acids. |
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Definition
A whopping three. His, Arg, Lys (HAL) |
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Term
What's the average length of proteins, in amino acids? |
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Definition
| Between 50 and 2000 (p. 125) |
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Term
| T/F: All of the information needed to specify the three-dimensional shape of a protein is contained in its amino acid sequence. |
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Definition
True. (p. 124) Sometimes it needs to be sequestered away from other ions by a chaperone protein, but that doesn't mean it doesn't contain all the info it needs. |
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Term
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Definition
It's a single amino acid that has a net 0 charge (b/c it has a COO- group and an NH3+ group). Generally, at neutral pH, amino acids are zwitterions (save for the 5 acidic/basic ones) |
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Term
| T/F: Histidine can serve as a biological buffer. |
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Definition
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Term
| T/F: Tyrosine, in an amino acid sequence, serves as a turning point (i.e., in the secondary structure). |
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Definition
| False. Proline does that. (slide 10) |
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Term
What's the pI (isoelectric point) of an amino acid? |
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Definition
The pH of an amino acid where the net charge is zero. |
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Term
What's the pI of His? pKaα-carboxylic acid = 1.8 pKaα-amino = 9.2 pKaside chain = 6.0 |
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Definition
Because His has an ionizable side chain, the pI is the average between the pKa of the side chain and one other pKa. Because His is basic, it's between the R and the NH2 pKas. pI = (9.2+6.0) / 2 = 7.6 |
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Term
What's the pI of Ile? pKaα-carboxylic acid = 2.3 pKaα-amino = 9.7 |
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Definition
| pI = (2.3 + 9.7) / 2 = 6.0 |
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