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BIOPHYSICS > Lecture 3.5 (Proteins) > Flashcards

Lecture 3.5 (Proteins) Flashcards

1
Q

Describe the formation of a peptide bond

A

A hydrogen atom from an AMINE GROUP from one amino acid is combined with an OH from a CARBOXYL GROUP of another amino acid to form WATER and leaves behind a PEPTIDE BOND

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2
Q

What does an amino acid consist of?

A
  • Central carbon atom
  • Carboxyl group
  • Amine group
  • Variable group
  • Hydrogen atom
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3
Q

What is the difference between Primary, Secondary, Tertiary and Quaternary protein structure?

A

PRIMARY STRUCTURE = sequence of a chain of amino acids

SECONDARY STRUCTURE = Local folding of the polypeptide chain into a-helices or b-pleated sheets

TERTIARY STRUCTURE = three-dimensional folding pattern of a protein due to side chain interactions

QUATERNARY STRUCTURE = protein consisting of more than one amino acid chain

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4
Q

What does “self assembly” mean?

A

The forces driving the molecules to assemble in the appropriate configuration or quaternary structure exist in the molecules themselves and in their interactions with solvent molecules

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5
Q

How can proteins be denatured?

A
  • pH changes
  • Temperature
  • Chemical changes
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6
Q

How can folding moderators/chaperones help with protein assembly?

A
  • Catalyse a step in the folding process
  • Temporarily bind to peptide chain and bring certain parts of the molecule closer together
  • Provide sequestered environment that foster’s protein’s native state
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7
Q

How many major amino acids are commonly found in proteins?

A

20

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8
Q

List the Non-polar, hydrophobic amino acids

A
  • Glycine
  • Alanine
  • Valine
  • Leucine
  • Isoleucine
  • Methionine
  • Proline
  • Phenylalanine
  • Tryptophan
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9
Q

What is significant about Tryptophan?

A

Large which creates the STERIC FORCES that limit the possible conformations available to the peptide chain

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10
Q

What is significant about Glycine and Alanine?

A

Small which allows the possibility of tightly packed configurations

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11
Q

Which amino acids are aromatic?

A
  • Phenylalanine (hydrophobic)
  • Tryptophan (hydrophobic)
  • Tyrosine (polar)
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12
Q

List the Uncharged, Polar amino acids

A
  • Serine
  • Threonine
  • Asparagine
  • Glutamine
  • Tyrosine
  • Cysteine
  • Lysine
  • Arginine
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13
Q

List the charged, polar amino acids

A
  • Histidine
  • Aspartate
  • Glutamate
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14
Q

How do charges occur in proteins?

A
  • Ionisation of the amine and carboxyl groups of amino acids at the ends of the polypeptide chain
  • Ionisation of various amino acid side chains
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15
Q

What do the charges cause the protein to do?

A

Fold in a way that maximises the distance between like charges while bringing opposite charges as close together as possible -> minimises FREE ENERGY and STABILISES the protein structure

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16
Q

What is a Zwitterion?

A

An ionised molecule that has both a positive and negative charge on it but a net charge of zero

[formed by adding a proton to the amine group + the carboxyl group losing a proton]

17
Q

What is the difference between a Primary, Secondary and Tertiary amine?

A

PRIMARY AMINE = has only one connection to the rest of the molecule

SECONDARY AMINE = has only one H atom attached and two covalent bonds to the rest of the molecule

TERTIARY AMINE = three connections to the rest of the molecule

18
Q

What are the properties of Amines?

A
  • Slightly -ve on nitrogen atom and +ve on hydrogen atom
  • Participate in H bonding on either +ve or -ve side of bond
  • One amine group can participate in up to 3 H bonds at once
19
Q

Describe the Hydrophobic effect

A

Hydrophobic functional groups create a FREE-ENERGY PENALTY by forcing water molecules adjacent to the hydrophobic molecule into a more ORDERED STATE -> Lowering ENTROPY -> FREE-ENERGY benefit to moving these functional groups away from water, into the center of the protein

20
Q

What decreases the hydrophobic effect?

A
  • Hydrophobic solvents
  • Cooler temperatures
    [order all of the H2O molecules so the cost of ordering the H2O molecules adjacent to a hydrophobic functional group becomes negligible]
21
Q

Disulphide bonds between _____________ residues help stabilise and add rigidity to protein structure

A

Cysteine

22
Q

Describe a Disulphide bond

A

When a sulphur atom attached to one amino acid forms a covalent bond with another sulphur atom on another amino acid

23
Q

Describe dipoles

A

Lined up in parallel will repel each other while those lined up antiparallel will attract one another. HOWEVER, dipoles lined up end to end with the +ve end of one dipole facing the -ve end of another dipole will be more favourable than other configurations

24
Q

Why cannot the bond between the carbonyl carbon and the amide nitrogen not rotate?

A

The pair of non-bonded electrons on the nitrogen spends a portion of its time within that bond -> gives bond double-bond characteristic -> Prevents free rotation around the bond

25
Q

What are the two biggest contributors to the limits on bond between amide nitrogen & a-carbon and a-carbon & carbonyl carbon?

A
  • Steric hindrances
  • Dipole-dipole interactions from adjacent peptide bonds
26
Q

What is Sickle Cell Anaemia?

A

One of the polypeptide chains that make up haemoglobin has a slight change with GLUTAMIC ACID (the sixth amino acid of haemoglobin B) is replaced by VALINE.

CAUSES:
Glutamic acid-to-valine amino acid change makes the haemoglobin molecules assemble into long fibers -> Distort disc-shaped red blood cells into crescent shapes -> Sickled cells get stuck as they pass through blood vessels impairing blood flow

SYMPTOMS:
- Breathlessness
- Dizziness
- Headaches
- Abdominal pain
- Extreme tiredness

27
Q

Describe an a-helix

A

The carbonyl of one amino acid is hydrogen bonded to the amino of an amino acid FOUR down the chain -> HELICAL STRUCTURE with each turn of the helix containing 3.6 amino acids

28
Q

Describe b-pleated sheets

A

Hydrogen bonds form between CARBONYL and AMINO GROUPS of backbone while the R GROUPS extend above and below the plane of the sheet -> Strands may be PARALLEL or ANTIPARALLEL

29
Q

Why is proline called a “helix breaker”?

A
  • Unusual R group creates a bend in chain
  • Not compatible with helix formation

[hence why proline is typically found in bends and unstructured regions between secondary structures]

30
Q

Which R group interactions contribute to the tertiary structure?

A
  • Hydrogen bonding
  • Ionic bonding
  • Dipole-dipole interactions
  • London dispersion forces
  • Hydrophobic interactions
  • Disulphide bonds
31
Q

What is the difference between Peripheral membrane proteins and Integral membrane proteins?

A

Peripheral membrane proteins = attach to integral membrane proteins or penetrate the peripheral regions of the lipid bilayer

Integral membrane proteins = embedded through the whole lipid bilayer cross-section

32
Q

What are the major functions of membrane proteins?

A
  • Transport
  • Enzymatic activity
  • Signal transduction
  • Cell-cell recognition
  • Intercellular joining
  • Attachment to the cytoskeleton and extracellular matrix (ECM)

BIOPHYSICS (15 decks)

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