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PL1003 > Topic 1 Biomolecules - Amino Acids, Peptides and Proteins > Flashcards

Topic 1 Biomolecules - Amino Acids, Peptides and Proteins Flashcards

1
Q

What are amino acids?

A

Amino acids are compounds containing an amino group, a carboxylic acid group and a side chain.
Amino acids are essential for life as they are the building blocks of protein.

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2
Q

what can 19 of the 20 amino acids be described as?

A

19 of the 20 amino acids are chiral and exist as pairs of enantiomers but all naturally occurring amino acids are L amino acids

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3
Q

Amino acids are amphoteric. what does amphoteric mean?

A

means all amino acids have both an acidic group (COOH) and a basic group (NH2)

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4
Q

what is the isoelectric point?

A

The pH at which the amino acid is exactly balanced between an ionic and cationic forms and is primarily in the neutral zwitter ionic form.

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5
Q

Why is glycine unique?

A

it doesn’t have a chiral carbon, it has a H as its R-group instead

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6
Q

What groups are defined as non-polar/hydrophobic?

A

alkyl groups (alkane branches) or aromatic (benzene ring)

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7
Q

what groups are defined as polar/hydrophilic?

A

uncharged chains with polar groups such as OH, negatively charged chains, positively charged chains

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8
Q

What effect does changing the pH have on amino acids?

A

Neutral/basic solutions - groups lose hydrogen

Neutral/acidic solutions - groups gain hydrogen

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9
Q

What are properties of side chains of amino acids?

A

in neutral amino acids the side chain charge doesn’t change with pH.

In acid and basic amino acids it does. e.g. aspartic acid

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10
Q

What is the general rule for pH and pKa of amino acids?

A

If the pH of a solution is less than the pKa, the H+ ion is on. If the pH is higher than the pKa the H+ is off.

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11
Q

How can amino acids be linked together?

A

linked together by an amide bond (peptide bond) between the carboxylic acid of one amino acid and the alpha-amino group of another amino acid to form peptides and proteins

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12
Q

What is Enkephalin?

A

a pentapeptide endorphin, a natural brain opioid, can bind to the body’s opioid receptor and affect pain perception

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13
Q

What are opioids?

A

opioids are molecules which interact with the opioid receptors in the central nervous system

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14
Q

Where are hormones produced?

A

produced by many organs and tissues.

e.g. insulin-causes cells to take up glucose from the blood

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15
Q

What are antibiotic fungal peptides and there function?

A

cyclic decapeptides that are active against gram positive bacteria

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16
Q

What does the natural peptide venom do?

A

induces paralysis by interfering with acetyolcholine receptors in nerves

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17
Q

What are proteins?

A

they are biopolymers made from amino acid monomers

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18
Q

what are proteins functions?

A

transport, catalysis, structure-ligaments, tendons etc, storage, hormones, locomotion-the movement of an organism from one place to another?

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19
Q

What is primary structure of proteins?

A

The sequence in which amino acids are synthesised into the polypeptide chain

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20
Q

What does primary structure determine?

A

determines the physiological, structural, and biological properties and functions of a protein.

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21
Q

What is sickle cell anaemia caused by?

A

caused by a mutation in the gene that instructs the body to produce haemoglobin

The sixth position in the normal b chain of haemoglobin has glutamic acid (amino acid), while a sickle b chain has valine.
Blocked blood vessels can cause pain, serious infections, and organ damage.

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22
Q

What is secondary structure?

A

The secondary level of structure is the arrangement in space of the atoms in the backbone of the protein.

can also be described as the repetitive three-dimensional arrangement of parts of the primary structure

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23
Q

What is secondary structure stabilised by?

A

hydrogen bonds along the backbone of the polypeptide

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24
Q

In secondary structure, what does the shape of the protein depend on?

A

The shape depends on the geometry of the peptide bond and local hydrogen bonding

25
Q

What are the different types of secondary stucture?

A

alpha-helix, antiparallel and parallel beta sheets, and turns

26
Q

Why do proteins not exist in linear chains?

A

As they fold into more complex structures due to free rotation in the other bonds.

In addition there are hydrogen bonds, ionic bonds, LDFs, and covalent bonds, all essentials for maintaining the proteins unique shape.

27
Q

where does local hydrogen bonding occur in secondary structure?

A

Between the H on the N of one amide in a peptide bond with the carbonyl O of another amide in the second peptide bond

28
Q

What is the importance of secondary structure?

A

adds properties such as strength and flexibility to a protein

29
Q

How are alpha-helixes formed?

A

results from the folding of a single backbone strand of the peptide backbone into a coil around a central axis to form a single helix.

the coil is tight, and just 3.6 amino acids are required for each complete turn.

30
Q

What are alpha-helixes stabilised by?

A

stabilised by hydrogen bonds between the amide hydrogen of one peptide and the carbonyl oxygen above it, which is located in the next turn of the helix

31
Q

Describe the arrangement of side chains in an alpha-helix?

A

side chain (R group) are directed outwards.

32
Q

what does a large amount of alpha-helix result in?

A

results in a strong, insoluble, fibrous, flexible product

33
Q

How are beta sheets formed?

A

forms when two or more adjacent segments of a peptide backbone interact with each other. usually several sections of the backbone, called beta-strands interact with each other to form a relatively flat, sheet-like structure.

34
Q

What are beta-sheets stabilised by?

A

hydrogen bonds between the peptide bonds

35
Q

What is tertiary structure?

A

Further folding of secondary structure which gives an overall 3-dimensional shape

36
Q

What does each protein fold into in tertiary structure?

A

Each proteins folds into a very specific shape known as the native conformation which is often the biological active form.

37
Q

What does the 3D arrangement allow for in tertiary structure?

A

The 3D arrangement of helixes and sheets creates a unique shape for every protein. Most are spherical or globular in shape and contain a cleft in the surface known as the active site.

38
Q

What types of bonding is involved (in tertiary) in the side chain?

A

Disulphide crosslinks – covalent bonds between cysteine residues. Important in structural proteins and gluten, therefore bread texture.

Hydrophobic attractions - attractions between R groups of non-polar amino acids

Hydrogen bonding - interaction between polar amino acid R groups

Ionic bonding - bonding between oppositely charged amino acid R groups.

LDF’s

39
Q

What is quaternary structure?

A

describes the formation of proteins containing multiple interacting polypeptide chains called subunits.

These may exist as dimers, trimers, tetramers etc??

40
Q

What are fibrous proteins?

A

Water insoluble structural materials in animals e.g. keratins, collagens (cartilage and tendons)

41
Q

What are fibrous proteins a major component of?

A

hair, nails and skin

42
Q

What are some properties a fibrous protein?

A

usually the primary structure is repetitive and tends to lack chemically-reactive side groups

43
Q

Describe alpha-keratins structure?

A

Rope-like structure - based on the alpha helix, cross-linked into bundles.

44
Q

What are some properties of alpha-keratin?

A

Can be very extensible - a wool fibre can be stretched to twice its length as hydrogen bonds between turns of the a-helix are broken.

In hair alpha-helices are held together by disulphide crosslinks.

S-S bonds help resist the stretch and restore a stretched fibre to its original length.

has rope like structure

45
Q

The degree of S-S bridging determines the properties of the Keratin. describe soft and hard keratins

A

Soft Keratins flexible, extensible – low sulphur e.g. skin

Hard Keratins - high sulphur e.g. horn (less flexible, less extensible)

46
Q

What is collagen a major component of?

A

cartilage, skin, blood vessels and bone

47
Q

What structural form does collagen occur in?

A

triple helix

(3 left-handed helices) (known as “Tropocollagen”).

The triple helix tightens under tension, resisting stretching, making collagen inextensible.

48
Q

What does the repetitive primary structure cause in collagen?

A

Bulky Proline and Hydroxyproline side chain rings point outwards and are responsible for the tendency to form left-handed helices.

Glycine at every third position sits in the interior of the helix, where there is little space.

49
Q

What are collagen fibre stabilised by?

A

Collagen fibres are stabilised by extensive inter-chain hydrogen bonding and some covalent S-S cross-links.

Fibres have stability, tensile strength and rigidity.

50
Q

What are some examples of globular proteins?

A

Enzymes, hormones, transport, storage etc

51
Q

Describe structure and properties of globular proteins

A

Globular Proteins are water soluble and roughly spherical in shape.

Intricately folded so that hydrophobic side chains are tucked inside - away from water

52
Q

What is myoglobin?

A

Is the oxygen-holding protein in muscle tissue.

53
Q

What does myoglobin consist of?

A

Consists of one polypeptide unit, of which 75% is an a-helix, which is further folded.

54
Q

What is a prosthetic group?

A

non-protein group which is tightly bound to a polypeptide unit and it is essential for the proteins function

55
Q

What prosthetic group does myoglobin contain?

A

haem which hold oxygen in the molecule

56
Q

Describe haemoglobin

A

Quaternary structure: 4 polypeptide molecules (Globins).

Sub units are held together by hydrophobic interactions, electrostatic (ionic) attraction and hydrogen bonds.

Haemoglobin is a transporter of blood. It has two identical alpha subunits and two identical beta subunits

Carries oxygen and carbon dioxide between the lungs and the muscle.

57
Q

Describe isoelectric point of a protein

A

The isoelectric point is the pH at which the total charge on the protein molecule is zero (no net electric charge) and this varies between proteins. At pH’s below the isoelectric point it has +ve charge overall and at pH’s above it has –ve charge overall. Charged proteins repulse each other, preventing aggregation. At the isoelectric point proteins tend to aggregate and are in their least soluble undenatured form.

58
Q

Describe separation by electropheresis

A

Proteins are loaded on a gel and given a negative charge by using a suitable buffer. A potential difference is applied. Large proteins move slowly, smaller ones move more quickly. The gel is stained eg. with Coomassie blue.

PL1003 (8 decks)

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