assignment 2 Flashcards
What are the 5 major classes of amino acids? Give an example of an amino
acid in each class.
- non-polar (alkyl - alanine, valine, leucine, isoleucine; aromatic –
phenylalanine, tyrosine, tryptophan) - acidic (aspartic acid, glutamic acid)
- basic (lysine, arginine, histidine)
- polar (asparagine, glutamine, serine, cysteine, threonine)
- special (glycine, proline)
18 of the common amino acids have an S configuration at the alpha-carbon, however one amino acid exists in the R configuration at this position. Which
one and why?
cysteine. The sulfur has a higher atomic number than oxygen which
reverses the priority for the CIP system
Briefly explain what constitutes each of the following with respect to proteins. primary, secondary, tertiary, quaternary structures
primary structure= list of amino acids in a protein in order from the N-terminus towards the C-terminus
secondary structure= areas of local order in the backbone chain. These regions tend to hold a particular shape such as a helix or sheet
tertiary structure= -overall three dimensional structure of a protein
quaternary structure= structure of a protein formed by the association of two or more subproteins
Briefly describe each of the four types of secondary protein structure with
respect to overall structure, what causes each structure to form and
appearance on a ribbon diagram. ALPHA HELIX
alpha helix is a corkscrew-shaped region. It forms from hydrogen bonds
between amide groups approximately 4 amino acids apart. On a ribbon
diagram is represented by a coiled, flat ribbon. The plane of the ribbon
follows the plane defined by the amide groups in the backbone, and there is
an arrow on the ribbon pointing from the N to the C terminus
Briefly describe each of the four types of secondary protein structure with
respect to overall structure, what causes each structure to form and
appearance on a ribbon diagram. BETA SHEET
beta sheet is a linear strand made up of the chain of atoms in the backbone
forming a flat zig-zag structure, which form because amide bonds tend to
prefer extended s-trans conformations. Several strands can associate
together forming a -sheet in which the individual strands can be parallel or
antiparallel. Large sheets may curl upon themselves to form -barrels
Briefly describe each of the four types of secondary protein structure with
respect to overall structure, what causes each structure to form and
appearance on a ribbon diagram. TURNS
turns are areas which change direction by almost 180° within a length of 3
or 4 amino acids. These form because of hydrogen bonding between nearby
amide groups, and are favored by amino acids such as glycine or proline.
There is no special designation for a turn on a ribbon diagram, but the
regions can be identified by their tight-turn shape
Briefly describe each of the four types of secondary protein structure with
respect to overall structure, what causes each structure to form and
appearance on a ribbon diagram. LOOPS
loops are areas of otherwise undefined secondary structure. They are
represented by thin tubes
the amide bonds in peptides are capable for adopting one of two
conformations, called s-cis and s-trans respectively.
explain why this functional group only adopts one of these conformations
draw three resonance forms. the third one with an O- and NH+, with a double bond between O and N largest contributor.
all atoms have octets. this form gives C-N bond double bond character, to the degree that N, C, O are all nearly fully sp2 hybridized. the double bond character limits rotation about this bond, much like C=C bond. this gives cis and trans conformations, like a regular double bond. s-cis and s-trans because the bond is formally a sigma bond.
which conformation is most common and why?
the s-trans conformation because large groups are far apart.
What are the four types of non-bonding interactions responsible for maintaining tertiary structure?
- electrostatics
- hydrogen bonding
- dipole-dipole interactions
- Van der Waals forces (dispersion forces)
One type of interaction, which controls tertiary structure, involves the
formation of a covalent bond. What is the name of this interaction and what
type of amino acid(s) are involved?
disulfide bond, formed between two cysteine side chains
Explain why Van der Waals interactions are so important in the maintenance
of tertiary structure
- water tends to be excluded from between two areas that are attracted by
VdW interactions. “squeezing” the water out from between the chains helps
to hold the chains together and provide structure. - VdW interactions are found in areas with lots of non-polar side chains.
These groups are only capable of interacting using VdW interactions, and
cannot participate in other types of non-bonding interactions such as
hydrogen bonding. Groups that interact through polar non-bonding
interactions (such as hydrogen bonding) experience stronger attractive
forces because the attraction between these groups is not “diluted” by
interactions with the non-polar groups
In general, how do enzymes catalyze reactions? Use an energy diagram in
your explanation, and show the key stages in an enzymatic reaction.
they bind to transition states. This binding lowers the energy of the
transition state and accelerates the reaction by reducing the activation
energy for enzyme-catalyzed processes.
Describe the four different types of enzyme inhibitor. Include a simple
diagram showing how each mode operates, and briefly explain how each can be identified. COMPETITIVE INHIBITOR
Competitive inhibitor competes with substrate for the same site
(active site) on the enzyme. This type of inhibitor alters Km and kcat
but does not affect Vmax.
Describe the four different types of enzyme inhibitor. Include a simple
diagram showing how each mode operates, and briefly explain how each can be identified. NON COMPETITIVE INHIBITOR
Non-competitive inhibitor binds to a different location on the enzyme
than the substrate does. Inhibitor binding prevents formation of the
ES complex. This type of inhibitor alters kcat and Vmax but does not
affect Km
