Protein section 2

Question 1 of 45

1

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Amino acids are grouped according to their ( physico-chemical, binding, structural, biological ) properties and this is reflected in the genetic code

Explanation

Question 2 of 45

1

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A single base change in the ( third, first, second ) position of the codon will often produce the same amino acid and in the ( second, third, first ) position often one with very similar physico-chemical properties.

Explanation

Question 3 of 45

1

The second base of the codon specifies whether an amino acid is...

Select one of the following:

polar or hydrophobic
basic or acidic
primary or secondary
aromatic or non-aromatic

Explanation

Question 4 of 45

1

Why are conservative substitutions good

Select one of the following:

because of them mutation events in the DNA sequence do not lead to a change in the function
they induce molecular evolution
they repair DNA

Explanation

Question 5 of 45

1

How many levels of protein structure are there

Select one of the following:

3
2
1
4
5

Explanation

Question 6 of 45

1

Match the level of the structure with the image

Drag an answer into the correct orange point.

Secondary

Primary

Tertiary

Quaternary

Explanation

Question 7 of 45

1

The amino acid sequence of the protein, dictated by the genetic code. This sequence contains all the information needed to specify:

Select one of the following:

Primary structure
Secondary structure
Tertiary structure
Quaternary structure

Explanation

Question 8 of 45

1

Regular repeating patterns of hydrogen-bonded backbone conformations such as alpha-helices and beta-sheets.

Select one of the following:

Primary structure
Secondary structure
Tertiary structure
Quaternary structure

Explanation

Question 9 of 45

1

The primary structure also dictates how these the structural elements pack together to form the overall shape of the protein in the form of folds. This is called the...

Select one of the following:

Tertiary structure
Quaternary structure
Folding structure

Explanation

Question 10 of 45

1

This represents the overall relative arrangement of two or more individual tertiary folded polypeptides.

Select one of the following:

Primary structure
Secondary structure
Tertiary structure
Quaternary structure

Explanation

Question 11 of 45

1

Reactivities of the elements involved in the primary structure

Select one or more of the following:

The overall polypeptide chain
The peptide bond
The amino acid R groups of the primary structure
The size of the amino acid sequence

Explanation

Question 12 of 45

1

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Resonance is the result of ( delocalisation, deprotonation, protonation ) of ( electrons, side chains, hydrogen atoms ) over several ( atoms, molecules )

Explanation

Question 13 of 45

1

Resonance decreases the polarity of the peptide bond and each has a dipole moment.

Select one of the following:

True
False

Explanation

Question 14 of 45

1

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As we mentioned previously there is rotation allowed around ( N-Cα, N-Cb ) and ( Cα-C, Cb-C ) by angles phi and psi
Thus we have a polymer with rotatable covalent bonds which alternate with rigid planar ones
This ( restricts, increases ) the number of ( conformations, bonds ) the polypeptide can adopt.

Explanation

Question 15 of 45

1

Apart from the properties of the peptide bond what other chemical reactivities does the polypeptide exhibit?

Select one or more of the following:

The reactivity of the carbonyl oxygen and amide nitrogen of the peptide bond
The various reactivities of the R groups attached to the α-carbon of the amino acids in the primary structure.
The London dispersion interactions between the amino acids
Hydrophobic effect

Explanation

Question 16 of 45

1

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( Hydrophobic, Hydrophilic ) side chains engage in van der Waals interactions. They have a tendency to ( avoid, go into ) contact with water and pack against each other. This is the basis for the ( hydrophobic, hydrophilic ) effect.
Tendencies: ( Alanine, Methionine, Serine ) and ( leucine, Aspargine, Histidine )- helix favouring residues, proline -helix breaking residue

Explanation

Question 17 of 45

1

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( Hydrophilic, Hydrophobic ) side chains are able to make ( hydrogen, covalent ) bonds with each other, with the peptide bond, with polar organic molecules and with water. Also because some are ( charged, neutral ) and exhibit ( pKa’s, pH ) they can change their charge depending on the ( pH, pKa ) or the microenvironment.

Explanation

Question 18 of 45

1

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( Amphipathic, Acidic, Basic ) side chains have both polar and non-polar character and are ideal at interfaces and may be involved in both ( H-bonding, Covalent bonding ) and ( van der Waals interactions., hydrophobic interactions )

Explanation

Question 19 of 45

1

Hydrogen bonds are formed when a hydrogen atom has a significant partial negative charge by virtue of being bound to a more electronegative atom such as oxygen or nitrogen and is attracted to a near neighbour (less than 0.35nm) that has significant partial positive charge.

Select one of the following:

True
False

Explanation

Question 20 of 45

1

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The atom to which the hydrogen is attached is called the H-bond ( donor, acceptor )

Explanation

Question 21 of 45

1

The charge state of the donor and acceptor changes the strength of the H-bond.

Select one of the following:

True
False

Explanation

Question 22 of 45

1

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To the right are some examples of H-bonding in proteins, the most important of which in the context of primary structure and its influence on the secondary structure of proteins is that between the amide ( donor, acceptor ) and the carbonyl ( acceptor, donor ) of the main chain peptide bond. The other shown are more important in tertiary structure.

Explanation

Question 23 of 45

1

ALTHOUGH PROTEINS ARE LINEAR POLYMERS THE STRUCTURES OF MOST OF THEM ARE NOT THE RANDOM COILS SEEN IN SYNTHETIC NON-NATURAL POLYMERS.

Select one of the following:

True
False

Explanation

Question 24 of 45

1

Most proteins are observed to be ❌ and have a ❌ hydrophobic core which consists primarily of hydrophobic amino acids. One very striking feature of the folded polypeptide chain is that the chain of amino acids takes up conformations in which the torsion angles phi and psi of the backbone chain repeat in regular patterns.

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globular

linear

tightly packed

loose

Explanation

Question 25 of 45

1

Types of secondary structure

Select one or more of the following:

Helices
Beta sheets
Beta turns
Globulin

Explanation

Question 26 of 45

1

The most common of these is alpha helix

Select one of the following:

Helices
Beta-sheets
Beta-turns

Explanation

Question 27 of 45

1

Sometimes known as pleated sheets. These sheets can exist as parallel or anti-parallel.

Select one of the following:

Beta sheets
Beta turns
Helices

Explanation

Question 28 of 45

1

here the chain is forced to turn sharply in a reverse direction, this small secondary structure element allows for the compact folding of proteins.

Select one of the following:

Helices
Beta sheets
Beta turns

Explanation

Question 29 of 45

1

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The network of regular ( secondary, primary ) structures contributes very significantly to the ( stability, conformation, size ) of the overall folded protein providing extensive networks of ( hydrogen, covalent ) bonds in which many consecutive residues are involved. All of the ( hydrogen, covalent ) bonding capability in the secondary structure of a protein is contributed from the amide nitrogen and carbonyl oxygen of the main chain peptide bond as ( donor, acceptor ) and ( acceptor, donor ) respectively.
This hydrogen bonding provides much of the stabilising ( enthalpy, entropy ) which allows the polar backbone amide and carbonyl groups to exist in the very ( hydrophobic, hydrophylic ) environment in the interior of a folded protein.

Explanation

Question 30 of 45

1

The carbonyl oxygen atom (n) of each residue accepts an H bond from the amide nitrogen four residues further along (n+5)

Select one of the following:

True
False

Explanation

Question 31 of 45

1

All of the polar amide groups of this helix are hydrogen bonded to each other except the ❌ amide hydrogen and the ❌ carbonyl oxygen.

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first

second

third

last

fifth

fourth

Explanation

Question 32 of 45

1

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The helix forms a ( cylindrical, tetrahedral, spherical ) structure with the walls formed by the H bonded backbone with the side chains pointing ( outwards, inwards ).

Explanation

Question 33 of 45

1

What is amphipathic, in what type of secondary structure can it be seen

Select one of the following:

hydrophobic nature on one side of the helix and hydrophilic on the other; helices
hydrophobic nature on one side of the helix and hydrophilic on the other; beta turns
acidic nature on one side of the helix and basic on the other; beta sheets
acidic nature on one side of the helix and basic hydrophilic on the other; coils

Explanation

Question 34 of 45

1

Steric factors favour the left handed helix.

Select one of the following:

True
False

Explanation

Question 35 of 45

1

No theoretical limit to the length of helices, very long ones up to hundreds of Angstroms have been observed in keratin (Hair protein).

Select one of the following:

True
False

Explanation

Question 36 of 45

1

formed between main chain amide hydrogen and carbonyl oxygen come from backbone groups distant from each other in the primary sequence.

Select one of the following:

Helices
Beta sheet
Beta turns

Explanation

Question 37 of 45

1

The strands can run in the same direction and be parallel beta sheets or in opposite directions and be anti-parallel beta sheets. It is also possible to get mixed sheets with both parallel and anti-parallel strands together. What direction is more stable?

Select one of the following:

anti-parallel
parallel

Explanation

Question 38 of 45

1

Click on each orange point and select the correct answer.

indicate the directionality of the sequence

Explanation

Question 39 of 45

1

Nearly all polar amide groups are ❌ bonded to one another in a sheet structure
The N-H and C=O groups on the outer sides of the sheets, the edge strands are not H bonded to other strand members.
These residues can H bond to ❌, or may pack against polar side chains in perhaps a nearby ❌.
❌ sheets are always buried.
Anti-parallel sheets are however frequently exposed to solvent and are probably ❌ stable structures than parallel sheets.

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hydrogen

covalently

water

substrate

helix

beta sheet

Parallel

Anti-parallel

more

less

Explanation

Question 40 of 45

1

parallel sheets are always separated by another structural element usually ❌.
beta sheet polypeptide chains are nearly fully extended (unlike helices) with distances between residues being up to ❌Angstroms.
beta strands always have a pronounced ❌ handed twist due to steric factors arising from the ❌ acid configuration.
❌ and ❌ are residues more commonly found in sheets.
Beta strands can be ❌ due to the alternating consecutive side chain configuration. These strands are found on the ❌ of proteins.

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helices

beta turns

3.3

3.4

3.5

right

left

L-amino

D-amino

Valine

Threonine

Cysteine

isoleucine

Alanine

Glycie

amphipathic

amphoteric

surface

inside

Explanation

Question 41 of 45

1

BETA SHEETS CANNOT FORM BARREL STRUCTURES

Select one of the following:

True
False

Explanation

Question 42 of 45

1

What kind of protein is it?

Drag the answer into the correct orange point.

Retinol binding protein

Retinol inhibiting protein

Cadherin binding protein

Cadherin inhibiting protein

Explanation

Question 43 of 45

1

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Here we see retinol binding protein with a distinct ( beta barrel, alpha helix ) structure.
A large ( anti-parallel, parallel ) beta ( sheet, turns ) curves all the way round with the last strand ( hydrogen, nitrogen ) bonded to the first thus forming a closed cylinder.
The interior of the cylinder is lined with ( hydrophobic, hydrophylic ) residues and can accommodate retinol which is ( non-polar, polar ).

Explanation

Question 44 of 45

1

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The simplest secondary structural element is the beta turn and usually involves just ( four, five ) residues. It is very important in allowing compact folding of proteins and is often found connecting the strands of ( anti-parallel, parallel ) beta sheets.
The beat turn comprises a hydrogen bond from the carbonyl oxygen of one residue (n) to the amide N-H of residue ( n+3, n+4 ). This reverses the direction of the chain.
Beta turn are most commonly found on the ( surface, interior ) of proteins in contact with the aqueous environment.
The tight geometry of the turn means that some amino acids such as ( glycine, phenylalanine, glutamine ) are found more commonly in turns than other bulkier groups.

Explanation

Question 45 of 45

1

What limits the number and positioning of secondary structural elements

Select one or more of the following:

size of R group
steric constraints
nature of R group
Directionality
The amount of peptide bonds

	Created by MrSujg about 9 years ago

1st year Biochemistry and molecular biology Quiz on Protein section 2, created by MrSujg on 22/11/2015.

Protein section 2

Protein section 2

Question 1 of 45

Select from the dropdown list to complete the text.

Amino acids are grouped according to their physico-chemical binding structural biological( physico-chemical, binding, structural, biological ) properties and this is reflected in the genetic code

Explanation

Question 2 of 45

Select from the dropdown lists to complete the text.

A single base change in the third first second( third, first, second ) position of the codon will often produce the same amino acid and in the second third first( second, third, first ) position often one with very similar physico-chemical properties.

Explanation

Question 3 of 45

The second base of the codon specifies whether an amino acid is...

Select one of the following:

Explanation

Question 4 of 45

Why are conservative substitutions good

Select one of the following:

Explanation

Question 5 of 45

How many levels of protein structure are there

Select one of the following:

Explanation

Question 6 of 45

Match the level of the structure with the image

Drag an answer into the correct orange point.

Explanation

Question 7 of 45

The amino acid sequence of the protein, dictated by the genetic code. This sequence contains all the information needed to specify:

Select one of the following:

Explanation

Question 8 of 45

Regular repeating patterns of hydrogen-bonded backbone conformations such as alpha-helices and beta-sheets.

Select one of the following:

Explanation

Question 9 of 45

The primary structure also dictates how these the structural elements pack together to form the overall shape of the protein in the form of folds. This is called the...

Select one of the following:

Explanation

Question 10 of 45

This represents the overall relative arrangement of two or more individual tertiary folded polypeptides.

Select one of the following:

Explanation

Question 11 of 45

Reactivities of the elements involved in the primary structure

Select one or more of the following:

Explanation

Question 12 of 45

Select from the dropdown lists to complete the text.

Resonance is the result of delocalisation deprotonation protonation( delocalisation, deprotonation, protonation ) of electrons side chains hydrogen atoms( electrons, side chains, hydrogen atoms ) over several atoms molecules( atoms, molecules )

Explanation

Question 13 of 45

Resonance decreases the polarity of the peptide bond and each has a dipole moment.

Select one of the following:

Explanation

Question 14 of 45

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Explanation

Question 15 of 45

Apart from the properties of the peptide bond what other chemical reactivities does the polypeptide exhibit?

Select one or more of the following:

Explanation

Question 16 of 45

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Explanation

Question 17 of 45

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Explanation

Question 18 of 45

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Explanation

Question 19 of 45

Hydrogen bonds are formed when a hydrogen atom has a significant partial negative charge by virtue of being bound to a more electronegative atom such as oxygen or nitrogen and is attracted to a near neighbour (less than 0.35nm) that has significant partial positive charge.

Select one of the following:

Explanation

Question 20 of 45

Select from the dropdown list to complete the text.

The atom to which the hydrogen is attached is called the H-bond donor acceptor( donor, acceptor )

Explanation

Question 21 of 45

Amino acids are grouped according to their ( physico-chemical, binding, structural, biological ) properties and this is reflected in the genetic code

A single base change in the ( third, first, second ) position of the codon will often produce the same amino acid and in the ( second, third, first ) position often one with very similar physico-chemical properties.

Resonance is the result of ( delocalisation, deprotonation, protonation ) of ( electrons, side chains, hydrogen atoms ) over several ( atoms, molecules )

The atom to which the hydrogen is attached is called the H-bond ( donor, acceptor )

The helix forms a ( cylindrical, tetrahedral, spherical ) structure with the walls formed by the H bonded backbone with the side chains pointing ( outwards, inwards ).