Bmb 401 Exam 1 (6)

What is the range of the number of amino acids a polypeptide can contain?

What is the mean molecular weight of an amino acid?

What mass unit is used for amino acids?

1 dalton = how many gm/mol?

What is the protein structural hierarchy?

The ___ (primary/secondary/tertiary/quaternary) structure is the ordered sequence of amino acids in that protein

A ___ (hydrogen/peptide) bond arises from the carboxyl group of one amino acid and the amino group of another

Water is liberated in the formation of peptide bonds in a process called what? Hint: 2 names

Is there rotation around peptide bonds?

Peptide bonds are ___ (rigid/flexible) and have partial ___ (single/double/triple) bond characteristics

Why do peptide bonds have partial double bond characteristics?

Peptide bonds are ___ (shorter/longer) than a single bond, but ___ (shorter/longer) than a double bond

How many atoms lie within the same plane in a peptide bond?

What are the 6 atoms that lie within the same plane in a peptide bond?

Cis and trans configurations in a peptide bond refer to the positions of what carbons?

What configuration, cis or trans, is favored in peptide bonds?

The trans position is favored in peptide bonds because there is ___ (more/less) steric interference between ___ (alpha carbons/R groups)

What amino acid is an exception to the trans favorability rule and both the trans and cis configuration is seen?

In the case of proline, cis configurations are seen as relatively ___ (more/equal/less) than trans configurations in terms of steric clash

The amino acid that is ___ (N/C)-terminal to the proline can be cis or trans configuration

Peptide bonds are rigid and ___ (triangular/planar)

What must be able to occur for proteins to be able to fold into their 3D shapes?

Rotation occurs between the alpha amino nitrogen and the ___ (alpha carbon/alpha carbonyl carbon)

Rotation occurs between the alpha carbonyl carbon and the ___ (alpha carbon/alpha carbonyl carbon)

Bond angles made between the alpha amino nitrogen and the alpha carbon are called ___ (psy/phi) angles

Bond angles made between the alpha carbonyl carbon and the alpha carbon are called ___ (psy/phi) angles

What are the two major secondary structural elements of proteins?

For an alpha helix, the path is ___ (compact/loose) and winds around a central ___ (peptide bond/axis) of rotation

Alpha helices are stabilized by ___ (hydrogen/peptide) bonds that are ___ (parallel/perpendicular) to the central axis of rotation

Alpha helix hydrogen bonds arise between what 2 groups in the peptide backbone?

Alpha helix hydrogen bonds arise between amino acids that are how many residues apart in the peptide chain?

How many amino acids are there per 360 degree turn in an alpha helix?

R groups of an alpha helix point ___ (toward/away) from the central axis of rotation, ___ (outward/inward) from the helix

What is the center of an alpha helix filled with?

___ (Right/Left)-handed alpha helices are the most common type of helices

What amino acid is an alpha helix breaker?

A series of ___ (charged/uncharged) amino acids is an alpha helix breaker

Amino acids with ___ (small/large) side chains are helix breakers

Amino acids that branch at the ___ (alpha/beta) carbon are helix breakers

What are beta sheets made up of?

Beta strands have a directionality that ___ (corresponds to/is opposite to) the direction of the peptide backbone

Beta strands run from the ___ (amino/carboxyl) group to the ___ (amino/carboxyl) group

Beta strands run ___ (C/N) to ___ (C/N)

In beta sheets, adjacent R groups are on the ___ (same/opposite) side of the backbone, and are ___ (above/inward) and ___ (below/outward) strands

In beta sheets, the hydrogen bonds extend between the beta strands from the carbonyl ___ (hydrogen/oxygen) of one strand to the amino ___ (hydrogen/oxygen) of another strand

Beta sheets are stabilized by ___ (hydrogen/peptide) bonds that are ___ (parallel/perpendicular) to the direction in which the peptide backbone is going

___ (Parallel/Antiparallel) beta strands have stronger hydrogen bonding between the beta strands

Antiparallel beta strands have stronger hydrogen bonding between the beta strands because there is greater ___ (circularity/linearity) in these bonds than in parallel strands

What is the more stable configuration of beta strands: parallel or antiparallel?

What type of repetitive secondary structure is located in a place where the peptide backbone is making a sharp turn?

Beta turns allow for compact conformation of what type of proteins?

Where on a protein are beta turns usually located?

What amino acid is often found in beta turns?

What is the start of a beta turn referred to as?

What is the end of a beta turn referred to as?

In beta turns, i corresponds to what terminus?

In beta turns, i+3 corresponds to what terminus?

In an alpha helix, each right-handed turn is how many amino acids?

In alpha helices, each main chain N-H (amino group) is hydrogen bonded to the ___ (alpha carbon/oxygen) (carbonyl group) 3-4 amino acids away

On a ramachandran diagram, what quadrant are beta sheets located in?

On a ramachandran diagram, what quadrant are alpha helices located in?

On a ramachandran diagram, what quadrant are right-handed alpha helices located in?

On a ramachandran diagram, what quadrant are left-handed alpha helices located in?

On a ramachandran diagram, ___ (light/dark) green represents psy and phi angles that are seen most often

What are 2 types of non-repetative structures?

Loops and coils are ___ (more/less) ordered than alpha helices and beta sheets, and ___ (are/are not) random

What is another name for super-secondary structures?

Motifs are in between what 2 structures?

What 3 characteristics do motifs have?

Angiostatin, topoisomerase, and myoglobin are all examples of ___ (primary/secondary/tertiary) structures

The ___ (primary/secondary/tertiary) structure is the overall 3D structure that the peptide chain adopts

What is the name of the unit of organization that makes up the tertiary structure?

True or false: Protein domains are functional units within the protein

Motifs are ___ (smaller/bigger) than protein domains

What effect is the largest driving force in tertiary and quaternary protein folding?

With proteins in aqueous solution, hydrophilic amino acid side chains will seek to be ___ (buried within the protein/facing the solution)

With proteins in aqueous solution, hydrophobic amino acid side chains will seek to be ___ (buried within the protein/facing the solution)

With proteins in lipid environment, hydrophobic amino acid side chains will seek to be ___ (buried within the protein/facing out)

With proteins in lipid environment, hydrophilic amino acid side chains will seek to be ___ (buried within the protein/facing out)

What property of secondary structural elements promotes formation of higher order structures?

What effect of water drives the formation of higher order structures?

When proteins fold, there is a ___ (increase/decrease) in entropy

The amino acids found in a peptide chain in unfolded protein have ___ (more/less) of a chance for randomness in their position than they would in a folded protein

As proteins fold and entropy decreases, what also decreases in order to counteract this?

What are 4 interactions that must be formed to help stabilize proteins?

Disulfide bonds are ___ (covalent/noncovalent) linkages between two S-H groups of two ___ (prolines/cysteines) in ___ (reducing/nonreducing) environments

What are 2 examples of non-reducing environments that disulfide bonds can form in?

Ionic interactions can form between two ___ (charged/uncharged) R groups and in ___ (acidic/basic) conditions

Ionic interactions between R groups and termini are also called what?

___ (Primary/Secondary/Tertiary/Quaternary) structure is only found in those proteins that are made up of more than one peptide chain

In quaternary structures, each peptide chain folds into what?

Quaternary structure is made up of two or more ___ (monomers/dimers/trimers) that come together to make up the whole protein

What are the subunits of quaternary structure?

True or false: Monomers may be identical or different

Subunits (monomers) of quaternary structure add to what 2 characteristics of a protein?

What 3 options may subunits (monomers) have in terms of effect on the activity of other subunits?