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Cell Biology and Genetics > Proteins > Flashcards

Proteins Flashcards

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1
Q

What is the structure of an amino acid?

A

Central carbon atom, covalently bound to

  • Amino group
  • Carboxyl group
  • Hydrogen atom
  • R group (side chain)
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2
Q

How do amino acids ionise?

A

Amino group gains hydrogen ion
NH2 + H+ —–> NH3+

Carboxyl group gives up hydrogen ion
COOH —–> COO- + H+

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3
Q

Which group in the amino acid is acidic?

A

The carboxyl group

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4
Q

Which group in the amino acid is basic?

A

The amino group

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5
Q

How are amino acids classified? Why?

A

Based on the properties of the R groups

Because in polypeptide chains, only the hydrogen atom and the R group of the amino acids remains

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6
Q

What is an amino acid residue?

A

What remains of an amino acid after it has been jointed to another amino acid

  • R group
  • hydrogen atom
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7
Q

What are the types of properties of the R group?

A

Chemical properties

Physical properties

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8
Q

What are the possible chemical properties of the R group?

A

Polar/non-polar

Hydrophobic/hydrophilic

Acidic/basic/neutral

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9
Q

What are the possible physical properties of the R group?

A

Aliphatic/aromatic

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10
Q

What does the pKa value of amino acids measure?

A

How acidic the amino acids are

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11
Q

What does a low pKa value mean?

A

The amino acid is more acidic

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12
Q

What does a high pKa value mean?

A

The amino acid is less acidic

more basic

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13
Q

What happens to the amino acid if pH > pKa? Why?

A

Higher pH means fewer hydrogen ions present
amino acid gives up hydrogen ions
becomes deprotonated

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14
Q

What happens to the amino acid if pH < pKa? Why?

A

Lower pH means more hydrogen ions present
amino acid takes up hydrogen ions
becomes protonated

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15
Q

What is physiological pH?

A

7.4

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16
Q

What is the primary structure of a protein?

A

Amino acids joined together in a linear chain

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17
Q

What reaction occurs when two amino acids are joined together?

A

amino acid1 + amino acid 2 —–> polypeptide + water

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18
Q

What bond joins two amino acids together?

A

Peptide bond

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19
Q

What is the amino terminus of a polypeptide?

A

The amino group NH2 end of the polypeptide chain

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20
Q

What is the carboxyl terminus of a polypeptide?

A

The carboxyl group COOH end of the polypeptide chain

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21
Q

What are the properties of peptide bonds?

A

Planar

Rigid

Trans conformation

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22
Q

What is meant by peptide bonds being planar?

A

The central carbon atom
N-H
C=O

are all in the same plane

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23
Q

What is meant by peptide bonds being rigid?

A

No rotation about the peptide bond

24
Q

What atoms are involved in a peptide bond?

A

C-N

C from C=O
N from N-H

25
Q

What is meant by the peptide bond having a trans conformation?

A

Heavier groups are on opposite sides of the peptide bond

the heavier groups are the central carbon atom, R group, H atom altogether

26
Q

What is the importance of the amino acid sequence in the primary structure?

A

Determines the way the polypeptide chain folds
the structure of the protein
and hence its function

27
Q

What are peptides/oligopeptides?

A

Chains of a few amino acids joined together

28
Q

What are polypeptides/proteins?

A

Chains of many amino acids joined together

29
Q

What type of bond is a peptide bond?

A

Covalent bond

30
Q

What is the secondary structure?

A

The spatial arrangement of the polypeptide backbone

31
Q

What are the types of secondary structures?

A

Alpha helix

Beta strand

32
Q

What do layers of beta strands form?

A

Beta pleated sheet

33
Q

What holds the alpha helix and the beta pleated sheets together?

A

Hydrogen bonds between C=O and N-H

34
Q

What are the types of beta sheets? What do they each mean?

A

Parallel - run in same direction

Anti parallel - run in opposite directions

35
Q

How does the polypeptide chain fold up into an alpha helix or beta pleated sheet if peptide bonds are rigid?

A

Bonds next to peptide bonds are free to rotate

36
Q

What is the tertiary structure?

A

Secondary structure folds up to form a 3D conformation

37
Q

What are the types of tertiary structures? What do they each mean?

A

Globular - spherical shape

Fibrous - long strand-like shape

38
Q

What is the general function of fibrous proteins?

A

Structural support

Maintain shape

39
Q

How many types of secondary structures are there in fibrous proteins?

A

Single repeating secondary structure

40
Q

How many types of secondary structures are there in globular proteins?

A

Several different types

41
Q

What is a classic example of a fibrous protein?

A

Collagen

42
Q

What is a protein domain?

A

Part of polypeptide chain that folds into a distinct shape

has a specific function

43
Q

How do water-soluble proteins generally fold up?

A

Non-polar hydrophobic side chains are buried within

Polar/charged hydrophilic side chains are on surface

44
Q

How do integral membrane proteins generally fold up? Why?

A

Non-polar hydrophobic chains are on the surface
interact with hydrophobic tails

Polar/charged hydrophilic chains form a channel within
interact with water in and out of cell

45
Q

What is the quarternary structure?

A

Different polypeptide chains coming together to form a multi-subunit protein

46
Q

What is an example of a protein with a quarternary structure?

A

Hb

47
Q

What is an example of a protein with a tertiary structure?

A

Myoglobin

48
Q

What does pI stand for?

A

Isoelectric point

49
Q

What is the pI of proteins?

A

pH at which protein has no overall charge

50
Q

Do acidic proteins have a low or high pI value? Why?

A

Low

low pH means more hydrogen ions, neutralises negative charge of acidic amino acid

51
Q

Do basic proteins have a low or high pI value? Why?

A

High

high pH means fewer hydrogen ions, because already have positively charged amino acids

52
Q

What happens to the protein if pH > pI? Why?

A

High pH means fewer hydrogen ions
amino acid gives up hydrogen ions
becomes deprotonated

53
Q

What happens to the protein if pH < pI? Why?

A

Low pH means more hydrogen ions
amino acid takes up hydrogen ions
becomes protonated

54
Q

What are conjugated proteins?

A

Proteins covalently linked to additional chemical components that are not amino acids

55
Q

What are some examples of roles of proteins? Give examples for some roles

A

Structural support e.g. collagen

Enzymes e.g. hexokinase

Transporters e.g. Hb

Carriers, channels etc.

Receptors, ligands etc.

Cell Biology and Genetics (32 decks)

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