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MCBG > Protein Structure & Function > Flashcards

Protein Structure & Function Flashcards

1
Q

What happens to an amino acid in solution?

A

Both the amino and carboxyl groups ionise

NH3+
COO-
Groups created

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2
Q

What is the charge on a zwitterion (ignoring the presence of the amino acid R group)?

A

No overall net charge

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3
Q

Out of the NH2 and COOH groups of the amino acid, which is basic and which is acidic?

A

NH2 = basic

COOH = acidic

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4
Q

What is meant by terms acidic and basic in terms of protein transfer?

A 
Acidic = Proton donor
Base = proton acceptor
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5
Q

Classification of an amino acid is dependent on the amino acid’s…

A

R group

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6
Q

Negatively charged groups are acidic or basic?

A

Acidic

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7
Q

Positively charged groups are acidic or basic?

A

Basic

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8
Q

What does pKa give an indication of?

A

How likely something is to ionise

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9
Q

The pKa value is equal to…

A

The pH at which the…

protonated form = deprotonated form

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10
Q

What is the relationship between the pH of a solution and the pKa of a BASIC amino acid?

A

If the pH < the pKa of a amino acid, the r group will be protonated

R group —> +ve —-> basic

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11
Q

What is the relationship between the pH of a solution and the pKa of an ACIDIC amino acid?

A

If the pH of a solution>greater than the pKa value then the R group will be deprotonated

Therefore -ve charged —-> acidic

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12
Q

What is the primary structure of a protein?

A

The linear amino acid sequence of the polypeptide chain

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13
Q

What is the secondary structure of an amino acid? Give 2 examples of ways a protein can arrange itself in its secondary structure.

A

The local spatial arrangement of the polypeptide backbone

Into a-helical, b-sheets

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14
Q

What does the tertiary structure of the protein refer to?

A

The overall 3d shape of a protein

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15
Q

What does the quaternary structure of a protein refer to?

A

Association between different polypeptide chains to form a multi subunit protein

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16
Q

What is the bond connecting two amino acids together called? What molecule is produced when this bond is created?

A

Peptide bond

Water molecule

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17
Q

Peptide bonds are planar, what does this mean?

A

C-alpha, C, O, N, H and C-alpha are all in the same plane

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18
Q

As well as being planar, peptide bonds are rigid and demonstrate partial double bond characteristics - what is meant by this?

A

They are unable to rotate

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19
Q

What sort of conformation do peptide bonds show?

A

Trans conformation

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20
Q

What is meant by the trans conformation of peptide bonds?

A

The c-alpha’s on each side of the peptide bond are on opposite sides of the peptide bond

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21
Q

Why can’t peptide bonds show a cis conformation?

A

Would result in steric clashes

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22
Q

Are bonds on each side of the peptide bond able to rotate?

A

Yes - free to rotate

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23
Q

What are Psi and Phi bonds?

A 
Psi = bond between c-alpha and carbon 
Phi = bond between c-alpha and N
24
Q

What is the isoelectric point (pI) of a protein?

A

The pH at which there is no net overall charge on a protein

25
Q

Basic proteins have a pI…

A

pI greater than 7

26
Q

Acidic proteins have a pI…

A

pI smaller than 7

27
Q

If pH>pI then the protein will be…

A

Deprotonated

28
Q

If pH

A

Protonated

29
Q

What are conjugated proteins?

A

Proteins containing covalently linked chemical components in addition to amino acids

30
Q

What determines the initial conformation of a protein?

A

The angles of the Phi and Psi bonds

31
Q

What type of helix is an alpha-helix?

A

Right handed helix

32
Q

How many amino acids are seen per turn in an alpha helix?

A

3.6 aa per turn

33
Q

What is meant by the pitch of an alpha helix?

A

Distance to go up 1 complete turn of the alpha helix

34
Q

What is the pitch in an alpha helix?

A

0.54nm

35
Q

What stabilises the structure of an alpha helix?

A

Hydrogen bonds between the N-H and C=O

The C=O group of one residue makes hydrogen bonds with the N-H group 4 amino acid’s away

36
Q

Which sorts of amino acid residues tend to form alpha helices? Give two examples

A

Small hydrophobic residues

Alanine
Leucine

37
Q

Give two amino acid residues that act as helix breakers

A

Proline

Glycine

38
Q

What is the distance between adjacent amino acids in a B-strand? What is the position of the R groups at these strands?

A

0.35nm

R groups alternate between opposite sides of the strand

39
Q

What results in the formation of a beta-sheet?

A

Side by side arrangement of beta strands

40
Q

What two different forms of beta sheet exist? What stabilises their structure?

A

Anti-parallel
Parallel

Hydrogen bonds

41
Q

Give an example of a protein that is largely alpha-helical.

A

Ferritin - iron storage molecule

42
Q

Give an example of a protein that is mainly b-sheets

A

Fatty acid binding protein

43
Q

What is the difference in secondary structures between globular and fibrous proteins?

A 
Fibrous = single type of repeating secondary structure
Globular = several types of secondary structure
44
Q

What is the general 3D shape of membrane proteins?

A

They have an ‘inside-out’ configuration, with hydrophobic groups on the outside rather than buried on the inside

45
Q

What bonds are found in the primary structure of a protein?

A

Peptide (covalent)

46
Q

What bonds are found in the secondary structure of a protein?

A

Hydrogen bonds

47
Q

Which bonds are found in the tertiary and quaternary structures of proteins?

A

Ionic, hydrogen bonds, hydrophobic interactions, and disulphides bonds

48
Q

Disulphides bonds are formed between which amino acid residues? What can be used to break them?

A

Cysteine residues

Reducing agents

49
Q

Ionic bonds are formed between…

A

Charged groups

50
Q

A normal, functional protein is said to be in its ______ conformation

A

Native

51
Q

What 3 things can denature a protein?

A

Heat
pH
Detergents/organic solvents

52
Q

How can heat denature a protein?

A

Increased vibrational energy —> breaks bonds

53
Q

How can pH denature a protein?

A

Affects ionic/hydrogen bonds

Alters ionisation states of amino acids

54
Q

How can detergents denature a protein?

A

Disrupt hydrophobic interactions

55
Q

Where is information for folding of a protein found? What is this ordered folding process driven by?

A

In the primary sequence

The need to find the most stable conformation

56
Q

What are amyloid fibres?

A

Misfolded, insoluble forms of normally soluble proteins

MCBG (15 decks)

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