exam 1

Question 1

True or false: Protein folding can be entropically favorable because biological systems are open systems

Answer 1

True

Question 2

True or false: Co-factors are only involved in catalysis and have no role in protein folding and structural stability

Answer 2

False - Co-factors are involved in protein folding and structural stability

Question 3

True or false: HSP proteins aid in folding, and HSP stands for “Hot solution protein”

Answer 3

False - HSP proteins do aid in folding, but HSP stands for Heat Shock Protein

Question 4

True or false: Protein folding can never happen spontaneously because it is always thermodynamically unfavorable

Answer 4

False - Protein folding is an open system and can therefore happen spontaneously

Question 5

True or false: Delta G prime naught is CONSTANT for any reaction under a given set of conditions (pH, temp, etc are stable)

Answer 5

True

Question 6

True or false: Large proteins never require a molecular chaperone to help them fold correctly

Answer 6

False - Large proteins specifically need chaperones for proper folding. The only proteins which might not need chaperones are small, globular proteins

Question 7

True or false: Proteins never act as molecular chaperones

Answer 7

False

Question 8

True or false: Molecular chaperones commonly bind hydrophobic amino acids in proteins and help them to fold correctly

Answer 8

True

Question 9

True or false: The coiled coil structure of two separate keratin polypeptide alpha helices is a monomer

Answer 9

False

Question 10

True or false: The coiled coil structure of two separate keratin polypeptide alpha helices is an example of a tertiary structure

Answer 10

False - It is a quaternary structure

Question 11

True or false: The primary sequence of the keratin polypeptide plays no role in the formation of the coiled coil structure

Answer 11

False

Question 12

Which of the following four terms would not be an acceptable way to label a protein made up of 3 subunits, each having the exact same primary sequence: Multimer, Oligomer, Heterotrimer, Homotrimer

Answer 12

Heterotrimer is incorrect because the 3 subunits have identical primary structures

Question 13

True or false: The membrane anchor binds with the hydrophobic interior of the lipid bilayer

Answer 13

True

Question 14

True or false: The membrane anchors are added after proteins are translated

Answer 14

True

Question 15

True or false: Proteins modified with these groups are not directly anchored to the lipid membrane, and are thus considered peripheral membrane proteins

Answer 15

False

Question 16

True or false: Membrane anchors are added enzymatically to specific amino acids

Answer 16

True

Question 17

True or false: Separate protein domains may carry our different functions

Answer 17

True

Question 18

True or false: A protein never contains common secondary structures such as beta sheets

Answer 18

False

Question 19

True or false: Proteins never contain more than one domain in their tertiary structure

Answer 19

False

Question 20

True or false: Protein domains only act to bind other molecules, and never participate in enzymatic reactions

Answer 20

False

Question 21

True or false: A process with a +H term and a -S term is spontaneous only at low temperatures

Answer 21

False

Question 22

True or false: A process with +H and -S is spontaneous only at high temperatures

Answer 22

False

Question 23

True or false: A process with -S has a favorable change in entropy, creating a less order system

Answer 23

False - A positive S value is indicative of an increase in entropy

Question 24

True or false: A process with -H is exothermic

Answer 24

True - -H is hot!

Question 25

Hydrogen bonds most responsible for stabilizing the alpha helix structure occur between which chemical groups?

Answer 25

The C=O and N-H grups of amino acids separated by four amino acids in the primary sequence

Question 26

True or false: Amphipathic secondary structures are never a part of proteins that interact with membranes or lipids

Answer 26

False - Amphipathic always interact with one hydrophobic face, including membranes or lipids

Question 27

True or false: Amphipathic secondary structures include hydrophobic and hydrophilic side chains

Answer 27

True - This is essentially the definition of an amphipathic structure

Question 28

Which two amino acid side chains absorb UV light at 280 nm?

Answer 28

Tryptophan (Trp, W) and Tyrosine (Tyr, Y). Both contain an aromatic ring

Question 29

True or false: Amphipathic secondary structures have no impact on how proteins bind to other proteins and molecules

Answer 29

False

Question 30

True or false: Amphipathic secondary structures are never a part of proteins that interact with water

Answer 30

False - One face of the amphipathic structure commonly interacts with water

Question 31

An amide bond in a peptide is formed by which type of reaction between two amino acids?

Answer 31

Condensation

Question 32

True or false: The addition of SDS in SDS PAGE separation disrupts the interaction between non-covalently bound peptide chains

Answer 32

False

Question 33

True or false: One SDS molecule interacts with two molecules of polyacrylamide in SDS PAGE separation

Answer 33

False - Two molecules of SDS interact with one molecule of polyacrylamide

Question 34

True or false: The interaction of SDS with proteins in SDS PAGE separation leads to an overall negative charge on all proteins

Answer 34

True

Question 35

True or false: SDS in SDS PAGE separation separates proteins that differ in molecular weight

Answer 35

False

Question 36

True or false: Covalent bonds made between two cystiene side chains are part of the primary structure of a protein

Answer 36

True

Question 37

True or false: The sequence of covalently bonded amino acids is part of the primary structure of a protein

Answer 37

True

Question 38

True or false: Covalent modifications to amino acid side chains are part of the primary structure of a protein

Answer 38

True

Question 39

True or false: Electrostatic interactions between charged amino side chains located adjacent to one another are part of the primary protein sequence of a protein

Answer 39

False

Question 40

What two amino acids does Trypsin cleave at?

Answer 40

Arginine (Arg, R) and Lysine (Lys, K)

Question 41

What amino acid does Cyanobromide cleave at?

Answer 41

Methionine (Met, M)

Question 42

True or false: Phi and Psi angles are constrained by amino acid side chain properties

Answer 42

True

Question 43

True or false: The planar nature of the peptide bond impacts the secondary structures

Answer 43

True

Question 44

True or false: The chemical properties of amino acid side chains have no role in determining secondary structure

Answer 44

False

Question 45

True or false: Hydrogen bonds are key to the formation of secondary structures, such as alpha helices

Answer 45

True

Question 46

What is the structure of a primary amine?

Answer 46

NH3+

Question 47

Which biomolecule is not considered a polymer: Nucleic acids, lipids, polysaccharides, or proteins?

Answer 47

Lipids are not considered polymers

Question 48

True or false: Bases are generally though to have an affinity for binding protons (H+)

Answer 48

True

Question 49

True or false: Strong acids fully dissociate their proton(s) in pure water

Answer 49

True

Question 50

True or false: The dissociation constant (Ka) of a strong acid is lower than for a weak acid

Answer 50

False - The dissociation constant is higher for stronger acids

Question 51

True or false: The pKa of a strong acid will be a smaller number than that for a weak acid

Answer 51

True - Think of pKa and pH as being similar in that the stronger the acid, the smaller the number

Question 52

True or false: Non-covalent interactions and bonding in molecules involve sharing a pair of electrons between atoms

Answer 52

False

Question 53

True or false: Non-covalent interactions and bonding in molecules form stronger bonds bonds than covalent interactions

Answer 53

False

Question 54

True or false: Non-covalent interactions and bonding in molecules includes ionic and electrostatic interactions

Answer 54

True

Question 55

True or false: The cumulative effect of many non-covalent interactions can lead to highly stale binding and structures

Answer 55

True

Question 56

True or false: The pH in a cellular environment is kept at a steady value by the presence of molecules such as H2PO4

Answer 56

True

Question 57

True or false: The pH in a cellular environment is kept at a specific pH in order to keep biomolecules from carrying positive or negative charges

Answer 57

False

Question 58

Which of the following four types of bonds is the strongest: Hydrogen, Ionic, Van der Waals, or Brownian?

Answer 58

Ionic

Question 59

True or false: Hydrogen bonds must always include at least one water molecule

Answer 59

False

Question 60

True or false: Hydrogen bonds can have different bonding strength based on the spatial orientation of the donor and acceptor atoms involved

Answer 60

True

Question 61

True or false: For water, the different electronegativities of oxygen and hydrogen results in the unequal sharing of electrons between them, making hydrogen bonding possible

Answer 61

True

Question 62

What amino acid side chains have a negative charge on them? Note: These are considered acidic

Answer 62

i) Aspartic Acid (Asp, D) | ii) Glutamic Acid (Glu, E)

Question 63

What amino acid side chains have a positive charge on them? Note: These are considered basic

Answer 63

i) Lysine (Lys, K) ii) Arginine (Arg, R) iii) Histidine (His, H)

Question 64

What are the five uncharged, polar amino acid side chains?

Answer 64

i) Serine (Ser, S) ii) Threonine (Thr, T) iii) Cysteine (Cys, C) iv) Asparagine (Asn, N) v) Glutamine (Gln, Q)

Question 65

What are the seven nonpolar, aliphatic amino side chains?

Answer 65

i) Glycine (Gly, G) ii) Valine (Val, V) iii) Leucine (Leu, L) iv) Isoleucine (Ile, I) v) Proline (Pro, P) vi) Methionine (Met, M) vii) Alanine (Ala, A)

Question 66

What three amino acid side chains have an aromatic ring?

Answer 66

i) Phenylalanine (Phe, F) ii) Tyrosine (Tyr, Y) iii) Tryptophan (Trp, W)

Question 67

Describe the two shapes that lipids create when in a polar environment

Answer 67

i) Micelle - Creates a ball with the heads outside and the hydrophobic tails inside ii) Lipid bilayer (you know what this looks like)

Question 68

What is the order of electronegativity of the five main elements which support life?

Answer 68

O > N > S > C > H

Question 69

True or false: A hydrogen bond distance is defined as the distance between the donor and acceptor atoms

Answer 69

True

Question 70

True or false: A hydrogen bond distance is defined as the distance between the hydrogen and the acceptor atom.

Answer 70

False - It is the distance between the donor and acceptor atoms

Question 71

What two types of interactions make up a hydrogen bond?

Answer 71

Electrostatic interactions and Van der Waals forces

Question 72

True or false: A hydrogen bond is shorter than the associated Van der Waals interaction

Answer 72

True

Question 73

Define hydration

Answer 73

Water molecules cluster around ions and polar groups, stabilizing them-- this dissolves them

Question 74

How would you find the pH of a solution using the concentration of hydrogen atoms?

Answer 74

pH = log (1 / [H+]) OR pH = -log ([H+]

Question 75

How would you find the pKa of a solution using the dissociation constant (Ka)?

Answer 75

pKa = - log (Ka) = -log ([H+][A-] / [HA])

Question 76

True or false: The pKa is the solution pH at which the molar concentrations of the undissociated acid and its conjugate base are equal

Answer 76

True

Question 77

For acids, describe charges and ionization states for far below the pH and far above the pH

Answer 77

Far below: Unionized (not attached to H) and no charge | Far above: Ionized and negatively charged

Question 78

For bases, describe charges and ionization states for far below the pH and far above the pH

Answer 78

Far below: Ionized (atttached to H) and positively charged | Far above: Unionized and no charge

Question 79

What four groups are attached to the alpha carbon in amino acid structure?

Answer 79

i) A hydrogen ii An amino group (NH2) - Ionized at pH 7 (+NH3) iii) A carboxyl group (COOH) - Ionized at pH 7 (COO-) iv) A side chain residue - changes between every amino acid

Question 80

Describe the structure of a peptide bond

Answer 80

This bond is between the COO- and +NH3 groups on the amino acids. The C becomes a double bond with one O, then is attached with one bond to the alpha carbon of its own amino acid, and with one bond to the N of the other amino acid. The N becomes NH, and is attached on its other side to the alpha carbonof its own amino acid by a single bond

Question 81

What is a residue called which does not serve a necessary function and therefore may be mutated?

Answer 81

Hypervariable residue

Question 82

What is a residue called which performs a necessary function and cannot mutate at all?

Answer 82

Invariant residue

Question 83

What is a residue called which performs a necessary function, but may be mutated to a similar residue (i.e. from Ser to Thr)

Answer 83

Conservative residue