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Biochem 1 > Bonding and protein structure > Flashcards

Bonding and protein structure Flashcards

1
Q

What is a protein?

A

A polymer of amino acids

Different protein molecules can have vastly different structures.

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2
Q

What does the nucleus of an atom contain?

A

Protons and neutrons

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3
Q

How are electrons arranged in an atom?

A

Electrons occupy energy levels or shells composed of atomic orbitals.

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4
Q

What are atomic orbitals?

A

Particular regions of space within which electrons mostly reside.

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5
Q

What is an ionic bond?

A

A bond formed when an electron is transferred from one atom to another.

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6
Q

What is a covalent bond?

A

A bond formed when 2 electrons are shared in 2 overlapping orbitals of similar energy from 2 atoms.

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7
Q

What leads to noble gas configuration?

A

Chemical bonding

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8
Q

What are sigma and pi bonds?

A

Types of covalent bonds formed by the overlap of atomic orbitals.

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9
Q

How many covalent bonds does carbon typically form?

A

4 covalent bonds

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10
Q

What is hybridization in atomic orbitals?

A

The combining of atomic orbitals within an atom to form new orbitals.

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11
Q

What is the geometry of sp3 hybridized orbitals?

A

Tetrahedral

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12
Q

What is the structure of methane related to?

A

sp3 hybridization

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13
Q

Fill in the blank: Bonds involving hybrid orbitals are more stable than those involving _______.

A

pure atomic orbitals

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14
Q

What type of bond is formed by the overlap of orbitals along a line between two atomic nuclei?

A

σ - bond

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15
Q

True or False: Both oxygen in water and nitrogen in ammonia are sp2 hybridized.

A

False

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16
Q

What defines the region of space in which electrons mostly reside?

A

Orbitals

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17
Q

What is the relationship between molecular orbitals and atomic orbitals?

A

Molecular orbitals are the combination of atomic orbitals of similar energy within a molecule.

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18
Q

How many lone pairs of electrons does water have?

A

2 lone pairs of electrons

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19
Q

What type of hybridization do ammonia and water exhibit?

A

sp3 hybridization

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20
Q

What are the essential building blocks used to assemble proteins?

A

Amino acids

Proteins are linear polymers made from amino acids.

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21
Q

What is the nature of the peptide bond?

A

Planar and very stable

The peptide bond exhibits partial double bond character and is cleaved by proteolytic enzymes.

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22
Q

What are the three types of atomic orbital hybridization mentioned?

A
  • sp^3
  • sp^2
  • sp

Each type has a distinct geometry: tetrahedral for sp^3, trigonal for sp^2, and linear for sp.

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23
Q

How many common amino acids are used in protein construction?

A

20

Each amino acid has unique physical and chemical properties.

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24
Q

What type of bond is formed by the overlap of atomic orbitals along a line between two nuclei?

A

Sigma bond (σ)

Sigma bonds are stronger due to greater electron density in the overlap region.

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25
Q

What is the arrangement of sp^2 hybrid orbitals?

A

Planar trigonal

This arrangement is typical in compounds like ethene.

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26
Q

What is the significance of the Ramachandran Plot?

A

Describes allowed combinations of torsion angles

It indicates steric clashes and helps predict protein folding.

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27
Q

What is the directionality of polypeptides?

A

N-terminus to C-terminus

The sequence of amino acids is always written from the amino end to the carboxyl end.

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28
Q

What type of bond can cystine form?

A

Disulfide bond

This bond can provide stability to protein structures.

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29
Q

What is the main characteristic of polar covalent bonds?

A

Unequal sharing of electrons

This typically occurs between atoms with different electronegativities.

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30
Q

True or False: All natural amino acids are in the D-form.

A

False

All natural amino acids are L-form.

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31
Q

Fill in the blank: The _______ is the repeating unit in polypeptides.

A

Backbone

The backbone is formed by the peptide bonds between amino acids.

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32
Q

How does the character of hybrid orbitals affect bond strength?

A

More s character results in shorter and stronger bonds

Greater s character also increases bond angles.

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33
Q

What defines the 3D shape of a protein?

A

The sequence and types of side chains

The specific arrangement of amino acids determines protein functionality.

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34
Q

What is the role of proteolytic enzymes?

A

Cleavage of peptide bonds

These enzymes facilitate the breakdown of proteins into amino acids.

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35
Q

What bond arrangement is found in ethyne (C2H2)?

A

Linear

This is due to sp hybridization of carbon atoms.

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36
Q

Why do organic compounds have linear, planar or tetrahedral structures?

A

This is due to bonding patterns and spatial arrangements of the atoms, which are dictated by electron pair repulsion and hybridisation of atomic orbitals.
Linear geometry is due to sp hybrisation of the central atom ( I s orbital and s p orbital combine to form 2 sp hybrid orbitals aligning at 180° to minimise electron repulsion.
Planar geometry is due to spy hybrisation ( 1 s and 2 p orbitals combine forming sp2 orbital arranges themselves at 120°, angle is flat, triangular planar structure.
Tetrahedral geometry arises from sp3 hybridisation ( 1 s and 3 p orbitals hybridise to form four sp 3 hydride orbitals that orientate at 109.5°

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37
Q

Glysine

A

Gly, G (non-polar side chains)
H

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38
Q

Alanine

A

Ala, A (non-polar side chains)
CH3

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39
Q

Valine

A

Val,V (non-polar side chain)
C3H7

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40
Q

leucine

A

Leu,L (non-polar side chain)
C4H9

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41
Q

Isoleucine

A

Ile,I (non-polar side chain)
C4H9

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42
Q

Methionine

A

Met,M (non-polar side chain)
CH2CH2SCH3

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43
Q

Proline

A

Pro,P (non-polar side chain - contains 2nd amine)
(N)-CH2-CH2-CH2-

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44
Q

Phenylalanine

A

Phe,F (non-polar side chain)
-CH2-C6H6

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45
Q

Tryptophan

A

Trp,W (non-polar side chain)
-C=C-NH-C=C-
| |
C6H6

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46
Q

Aspsrsgine

A

Asn,N (polar side chain)
CH2-C=O
|
NH2

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47
Q

Glutamine

A

Gln,Q (polar side chain)
CH2-CH2-C=O
|
NH2

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48
Q

Cysteine

A

Cys,C (polar side chain)
CH2-SH

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49
Q

Serine

A

Ser,S (polar side chain)
CH-OH

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50
Q

Threonine

A

Thr,T (polar side chain)
-CH-CH3
|
OH

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51
Q

Tyrosine

A

Tyr,Y (polar side chain)
CH2-C6H6-OH

52
Q

Lysine

A

Lys,K (+ polar side chain)
CH2-CH2-CH2-CH2-NH3+

53
Q

Arginine

A

Arg,R (+ polar side chain)
CH2-CH2-CH2–NH2-C(-NH2)=NH2+

54
Q

Histidine

A

His,H (+ polar side chain)
CH2-C(-NH)=CH
| |
HC=NH2+

55
Q

Aspartic acid

A

Asp,D (- polar side chain)
CH2-COO-

56
Q

Glutamic acid

A

Glu,E (- polar side chain)
-CH2-CH2-COO-

57
Q

What are the properties of a peptide bond

A

very stable
partial double bond character
cleaved by proteolytkc enzymes - proteases or peptidases

58
Q

What are the non-covalent forces that stabilize the folded state of proteins?

A

Electrostatic interactions, Van der Waals interactions, Hydrogen Bonds, The Hydrophobic Effect

59
Q

What is the main driving force of protein folding?

A

Entropy

60
Q

What is the typical free energy required to denature a protein with 100 residues?

A

Approximately 40 kJmol-1

61
Q

True or False: Native proteins are highly stable entities under physiological conditions.

A

False

62
Q

Which amino acid can form a disulfide bond?

A

Cysteine

63
Q

What is the role of the dielectric constant (D) in ionic interactions?

A

It measures the solvent’s ability to keep opposite charges apart.

64
Q

How does water impact protein stability?

A

Water solubilizes polar and ionic substances but not non-polar materials.

65
Q

Fill in the blank: The strongest non-covalent interactions in proteins are __________.

A

Hydrogen Bonds

66
Q

What types of non-covalent interactions stabilize protein structures?

A
  • Ionic interactions
  • Van der Waals interactions
  • Hydrogen bonds
  • The Hydrophobic effect
67
Q

What is the association energy range for hydrogen bonds?

A

4 – 13 kJmol-1

68
Q

True or False: Ionic interactions greatly stabilize proteins.

A

False

69
Q

What is the difference between dipole-dipole interactions and London dispersion forces?

A

Dipole-dipole interactions are permanent, while London dispersion forces are transient.

70
Q

What happens to water molecules when hydrophobic side chains are buried in protein folding?

A

Caged water molecules are released, increasing the entropy of the solvent.

71
Q

What is the formula that describes the spontaneity of protein folding?

A

ΔG = ΔH - TΔS

72
Q

In the context of protein folding, what does a negative ΔG indicate?

A

The process is spontaneous.

73
Q

What type of interaction is the hydrophobic effect primarily associated with?

A

Minimizing contact with water by nonpolar substances.

74
Q

Fill in the blank: The energy of association between two electric charges is given by __________.

A

E = k * q1 * q2 / (D * r)

75
Q

What is the typical strength of ionic interactions in the interior of proteins?

A

-86 kJmol-1

76
Q

What are the characteristics of hydrogen bonds compared to covalent bonds?

A

Weaker, longer bond distances (1.5-2.6 Å), and the strongest tend to be linear.

77
Q

What effect do non-polar molecules have in aqueous solutions?

A

They tend to minimize contact with water, leading to the formation of micelles.

78
Q

What is the stability of native proteins under physiological conditions?

A

Marginally stable

79
Q

What is the significance of the hydrophobic effect in protein folding?

A

It drives the burying of hydrophobic residues in the non-polar core.

80
Q

What is the hydrophobic effect ?

A

The influences that causes non polar substances to minimises their contact with water, and amphipathic molecules, such as soaps and detergents, to form micelles in aq solutions

81
Q

What is the primary structure of a protein?

A

The linear sequence of the amino acids in the polypeptide chain.

The primary structure has directionality.

82
Q

What stabilizes the secondary structure of proteins?

A

Hydrogen bonding between atoms of the polypeptide backbone.

Secondary structures include alpha helices and beta sheets.

83
Q

Define secondary structure in proteins.

A

Folding of the polypeptide backbone into regular structures such as the alpha helix and beta sheet.

Includes turns and loops.

84
Q

What is an alpha helix?

A

A coiled structure with all main chain CO and NH groups hydrogen bonded, with side chains pointing away from the helix axis.

Predicted by Pauling and Corey in 1951.

85
Q

What is the typical handedness of alpha helices found in proteins?

A

Right-handed.

Nearly all helices in proteins are right-handed.

86
Q

What is amphiphilicity in relation to alpha helices?

A

Alpha helices often have both hydrophobic and hydrophilic character.

Hydrophobic face packs to the interior, and hydrophilic face points towards the solvent.

87
Q

How are beta sheets constructed?

A

From 2 or more polypeptide strands hydrogen bonded to each other, each strand in a nearly extended conformation.

Can be parallel or antiparallel.

88
Q

What is the role of loops and turns in protein structure?

A

They connect secondary structure elements and contribute to protein function.

They often contain functional residues.

89
Q

What is tertiary structure?

A

The assembly of secondary structure elements into the native protein structure.

Connecting loops form the tertiary structure.

90
Q

Define quaternary structure of proteins.

A

The assembly of multiple polypeptide chains into multi-subunit structures.

Examples include hemoglobin and antibodies.

91
Q

What are domains in protein structure?

A

Structurally independent units within polypeptides, often with specific functions.

Domains can fold into globular clusters.

92
Q

What characterizes the immunoglobulin fold?

A

A pair of antiparallel beta sheets surrounding a hydrophobic core.

Each domain in IgG is structurally similar.

93
Q

True or False: All beta sheets are flat.

A

False.

Beta sheets can adopt a twisted shape due to steric repulsion.

94
Q

Fill in the blank: The compact structure that individual polypeptides attain is called the _______.

A

tertiary structure.

In water-soluble proteins, hydrophobic residues are usually interior.

95
Q

What interactions facilitate quaternary structure?

A

Non-covalent interactions such as hydrogen bonds and buried hydrophobic residues.

Sometimes disulfide bonds are also involved.

96
Q

What is a beta turn?

A

A common way of achieving a reversal in the direction of the polypeptide chains.

Stabilized by hydrogen bonds between CO of residue i and NH of residue i+3.

97
Q

What is a supersecondary structure?

A

Modules of secondary structural elements combined in various ways.

Examples include β-α-β units and helix-turn-helix motifs.

98
Q

What’s conformational change ?

A

Protein changing their 3D shape on binding a small ligand , can be driven driven by a number of events such as substrate binding or phosphorylation

99
Q

What are active site built from

A

Residues in various different positions on a primary sequence

100
Q

What’s phosphorylation ?

A

Phosphorylation - the hydroxyl groups of Ser, Thr and Tyr can be reversibly phosphorylated (kinase/phosphatase) and this process often acts as a molecular switch in regulating cellular processes.

101
Q

What’s glycosylation ?

A

Glycosylation many proteins found on the surface of cells, or that are secreted, acquire carbohydrate units on specific Asn residues, increasing hydrophilicity and the ability to interact with other molecules. Carbohydrate can also link to Ser and Thr.

102
Q

What’s hydroxyproline ?

A

Hydroxyproline the addition of a hydroxyl group to proline to form hydroxyproline stabilizes fibres of newly synthesised collagen. A lack of vitamin C inhibits this process, the fibres are weakened, and scurvy results

103
Q

What a protein family ?

A

A protein family consists of a number of members, each having a closely related amino acid sequence and three dimensional structure, but with differing functions.
• Arises from divergent evolution from a common ancestor

104
Q

What’s the serine proteases family

A

family of proteolytic enzymes including digestive enzymes and some proteases involved in blood clotting – contain the catalytic triad of Asp – His – Ser residues
(similar amino acid sequence, almost identical 3D structures, distinct enzymatic activities, each member has a distinct function)

105
Q

When does a sigma bond occur?

A

When an anion and a cation encounter one another

106
Q

What’s a nucleophile and an electrophile

A

Nucleophile: supplies e-
electrophile: accepts electrons

107
Q

When does the simultaneous making and breaking of sigma bonds occur

A

When a nucleophile approaches a carbon atom having a leaving groups in a direction anti and rearward to the leaving group

108
Q

What’s a lysozyme

A

An enzyme that’s invalid in the first line of defense against bacterial attack that cleaves peptidoglycan, the polysacchance complex in the cell was of gram-positive bacteria
Found in human tears

109
Q

What does lysozyme do?

A

Cut a glycosidic bond between NAM and NAG sugars in bacteria peptidoglycan

110
Q

What is the structure of lysozymes

A

Polypeptide chain of 129 AAs and tours s-s bridges, two lobes (domains) separated by a deep cleft on left Bsheet of mainly hydrophilic residues, on right a hydrophobic core surrounded by a short a-helices
The active site is in the top half of the cleft which binds six sugars , the glycosidic bond is between the 4th and 5th sugars which is the bond broken in this reaction

111
Q

What is the structure of lysozymes

A

Polypeptide chain of 129 AAs and tours s-s bridges, two lobes (domains) separated by a deep cleft on left Bsheet of mainly hydrophilic residues, on right a hydrophobic core surrounded by a short a-helices
The active site is in the top half of the cleft

112
Q

Explain the lysozyme active site

A

Lysozyme bonds the peptidoglycan carbohydrate polymer so nam ring is at D side and nag ring at site E in the binding site on the enzyme surface.

113
Q

How does lysozymes bind?

A

Cleared NAG-NAM polysaccharide from bacterial cell walls, 2 domains separated by-active site cleft. (Sett can bind 6 cleaves after 4

114
Q

What are the key residues of lysozymes

A

Glu 35: profaned (glutamic acid rather than glutamate) because its in an unusual hydrophobic environment - acts as an acid
Asp 52: unprotomated (normal at neutral pH) and acts as nucleophile.

115
Q

What is mechanism for lysozyme?

A

1) nucleophilic attack by asp 52 to create a covalent glycosyl-enzyme intermediate
2) Glu 35 donates a proton
3) followed by attack by water.

116
Q

What’s the Henderson-Hasselbach equation

A

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

117
Q

What’s the Henderson-Hasselbach equation

A

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

118
Q

What’s a zwitterion

A

An amino acid molecule with a negative coo group and positive nh3 group

119
Q

What is responsible for pH dependent reaction profiles

A

The protonation state of the side chain of a residue

120
Q

What’s the difference between transition states and reaction intermediates?

A

Transition states exist at top reaction curve for very short femtoseconds timescales.
Reaction intermediates exist at the middle of the reaction curve are more stable than transition states and can be isolated

121
Q

What do enzymes prefer to bind too?

A

Transition states and therefore facilitate their formation- many of best enzymes inhibiton are transition state analogues

122
Q

What’s the induced fit model

A

Where an enzyme will go through a conformational change to better fit to its substrate, this happens as enzyme is strained substrate first when binds and strain is relieved by reaching the transitional state is reached.

123
Q

What are the common steps which recur in enzyme catalyzed reactions that further enhance the rate

A
  1. General acid-base catalysis 2. Covalent catalysis 3. Use
    of metal ions in catalysis.
124
Q

Explain general acid- base catalysis?

A

Invokes donation of a proton by a group on the enzyme acting acid or abstraction of a proton by a group on the enzyme acting as a base both processes lower the free energy pathway to the transition state in a reaction this process may combined in to a single reaction cycle.

125
Q

Explain covalent catalysis

A

Enzyme forms covalent bonds with substrates to generate transient reactive intermediates. This will generally involve a strong nucleophile m the enzyme
Lysozymes use an covalent intermediate between asps2 and oxonium ion on the NAM sugar formed during the reaction cycle as part of its catalytic mechanism

126
Q

Explain metal ion catalysis

A

Enzymes often use bound metal ions in their reaction mechanisms, metals can be tightly bounds, metalloenzymes, these typically use transition metals ions (fe2+/fa3+) can also be loosely bound, metal activated, mesh enzymes typically use

127
Q

Explain metal ion catalysis

A

Enzymes often use bound metal ions in their reaction mechanisms, metals can be tightly bounds, metalloenzymes, these typically use transition metals ions (fe2+/fa3+) can also be loosely bound, metal activated, mesh enzymes typically use

Biochem 1 (2 decks)

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