Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

ESA 1 - Medical Cell Biology & Genetics > Session 4.3b - Lecture 1 - Protein Structure > Flashcards

Session 4.3b - Lecture 1 - Protein Structure Flashcards

Slides 12-23

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards USMLE® Step 1 flashcards
1
Q

Which amino acids have positively charged side chains?

A

Lysine
Arginine
Histidine (usually - although this is a little bit weird)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Which amino acids have negatively charged side chains?

A

Glutamate

Aspartate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is different about histidine compared to the rest of its group? Name the other members of its group.

A

Histidine is an amino acid with a positively charged side chain, so is basic. However, it is weakly basic compared to lysine and arginine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Glutamate and aspartate are part of which group?

A

Negatively charged side chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Why are some amino acids positively or negatively charged?

A

This depends on the nature of the group - comes down to the pKa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the pKa?

A

The negative log (-log or p) of the acid dissociation constant (Ka)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is Ka?

A

The acid dissociation constant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is the acid dissociation constant?

A

Ka

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the negative log of the acid dissociation constant named, and what does this determine?

A

pKa
(negative log [p] of acid dissociation constant [Ka])

Whether an amino acid is positively or negatively charged

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is pKR?

A

It is the pK specifically related to the pK value of the side chain of an amino acid, not thinking about the rest of the amino acid residue.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What do we denote the pK specific to an amino acid side chain?

A

pKR

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the pKR value of lysine?

A

10.5

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are the pK values of Lysine, Arginine and Histidine?

A

Higher

Lysine 10.5
Arginine 12.5
Histidine 6.0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What does the pK value mean?

A

The pK value is the pH at which there’s no overall net charge on an acid or a base

OR

The point where there’s equal amounts of protonated and deprotonated forms (1:1 relationship)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

The pH at which there’s no overall net charge on an acid or a base is called what?

A

pK

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

The point where there’s equal amounts of protonated and deprotonated forms (1:1 relationship) can be represented by what?

A

The pK value

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Lysine has a pK value of 10.5. At what pH will lysine have no net charge?

A

10.5

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Lysine has a pK value of 10.5. At what pH will there be equal protonated and deprotonated forms of lysine?

A

10.5

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

In what form does lysine appear at physiological pH?

A

Physiological pH is ~7.4.

Lysine has a pKa of 10.5.

This means it is always protonated at physiological pH (accepted a proton) and in positive charge form.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

How do glutamate and aspartate appear at physiological pH?

A

These appear as anions, ionised forms of glutamic acid and aspartic acid

This means they have donated their protons and have become negatively charged.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What does it mean for their pK value if glutamate and aspartate are negatively charged at physiological pH?

A

They have low pK values.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What are the pK values of Glutamate and Aspartate?

A

Glutamate 4.3
Aspartate 2.8

(Lower)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Positively charged R groups have a _____ pKR value?

A

higher

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Negatively charged R groups have a _____ pKR value?

A

lower

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

If the pH of the solution < the pK value then the group will be __________

A

protonated

general rule - note pK is lazy, should write pKa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

If the pH of the solution > the pK value then the group will be __________

A

deprotonated

general rule - note pK is lazy, should write pKa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

If the pH of the solution ____ the pK value then the group will be protonated

Fill in the blank, choose ONE:
Less than <
Equal =
More than >

A

Less than
<

(general rule - note pK is lazy, should write pKa)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

If the pH of the solution ____ the pK value then the group will be deprotonated

Fill in the blank, choose ONE:
Less than <
Equal =
More than >

A

More than
>

(general rule - note pK is lazy, should write pKa)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Why do lysine and arginine appear protonated at physiological pH?

A

Physiological pH ~7

Their pK values are higher than pH so they are protonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Why do glutamate and aspartate appear deprotonated at physiological pH?

A

Physiological pH ~7

Their pK values are lower than pH so they are deprotonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What charge do lysine and arginine have a physiological pH?

A

+ve because their pK values are higher than the pH, thus are protonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What charge do glutamate and aspartate have a physiological pH?

A

-ve because their pK values are lower than the pH, thus are deprotonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Protonated and deprotonated does not necessarily mean what?

A

That things have a positive or negative charge.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What is physiological pH?

A

7.4

~7

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What is the predominant form of each of the following amino acids shown below?

Lysine pK = 10.5
CH2CH2CH2CH2NH2 + H+ CH2CH2CH2CH2NH3+

A

CH2CH2CH2CH2NH3+

If the pH of the solution < the pK value then the group will be protonated

(positively charged)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is the predominant form of each of the following amino acids shown below?

Aspartate pK = 2.8
CH2COOH CH2COO- + H+

A

CH2COO-

If the pH of the solution > the pK value then the group will be deprotonated

(negatively charged)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Is lysine postively or negatively charged at physiological pH?

A

Physiological pH = 7.4

pH < pK so group is protonated

= positively charged

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Is aspartate postively or negatively charged at physiological pH?

A

Physiological pH = 7.4

pH > pK so group is deprotonated

= negatively charged

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What are the chemical structures for aspartate and aspartic acid?

A

Aspartate = CH2COO-

Aspartic acid = CH2COOH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Will you find lysine in its deprotonated form at physiological pH?

A

YES, just because the PREDOMINANT form of it will be protonated at physiological pH, doesn’t mean there aren’t any other molecules of the deprotonated form, just that the protonated form is much more likely.

(Remember it is an equilibrium equation, and Henderson-Hasselbach can be used to work out the ratio of protonated:deprotonated)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Will you find aspartate in its protonated form at physiological pH?

A

YES, just because the PREDOMINANT form of it will be deprotonated at physiological pH, doesn’t mean there aren’t any other molecules of the protonated form, just that the deprotonated form is much more likely.

(Remember it is an equilibrium equation, and Henderson-Hasselbach can be used to work out the ratio of protonated:deprotonated)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

Will you find lysine in its protonated form at physiological pH?

A

Yes, predominantly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Will you find arginine in its deprotonated form at physiological pH?

A

Yes, predominantly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

How can we work out the proportions of a protonated:deprotonated amino acid in solution, such as lysine?

A

Via the Henderson-Hasselbalch equation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

What can you use the Henderson-Hasselbalch equation for?

A

Working out the proportions of protonated:deprotonated amino acids in solution.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What do we get when put amino acids together?

A

A protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

When amino acids form a protein, what structural levels do we get?

A

4 different levels of protein structure (primary, secondary, tertiary and quaternary structure)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

The ‘beads on a string model’ refers to which level of protein structure?

A

Primary structure.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

What is the primary structure?

A

The linear amino acid sequence of the polypeptide chain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

What does the primary structure tell us?

A

Only tells us which different amino acids come on one after another.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

How do we notate the amino acid structure in a protein?

A

We write them down from N terminus to C terminus left to right, by convention.
- If not specified we assume it is this way around by convention (similar to 5’ and 3’ DNA).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

What is the secondary structure?

A

Local spatial arrangement of polypeptide backbone - the conformations like helices etc.

(small sequence of our protein folding into standard conformation)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

Which structure of the protein is responsible for a small sequence of the protein folding into standard conformation?

A

The secondary structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

What is the tertiary structure?

A

The overall 3- dimensional configuration of the protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

What gives us the overall 3D structure of the protein?

A

Localised regions can further fold up to give the overall 3D structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

Localised regions of the protein can further fold up to give us what?

A

The overall 3D structure/tertiary structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

In textbooks, which structure is typically depicted for proteins?

A

The tertiary structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

What is the quaternary structure?

A

Association between different polypeptides to form a multi-subunit protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

Which structure of proteins is not seen in all proteins?

A

The quaternary structure is not seen in all proteins but in probably quite a lot of them.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

Which structures involves interaction between >1 polypeptide?

A

The quaternary structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

In the quaternary structure, where is one linear amino acid chain?

A

One linear amino acid chain = one polypeptide sequence

So in the quaternary structure this is one subunit

> 1 subunit gives a quaternary structure, involving proteins fitting together

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

Fig. 14

Label the image

A

Primary structure
Secondary structure
Tertiary structure
Quaternary structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

Draw the four structures of a protein.

A

See slide 14

Primary - Lys-Lys-Gly-Gly-Leu-Val-Ala-His

Secondary - alpha-helix

Tertiary - 3D configuration

Quaternary - >1 subunit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

Why do proteins fold up/how can they fold up?

A

This comes down to do with the chemical nature of proteins themselves - the basis for all the folding is to do with the peptide bond which joins the 2 amino acids together.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

What is peptide bond formation?

A

The linking of two amino acids is accompanied by the abstraction of a molecule of water

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

What is the basis for all the folding in a protein?

A

The peptide bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

What type of reaction is a peptide bond?

A

Condensation reaction (removal of water)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

Which groups react to form a peptide bond?

A

The carboxyl group and amino group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

What atoms are bonded in a peptide bond?

A

Carbon - nitrogen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

What are the functional groups involved in a peptide bond?

A

Carboxyl group (COO-) to form a carbonyl oxygen (C=O)

Amino group (NH3+) to form an amide group (N-H)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

Fig. 15

Label the equation.

A

Amino acid 1 + amino acid 2
–removal of water–>
peptide with amino terminus, peptide bond and carboxyl terminus.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

Draw the formation of a peptide bond.

A 
[AA]R1 + [AA]R2
--H2O-->
NH3+ amino terminus
-H-C-R1-
O=C-N-H peptide bond
-H-C-R2-
COO- carboxyl terminus
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

Why is the peptide bond important?

A

Peptide bonds are:

  • planar
  • rigid
  • exhibit a trans conformation
  • bonds on either side of it are free to rotate
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

Fig. 16

What does this image show?

A

Several amino acids joined together, with alpha carbons from constituent amino acids together.

Peptide bond (C-N) visible from the carbonyl-oxygen (C=O) and amide-hydrogen (N-H)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

What is the peptide unit?

A

One central carbon to the next

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

Fig. 16

If we took a peptide unit and turned it around to face you, what would you see?

A

It is all in one plane; they’re flat (planar).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
77
Q

What part of a protein is planar?

A

Peptide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
78
Q

Which atoms all line in one plane?

A

Ca, C, O, N, H and Ca all aline in the same plane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
79
Q

Fig, 16

Label the image

A

Amino terminus

80
Q

Draw a peptide containing 4 amino acids in planar structure, and label.

A

See Fig. 16

81
Q

Is there movement in amino acids?

A

Peptide bonds are planar/flat in structure, but there is movement around some of the other things.

82
Q

What configuration do peptide bonds lie in?

A

PLANAR

83
Q

Can peptide bonds move?

A

No, they are RIGID

84
Q

Can C-N bonds rotate?

A

Normally, they can yes, but they are rigid in peptide bond.

85
Q

Why are peptide bonds unable to rotate?

A

Although C-N bonds can rotate in other molecules, peptide bonds undergo DELOCALISATION, creating resonance forms.

86
Q

Delocalisation does what to a peptide bond?

A

Makes it rigid and unable to rotate

87
Q

What are resonance structures in proteins?

A

Delocalisation of electrons in a peptide bond, causing rigidity of the C-N bond.

88
Q

Why do we get delocalisation in peptide bonds?

A

These electrons that are important to making up this carbonyl bond in the protein delocalise across the C-N bond.

89
Q

What does delocalisation/resonance forms mean for the peptide bond in proteins?

A

The electrons from the C=O bond can delocalise over the C-N bond, giving the C-N bond partial double bond characteristics (e.g. rigidity, planar, shorter)

90
Q

What are double bond characteristics, and how can they apply to peptide bonds?

A

The electrons from the C=O bond can delocalise over the C-N bond, giving the C-N bond partial double bond characteristics.

Double bonds in things like alkanes are inflexible, whereas things can rotate around a single bond, hence giving rigidity in the single C-N bond.

91
Q

Fig. 17

Label the image

A

Peptide-bond resonance structures

92
Q

What does delocalisation mean for bond length in the peptide bond?

A

Delocalisation of the C=O means C-N bond has double bond characteristics.

This means the C-N bond is a little bit shorter than you’d expect it to be (reminiscent more of a double bond than a single bond).

93
Q

What does a shorter bond length mean?

A

A shorter bond length means a bond is a little stronger.

94
Q

Draw the peptide-bond resonance structures

A

C-C=O-N-H-C

C-C-O-=N+-H-C

95
Q

Why are peptide bonds rigid?

A

Due to the delocalisation of electrons from the C=O to the C-N, giving it double bond characteristics.

96
Q

What does the delocalisation of a peptide bond mean for the partial charges?

A

The O=C-N becomes an O–C=N+

97
Q

What does the delocalisation of electrons from the C=O affect the properties of the peptide (C-N) bond?

A

The peptide bond C-N has partial double bond characteristics.

Unable to rotate - contributes to planarity

98
Q

Peptide bonds can feature in different conformations. What are they?

A
  • Trans

- Cis

99
Q

What is the trans conformation of a peptide bond?

A

Carbonyl-oxygen (C=O) on one side of the bond and amide-hydrogen (N-H) on another.

100
Q

What is the conformation when the C=O and N-H bonds are on opposite sides?

A

Trans

101
Q

What is the cis conformation of a peptide bond?

A

Carbonyl-oxygen (C=O) on one side of the bond and amide-hydrogen (N-H) on the SAME.

102
Q

What is the conformation when the C=O and N-H bonds are on the same side?

A

Cis

103
Q

As well as the C=O and N-H being on the same side on Cis conformations, what other groups are on the same side?

A

The R groups

104
Q

What conformation are proteins ALWAYS in?

A

Trans

105
Q

Why do we not find proteins in the Cis conformation?

A

The R groups are much closer together, thus causing steric hindrance

106
Q

Why is it important that proteins are in the trans orientation?

A

This allows the peptide bonds to have flexibility

107
Q

Which part of the protein is rigid and planar and which part can rotate?

A

Peptide bonds are rigid and planar but the bonds on either side of them can rotate.

108
Q

What are the properties of a trans conformation in peptide bonds?

A

Ca on opposite sides of peptide bond

109
Q

What are the properties of a cis conformation in peptide bonds?

A

Ca on same sides of peptide bond

Steric clashes

110
Q

Fig. 18

Label the image

A

Trans - Ca on opposite sides of peptide bond

Cis - Ca on same side of peptide bond
Steric clashes

111
Q

Draw a trans and cis conformation of proteins.

A

Trans - Ca on opposite sides of peptide bond (1)

Cis - Ca on same side of peptide bond (1)
Steric clashes (1)
112
Q

What is the Cα-N bond called in amino acids?

A

Phi bond

113
Q

What is the Phi bond?

A

Cα-N single bond

114
Q

What is the Cα-C bond called?

A

Psi bond

115
Q

What is the Psi bond?

A

Cα-C single bond

116
Q

What does this symbol notate?

ψ

A

Psi in the Greek alphabet

117
Q

What does this symbol notate?

φ

A

Phi in the Greek alphabet?

118
Q

What is the symbol for Psi in the Greek alphabet?

A

ψ

119
Q

What is the symbol for Phi in the Greek alphabet?

A

φ

120
Q

What is the significance of the Psi and Phi bonds?

A

These can rotate, allowing not any conformation but lots of different bond angles, leading to flexibility and therefore development of our 3D structure and proteins.

121
Q

What part of the protein can rotate to give us flexibility?

A

The Psi (C-C) and Phi (C-N) bonds

122
Q

Fig. 19

Label the image

A

Psi and Phi bond appropriately labelled

Psi - Cα-C
Phi - Cα-N

123
Q

Draw a short peptide depicted a psi and phi bond.

A

-N-H-C–H-R-C=O-N-H-phi-C-H–R-psi-C=O-N-H-C-H-R-C=O

124
Q

What forms a protein?

A

Amino acids joined by peptide bonds

125
Q

What does the amino acid sequence of a protein determine?

A
  • The way in which the polypeptide chain folds

- The physical characteristics of the protein

126
Q

What are the physical characteristics and the way a protein folds determined by?

A

The amino acid sequence of a protein

127
Q

What is the importance of amino acids in proteins?

A

It allows them to come in a huge variety of shapes, forms and have different characteristics.

128
Q

Fig. 20

Label this image

A

Amino-terminal end
Carboxyl-terminal end
Red = R groups
Yellow = Peptide bond

Serine, glycine, tyrosine, alanine and leucine

129
Q

Draw the protein of serine, glycine, tyrosine, alanine and leucine.

A

NH3+ Amino-terminal end

C-H-
O=C-N-H repeated

Coo- carboxyl-terminal end

Serine = CH2OH
Glycine = H
Tyrosine = CH2-benzene-OH
Alanine = CH3
Leucine = CH2-CH-CH3-CH3
130
Q

What are the electrical characteristics of a protein defined by?

A

Its isoelectric point (pI)

131
Q

What is the isoelectric point (pI) of proteins?

A

The isoelectric point, pI, of a protein is the pH at which there is no overall net charge.

132
Q

How is the pI calculated?

A

Basically, it is the pKa of the entire protein.

133
Q

Name a protein with a pI of ~1 and a protein with a pI of 11.

A

Pepsin, pI = <1.0

Lysozyme, pI = 11.0

134
Q

Name some acidic proteins.

A

Protein/pI

Pepsin <1.0
Egg albumin 4.6
Serum albumin 4.9
Urease 5.0
β-lactoglobulin 5.2
Haemoglobin 6.8
135
Q

Name a neutral protein

A

Protein/pI

Myoglobin 7.0

136
Q

Name some basic proteins.

A

Protein/pI

Chymotrypsinogen 9.5
Cytochrome c 10.7
Lysozyme 11.0

137
Q

Name the functions of the following proteins.

Pepsin
Egg albumin
Serum albumin
Urease
β-Lactoglobulin
A

Pepsin - digestive enzyme

Egg albumin - egg white

Serum albumin - found in blood

Urease - hydrolyses urea

β-Lactoglobulin - protein in cow/sheep’s milk

138
Q

Name the functions of the following proteins.

Haemoglobin
Myoglobin
Chymotrypsinogen
Cytochrome c
Lysozyme
A

Haemoglobin - transports oxygen in blood

Myoglobin - iron/oxygen binding in muscle tissue

Chymotrypsinogen - inactive precursor of chymotrypsin (digestive enzyme)

Cytochrome c - haem protein

Lysozyme - glycoside hydrolase, breaks down cell walls in peptidoglycans

139
Q

Why do proteins have different isoelectric points?

A

It depends on the amino acid residues that make them up, as all side chains have a certain pK value so will contribute to this.

i.e. basic proteins have lots of basic amino acids e.g. lysines, arginines

acidic proteins have lots of acidic amino acids e.g. glutamate, aspartate

140
Q

What does a pI > 7 mean?

A

Basic proteins

Contain many positively charged (basic) amino acids (accepted a proton)

141
Q

What does a pI < 7 mean?

A

Acidic proteins

Contain many negatively charged (acidic) amino acids (donated a proton)

142
Q

What are most protein’s pI?

A

~5-8, but certain ones will be much higher or much lower.

143
Q

Why do proteins have different pI points?

A

Due to the function of the protein in the cell.

e.g. a protein that’s positively charged will want to interact with something negatively charged

144
Q

Amino acids contribute to what in the protein?

A

Structure - chemical bonding

Function - due to electrical properties (pI) and what it can then interact with.

145
Q

If pH < pI protein is _________

A

protonated

146
Q

If pH > pI protein is _________

A

deprotonated

147
Q

If pH ___ pI protein is protonated

A
148
Q

If pH ___ pI protein is deprotonated

A

>

149
Q

What is the average size of a protein?

A

Biologically active peptides and proteins come in a varying range of sizes,

(When we’re talking about proteins <100 AA residues, we call them peptides)

150
Q

Define peptide/oligopeptide

A

A few amino acids in length, generally <100 amino acid residues

151
Q

Define polypeptide/protein

A

Many amino acids, generally >100 amino acid residues

152
Q

What is the word(s) for a small protein?

A

Peptide/oligopeptide

153
Q

What is the word(s) for a protein sequence longer than >100 amino acid residues?

A

Polypeptide/protein

154
Q

Give an example of an important small peptide in the body.

A

Angiotensin II (8 amino acids)

155
Q

What is angiotensin II derived from?

A

Angiotensinogen (~425 amino acids)

156
Q

What is angiotensin II?

A

A potent vasoconstrictor molecule which binds strongly to angiotensin receptors, regulating blood pressure

157
Q

Why is angiotensin II important clinically?

A

Angiotensin receptor blockers can be made which mimic the structure of angiotensin II, getting in the way of it binding to the receptors and its vasoconstriction.

This will lower the blood pressure and thus can be important in hypertension.

158
Q

What is angiotensin II structure be used to treat?

A

Hypertension

159
Q

How can angiotensin II structure be used to lower blood pressure?

A

Angiotensin receptor blockers can be made which mimic the structure of angiotensin II, getting in the way of it binding to the receptors and its vasoconstriction.

This will lower the blood pressure and thus can be important in hypertension.

160
Q

What is the amino acid sequence of angiotensin II?

A

Asp-Arg-Val-Tyr-Ile-His-Pro-Phe

161
Q

What is the function of cytochrome c important in?

A

The electron transport chain

162
Q

What is a Dalton?

A

A measure of molecule weight in a ratio related to the weight of a hydrogen atom.

163
Q

What is the function of Apolipoprotein B?

A

Important in transport of dietary lipids around body

164
Q

What do protein sizes range from?

A

e.g.

Molecular weight/number of residues/number of polypeptide chains

Cytochrome c = 13,000/104/1

Apolipoprotein B = 513,000/4,536/1

165
Q

Table 22

Label the proteins listed that are found in humans

A

Cytochrome c
Haemoglobin
Serum albumin
Apolipoprotein B

166
Q

Table 22

Label the proteins listed that are found in animals

A 
Ribonuclease A (bovine pancreas)
Lysozyme (chicken egg white)
Myoglobin (equine heart)
Chymotrypsin (bovine pancreas)
Chymotrypsinogen (bovine)
167
Q

Table 22

Label the proteins listed that are found in bacteria/yeast.

A 
Hexokinase (yesat)
RNA polymerase (E. coli)
Glutamine synthetase (E. coli)
168
Q

Table 22

Name the molecular weight ranges from humans, animals and bacteria/yeast

A

Human - 13,000 - 513,000

Animal - 13,700 - 22,000

Yeast/bacteria - 102,000 - 619,000

169
Q

Table 22

Name the number of residues ranges from humans, animals and bacteria/yeast

A

Human - 104 - 4,536

Animal - 124 - 245

Yeast/bacteria - 972 - 5,628

170
Q

Table 22

Name the proteins with no quaternary structure

A

= 1 polypeptide chain

Cytochrome c
Ribonuclease A
Lysozyme
Myoglobin
Chymotrypsinogen
Serum albumin
Apolipoprotein B
171
Q

Table 22

Name the proteins with a quaternary structure

A

= >1 polypeptide chain

Hexokinase (2)
Chymotrypsin (3)
Haemoglobin (4)
RNA polymerase (5)
Glutamine synthetase (12)
172
Q

How many residues does cytochrome c contain and what is its molecular weight?

(small)

A

104 residues

13,000 Daltons

(small)

173
Q

How many residues does apolipoprotein B contain and what is its molecular weight?

(large)

A

4,536 residues

513,000 Daltons

(large)

174
Q

What is the molecular weight of the largest known protein and how many amino acids does it contain?

Hint: we know glutamine synthetase has 619,000 amino acid residues

A

Hint: we know glutamine synthetase has 619,000 amino acid residues

Titin
Molecular weight = 2,993,000

1 polypeptide chain

175
Q

What is the function of titin?

A

It is an aptly named giant protein that is part of the sarcomeric apparatus in cardiac myocytes. It has 1 polypeptide chain

(almost 3 million Daltons in molecular weight/~27,000 amino acid residues)

176
Q

How many amino acid residues does titin contain?

A

Average Mw of 1 amino acid = 110

So approximately 27,000 amino acid residues

177
Q

What is the average molecular weight of 1 amino acid?

A

110 Da

178
Q

Protein sizes can range, give 2 examples

A

Cytochrome c - 104 amino acids

Titin - 27,000 amino acids

179
Q

What is a conjugated protein?

A

A protein that is covalently linked to chemical components in addition to amino acids.

180
Q

What do we call a protein that is covalently attached to other things?

A

Conjugated proteins

181
Q

What are lipoproteins attached to, and give an example.

A

Lipids

B1-Lipoprotein of blood

182
Q

What are glycoproteins attached to, and give an example.

A

Carbohydrates

Immunoglobulin G

183
Q

What are phosphoproteins attached to, and give an example.

A

Phosphate groups

Casein of milk

184
Q

What are hemoproteins attached to, and give an example.

A

Haem (iron porphyrin)

Haemoglobin

185
Q

What are flavoproteins attached to, and give an example.

A

Flavin nucleotides

Succinate dehydrogenase

186
Q

Give examples of prosthetic groups metalloproteins can be attached to.

A 
Iron
Zinc
Calcium
Molybdenum
Copper
187
Q

Give an example of an iron metalloprotein.

A

Ferritin

188
Q

Give an example of a zinc metalloprotein.

A

Alcohol dehydrogenase

189
Q

Give an example of a calcium metalloprotein.

A

Calmodulin

190
Q

Give an example of a molybdenum metalloprotein.

A

Dinitrogenase

191
Q

Give an example of a copper metalloprotein.

A

Plastocyanin

192
Q

What do lipo- and glycoproteins get attached to?

A

Important metabolic constituents

glyco- –> sugars
lipo- –> lipids

193
Q

What is the function of phosphoproteins?

A

These add phosphate groups

  • some of these are natural
  • other proteins, this is used as a key regulatory mechanism, where you can control many enzymes and proteins by phosphorylation status.
194
Q

What type of conjugate protein is often used to control enzymes and proteins?

A

Phosphoproteins - as they can be controlled by phosphorylation status.

195
Q

What is succinate dehydrogenase?

A

A flavoprotein (adds flavin nucleotides as a synthetic group) that is a glycolytic enzyme

196
Q

What do phospho- and flavoproteins have in common?

A

They contain synthetic groups which is important for the protein to be active.

197
Q

What is the significance of metal ions and proteins?

A

You can add a whole range of metal ions to some proteins that are important clinically.

ESA 1 - Medical Cell Biology & Genetics (21 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions