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Semester 2 Chemistry Revisions > Lecture 13 > Flashcards

Lecture 13 Flashcards

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1
Q

How many commonly occurring amino acids are there?

A

20

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2
Q

What isomer of amino acids are used in human metabolism?

A

L

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3
Q

What do L/D isomerism describe?

A

Configuration of the chiral carbon in relation to D- glyceraldehyde

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4
Q

When are amine groups ionised? Why? What happens?

A

pH decreases.

Amine groups are basic and accept H+

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5
Q

When are carboxylic groups ionised? Why? What happens?

A

pH increases.

Carboxylic acid are acids and donate a H+.

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6
Q

At what pH is needed for an amino acid to be a Zwitterion?

A

7.0- 7.4

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7
Q

What is a Zwitterion?

A

Amine group accepted a hydrogen and carboxylic acid group has donated a Hydrogen.

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8
Q

What is the Iso- Electric point?

A

The pH at which a molecule has a neutral charge and so equal amounts of positive and negative charges present.

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9
Q

How do you calculate the pI for an amino acid with only 2 ionisable groups?

A

Work out the average of the two pKs.

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10
Q

If the side chain is also ionisable and so there are 3 ionisable groups how do you calculate the pI?

A
  1. Draw molecule and work out charge.
  2. Imagine pH is lower than the lowest pH what is the charge of the molecule?
  3. Continue increase pH until the net charge is 0 and then average these two pKas.
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11
Q

List some common ways of categorising R groups:

A
  • SIZE (large / small)- Large amino acids facing outwards of the protein.
  • SHAPE (aliphatic / aromatic).
  • HYDROPHOBICITY (polar / non-polar)- Polar amino acids have strong interactions with water.
  • CHARGE AT PHYSIOLOGICAL PH (acidic / basic).
  • SULPHUR-CONTAINING (cysteine & methionine).
  • IMINO (proline is not actually an amino acid).
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12
Q

What is an essential amino acid?

A

Cannot be produced in the body so must be obtained from food sources.

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13
Q

What is a nonessential amino acid?

A

Can be synthesised by essential amino acids in the body.

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14
Q

What is a conditionally essential amino acid?

A

Essential in certain physiologic conditions.

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15
Q

Why is there a permanent trans configuration in the -CO-NH- system? How can a peptide be flexible?

A

ABSENCE of FREE rotation.

Other bonds give the peptide chain flexibility.

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16
Q

What hybridisation is the O, C and N in a peptide bond? What does this mean?

A

O, C, N are all sp2 hybridised so all have p orbitals. Nitrogen’s LONE PAIR interacts with the ELECTRONS in the pi bond. There is a bond occurring over 3 different atoms and contains 4 electrons.

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17
Q

Why is the trans isomer the most stable isomer?

A

Keeps the side chains away from each other which allows less sterohinderance.

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18
Q

How are peptides always drawn/ written?

A

From amino terminus at the top left the carboxyl terminus at the bottom right.

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19
Q

When is there covalent bonding/ non covalent bonding in protein structure?

A

Covalent Bonding: between adjacent Amino acids.

Non- Covalent bonding: Alpha helices and Beta Sheets, Compact 3-D folded shape and Multiunit Protein.

20
Q

What is the primary strucutre?

A

LINEAR sequence of amino acids linked together by peptide bonds.

21
Q

What is a residue?

A

Individual Amino Acid

22
Q

What determines the primary sequence?

A

Gene encoding the protein

23
Q

What is the Secondary strucutre?

A

REGIONS of REGULAR structure which is maintained by HYDROGEN BONDING between the C=O and the N-H atoms.

24
Q

In an alpha helix how many amino acids per 360o turn?

A

4

25
Q

In an alpha helix where do the side chains project? What does this allow?

A

Side chains project outwards to allow for large amino acids.

26
Q

What is a Parallel Beta Sheet?

A

Chain 1 & 2 start at the amino group and finish with the carboxylic acid.

27
Q

What is an Anti- parallel Beta Sheet?

A

Chain 1 starts with the amino group and finishes with the carboxylic acid whereas Chain 2 starts with the carboxylic acid and finishes with the amino group.

28
Q

How can you tell the difference between a parallel/ antiparallel beta sheet? Which sheet is more stable?

A

size of the rings formed by hydrogen bonds. Parallel= 12 & Antiparallel= Alternates between 10 and 14 which is MORE stable.

29
Q

In a Beta sheet where are the side chains?

A

Above and Below the Sheet.

30
Q

What does Proline do in a Beta sheet?

A

Causes a kink in the sheet which is needed for a Beta turn.

31
Q

What is the tertiary structure of a protein?

A

Protein FOLDS into compact THREE-DIMENSIONAL structures.

32
Q

Generally the most stable protein structures have _____________

A

the MINIMUM surface area accessible to water.

33
Q

Interior of proteins are ___________

Exterior of proteins are ___________

A

HYDROPHOBIC

HYDROPHILIC

34
Q

The tertiary structure of a protein is stabilised by ‘intermolecular’ bonds, describe these bonds:

A
  • ELECTROSTATIC INTERACTIONS between oppositely charged side-chains called a salt bridge, which forms an ionic bond.
  • HYDROGEN-BONDS stabilise tertiary structure by H-bonding between side-chains. Most polar residues can H-bond.
  • LONDON/VAN DER WAAL’S INTERACTIONS are non-covalent forces of attraction between neutral molecules. All amino acids form these forces.
  • HYDROPHOBIC INTERACTIONS are the most important in stabilising protein 3D shapes and involves burying the hydrophobic residues.
  • DISULPHIDE BONDS formed by the oxidation of 2 cysteine residues.
35
Q

What is the Quaternary structure?

A

Many proteins exist as 2 or more SEPERATELY folded peptide chains.

36
Q

Classification of Proteins- What are simple proteins?

A

Proteins are often small and have chains of amino acids joined by peptides.

37
Q

Classification of Proteins- What are Conjugated proteins?

A

Proteins are often bigger and are simple proteins united with a non- protein factor. E.g. a cofactor.

38
Q

Describe the properties of globular proteins:

A

COMPACT= shape Made of α-helices and β-sheets and polypeptide chains are held together BY INTRA-CHAIN HYDROGEN BONDS.
RANDOM Sequence of amino acids.
WATER SOLUBLE.
FUNCTIONAL rather than STRUCTURAL.

39
Q

What is Insulin?

A

It is a small protein and is made up of Chain A and Chain B. Chain A has 1 disulphide bond within its structure and another 2 holding both chains together

40
Q

Where and how is insulin stored? Stabilised by ….

A

Hexamer in the pancreas.

A Zinc ion.

41
Q

Describe the properties of fibrous proteins:

A 
FIBRE-LIKE structure.
Polypeptide chains are held together by INTER-CHAIN HYDROGEN BONDS. 
INSOLUBLE in water.
REPEATING sequence of amino acids. 
Adapted for a STRUCTURAL function.
42
Q

What are the two types of fibrous proteins?

A

Elastic (COILED) e.g. keratin, elastin, myosin.

Inelastic (SHEET STRUCTURES) eg. fibroin, collagen.

43
Q

What is the repeating amino acid sequence in collagen?

A

GXY (G= Glycerine, X= amino acid and Y= Proline/ Hydroxyamino acids).

44
Q

How are hydroxyamino acids formed?

A

From proline by enzymatic oxidation of proteins which requires VITIMIN C.

45
Q

What is the secondary structure in collagen?

A

LEFT HANDED helix which has NO hydrogen bonds and 3 residues per turn.

46
Q

What is the quaternary structure in collagen?

A

TRIPLE helix which is held together by Hydrogen bonds between helices.

Semester 2 Chemistry Revisions (12 decks)

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