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My ESA1 > MGD S1 - Amino Acids, Protein Folding and Function > Flashcards

MGD S1 - Amino Acids, Protein Folding and Function Flashcards

1
Q

Describe a prokaryotic cell

A

Bacteria have no separate nucleus, contain a cell wall and a plasma membrane, and lack most organelles

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2
Q

How do antibiotics work?

A

They exploit the differences between prokaryotes and eukaryotes

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3
Q

Name the Level 1 cell/organelle, Level 2 macromolecular complex, Level 3 macromolecules and Level 4 monomeric units of the nucleus, ER and ER/Golgi/membrane

A

Nucleus - chromatin - DNA/protein - nucleotides/amino acids ER - ribosome - protein/RNA - amino acids/nucleotides ER/Golgi/membrane - membrane - protein/oligosaccharide - amino acids/sugars

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4
Q

How are monomeric units joined?

A

By covalent bonds to form macromolecules

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5
Q

How are macromolecules/complexes held together?

A

By non-covalent interactions

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6
Q

Describe the weak interactions between biomolecules

A

Formation of macromolecules and complexes requires weak, non-covalent interactions. Multiple weak interactions increases the stability of these complexes. Breaking interactions causes loss of structure and function

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7
Q

What does electrostatic mean?

A

Involves charges

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8
Q

What does solubility depend on?

A

The ability to form hydrogen bonds. Polar biomolecules form H bonds and dissolve. Non-polar molecules cannot form H bonds and are insoluble

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9
Q

What happens to amphipathic molecules in aqueous solution?

A

Hydrophobic regions cluster together. Hydrophilic regions interact with water

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10
Q

What are amphipathic molecules?

A

They have polar and non-polar regions

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11
Q

Describe a micelle

A

Hydrophobic groups away from water. Ordered shell of water that interacts with hydrophilic head groups

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12
Q

Describe the fluid mosaic model of a membrane

A

Lipid bilayer. Proteins embedded in the bilayer

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13
Q

List some of the crucial roles that proteins play in virtually all biological processes

A
  • Catalysts - enzymes - Transporters (e.g. Fe, O2) - Structural support (e.g. collagen in skin and bones) - Machines (e.g. muscular contraction and motion) - Immune protection (e.g. immunoglobulins) - Ion channels - Receptors (for hormones, neurotransmitters etc) - Ligands in cell signalling (growth factors etc) CIRL MIST
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14
Q

Describe the key features of proteins

A
  • Proteins are polypeptides: macromolecules made up of amino acid residues - The amino acid sequence of a protein is encoded by a gene: the nucleotide sequence of a gene determines the amino acid sequence of a protein - The polypeptide chain folds into a complex and highly specific 3D structure, determined by the sequence of amino acids - The folding of proteins depends on the chemical and physical properties of the amino acids - The 3D shape is important for the function of the protein
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15
Q

What are amino acids?

A

The building blocks of proteins. They consist of a central carbon atom (the alpha carbon) covalently bonded to: - an amino group (-NH2) - a carboxyl group (-COOH) - a hydrogen atom (-H) - a distinctive R group (side chain)

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16
Q

Describe ionisation of an amino acid

A

Both the carboxyl group (-COOH) and the amino group (-NH2) can ionise Base: NH2 + H+ -> NH3+ Acid: COOH -> COO- + H+

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17
Q

Give the two stereoisomers of amino acids

A

L isomer = the isomer found in proteins. Non super-imposable and not a mixture. D isomer is not naturally occurring in proteins

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18
Q

How are amino acids classified?

A

According to the chemical properties of the R groups. Only one alpha-NH3+, at the N terminal end, and one alpha-COO-, at the C terminal end. Acid-base behaviour determined by the R groups

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19
Q

What is an amino acid residue?

A

The part of the amino acid left after a peptide bond is formed

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20
Q

Give the classifications of amino acids

A
  • Non-polar (hydrophobic) amino acids: glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tryptophan - Polar (hydrophilic) uncharged amino acids: serine, threonine, asparagine, glutamine, tyrosine, cysteine - Polar (hydrophilic) charged amino acids: lysine, arginine, histidine, aspartame, glutamate
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21
Q

What can cause problems with amino acids?

A
  • If a small amino acid is mutated to a big one - Big side chains
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22
Q

Describe the effects of the difference between the pH of the solution and the pK value

A
  • If the pH of the solution is bigger than the pK value then the group will be deprotonated
  • If the pH of the solution is smaller than the pK value then the group will be protonated
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23
Q

Describe peptide bond formation

A

The linking of two amino acids is accompanied by the abstraction of a water molecule

24
Q

Describe the features of peptide bonds

A
  • They are planar: alpha-carbon, C, O, N, H and alpha-carbon all lie in a plane - C-N has partial double bond characteristics which makes it rigid and planar - It is shorter than expected, so stronger due to delocalised electrons
25
Q

Describe the difference between cis and trans peptide bonds

A
  • Trans: alpha-carbons on opposite sides of peptide bond. Occurs naturally - Cis: alpha-carbons on same side of peptide bond, leading to steric clashes. Doesn’t occur naturally
26
Q

Outline the importance of amino acids in proteins

A

The amino acid sequence of a protein determines: - the way in which the polypeptide chain folds - the physical characteristics of the protein

27
Q

What is the isoelectric point (pI)?

A

The isoelectric point, pI, of a protein is the pH at which there is no overall net charge

  • Basic proteins, pI greater than 7, contain many positively charged (basic) amino acids
  • Acidic proteins, pI less than 7, contain many negatively charge (acidic) amino acids
  • pH less than pI, the protein is protonated
  • pH greater than pI, the protein is deprotonated
28
Q

Describe the size of different peptides and proteins

A
  • Peptides/oligopeptides: a few amino acids in length (less than 100)
  • Polypeptides/proteins: many amino acids
29
Q

What are conjugated proteins?

A

Some proteins contain covalently linked chemical components in addition to amino acids

30
Q

What are the different levels of protein structure?

A
  • Primary structure: the linear amino acid sequence of the polypeptide chain - Secondary structure: local spatial arrangement of polypeptide backbone - Tertiary structure: 3D arrangement of all atoms in a polypeptide - Quaternary structure: 3D arrangement of protein subunits
31
Q

Describe protein conformation

A

Covalent (peptide) bonds hold primary structure together. Angles determine the conformation of peptide backbone and hence the “fold” of the protein

32
Q

Describe the structure of an alpha helix (secondary structure)

A
  • 3.6 amino acids per turn - 0.54nm pitch (5.4Å) - Right-handed helix - R groups play no part in formation of the helix - 1.5nm between each residue - The backbone -C=O group of one residue is H bonded to the -NH group of the residue four amino acids away
33
Q

How does sequence affect alpha helix stability?

A
  • Not all polypeptide sequences adopt alpha-helical structures - Small hydrophobic residues such as Ala and Leu are strong helix formers - Pro acts as a helix breaker because the rotation around the N-alpha carbon bond is impossible - Gly acts as a helix breaker because the tiny R-group supports other conformations
34
Q

Describe the structure of a beta strand

A
  • Fully extended conformation - 0.35nm between adjacent amino acids - R groups alternate between opposite sides of chain
35
Q

Describe the structure of an antiparallel beta sheet

A

Adjacent beta strands run in opposite directions, with multiple inter-strand H bonds stabilising the structure

36
Q

Describe the bonds of a parallel beta sheet

A

H bonds at more of an angle Also get mixed beta sheets

37
Q

Describe the structure of ferritin and fatty acid binding protein

A
  • Iron storage protein ferritin - largely alpha helix - Fatty acid binding protein - largely beta sheet
38
Q

What is tertiary structure?

A

The spatial arrangement of amino acids far apart in the protein sequence

39
Q

Compare globular and fibrous proteins

A
  • Fibrous: role is support, shape, protection. Long strands or sheets. Single type of repeating secondary structure. For example collagen - Globular: role is catalysis and regulation. Compact shape. Several types of secondary structure. For example haemolytic
40
Q

What are the different specialised cell types?

A
  • Epithelial cells - Nerve cells - Adipocytes - Muscle cells - Red blood cells DNA same, differences due to proteins expressed
41
Q

Describe collagen

A

Triple helical arrangement of collagen chains. Contain Gly-X-Y repeating structure. Hydrogen bonds stabilise interactions between chains. Collagen fibrils formed from covalently cross-linked collagen molecules

42
Q

Describe the variety of tertiary structures of globular proteins

A
  • Motifs: folding patterns containing 1 or more elements of secondary structure. E.g. beta-alpha-beta loop, beta-barrel - Domains: part of a polypeptide chain that fold into a distinct shape. Often have a specific functional role. E.g. calcium-binding domains of troponin C
43
Q

Describe the folding of water-soluble proteins

A

Polypeptide chains fold so that the hydrophobic side chains are buried and polar, charged chains are on the surface e.g. myoglobin

44
Q

Describe the folding of membrane proteins

A

Membrane proteins often show “inside-out” distribution of amino acids e.g. porins: water-filled hydrophilic channel and largely hydrophobic exterior

45
Q

Describe the quaternary structure of haemoglobin and a ribosome

A
  • Haemoglobin - 2 alpha and 2 beta subunits - Ribosome - 55 protein subunits and 3 RNA molecules
46
Q

What are the forces involved in maintaining protein structure at the different levels?

A
  • Primary: covalent (peptide) - Secondary: H-bonds - Tertiary: covalent (disulphide), ionic, H-bonds, Van der Waals, hydrophobic - Quaternary: covalent (disulphide), ionic, H-bonds, Van der Waals, hydrophobic
47
Q

Describe covalent (disulphide) bonds

A
  • Formed between Cys residues - 214 kJ/mol - Can be broken by reducing agents e.g. beta-mercaptoethanol - Work for longer - strong bonds - Most proteins with disulphide bonds are secreted e.g. ribonuclease - Proteins are quite fragile
48
Q

Describe electrostatic interactions

A
  • Formed between charged groups e.g. Glu-, Asp- and Arg+, Lys+, His+ - 10-30 kJ/mol - Salt bridge
49
Q

Describe hydrogen bonds

A
  • Formed between electronegative atom and a hydrogen bound to another electronegative atom - 10-30 kJ/mol
50
Q

Describe the hydrophobic effect

A
  • Interactions between hydrophobic side chains - Due to displacement of water - ~10 kJ/mol - Not bonds
51
Q

Describe Van der Waals forces

A
  • Dipole-dipole interactions - 4 kJ/mol - Important when surfaces of 2 large molecules come together
52
Q

Describe protein denaturation

A
  • Proteins are not very stable - Disruption of protein structure is known as denaturation - Caused by breaking of forces that hold proteins together: - Heat increases vibrational energy - pH alters ionisation states of amino acids and changes ionic/H bonds - Detergents / organic solvents disrupt hydrophobic interactions
53
Q

How do proteins fold?

A
  • All the information needed for folding is contained in the primary sequence - Folding is not a random process but may proceed through localised folding - Some proteins need chaperones to assist in folding: stop a protein mis-folding by holding onto it
54
Q

What is the problem with protein mis-folding?

A
  • Can cause disease - Transmissible spongiform encephalopathies e.g. BSE, kuru, CJD - Altered conformation of a normal human protein promotes the conversion of the existing protein into a diseased state - e.g. PrPc -> PrPSc causes the formation of big aggregates
55
Q

What are amyloidoses?

A

Big clusters of mis-folded proteins

56
Q

Describe the formation of amyloid fibres

A
  • They are a mis-folded, insoluble form of a normally soluble protein that cause disease - Highly ordered with a high degree of beta-sheet - Core beta-sheet forms before the rest of the protein - late-onset diseases - Interchain assembly stabilised by hydrophobic interactions between aromatic amino acids
57
Q

When are amino acids aromatic and when are they aliphatic? Give examples of each

A

Aromatic when they contain a benzene ring, aliphatic when straight chain

  • Aromatic R groups: phenylalanine, tyrosine, tryptophan
  • Polar, uncharged R groups: serine, threonine, cysteine, asparagine, glutamine
  • Non-polar, aliphatic R groups: glycine, alanine, proline, valine, leucine, isoleucine, methionine
  • Negatively charged R groups: aspartate, glutamate
  • Positively charged R groups: lysine, arginine, histidine

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