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BIOCHEM 401 > Module 2 > Flashcards

Module 2 Flashcards

1
Q

What are the 5 main components of an amino acid?

A

An amino group, a carboxylic acid group, an alpha carbon, and a side chain

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2
Q

What is the chemical formula for an amino group?

A

H2N

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3
Q

What is the chemical formula for a carboxylic acid?

A

COOH

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4
Q

How is electrostatic charge distributed in an amino acid at neutral pH?

A

The amino group is positively charged and the carboxylic acid is negatively charged.

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5
Q

What does pH measure?

A

pH is a logarithmic scale which inversely indicates the concentration of hydrogen ions in a solution

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6
Q

What are the properties of a solution with high pH?

A

A high pH solution is basic, meaning it has a low concentration of hydrogen ions.

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7
Q

What are the properties of a solution with low pH?

A

A low pH solution is acidic, meaning it has a high concentration of hydrogen ions.

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8
Q

Are acids proton donors, or proton acceptors?

A

Proton donors

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9
Q

What are the 6 types of amino acid side chains?

A

Polar uncharged

Positively charged (basic)

Negatively charged

Aliphatic (Non-polar/hydrophobic)

Aromatic

H/Glycine

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10
Q

How many protein amino acids are there?

A

20

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11
Q

Which of the amino acids is actually an imino acid and what is the key impact this has on the protein?

A

Proline - it has an imino group rather than an amino group. The imino group is part of a cyclic structure. This limits the possible rotation between the nitrogen and the alpha carbon, which impacts the shape of the protein backbone.

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12
Q

What are the 6 nonpolar/aliphatic/hydrophobic amino acids?

A

Girls Always Vote Left If Provoked OR

GLaciers in ALAska VALiantly Locate ISOlated PROwlers

Glysine (G)

Alanine (A)

Valine (V)

Leucine (L)

Isoline (I)

Proline (P)

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13
Q

What are the 3 aromatic amino acids?

A

The AROma of fine Pine and yellow Timber is worth the TRYP

Phenylalanine (F)

Tyrosine (Y)

Tryptophan (W)

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14
Q

What are the two alcoholic amino acids?

A

ALCOHOL is a SERious THREat

Serine (S)

Threonine (T)

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15
Q

What are the three basic/positively charged amino acids?

A

BASICally, HIS Lost kid Always returned

Histidine (H)

Lysine (K)

Arginine (R)

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16
Q

What are the two sulfur-containing amino acids?

A

METhodically Check the path for SULFUR.

Methionine (M)

Cystine (C)

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17
Q

What bonds determine the primary structure of a protein?

A

Covalent bonds (aka dipeptide bonds or amide linkages)

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18
Q

What are the two ends of a protein called, and how do they differ?

A

The N terminus is at the amino group of the first amino acid added to the protein chain. The C terminus or carboxy end is at the free carboxyl group of the last amino acid

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19
Q

Which colour is the N terminus and which is the C terminus? At which end would you find the most recently added amino group?

A

Red is N terminus, blue is C terminus. The most recent amino group is at the C terminus.

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20
Q

***List 8 functions of proteins

A

Catalysis

Transport

Structure

Motion

Antibodies

Hormones

Messenger proteins

Genetic information stored in DNA

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21
Q

**Give two examples of proteins involved in catalysis

A

DNA polymerase (DNA replication)

Enolase (glycolysis)

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22
Q

**Give two examples of proteins involved in transport

A

Haemoglobin (oxygen transport)

Lactose permease (transports lactose across cell membrane)

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23
Q

**Give two examples of proteins involved in structure

A

Keratin (hair, nails, horns)

Collagen (connective tissue)

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24
Q

**Give two examples of proteins involved in motion

A

Myocin (muscle tissue)

Actin (muscle tissue and cell motility)

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25
Q

What is a dipeptide?

A

A polymer made up of 2 amino acids

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26
Q

What is a tripeptide?

A

A polymer made up of 3 amino acids

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27
Q

What is an oligopeptide?

A

A polymer made up of a few amino acids

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28
Q

What is a polypeptide?

A

A polymer made up of many amino acids

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29
Q

What kind of reaction occurs to form a peptide bond?

A

Condensation reaction

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30
Q

Draw the formation of a peptide bond

A
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31
Q
A
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32
Q

What is a chiral carbon?

A

A carbon linked to four distinct functional groups (none the same as each other)

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33
Q

What are enantiomers?

A

The two mirrored configurations of a molecule containing a chiral centre

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34
Q

An enantiomer is one of two kinds of:

A

Stereoisomers

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35
Q

You can obtain a mirror image of a ______ but not a _______ molecule without breaking covalent bonds

A

Achiral, chiral

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36
Q

What is the difference between conformation and configuration?

A

Conformation refers to the different shapes a molecule can take based on free rotation of its single bonds.

Configuration is the relative position of the atoms in a molecule and can only be changed by cleaving and forming new chemical bonds.

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37
Q

Molecular conformations with lower potential energy display _____ stability

A

Higher

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38
Q

___bolism generates energy and waste

A

Catabolism

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39
Q

____bolism uses energy

A

Anabolism

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40
Q

Metabolism is the combination of _______ and ________

A

Catabolic and anabolic biochemical reactions

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41
Q

All life on earth uses at least one of these two potential sources of energy:

A

Sunlight

Potential energy stored in food

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42
Q

Anabolism _____creases entropy

A

decreases

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43
Q

What is the first law of thermodynamics?

A

The universe contains a constant amount of energy.

Energy is not created nor destroyed, but it can change form.

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44
Q

What is the second law of thermodynamics?

A

Energy is transferred in a way that increases the randomness (entropy) of the universe.

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45
Q

How does a molecule contain potential energy?

A

In its bonds.

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46
Q

Increased entropy mostly occurs through the transformation of various forms of energy into _____________

A

Thermal energy

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47
Q

Give the two versions of the Gibbs free energy equation (including definitions)

A

G = H - TS

ΔG = ΔH - TΔS

G = Free energy

H = Enthalpy

T = Temperature

S = Entropy

Δ = Change (delta)

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48
Q

Define enthalpy

A

Enthalpy is the total energy of a system.

In the case of a biochemical reaction, it includes all the energy stored in the chemical bonds of all the molecules involved in the reaction, as well as the environment around the reaction.

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49
Q

How is the T in the Gibbs free energy equation measured?

A

Degrees Kelvin

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50
Q

Why does temperature amplify the entropy term in the Gibbs free energy equation?

A

Because raising the temperature intensifies random molecular motion, leading to an increased disorder.

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51
Q

Define free energy

A

The portion of energy in a system that is available to do work

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52
Q

Define phototroph and name its alternative

A

A living organism using sunlight as a source of energy

Chemotroph

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53
Q

Define chemotroph, and name its alternative

A

A living organism that extracts energy from chemical molecules

Phototroph

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54
Q

Name and define the two types of chemotroph

A

Lithotrophs extract energy from inorganic molecules

Organotrophs extract energy from organic molecules.

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55
Q

Define autotrophs and heterotrophs

A

To obtain carbon for building biomolecules, autotrophs fix carbon dioxide, while heterotrophs rely on organic molecules.

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56
Q

Describe the cyclical relationship between autotrophs and heterotrophs

A

Autotrophs generate organic molecules and oxygen that will be used by heterotrophs.

Heterotrophs produce water and carbon dioxide used by autotrophs.

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57
Q

The flow of energy is irreversible because living organisms cannot convert _____ into _____.

A

Heat, chemical energy

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58
Q

Which goes with which?

Phototroph and Chemotroph

Autotroph and Heterotroph

A

There are autotrophs and heterotrophs within both phototroph and chemotroph categories.

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59
Q

A system rich in free energy is _______ and _______ evolves towards a more ______ state with ______ free energy.

A

Unstable

Spontaneously

Stable

Lower

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60
Q
A
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61
Q

When the entropy of a system increases, how does this affect the free energy of the system?

A

The free energy decreases

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62
Q

Describe a spontaneous process

A

A spontaneous process is characterized by a decrease of free energy as the system evolves toward a more stable state.

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63
Q

A spontaneous biochemical reaction - also called ___________ - is thermodynamically __________.

A

an exergonic reaction

favourable

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64
Q

In a spontaneous reaction, the substrate - with a ____ potential energy - is converted into reaction products with a _____ potential energy.

A

High

Lower

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65
Q

A spontaneous biochemical reaction is characterized by _____ of free energy

A

a decrease

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66
Q

What does ΔG refer to?

A

The change in free energy

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67
Q

What kind of reaction does this equation describe?

A

A spontaneous reaction

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68
Q
A
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69
Q

If change of enthalpy is negative, the reaction _______

and is said to be ________.

If change of enthalpy is positive, the reaction _______ heat and is said to be ________.

A

releases, exothermic

consumes, endothermic

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70
Q
A
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71
Q

What is the carbon in an amino acid called?

A

The alpha carbon

72
Q

True or false: There are twenty amino acids

A

False. 20 amino acids are found in proteins, however there are others present in living organisms but not as constituents of proteins. Some Some residues can also be modified after a protein has been synthesized.

73
Q

How many of the amino acids are chiral and what are the exceptions?

A

19 are chiral - only glycine is the exception as the alpha carbon is bound to 2 hydrogens

74
Q

Which amino acids do not conform to this general structure, and why?

A

Proline, where the side chain is connected to the protein backbone twice, forming a five-membered nitrogen-containing ring - this limits the structural flexibility of proteins containing proline

75
Q

How are the bonding orbitals arranged around the alpha-carbon of an amino acid?

A

Tetrahedral

76
Q

How many stereoisomers can amino acids have, of what kind, and what are they called?

A

Two - enantiomers - L and D configurations

77
Q

What are these two configurations of an amino acid called?

A

The first is L configuration and the second is D configuration. You can remember the L configuration because, with the carboxyl group at the top, the L configuration has the amino group to the LEFT of the alpha carbon.

78
Q

Which stereoisomer of amino acids naturally occurs in proteins?

A

L configuration

79
Q

Where can amino acids in the D configuration be found?

A

D-Amino acid residues have been found only in a few, generally small peptides, including some peptides of bacterial cell walls and certain peptide antibiotics.

80
Q

How are cells able to specifically synthesize the L isomers of amino acids?

A

The active sites of enzymes are asymmetric, causing the reactions they catalyze to be stereospecific.

81
Q

Which four aliphatic non-polar side-chains tend to cluster together, and why?

A

The side chains of alanine, valine, leucine, and isoleucine
tend to cluster together within proteins, stabilizing protein structure by means of hydrophobic interactions.

82
Q

Which two amino acids contain sulfur?

A

Methionine and cysteine

83
Q

Which functional group of tyrosine tends to form hydrogen bonds?

A

The hydroxyl group

84
Q

Describe which aromatic R groups hydrophobic or hydrophilic?

A

They are all hydrophobic (non-polar) - Tyrosine and tryptophan are significantly more polar than phenylalanine, because of the tyrosine hydroxyl group and the nitrogen of the tryptophan indole ring.

85
Q

At which wavelength do most proteins absorb light?

A

280 nm

86
Q

Among amino acids, what is unique about histidine and what functions does this allow?

A

Histidine is the only common amino acid having an ionizable side chain with a pKa near neutrality. In many enzyme-catalyzed reactions, a His residue facilitates the reaction by serving as a proton donor/acceptor.

87
Q

Which amino acids are amides?

What change would be made to create an amide of the amino acid pictured?

A

Aspartate and asparagine

Glutamate and glutamine

The carbon of the carbonyl group binds with a nitrogen and two hydrogens (and forms a double-bond with the remaining oxygen)

88
Q

An acid is a proton ________

A base is a proton _________

A

Donor

Acceptor

89
Q

A zwitterion can act as either ______ or _______

A

Acid

Base

90
Q

What is a zwitterion?

A

A dipolar ion: a molecule or ion having separate positively and negatively charged groups.

91
Q

Under what conditions do amino acids predominantly occur as zwitterions?

A

In aqueous solutions at neutral pH.

92
Q

What do “amphoteric” and “ampholyte” describe?

A

Amphoteric - the ability to act as an acid or a base

Ampholyte - a substance that is amphoteric

93
Q

What does pKa indicate?

A

The pH at which 50% of the functional groups exist in their protonated state and 50% exist in their deprotonated state.

Therefore if the pH is below the pKa of a functional group, protonate it!

94
Q

What are the protonated and deprotonated forms of the amine functional group?

A

Protonated: NH3+

Deprotonated: NH2 + H+

95
Q

What are the protonated and deprotonated forms of the carboxyl functional group?

A

Protonated: COOH

Deprotonated: COO- + H+

96
Q

The _____ the pKa value, the stronger the acid

A

Lower

97
Q

What is the difference between Ka and pKa

A

Ka is the acid dissociation constant of a solution

pKa is the negative base-10 logarithm of Ka. This makes the Ka values larger and therefore easier to interpret, and means that the tendency of a group to give up a proton decreases tenfold as the pKa increases by one unit

98
Q

The tendency of a functional group to give up a proton decreases by ______ as the pKa _______ by one unit

A

tenfold

increases

99
Q

What is the normal pH of intracellular fluid and blood?

A

7.4

100
Q

Define isoelectric point

A

The characteristic pH at which the net electric charge of the molecule is zero

101
Q

Where is the isoelectric point on this titration curve?

A
102
Q

What do the blue boxes indicate in this titration curve?

A

The pH regions of greatest buffering power for the molecule

103
Q

In an aqueous environment, only _____ has an R group (pKa = 6.0) providing significant buffering power near the neutral pH usually found in the intracellular and extracellular fluids of most animals and bacteria

A

Histidine

104
Q

What is the reference molecule for the L and D configurations?

A

glyceraldehyde

105
Q

Draw the formation of a peptide bond

A
106
Q

Under standard biochemical conditions, does the equilibrium favour 2 amino acids or formation of a dipeptide?

A

2 amino acids

107
Q

What is the difference between a polypeptide and a protein?

A

Although the terms “protein” and “polypeptide” are sometimes used interchangeably, molecules referred to as polypeptides generally have molecular weights below 10,000, and those called proteins have higher molecular weights

108
Q

Peptide bonds in proteins are quite stable/unstable, with an average half-life (t1/2) of about ____ under most intracellular conditions.

A

Stable

7 years

109
Q

Which parts of a peptide contribute to the overall acid-base properties of the molecule

A

The terminal amino and carboxyl groups and ionizable side chains

110
Q

The pKa value for an ionizable R group changes/remains the same when an amino acid becomes a residue in a peptide

A

Changes - due to the loss of charge in the alpha-carboxyl and alpha-amino groups which have formed peptide bonds, the interactions with other peptide R groups, and other environmental factors

111
Q

What relationship exists between the molecular weights of biologically active peptides and proteins and their functions.

A

There is no generalizable relationship

112
Q

What do oligomeric and protomer mean when describing a protein

A

When describing a multi-subunit protein, oligomeric indicates that at least 2 of the subunits are identical. Protomer is the name for each identical subunit

113
Q

True or false: the different polypeptide chains in multi-unit proteins are always linked by non-covalent bonds

A

False - they are usually linked with non-covalent bonds but in some cases they can be linked with disulfide bonds

114
Q

How do you calculate the approximate number of amino acid residues in a simple protein?

A

Divide the molecular weight of the protein by 110

115
Q

What process breaks polypeptides back down into free amino acids?

A

Hydrolysis

116
Q

Define a simple protein, and name and define the alternative

A

Simple proteins contain only amino acid residues and no other chemical constituents.

Conjugated proteins proteins contain permanently associated chemical components in addition to amino acids - these are called prosthetic groups

117
Q

Name and define six classes of conjugated protein

A
118
Q

Amino groups on an amino acid are weakly acidic/basic?

A

Basic

119
Q

What kind of side chains do the non-polar aliphatic amino acids have?

A

Alkyl side chains

120
Q

Which amino acid is present in proteins much less frequently than others?

A

Methionine

121
Q

What does the ring structure of aromatic amino acid side chains allow them to do?

A

Absorb UV light

122
Q

Which positively charged amino acid could also be considered aromatic?

A

Histidine

123
Q

What kind of side-chain does cysteine have?

A

Thiol side-chain

124
Q

Describe the formation and function of cystine

A

Two cysteines can be oxidised to form cystine

Cystine can form covalent cross-links within proteins

Cystine is hydrophobic

125
Q

What kind of reactions is cysteine often involved in within cells?

A

Redox reactions

126
Q

What kind of bonds can amide amino acids form?

A

They can form hydrogen bonds as H donors or H acceptors

127
Q

What kinds of bonds can hydroxy amino acids form?

A

Hydrogen bonds with water or other H-acceptor groups on the protein

128
Q

What defines a hydroxy amino acid and what does this allow?

A

The presence of a hydroxy group (-OH) - these can form phosphate esthers

129
Q

What are peptide-hydrogen bonds?

A

hydrogen bonds between the carbonyl oxygen of one peptide bond and the amide hydrogen of another peptide bond within the same protein

130
Q

Membrane proteins are more ________ than globular proteins

A

Hydrophilic

131
Q

How are peptide bonds formed (what conditions are needed)?

A

Peptide bonds between amino acids are formed on the catalytic site of the ribosome, by peptidyl transferase

132
Q

Is haemoglobin water soluble?

A

Yes

133
Q

What defines an alpha amino acid?

A

Has the amino group and carboxyl group both bonded to the same alpha carbon. (Beta amino acids have the carboxyl group bonded to a carbon adjacent to the alpha carbon)

134
Q

Are basic amino acids positively or negatively charged at low pH?

A

Positively charged

135
Q

A protein with more acidic amino acids than basic amino acids will have a pI that is _____ 7

A

Below

136
Q

Which amino acids are dissolved in water at neutral pH?

A

Those without an ionizable side-chain

137
Q

At low pH, an amino acid will be _______ charged

A

positively

138
Q

What is another name for aromatic side chain rings?

A

Benzene rings

139
Q

Which two aliphatic amino acids are NOT usually found in the centre (away from water) of protein structures

A

Glycine and proline

140
Q

What are the aromatic amino acids used to synthesize?

A

Tryptophan: serotonin

Tyrosine: thyroid hormones

Phenylalanine: dopamine

141
Q

Which of the aromatic amino acids is not as good at absorbing UV light?

A

Phenylalanine

142
Q

What causes sickle cell anemia?

A

Glutamate 6 (polar0 is replaced by valine (non-polar) in the beta subunit of haemoglobin. The creation of a new hydrophobic region causes multiple subunits to attract by hydrophobic forces, meaning the haemoglobin is polymerised beyond its usual tetramer quarternary structure. The polymerized hemoglobin distorts red blood cells into an abnormal sickle shape.

143
Q

State the main functions and level of conservation of cytochrome c and cytochrome p450

A

Cytochrome c is mainly found in the mitochondria and acts as an electron transporter between membranes. It’s primary structure is highly conserved across related species.

Cytochrome p450 is a liver enzyme needed for detoxification pathways, include metabolism of medications. Cytochrome p450 shows polymorphisms between individuals within a species.

144
Q

Describe the evolution of myoglobin and haemoglobin

A

(see module 2 lecture 2)

145
Q

What bonds stabilise secondary structure?

A

Hydrogen peptide bonds

146
Q

Describe the properties of peptide bonds as they relate to secondary structure

A

They are rigid and planar from alpha-carbon to alpha-carbon (usually trans).

They have a partial double bond character.

Rotation of the planes is possible around the phi and psi bonds linking the amino and carboxyl groups respectively to the alpha carbon.

This rotation is limited by steric hindrance.

147
Q

How are the peptide-hydrogen bonds aligned in an alpha-helix?

A

Roughly parallel with the helical axis

148
Q

How are R-groups arranged in an alpha-helix?

A

They protrude outwards and slightly towards the N terminus

149
Q

Which direction of alpha-helix is found in proteins?

A

Right handed - as if you were going up a spiral staircase and the outside rail was in your right hand

150
Q

Which protein amino acids can participate in the alpha-helix structure?

A

All of them to some extent, although proline disrupts the structure by limiting rotation around the phi angle bond and glycine because its side-chain supports other conformations.

151
Q

Which four amino acids are most often found in alpha-helices?

A

Alanine, Glutamate, Leucine, and Methionine

152
Q

What kinds of bonds stabilise beta-sheets?

A

Peptide hydrogen bonds between strands

153
Q

Which is stronger - parallel or antiparallel beta sheet - and why?

A

Antiparallel is stronger as the peptide-hydrogen bonds are better aligned (more linear)

154
Q

How are R groups arranged in a beta-sheet?

A

They protrude above and below the sheet, perpendicular to the hydrogen bonds. On each strand, they alternate between above and below.

155
Q

How are beta-turns stabilised?

A

Hydrogen bonds from a carbonyl oxygen to an amide nitrogen three residues down the sequence

156
Q

Over how many residues is a beta turn formed, and which amino acids are commonly found in beta turns?

A

A 180 degree turn is achieved over four amino acids

Proline is often found in position 2, or glycine in position 3.

157
Q

Where in a protein to beta turns often occur?

A

Near the surface, and in crevices between domains.

158
Q

What is the difference between a type 1 and type 2 beta turn?

A

Type 1 contains proline at position 2

Type 2 contains glycine at position 3

159
Q

Which amino acids can participate in peptide-hydrogen bonds?

A

All except proline

160
Q

How many amino acid residues are in each turn of an alpha-helix?

A

3.6

161
Q

Where are beta sheets most often found in a protein?

A

At its core

162
Q

What types of R-groups are more likely to participate in beta sheets?

A

Hydrophobic R-groups e.g. valine and isoleucine

163
Q

What is another name for a negatively charged carboxyl group?

A

A carboxylate

164
Q

Which is the strongest and which is the weakest non-covalent bond?

A

Strongest - ionic

Weakest - van der Waals

165
Q

Which non-covalent bond is directional?

A

Hydrogen bond - is strongest when the two dipoles are aligned

166
Q

Is a disulfide bond more likely to occur in extracellular or intracellular space?

A

Extracellular - disulfide bonding is an oxidisation reaction and requires an oxidising environment which is found extracellularly

167
Q

How many conformations can the peptide bond take and what greek letter represents this bond?

A

Two only - cis and trans (defined by position of the alpha carbon) - due to the planar nature of the bond, aka its partial double bond character

It is represented by omega (ω) and is either 180 degrees or 0 degrees.

168
Q

Which conformation does the peptide bond usualy take, why, and what is the exception?

A

Trans - meaning the alpha carbons are on opposite sides. This is because when the carbons are in cis conformation, their side chains tend to clash.

The exception is the peptide bond on the n-terminal side of a proline, which can be cis or trans.

169
Q

What is the geometric term to describe the phi and psi bonds on the amino acid backbone?

A

Dihedral

170
Q

Hydrogen bonds between what and what stabilise alpha helices?

A

Between the carbonyl of residue N, and the amino group of residue N+4

171
Q

Which of the three types of secondary structure often contributes to the actives sites of a protein and why?

A

Beta loops/turns as they have a lot of conformational flexibility to shape themselves around ligands

172
Q

Why does a proline often break an alpha helix?

A

Because of the imino ring, it has no free hydrogen to bond with a carbonyl group

173
Q

What motif is this?

A

Beta alpha beta - two beta strands joined by an alpha helix

174
Q

Define a domain

A

This is an independent folding unit within a single polypeptide, usually comprised of several motifs. It can form and maintain its tertiary structure independent to the rest of the protein.

175
Q

Describe the quarternary structure of alcohol dehydrogenase

A

It is a homodimer of two polypeptides, each containing two domains. It has two active sites - one at the intersection of the two domains in each subunit.

176
Q

If protein folding reduces entropy, why is it thermodynamically favourable?

A

Because when water molecules encounter hydrophobic surfaces, this limits their possible movements and reduces entropy. When the hydrophobic elements of a protein are folded away into the protein’s core, more water molecules can move freely, so overall system entropy is increased.

BIOCHEM 401 (2 decks)

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