Biochem U4: 1°, 2° Structure, Ramachandran Diagrams

Learning objectives 4.1, 4.2, 4.3, 4.4, 4.5

If a residue is the same in a similar protein in many different organisms, which term describes it?

Invariant

Variant

Conservative

Variable

Invariant

Which of the following functional groups is the peptide bond?

Question 2 options:

Carboxylate

Imine

Amine

Amide

Amide

The first amino acid in a peptide chain contains which of the following groups?

Question 3 options:

Gene

Codon

N-terminus

C-terminus

N-terminus

Which of the following changes is an example of a conservative substitution?

Question 4 options:

Val → Leu

Ile → Lys

Met → Cys

Asp → Asn

Val → Leu

Which of the following information can be observed in protein sequence alignments?

Question 1 options:

DNA sequence

Conserved residues

All of these options

3-D structure

Conserved residues

Which of the following phrases describes the components of a codon?

Question 2 options:

One amino acid

Three amino acids

Nine RNA nucleotides

Three DNA nucleotides

Three DNA nucleotides

Which of the following mutations is an example of a single nucleotide polymorphism?

Question 3 options:

CAC → CTC

CAC → CAAC

CAC → CC

All of these options

CAC → CTC

A single nucleotide polymorphism can be characterized as which of the following terms?

Question 4 options:

Transgene

Mutation

Homologous

Expression

Mutation

Which of the following terms describes a residue that is in the same sequence position in a protein but is two amino acids with different polarity when compared across organisms?

Question 1 options:

Alignment

Conservative substitution

Mismatched

Non-conservative substitution

Non-conservative substitution

When is a residue invariant?

Question 2 options:

When that position is found to mutate to other amino acids in a single protein

When different amino acids appear at that position in all proteins within a sequence alignment

When the same amino acid appears at that position in all proteins within a sequence alignment

When similar amino acids appear at that position in all proteins within a sequence alignment

When the same amino acid appears at that position in all proteins within a sequence alignment

In one member of a species, part of a gene has the sequence TATCG. In another member of the species, the sequence is TAACG. This observation is an example of which of the following terms?

Question 3 options:

Conservative substitution

Single nucleotide polymorphism

Codons

Irregular structure

Homologous proteins

Single nucleotide polymorphism

The peptide bond exists between which of the following backbone atoms?

Question 4 options:

CO of the first amino acid, NH of the second amino acid

Cα of the first amino acid, CO of the second amino acid

Cα of the first amino acid, NH of the second amino acid

NH of the first amino acid, Cα of the second amino acid

NH of the first amino acid, CO of the second amino acid

CO of the first amino acid, NH of the second amino acid

An alignment can be made to compare which types of information?

Nucleotide sequence and amino acid sequence

Amino acid sequence and protein structure

All of these options

Nucleotide sequences from two different organisms

When are two genes homologous?

Question 2 options:

None of these options

When they are evolutionarily related

When they have both of these traits

When they produce proteins with similar functions

When they have both of these traits

Which of the following changes is an example of a conservative substitution?

Question 3 options:

All of these options

K to R

Asparagine to glutamine

Leu to Ile

All of these options

Which of the following terms describes the first amino acid residue in a peptide?

Question 4 options:

Cα

C-terminus

N-terminus

Peptide bond

N-terminus

Which of the following information can be learned using a protein sequence alignment?

Question 1 options:

Which residue positions exhibit variation between organisms

All of these options

Which residues are likely important for the function of the protein

Which positions in the sequence are highly conserved

All of these options

Protein primary structure describes which of the following information?

Question 2 options:

All of these options

The 3-D arrangement of the backbone atoms

The type of bond used to connect amino acid residues

The order of the amino acids in a protein

The order of the amino acids in a protein

Which of the following statements describes a protein sequence alignment?

Question 3 options:

A comparison of sequence of several proteins

A method for determining the primary structure of a protein

A mechanism to convert amino acids back into codons

A particular type of protein

A comparison of sequence of several proteins

Which term describes the basic nucleic acid unit that corresponds to an amino acid?

Question options:

Nucleotide

mRNA

Codon

Gene

Codon

Which of the following statements must be true for two proteins to be homologous?

They come from the same gene

They must have the same function

They must have the same function and similar sequences

They must have similar sequences

They must have the same function and similar sequences

Which of the following statements describes a protein sequence alignment?

A determination of the sequence of some protein from the gene codons

A technique for determining protein sequence

A comparison of sequences of several proteins

A type of protein

A comparison of sequences of several proteins

Protein primary structure describes which of the following features?

The sequence of amino acids

The codons

Mutations that can occur in the sequence

Which positions are invariant

The sequence of amino acids

Which type of information can be learned from a sequence alignment?

Question 1 options:

None of these options

Protein function

Evolutionary relationships

3-D shape of a protein

Evolutionary relationships

Which of the following statements correctly defines the primary structure of a protein?

Question 2 options:

The alphabetical list of amino acids in a protein

The sequence of nucleotides in the gene

The amino acid sequence

The mRNA sequence

The shape of the amino acid backbone

The amino acid sequence

When should a change in amino acid sequence be described as conservative?

Question 4 options:

The original and new amino acids are highly similar in structure to each other

The amino acids both vote Republican

The change does not affect the protein 3-D structure

The original and new amino acids have substantially different structures

The original and new amino acids are highly similar in structure to each other

Which of the following changes is an example of a conservative substitution?

Question 1 options:

Ser → Thr

All of these options

Phe → Ala

Glu → Lys

None of these options

Ser → Thr

Which of the following statements describes a codon?

Question 2 options:

A ring found in cereal boxes for writing secret messages

The first amino acid in a growing peptide chain

A nucleic acid sequence that codes for an entire protein

A 3-nucleotide unit that codes for a single amino acid

A 3-nucleotide unit that codes for a single amino acid

Which of the following changes is an example of a conservative substitution?

Question 4 options:

Met → Cys

Val → Leu

Ile → Lys

Asp → Asn

Val → Leu

Which of the following phrases describes the components of a codon?

Question 2 options:

Three DNA nucleotides

Nine RNA nucleotides

One amino acid

Three amino acids

Three DNA nucleotides

Which of the following terms describes a residue that is in the same sequence position in a protein but is two amino acids with different polarity when compared across organisms?

Question 4 options:

Conservative substitution

Alignment

Non-conservative substitution

Mismatched

Non-conservative substitution

Which of the following information can be observed in protein sequence alignments?

Question options:

3-D structure

DNA sequence

All of these options

Conserved residues

Conserved residues

If a residue is the same in a similar protein in many different organisms, which term describes it?

Question options:

Conservative

Variant

Variable

Invariant

Invariant

Which of the following changes is an example of a conservative substitution?

Question 2 options:

Leu to Ile

All of these options

K to R

Asparagine to glutamine

All of these options

When is a residue invariant?

When the same amino acid appears at that position in all proteins within a sequence alignment

When similar amino acids appear at that position in all proteins within a sequence alignment

When that position is found to mutate to other amino acids in a single protein

When different amino acids appear at that position in all proteins within a sequence alignment

When the same amino acid appears at that position in all proteins within a sequence alignment

Which of the following is an example of a post-transcriptional modifications (select all correct answers)?

Question 2 options:

Covalently modifying a base in a mRNA sequence

Mutating a gene

Deleting 3 amino acids from a protein chain

Removing a section of a mRNA sequence

Covalently modifying a base in a mRNA sequence

Removing a section of a mRNA sequence

In the dipeptide Glu-Lys, the peptide bond could exist between which two atoms (select all correct answers)? (Hint: remember that sequence order matters.)

Question 4 options:

C of the γ-carboxylate of Glu and N of the ε-amine of Lys

The two Cα

N of the Glu backbone amine and C of the Lys backbone carboxylate

C of the Glu backbone carboxylate and N of the Lys backbone amine

N of the Glu backbone amine and N of the ε-amine of Lys

C of the Glu backbone carboxylate and N of the Lys backbone amine

Which of the following conclusions is valid when observing highly conserved residues in proteins?

Question 2 options:

There has not been sufficient time for that position to evolve into another amino acid

The amino acid is probably important for protein function

The residue cannot be mutated in the lab

The amino acid is the same in all copies of the protein produced by an organism

The amino acid is probably important for protein function

In the tripeptide AGK, which amino acid residue has the C-terminus?

Question 4 options:

K

There is insufficient information to answer this question

All three

G

A

K

All post-transcriptional modifications result in a change in which of the following molecules?

Question 1 options:

All of these options

mRNA

Protein

DNA

mRNA

Which of the following events could result in a specific protein (i.e., always the same) that is not exactly as predicted by the codons of the gene (select all correct answers)?

Question 3 options:

Random errors during transcription

Post-transcriptional modification of the RNA

Random errors during translation

A mutation in the DNA

Substitution of Se for S in a Cys residue

Post-transcriptional modification of the RNA

Substitution of Se for S in a Cys residue

In the sequence alignment of a protein, position 94 is always L, I, V, or F. Which of the following conclusions is a reasonable based on this information?

Question options:

The position is probably on the surface (water-exposed portion) of the protein

The position forms a critical hydrogen bond

None of these options

The position has no function and the side chain is irrelevant

The position is certainly critical for the function of the protein

None of these options

Which of the following is an example of a post-transcriptional modifications (select all correct answers)?

Question 4 options:

Deleting 3 amino acids from a protein chain

Mutating a gene

Removing a section of a mRNA sequence

Covalently modifying a base in a mRNA sequence

Removing a section of a mRNA sequence

Covalently modifying a base in a mRNA sequence

With respect to proteins, "irregular secondary structure" means which of the following statements?

Question 1 options:

A protein that is not symmetrical

A region of a protein that lacks regular secondary structure

A protein that contains unusual amino acids

All of these options

A region of a protein that lacks regular secondary structure

Which of the following structures is an example of an irregular secondary structure (select all correct answers)?

Question 2 options:

β-sheet

Loop

Polyproline helix

α-helix

Loop

Which of the following structures is an example of secondary structure (select all correct answers)?

Question 3 options:

Polyproline helix

Loop

α-helix

Subunit

Polyproline helix

loop

α-helix

Which of the following shapes is a type of regular secondary structure?

Question 4 options:

Loop

310-sheet

All of these options

None of these options

β-helix

None of these options

The angles phi and psi describe rotation around which amino acid bonds?

Question 3 options:

N-Cα and Cα-C in the protein backbone

The atoms in the amine end

The peptide bond and Cα-Cβ in the side chain

The atoms in the carboxylate end

N-Cα and Cα-C in the protein backbone

Why is proline rarely found in most regular secondary structures (select all correct answers)?

Question 1 options:

The use of the backbone amine in the side chain means proline cannot easily form peptide bonds

The side chain of proline is too bulky

Proline is unable to adopt the correct phi and psi angles

Proline distorts the phi and psi bonds in adjacent residues in a peptide chain

Proline is unable to adopt the correct phi and psi angles

The amino acid leucine is quite soluble in water. However, a peptide consisting of 5 consecutive leucine residues is much less soluble. Which of the following observations accounts for both of these observations (select all that apply)?

Question 1 options:

The peptide backone is less polar than the backbone of individual amino acids

The hydrophobic effect causes the peptide to aggregate

Leu is a non-polar amino acid

5 leucine amino acids have a total of 10 charges, while Leu5 only has 2

The peptide backone is less polar than the backbone of individual amino acids

5 leucine amino acids have a total of 10 charges, while Leu5 only has 2

Which of the following statements about peptides is true (select all correct answers)?

Question options:

The peptide Val-Leu-Ile has at least one charged functional group at all pH values

Asn and Gln are observed to form peptide bonds with either their backbone or side chains within proteins

All peptides with several aromatic side chains will have low solubility in water

In water, peptides spontaneously hydrolyze into amino acids

The peptide Val-Leu-Ile has at least one charged functional group at all pH values

In water, peptides spontaneously hydrolyze into amino acids

Which of the following statements about the hydrolysis of proteins is true (select all correct answers)?

Question options:

The products of protein hydrolysis are short peptides or individual amino acids

The rate of the reaction can be increased with specific enzymes

The reaction must be coupled to ATP hydrolysis

This process is usually spontaneous

The products of protein hydrolysis are short peptides or individual amino acids

The rate of the reaction can be increased with specific enzymes

This process is usually spontaneous

Why are Asn and Gln observed at the end of an α-helix more often than other amino acids (select all correct answers)?

Question 1 options:

Asn and Gln are not observed more frequently at the ends of α-helices

The side chains of these residues are of an optimal size for forming an α-helix

The side chains can form hydrogen bonds with the backbone of the same type as observed between backbone atoms in the helix

When positively charged, these residues help stabilize the negative charge of the backbone

The side chains can form hydrogen bonds with the backbone of the same type as observed between backbone atoms in the helix

Why is reaction coupling necessary to synthesize a protein?

Question 2 options:

The condensation reaction is spontaneous, but reaction coupling makes it faster

None of these options

The condensation reaction to form the protein is non-spontaneous

The hydrolysis reaction is spontaneous, but reaction coupling makes it faster

The hydrolysis reaction to from the protein is non-spontaneous

The condensation reaction to form the protein is non-spontaneous

The amino acids Cys, Ala, and Val are in solution. Which of the following actions would increase the chance that the amino acids will react to form a peptide, of any sequence (select all correct answers)?

Question 2 options:

Heating the solution to evaporate some water

Removing the Val amino acids

Adding some Trp

Diluting the solution with more water

Heating the solution to evaporate some water

Adding some Trp

Why is glycine infrequently observed in most regular secondary structures (select all correct answers)?

Question 1 options:

Glycine cannot correctly hydrogen bond to match regular secondary structures

The side chain of glycine is too small to fit correctly in most secondary structures

The flexibility of glycine means that the loss of entropy upon adopting a particular conformation is larger than usual

Glycine distorts the phi and psi bonds in adjacent residues in a peptide chain

The flexibility of glycine means that the loss of entropy upon adopting a particular conformation is larger than usual

Secondary structure describes which of the following features (select all correct answers)?

Question 1 options:

The sequence of the amino acids

The orientation of the backbone atoms

The orientation of the side chain atoms

The interaction between two peptide chains

The orientation of the backbone atoms

Which of the following features is an example of secondary structure?

Question 2 options:

The interactions between the A chain and B chain of insulin

The fact that alanine follows valine in the sequence of a protein

The hydrogen bonding within the backbone of an α-helix

The formation of a disulfide bond in the core of a protein

The hydrogen bonding within the backbone of an α-helix

Which of the following structures is an example of a regular secondary structure?

Question 3 options:

None of these options

Loop

B-form duplex

Polyproline helix

Polyproline helix

Which type of structure connects other secondary structure elements?

Question 4 options:

None of these options

α-helix

β-sheet

Loop

Loop

The phi and psi angles of amino acids refer to which of the following rotations?

Question 1 options:

Rotation of the bonds along the protein backbone

Rotation of the bonds in the side chains

All of these options

Rotation of the bonds connecting amino acids together

Rotation of the bonds along the protein backbone

Irregular secondary structures lack which of the following features?

Question 2 options:

Hydrogen bonds

All of these options

Repeating phi and psi angles

Specific backbone conformations

None of these options

Repeating phi and psi angles

Which of the following structures is an example of a regular secondary structure?

Question 3 options:

α-helix

All of these options

π helix

310 helix

All of these options

Torsion angles are used to describe which of the following protein features?

Question 4 options:

All of these options

The steric clashes that occur in regular secondary structure

The rotation of backbone bonds

The rotation of side chain bonds

The rotation of backbone bonds

Protein secondary structure is a description of which of the following features?

Question 1 options:

Φ and ψ rotations

The position of side chain atoms

None of these options

Amino acid sequence

All of these options

Φ and ψ rotations

Phi and psi angles primarily determine which type of structure?

Question 2 options:

Quaternary

Tertiary

Primary

Secondary

Secondary

Torsion angles of a protein refer to which of the following features?

Question 3 options:

π-π interaction angles

How tightly the protein is wound up

Φ and ψ rotations

The angle between the side chain and the Cα

Φ and ψ rotations

In the phrase regular secondary structure, "regular" means which of the following ideas?

Question 4 options:

Most likely to form spontaneously

Commonly observed

All of these options

A repeating structural pattern

None of these options

A repeating structural pattern

Which of the following shapes is a type of regular secondary structure?

Question 1 options:

β-helix

All of these options

None of these options

310-sheet

Loop

None of these options

Which of the following statements is true for all irregular secondary structures?

Question 2 options:

All of these options

Each amino acid has a backbone conformation different than its neighbors

The structures are rarely observed

The structures have random motion of the amino acids

All of these options

Which of the following structures is an example of an irregular secondary structure (select all correct answers)?

Question 4 options:

β-sheet

Polyproline helix

Loop

α-helix

Loop

Which of the following structures is an example of a regular secondary structure?

Question 1 options:

α-helix

All of these options

π helix

310 helix

All of these options

Which of the following structures is an example of secondary structure (select all correct answers)?

Question 2 options:

α-helix

Subunit

Polyproline helix

Loop

α-helix

Polyproline helix

Loop

With respect to proteins, "irregular secondary structure" means which of the following statements?

Question 3 options:

A protein that is not symmetrical

All of these options

A protein that contains unusual amino acids

A region of a protein that lacks regular secondary structure

A region of a protein that lacks regular secondary structure

Irregular secondary structures lack which of the following features?

Question 4 options:

Repeating phi and psi angles

Hydrogen bonds

All of these options

Specific backbone conformations

None of these options

Repeating phi and psi angles

Which of the following terms is an example of 3-D protein structure?

Question 1 options:

All of these options

β-sheet

α-helix

Loop

Secondary structure describes which of the following features (select all correct answers)?

Question 2 options:

The interaction between two peptide chains

The orientation of the side chain atoms

The sequence of the amino acids

The orientation of the backbone atoms

The orientation of the backbone atoms

Which of the following terms is an example of 3-D protein structure?

Question 1 options:

Loop

β-sheet

All of these options

α-helix

All of these options

Which of the following structures is an example of a regular secondary structure?

Question 2 options:

310 helix

α-helix

All of these options

π helix

All of these options

Why is an α-helix more stable than a 310 helix?

Question 1 options:

Because the 310 helix is observed less commonly

Because the 310 helix has n to n+3 hydrogen bonding

All of these options

Because the 310 helix has more steric clash

Because the 310 helix has n to n+3 hydrogen bonding

How is a turn different from a loop?

Question 3 options:

A turn is a type of tertiary structure, whereas a loop is a secondary structure

A loop is a relatively short sequence connecting two regular secondary structures, while a turn is less constrained and does not necessarily connect regular secondary structures

A turn is a relatively short sequence connecting two regular secondary structures, while a loop is less constrained and does not necessarily connect regular secondary structures

A loop is a type of tertiary structure, whereas a turn is a secondary structure

A turn is a relatively short sequence connecting two regular secondary structures, while a loop is less constrained and does not necessarily connect regular secondary structures

Why is G frequently conserved in protein sequences (select all correct answers)?

Question 2 options:

The backbone of G has greater conformational flexibility than other amino acids

The side chain of G is significantly smaller than all other amino acids

G is unable to form α-helices and β-sheets

The side chain of G can hydrogen bond better than any other amino acid

The backbone of G has greater conformational flexibility than other amino acids

The side chain of G is significantly smaller than all other amino acids

Which of the following structures is an example of irregular secondary structure (select all correct answers)?

Question 4 options:

Loop

β-sheet

α-helix

Turn

Loop

Turn

Which of the following statements about a β-sheet is false?

Question 1 options:

β-sheets are a type of secondary structure

All of these options

Antiparallel β-sheets have shorter hydrogen bonds than parallel β-sheets

All the residue side chains are oriented in the same direction

None of these options

All the residue side chains are oriented in the same direction

Which of the following statements describes the role of loops in protein structure?

Question 3 options:

To connect other secondary structure elements

None of these options

All of these options

To stabilize nearby primary structure

To decrease the entropy of the protein

To connect other secondary structure elements

Which of the following bonds is not associated with torsion angles of the protein backbone?

Question 1 options:

C-Cα

C-N

Cα-N

None of these options

C-N

Which of the following statements about an α-helix is true?

Question 2 options:

Hydrogen bonds are formed between the backbones of two neighboring helices

There are 7.2 residues per turn

All of these options

The helix is left-handed

None of these options

None of these options

Which of the following statements about β-sheets is true?

Question 4 options:

Hydrogen bonds in an β-sheet occur between backbone atoms

Side chains alternate projecting up and down along a β-sheet

None of these options

All of these options

The strands that make up β-sheets can be either parallel or anti-parallel

All of these options

Where are the side chains of residues located in an α-helix?

Question 1 options:

Alternating one side and the other

There is no specific arrangement

Pointed away from the center of the helix

Inside the center region of the helix

Pointed away from the center of the helix

A Ramachandran diagram presents which of the following information?

Question 2 options:

The number of α-helices and β-sheets in a protein

The number of amino acids with particular phi and psi angle combinations

The stable combinations of phi and psi angles for a single amino acid

The number of phi and psi angles in a single amino acid

The stable combinations of phi and psi angles for a single amino acid

Which of the following statements is true?

Question 3 options:

Irregular secondary structure appears on a Ramachandran plot as unshaded areas

Intrinsically unstructured proteins lack irregular secondary structure

None of these options

All of these options

Loops are one example of irregular secondary structure

Loops are one example of irregular secondary structure

How does a π helix differ from an α-helix (select all correct answers)?

Question 4 options:

The π helix is left-handed instead of right-handed

The π helix has a less compact structure of backbone atoms

The π helix has fewer backbone hydrogen bonds than an α-helix does

The π helix has n+5 hydrogen bonding instead of n to n+4

The π helix has a less compact structure of backbone atoms

The π helix has n+5 hydrogen bonding instead of n to n+4

Which of the following statements is false?

Question 1 options:

All of these options

The backbone of each residue in an α-helix hydrogen bonds to the backbone of the residue that is four amino acids later in the sequence

The side chains of neighboring residues in an antiparallel β-sheet are on alternate sides of the β-sheet

None of these options

All the amino acids in a parallel β-sheet have approximately the same ψ and ϕ angles

None of these options

Which of the following statements about α-helices is true?

Question 2 options:

Side chains project out perpendicular to the central axis of the α-helix

None of these options

The α-helix is a right-handed structure

All of these options

Hydrogen bonds in an α-helix occur between backbone atoms

All of these options

Which of the following features has a major impact on the observed types of secondary structure in proteins (select all correct answers)?

Question 3 options:

Phi and psi angles

Planarity of the peptide bond

Charge of the protein backbone

Zwitterions

Phi and psi angles

Planarity of the peptide bond

Where are the side chains of residues located in a β-sheet?

Question 1 options:

All on the same side

There is no specific arrangement

Inside the center region of the sheet

Alternating one side and the other

Alternating one side and the other

Which type of structure involves n and n+4 hydrogen bonds?

Question 3 options:

Turn

β-sheet

None of these options

α-helix

α-helix

Which of the following statements about β-sheets are false (select all correct answers)?

Question 3 options:

The repeating φ and φ of β-sheets provide a pleated sheet-like backbone structure

Anti-parallel β sheets have shorter hydrogen bonds than parallel β sheets

β-sheets are a type of regular secondary structure

All of the residue side chains are oriented in the same direction

All of the residue side chains are oriented in the same direction

Which of the following statements about a β-sheet is false?

Question options:

Antiparallel β-sheets have shorter hydrogen bonds than parallel β-sheets

β-sheets are a type of secondary structure

None of these options

All of these options

All the residue side chains are oriented in the same direction

All the residue side chains are oriented in the same direction