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MCBG - SEM1 > Session 2: Proteins > Flashcards

Session 2: Proteins Flashcards

1
Q

What is the isoelectric point?

A

The point at which the pH of a protein has not net electrical charge

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2
Q

What is the Henderson-Hasselbalch equation?

A

pH = pK + log10([base]/[acid])
OR
pH = pK + log10[deprotonated]/[protonated]

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3
Q

How do you get rid of log10 on one side when doing a calculation using Henderson-Hasselbalch equation?

A

Make the number on the other side the power of 10
eg 1 = log10([deprotonated]/[protonated]) => 10^1 = [deprotonated]/[protonated]

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4
Q

What is the functional importance of a positive charge on Histone proteins?

A

Allows them to associate with DNA which is negatively charged via electrostatic interactions to form chromatin

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5
Q

What is the relationship between pH, isoelectric point, and the charge if a protein?

A

pH < pH of isoelectric point = POSITIVE (cation)

pH> pH of isoelectric point = NEGATIVE (anion)

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6
Q

What does ph>pI tell us about how a protein will move in an electric field?

A

When pH is greater than pI = protein is deprotonated and has a negative charge so it will move towards the positive electrode (anode)

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7
Q

What does pH<pI tell us about how a protein will move in an electric field?

A

When pH is less than pI = protein is protonated and has a positive charge so it will move towards the negative electrode (cathode)

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8
Q

What does pH=pI tell us about how a protein will move in an electric field?

A

No overall net charge so protein cannot be attracted to either positive or negative electrodes so will not move

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9
Q

What are the characteristics of basic proteins?

A
  • positively charged
  • large proportion of positively charged amino acids (high pI)
  • high pK values
  • positively charged at physiological pH
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10
Q

Based on pH and pKa values, how can you tell if a protein will be in an acidic form & a proton donor?

A

When pH > pKa
Release H+
Deprotonate
Migrate towards the positive electrode

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11
Q

Based on pH and pKa values, how can you tell if a protein will be in a basic form & a proton acceptor?

A

When pH < pKa
Accepts H+
Protonate
Migrate towards negative electrode

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12
Q

What does pH=pKa suggest? What causes that equilibrium to shift?

A

Equal numbers of protonated and unprotonated groups.
pH shifts the equilibrium to either side

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13
Q

What does the pKa value of an amino acid side chain tell us about that chemical group?

A
  • Likelihood for amino acid side chain will become deprotonated (release H+)
  • Provides info on side chain charge & effect of pH on side chain
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14
Q

What are the types of bonds involved in maintaining the different levels of protein structure? What are the consequences of their disruptions

A
  • Primary = covalent peptide bonds
  • Secondary = H bonds between polypeptide backbone (amide H and carbonyl O)
  • Tertiary & quaternary = different types of non-covalent forces (eg disulphide bridges, Van der Waals & ionic bonds)

Protein would turn into flexible polypeptide chain that has lost its natural shape

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15
Q

What are the different arrangements of beta sheet in secondary structure?

A
  • extended beta-strand structure
  • antiparallel
  • mixed
  • parallel
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16
Q

How are beta sheets stabilised?

A

Hydrogen bonds

17
Q

Describe the structure of beta sheets.

A

Beta sheets are composed of adjacent beta stands

18
Q

What are the features of peptide bonds which are important for protein structure?

A
  • Planar
  • Rigid => C-N has partial double bond characteristics due to delocalised electrons
  • Trans conformation => carbonyl O and amide H are always on opposite sides of the peptide bond
  • Bonds are free to rotate - Psi & Phi bonds
19
Q

Why are peptide bonds rigid?

A

C-N has partial double bond characteristics due to delocalised electrons

20
Q

What does the amino acid sequence of a protein determine?

A
  • the way in which the polypeptide chain folds
  • physical characteristics of a protein
21
Q

What are the key properties of proteins?

A

Size
- number of amino acid residues
- molecular weight
Isoelectric point

22
Q

What are Psi and Phi bonds?

A

Psi = C(alpha)-C bond
Phi = C(alpha)- N bond

23
Q

What are globular and fibrous structures? How do they differ?

A

They are types of tertiary structures.
Globular = compact structure & made up of several types of secondary structure
Fibrous = extended conformation & made up of single type of repeating secondary structure

24
Q

What is a quaternary structure?

A

Spatial arrangement of subunits and their interactions

25
Q

What are amyloid fibres and how are they formed

A

Insoluble form of normally soluble protein
Due to misfolding of protein

26
Q

Describe the structure of amyloid fibres.

A
  • highly ordered with a high degree of beta-sheet
  • interchain assembly stabilised by hydrophobic interactions between aromatic amino acid residue
27
Q

How do proteins fold?

A
  • Folding must be ordered (NOT random)
  • Each step involves localised folding with stable confirmations maintained
  • driven by the need to find the most stable conformation
28
Q

Where is all the information needed for folding contained in?

A

Primary sequence

29
Q

What happens to proteins when they denature?

A
  • Becomes a simple polypeptide chain
  • Lost structure & function
30
Q

What determines how proteins can fold?

A

Primary sequence

31
Q

How are amino acids joined together to give a sequence?

A

Covalent peptide bonds

32
Q

What are disulphide bonds?

A

bonds formed between sulphydryl (SH) groups of cysteine AA residue

33
Q

Why are disulphide bonds needed?

A

help maintain structure of molecule in harsh environment outside the cell

34
Q

How can disulphide bonds be broken?

A

can be broken down with reducing agents like mercaptoethanol

35
Q

What does pKa describe?

A

acid dissociation constant, the pH at which there is an equal balance of an AA in solution

MCBG - SEM1 (6 decks)

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