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Cell biology > B2 Chapter 1: Proteins > Flashcards

B2 Chapter 1: Proteins Flashcards

1
Q

What are 2 causes of a variation of proteins encoded by a single gene?

A
  • Alternative splicing
  • Post-translational modifications
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2
Q

Approximately how many amino acids form a polypeptide?

A

40 - 5 000

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3
Q

What is the approximate range of relative molecular mass of a polypeptide?

A

4 000 - 580 000

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4
Q

What is relative molecular mass?

A

The ratio of the sum of atomic masses within a molecule to the 1/12 the mass of a carbon-12 atom.

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5
Q

Name 10 major groups of proteins.

A
  • Enzymes
  • Structural proteins
  • Adhesion proteins
  • Signalling proteins
  • Receptor proteins
  • Transport proteins
  • Motor proteins
  • Immunoglobulins
  • Storage proteins
  • Gene regulatory proteins
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6
Q

What is the function of adhesion proteins?

A

To mediate the cell-cell or cell-extracellular matrix contact.

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7
Q

What is the function of signalling proteins?

A

To faciliate inter- and intracellular communication through being recognised by the relevant receptor molecules.

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8
Q

What is the function of receptor proteins?

A

To recognise specific signalling molecules in the extracellular or intracellular environment in order to faciliate communication.

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9
Q

Name two types of receptor proteins?

Not specific names, just types.

A
  • Cell surface receptors
  • Intracellular receptors
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10
Q

What is the function of transport proteins?

A

To facilitate transport of substances within, to, and from the cell. E.g., membrane transport proteins

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11
Q

What is the function of motor proteins?

A

Moving vesicles along mictrotubules to their destination to be released. Faciliates movement.

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12
Q

What is the function of Immunoglobulins?

A

Also known as antibodies, they recognise specific antigens on the surface of infected cells or foreign bacteria.

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13
Q

What is the function of storage proteins?

A

To bind to and store nutrients.

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14
Q

What is the function of gene regulatory proteins?

A

Bind to DNA to regulate gene expression.

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15
Q

What type of protein is ferritin?

A

Storage protein - specifically iron.

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16
Q

Give one example of a gene regulatory protein.

A

Lac repressor.

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17
Q

What are ligands?

A

An ion or molecule that binds to a specific associated protein at its binding site.

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18
Q

What is ‘Primary structure’?

In proteins

A

The amino acid sequence

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19
Q

What is a proteins secondary structure?

A

The stable three-dimensional arrangements stretches of a polypeptide makes. (alpha helices and beta sheets)

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20
Q

What is a proteins tertiary structure?

A

The arrangement of a proteins secondary structures.

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21
Q

What is a proteins Quarternary structure?

A

The arrangement of subunits of a multimeric protein.

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22
Q

What is the difference between a homomeric protein and a heteromeric protein?

A

A homomeric protein contains identical subunits.
A heteromeric protein contains different subunits.

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23
Q

If a protein is formed of 4 subunits that are all the same, how could you describe it?

A

Homotetrameric

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24
Q

What is a cytokine?

A

A type of signalling protein

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25
Q

What is a cofactor?

A

A non-protein group that is associated with a protein. Essential for the proteins function.

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26
Q

Give one example of a cofactor.

A

Haem in haemoglobin

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27
Q

If a protein is formed of only one polypeptide chain, how can it be described?

A

Monomeric

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28
Q

What is a protein domain?

A

Dictinct units within a protein that have particular function.

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29
Q

What are disulfide bridges?

A

Covalent bonds between two cysteine residues.

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30
Q

What is the function of disulfide bridges in a protein?

A

Stabilises the arrangement of the protein by holding sections together - within a subunit or between subunits.

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31
Q

Are alpha helices right handed or left handed?

A

Right handed

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32
Q

What are protein folds/motifs?

A

Extensive arrangements of a proteins secondary structures.

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33
Q

What is a β barrel?

A

A protein fold/motif in which β sheets wrap around to form a barrel-shaped structure where the inner surface is often hydrophobic.

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34
Q

What can a β barrel be used for?

A

To carry molecules.

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35
Q

What is a rossman fold/dinucleotide binding fold?

A

α helices arranged alternately on either side of β sheet

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36
Q

What are the repeating atoms in a polypeptide backbone?

A

N, C, C with O

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37
Q

What is the proper term for the central carbon atom within an amino acid?

A

α-carbon/ Cα

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38
Q

In an amino acid what is attached to the α-carbon?

Not including the carboxyl and amino group

A

A hydogren and the side chain of the amino acid/

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39
Q

What is on either end of a polypeptide?

A

Amino group (-NH2) / N-terminus
Carboxyl group (-COOH) / C-terminus

40
Q

What is the convention when numbering amino acids in a polypeptide?

A

Start counting from N-terminus.

41
Q

When would a protein go through conformational change?

A

When interacting with specific molecules or going through modificiation.

42
Q

In translation, what occurs to EF-Tu, it’s attached GTP, and it’s attached tRNA when the EF-Tu binds to a ribosome?

A

The EF-Tu undergoes conformation chainge, hydrolyses the GTP to GDP causing the release of the tRNA, and EF-Tu to dissociate from the ribosome.

43
Q

At cytolsolic 7.2 pH what occurs to the amino and carboxyl groups of an amino acid?

Name the overall process and then describe the process of each group.

A

They are ionised.
- The carboxyl group loses a proton and becomes negatively charged.
- The amino group gains a proton and becomes positively charged.

44
Q

What type of reaction occurs in the formation of C-N peptide bonds between amino acids?

A

Condensation reaction

Water molecule is produced

45
Q

What is a CO-NH group also known as?

A

A peptide group.

Formed through peptide bonding between amino acids.

46
Q

What are the four chemically distinct groups amino acid side chains can be sorted into?

A
  • Negatively charged (acidic)
  • Positively charged (basic)
  • Uncharged polar (no net charge but charge distributed unevenly in the side chain)
  • Non-polar (charge is distributed evenly in the side chain)
47
Q

What are the levels of protein heirarchy?

Give brief descriptions

A
  • Primary | Amino acid sequence
  • Secondary | Basic stable structures (alpha helix, beta pleated plates etc.)
  • Tertiary | Three-dimernsional arrangements of secondary structures
  • Quaternary | Closely associated polypeptide chains forming mutlimeric proteins
48
Q

Why is the rotation of the polypeptide backbone limited?

Name the process that limits it and give brief outline of what this is.

A

Steric interference | Repulsive forces between atoms due to the space occupied by their electron clouds.

49
Q

What would be required to overcome steric inteference?

A

Energy input

50
Q

Name the two most common secondary structures in proteins.

A
  • α helices
  • β pleated sheets
51
Q

Describe α helices

A
  • Common secondary structures of proteins
  • Right handed helical conformation
  • Hydrogen bonds between N-H of one peptide group and C=O of fourth peptide group along
  • R-chains point outwards
52
Q

Desribe β pleated sheets

A
  • Hydrogen bonding between adjacent strands
  • Can run parallel or anti-parallel to one another
53
Q

What bonds are involved in the formation of a proteins secondary structures?

A

Hydrogen bonding

54
Q

In globular proteins what are the distinct regions of secondary structures linked by?

A

Random coils

55
Q

What are the steps involved in X-ray crystallography?

A
  1. Protein is crystallised
  2. Protein crystal irradiated with beam of X-rays
  3. X-rays scattered by diffraction (more electrons = more scattering)
  4. Analysis of x-ray diffraction pattern
  5. Formation of electron density map
  6. Molecular model formation
56
Q

What is a protein domain?

A

A distinct sub-structure composed of secondary structures. They are often linked by a flexible hunge, and have distinct functions that contribute to the overall protein function.

57
Q

If a globular protein is within an aqueous environment, how would charged groups within the hydrophobic core stabilise themselves?

A

Through ionic interaction with oppositely charged groups.

58
Q

What non-covalent and covalent bonds are involved in stabilising teritary structure?

A

Non-Covalent
- Hydrogen bonds
- Hydrophobic interactions
- Ionic bonds

Covalent
- Disulfide bonds/bridges

59
Q

What are disulfide bridges?

A

A covalent bond between 2 sulfur atoms within cysteine side chains.

60
Q

In what circumstance would polypeptide residues tolerate unfavourable conditions?

A

If the overall stability of the polypeptide is improved.

61
Q

What are cofactors?

A

Non-protein molecules that associate with proteins and are essential for their function.

62
Q

In terms of quaternary structure of a protein, what is the difference between homomeric and heteromeric proteins?

A

Homomeric proteins are formed of identical subunits.

Hetermomeric proteins have non-identical subunits.

63
Q

In multimeric proteins, what types of proteins are often found to contain covalent disulfide bonds?

A

Secreted and extracellular proteins.

64
Q

Non-covalent interactions between surfaces of subunits drive what protein heirarchal structure?

A

Quaternary

65
Q

What is the function of a chaperone protein?

A

To help large, or multiple domain contaning proteins to fold into the correct conformation by:
- Preventing innaportpriate interactions by aggreagrating between the protein and other molecules, or between the protein molecules themselves.
- Recover and refold misfolded proteins

66
Q

What is the name of the the type of enzymez that breaks down polypeptides?

A

Proteases

67
Q

How is a polypeptide prepared for its breakdown?

A

The covalent attachment of ubiquitin (protein)

68
Q

What are proteases?

A

Proteolytic enzymes that break down proteins by catalysing the cleavage of peptide bonds.

69
Q

Name two reasons proteases would break down a protein within a cell.

A
  • If the protein is no longer needed by the cell.
  • If the protein has been misfolded.
70
Q

What is the danger of misfolded proteins? What do they do and why do they do this?

A

They tend to aggregate together to form more stabile formations.

71
Q

Where may misfolded proteins have less chance of being broken down?

A

Outside of the cell.

72
Q

Which proteins are fully functional upon release from the ribsosome and subsequent folding has occured?

A

Proteins that function within the cytosol.

73
Q

What type of eukaryotic proteins require post-translational modification?

A
  • Those synthesised in the RER
  • Proteins to be secreted
  • Those to be incorporated into the lumen
74
Q

For eukaryotic proteins, where does post translational modifications occur?

A

The lumen of the endoplasmic reticulum.

75
Q

Are covalent post-translational modifications of proteins reversible or irreversible?

A

Irreversible.

76
Q

Name two covalent post-translational modifications of proteins and describe the mechanism. What are each of the products of these mechanisms used for?

A
  • Protein glycosylation | The formation of a glycoprotein by the attachment of short sugar chains through reaction with, either the -NH2 group of the protein or the -OH group of an amino acid side chain. Glycoproteins are incorporated into cell membranes for cell communication, or secreted out of the cell to be used elsewhere.
  • Protein lipidation | Lipid groups being covalently attached to the protein to form a lipid-linked protein. The lipid part anchors the protein into membranes, with the properties of the attached lipid determining which sheet of the membrane the protein will be located.
77
Q

What are zymogens?

A

Proteins that are secreted in an inactive form.

78
Q

What type of reaction occurs to zymogens, and to what bonds does it occur, for them to become active?

A

Hydrolysis of specific peptide bonds (proteolytic cleavage)

79
Q

Why may some proteins secreted from the cell in an inactive form?

A

To prevent damage or interaction within the cell.

80
Q

What is chromatography?

A

A process of separating constituent parts of a mixture (mobile phase) depending on how quickly they travel through a column containg the stationary phase material.

81
Q

Name three types of chromatrography and what each is based on.

A
  • Ion exchange chromatography | relative charge
  • Hydrophobic interaction chromatography | relative hydrophobicity
  • Gel filtration/size exclusion chromatography | relative size
82
Q

What are enzymes?

A

Proteins that act as biological catalysts.

83
Q

What are some common protein-binding ligands?

4 are listed

A
  • cofactors
  • small organic or inorganic molecules
  • ions
  • macromolecules
84
Q

What type of interactions facilitate protein-ligand interactions?

A

Non-covalent

85
Q

What must be compatible for a protein-ligand interaction?

A

Their chemical and physical properties.

86
Q

What is site-directed mutagenesis (SDM)?

A

A technique used to study protein function and demonstrate the relationshio between a proteins structure and function.
Uses recombiant DNA texhniques to slectively replace the of interest residue with a critically different amino acid, allowing assessment of the importance of the initial amino acid by comparison of the mutated protein and the wild type protein.

87
Q

What are conserved domains?

A

Areas of homologous amino acid sequences within proteins found across species that have been conserved through evolution.

88
Q

What do homologous proteins share?

A

A common ancestor.

89
Q

Why can enzymes be reused?

A

They are unaltered by reactions.

90
Q

What is the lock and key hypothesis?

A

The idea that the specificity of the substrate and the active site of the enzyme act in a lock and key manner. (they dont really)

91
Q

Why may an enzyme catalysed reaction not be reversible?

A

If the product do not bind as easily to the enzyme as the substrate once did.

92
Q

What mayd ifferent enzymes show different levels of specificity for?

A
  • The substrate
  • The types of reactions
93
Q

What must be overcome for a chemical reaction to occur?

A

An energy barrier.

94
Q

What is an enzymes catalytic power?

A

The measure of its ability to speed up a reaction.

95
Q

How do enzymes catalyse chemical reactions in terms of energy?

A

Enzymes offer an alternative pathway with less required energy to be expended in order to reach the transition state / they decrease the energy barrier.

96
Q

In a chemical reaction between two reactants, what is the transition state?

A

The unstable intermediate.

97
Q

What can influence the rate of enzyme-catalysed reactions occuring in a cell?

4 listed

A
  • Temperature
  • pH
  • presence of cofactors
  • presence of inhibitors

Cell biology (9 decks)

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