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MGD > Amino Acids and Proteins > Flashcards

Amino Acids and Proteins Flashcards

0
Q

What is the function of the cytoplasm?

A

Metabolism of carbohydrates, amino acids and nucleotides. Fatty acid synthesis.

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1
Q

What is the function of the Golgi body?

A

Detoxification reactions and export of proteins. Involved in protein targeting and post translational modification.

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2
Q

What is the function of a lysosome?

A

Cellular digestion.

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3
Q

What is the function of mitochondria?

A

ATP synthesis.

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4
Q

What is the function of rough endoplasmic reticulum?

A

Manufacture proteins for membrane or secretory pathway or for lysosomes. Initiates glycolysation.

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5
Q

What so the function of smooth endoplasmic reticulum?

A

Synthesis of lipids, phospholipids and steroids. Metabolises carbohydrates and steroids. Detoxifies drugs. Attaches receptors to membrane proteins.

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6
Q

What is the function of the nucleus?

A

Synthesis of DNA & RNA. Repair of DNA. RNA processing. Ribosome assembly (in nucleolus).

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7
Q

What is the function of the plasma membrane (plasmalemma)?

A

Cell morphology and movement. Transport of ions and small molecules.

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8
Q

What is the function of ribosomes?

A

Protein synthesis.

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9
Q

What is a macromolecular complex?

A

Something made up of macromolecules.

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10
Q

What bonds and interactions are important for macromolecular structure?

A

Covalent bonds between monomers, hydrogen bonds, ionic interactions (attraction/repulsion), hydrophobic interactions, Van der Waals.

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11
Q

Why are weak interactions important in macromolecules?

A

They increase stability of the complexes; breaking/disrupting interactions causes loss of structure and function.

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12
Q

What is the difference between hydrophobic and hydrophilic molecules in water?

A

Polar, hydrophilic molecules form hydrogen bonds with, and dissolve in, water. Non-polar, hydrophobic molecules cannot form hydrogen bonds so are insoluble one water.

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13
Q

What are amphipathic molecules?

A

Molecules with polar and non-polar regions. The hydrophobic molecules cluster together to form a micelle.

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14
Q

Which amino acid isomers do humans have?

A

L isomers.

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15
Q

How do you draw a trans peptide bond?

A

C=O and N-H bonds on opposite sides.

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16
Q

What classifications of amino acids are there?

A

R groups can be: non-polar (hydrophobic), polar & uncharged (hydrophilic), or polar & charged (hydrophilic).

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17
Q

What is the pK value of an amino acid?

A

It is pH at which it has no charge.

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18
Q

What is the pK of acidic and alkaline amino acids?

A

Alkaline: pK > 7
Acidic: pK < 7

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19
Q

What is the significance of the pK value?

A

If the pH is lower than the pK, the amino acid will be protonated.
If the pH is higher than the pK, the amino acid will be deprotonated.

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20
Q

Why don’t peptide bonds form in the cis form?

A

Steric clashes.

21
Q

Explain the key features of a peptide bond.

A

The electrons in the C-N bond are delocalised, giving it partial double bond characteristics; this makes the peptide bond rigid and planar.

22
Q

What is the primary structure of an amino acid?

A

The linear amino acid sequence of the polypeptide chain.

23
Q

What is the secondary structure of a protein?

A

The local special arrangement of the polypeptide back bone.

24
Q

What is the tertiary structure of a protein?

A

3 dimensional arrangement of all the atoms in the polypeptide.

25
Q

What is the quaternary structure of a protein?

A

3 dimensional arrangement of protein subunits.

26
Q

What are the features of the alpha helix?

A

3.6 amino acids per turn, 0.54nm pitch, right-handed, C=O group of on residue is hydrogen bonded to NH group 4 amino acids away - these hydrogen bonds hold the helix together.

27
Q

What sort of amino acids are strong helix formers?

A

Small hydrophobic residues such as Ala and Leu.

28
Q

What are the features of the beta strand?

A

Fully extended conformation, 0.35nm betweens adjacent residues. R groups alternate between opposite sides of the chain.

29
Q

What is a beta sheet?

A

The side by side arrangement of beta strands. Many hydrogen bonds stabilise the structure?

30
Q

What is the difference between a parallel and an antiparallel beta strand?

A

In antiparallel the adjacent beta strands run in opposite directions. Whereas in parallel all strands run in the same direction.

31
Q

What are the features of fibrous proteins?

A

They are long strands or sheets. Single type of repeating secondary structure.
Roles are: support, shape & protection.
Example: collagen.

32
Q

What are the features of globular proteins?

A

Compact shape. Secondary types of secondary structure.
Roles: catalysis, regulation.
Example: haemoglobin.

33
Q

What is the structure of collagen?

A

Collagen chains - Gly-X-Y repeating primary structure - form triple helical arrangement called a collagen molecule with H bonds stabilising the interactions between chains. Many of these collagen molecules are cross linked to form a collagen fibril.

34
Q

What is a motif?

A

A folding pattern of a polypeptide containing 1 or more elements of secondary structure.

35
Q

What is a domain?

A

Part of a polypeptide chain that folds into a distinct shape and often has a specific functional role.

36
Q

How do water soluble proteins fold?

A

Hydrophobic amino acids are buried. Polar and charged amino acids are on the surface.

37
Q

How do membrane proteins fold?

A

Largely hydrophobic exterior with water filled, hydrophilic channel in which ions and solutes can pass through the membrane.

38
Q

What is the force involved in maintaining primary structure?

A

Covalent (peptide) bonds.

39
Q

What is the force involved in maintaining secondary structure?

A

Hydrogen bonds.

40
Q

What are the forces involved in maintaining tertiary and quaternary structure?

A

Covalent (disulphide) bonds, ionic attraction/repulsion, hydrogen bonds, Van der Waals, hydrophobic interactions.

41
Q

What sort of proteins have disulphide bonds?

A

Mainly secreted ones: they secreted into harsher conditions they need strong bonds to maintain structure.

42
Q

What disrupts disulphide bonds?

A

Reducing agents.

43
Q

What amino acids form disulphide bonds?

A

Cystine.

44
Q

What type of amino acid forms electrostatic/Ionic interactions?

A

Ones with charged R groups. These interactions can also be called salt bridges.

45
Q

What is hydrophobic effect?

A

Interaction of two hydrophobic sidechains due to displacement of water.

46
Q

What can pH change disrupt leading to denaturation?

A

Changes ionisation state of amino acids, disrupting ionic and hydrogen bonds.

47
Q

What disrupts hydrophobic interactions?

A

Detergents and organic solvents.

48
Q

How is protein misfolding bad?

A

Altered confirmation of normal human protein means it cannot perform necessary functions - disease state.

49
Q

What are amyloid fibres?

A

Misfolded, insoluble form of normally soluble protein.

50
Q

What are the features of amyloid fibres?

A

Highly ordered with high proportion of beta sheet. Core beta sheet forms before rest of the protein. Inter-chain assembly stabilised by hydrophobic interactions between aromatic amino acids.

MGD (4 decks)

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