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Biology Module 2 > Proteins & Chromatography > Flashcards

Proteins & Chromatography Flashcards

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1
Q

What is a peptide?

A

Peptides are polymers which consist of many amino acid molecules.

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2
Q

What is a dipeptide?

A

A dipeptide is formed when two amino acids join together.

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3
Q

What is a polypeptide?

A

A polypeptide is formed when more than two amino acids join together.

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4
Q

What are proteins?

A

Proteins consist of multiple polypeptides arranged as complex macromolecules. All proteins contain hydrogen, carbon, oxygen and nitrogen.

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5
Q

What is the general structure of an amino acid?

A

Amino acids contain:

  • amine group (-NH2)
  • carboxylic acid group (-COOH)
  • one hydrogen atom (H)
  • R-group

All are attached to a central carbon atom

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6
Q

How many R-groups are there?

A

20 - meaning there are 20 different naturally occurring amino acids found in cells.

9 are essential, 5 non essential, and 6 only essential in infants and young children.

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7
Q

What is an R-group?

A

A variable side chain which consists of a range chemical groups different in each amino acid. Different R groups result in different amino acids.

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8
Q

How do amino acids form?

A

Amino acids form when the amine and carboxylic acid groups react in adjacent amino acids.

The hydroxyl in the carboxylic group reacts with the hydrogen in the amine group of another amino acid.

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9
Q

What does peptide synthesis produce?

A

A peptide bond between the two amino acids and a molecule of water. This makes this a condensation reaction.

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10
Q

How is peptide synthesis catalysed?

A

The reaction is catalysed by the enzyme “peptidyl transferase” which is present in ribosomes.

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11
Q

What do R-group interactions lead to?

A

They lead to the formation of polypeptides which fold into complex structures (proteins). Different amino acid sequences lead to different structures and shapes being produced.

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12
Q

What are the 4 levels of protein structure?

A
  • Primary structure
  • Secondary structure
  • Tertiary structure
  • Quaternary structure
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13
Q

What is the primary structure of a protein?

A

The number of and sequence in which the amino acids are joined. This is determined by the gene.

The amino acids involved and their sequence will influence how the polypeptide folds to give the final shape - this determines it’s function. The only bonds in primary structure are peptide bonds.

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14
Q

What is the secondary structure of proteins?

A

Hydrogen bonds between non-adjacent amine and carboxyl groups within the amino acid chain which pulls it into one of two shapes.

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15
Q

What are the two shapes hydrogen bonds can pull amino acids into?

A
  • alpha helices (strong, helical shape)
  • beta pleated sheets (weak, strength achieved by layering and bonds between layers)
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16
Q

How do beta pleated sheets form?

A

Depending on the amino acid composition, polypeptide chains can lie parallel to one another, joined by hydrogen bonds. This pattern causes the structure to appear pleated.

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17
Q

What is the tertiary structure of a protein?

A

The folding of a protein into it’s final 3D shape. Coiling / folding of proteins into secondary structures brings the R-groups closer together, and they can now interact. Further folding will occur.

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18
Q

What interactions can occur between R-groups?

A
  • disulphide bridges - interactions between sulphur in the R-group of the amino acid cysteine - strong and not broken easily
  • ionic bonds - form between the carboxyl and amine groups not involved in peptide bonding. They are broken easily by pH and are weaker than disulfide bridges
  • hydrogen bonds - numerous, weakest of the bonds formed
  • hydrophobic / hydrophilic interactions - weak interactions between polar and non-polar R-groups
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19
Q

What is the quaternary structure of a protein?

A

An interaction between 2 or more polypeptides, meaning quaternary structures only exist in proteins which contain at least 2 polypeptides.

These individual proteins are known as subunits. Interactions between subunits are the same as within a tertiary structure but are between different protein molecules rather than within one molecule.

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20
Q

What can protein subunits be?

A

Identical or different:

  • enzymes = 2 identical
  • insulin = 2 different
  • haemoglobin = 4 - 2 sets of 2 identical
21
Q

What do protease enzymes do?

A

They catalyse the breakdown of peptides - a water molecule is added to break the peptide bond in a hydrolysis reaction which reforms the amine and carboxylic acid groups.

22
Q

What coloured complexes do peptide bonds form with Cu ions?

A

They form violet complexes in an alkaline solution.

23
Q

How do hydrophobic and hydrophilic properties affect protein shape?

A

Proteins are assembled in the aqueous environment of the cytoplasm. The way in which a protein folds depends on whether or not the R-group is hydrophobic or hydrophilic.

hydrophilic = outside of the protein
hydrophobic = inside (shielded from water)

24
Q

Describe the Biuret test to test for proteins:

A
  1. 3cm3 of a liquid sample is mixed with 3cm3 of a 10% concentration sodium hydroxide solution.
  2. 1% concentration copper sulphate is added a few drops at a time until the solution turns blue.
  3. Protein is present if the solution turns from blue to lilac.
25
Q

What are the two main types of proteins?

A
  • Globular proteins
  • Fibrous proteins
26
Q

What are the properties of globular proteins?

A

They are compact, water soluble and roughly spherical in shape. They form when proteins fold into their tertiary structures so the hydrophobic R-groups are kept away from the aqueous environment.

27
Q

Why are globular proteins soluble in water?

A

The hydrophilic R-groups are on the outside, making the protein soluble. Solubility is essential to regulating many life processes.

28
Q

What type of protein is insulin?

A

A globular protein - hormone involved in the regulation of blood glucose concentration.

29
Q

Why do hormones need to be soluble and precisely shaped?

A

They need to be soluble as they are transported in the bloodstream, and precisely shaped to fit into specific receptors on cell surface membranes.

30
Q

What is a conjugated protein?

A

A globular protein that contains a non-protein component called a prosthetic group.

Examples of prosthetic groups include lipoproteins and glycoproteins. Metal ions and molecules derived from vitamins can also form prosthetic groups (e.g. haem groups which contain iron (II) ions).

31
Q

What is haemoglobin?

A

A globular conjugated protein with a haem group attached to each of it’s 4 polypeptide chains (2 alpha subunits, 2 beta subunits).

Haem groups contain iron, which is what the oxygen binds to.

32
Q

What are the properties of haemoglobin?

A
  • hydrophobic groups inside, hydrophilic outside
  • quaternary protein
  • 2 alpha and 2 beta chains
  • similar proportion of glycine to that of other amino acids in other proteins
  • the haem groups’ iron (II) ions can combine reversibly with O2 molecules
33
Q

What is catalase?

A

A quaternary protein and enzyme containing 4 haem prosthetic groups. The iron (II) ions allow catalase to interact with hydrogen peroxide and speed up it’s breakdown.

Catalase is a byproduct of metabolism and is damaging to cells if allowed to accumulate.

34
Q

What are fibrous proteins?

A

They are regular, repetitive sequences of amino acids which form fibres.

They tend to make strong, long molecules which are not folded into complex 3D shapes like globular proteins.

35
Q

Why are fibrous proteins usually insoluble?

A

They have a high proportion of amino acids with hydrophobic R-groups in their primary structures.

36
Q

What are generally the roles of globular and fibrous proteins?

A
  • globular proteins usually have metabolic roles
  • fibrous proteins usually have structural roles
37
Q

How is collagen structured?

A

It is a connective tissue found in skin, tendons, ligaments and the nervous system. One molecule of collagen is made up of 3 polypeptide chains twisted around each other in a long, strong, rope-like structure.

38
Q

What is keratin?

A

A group of fibrous proteins found in skin, nails and hair which contains a large proportion of the amino acid cysteine.

This results in the formation of strong disulphide bridges.

39
Q

How do disulphide bridges affect flexibility?

A

They typically help form a strong, inflexible and insoluble material. The degree of disulphide bridges determines flexibility - e.g. hair contains fewer bonds than nails and is therefore more flexible.

40
Q

What is elastin?

A

A fibrous protein found in elastic fibres - present in the walls of blood vessels and the alveoli.

It is a quaternary protein formed from stretchy molecules called tropoelastin.

41
Q

How does elastin form?

A

Tropoelastin molecules contain alternate hydrophobic and lysine rich areas (lysine is an amino acid).

Elastin forms when tropoelastin molecules aggregate via intersections between hydrophobic areas.

Elastin is stabilised by cross-linking covalent bonds involving lysine.

42
Q

What is chromatography used for?

A

It is used to separate and identify chemicals in a mixture which relies on the movement of a liquid or a gas through a medium.

The liquid or gas that moves is the mobile phase, while the medium that does not move is the stationary phase.

43
Q

What are the two types of chromatography?

A
  • Paper chromatography
  • Thin-layer chromatography
44
Q

What are the mobile and stationary phases in each type of chromatography?

A

Paper:
- mobile phase = liquid solvent (ethanol, water, etc)
- stationary phase = chromatography paper

Thin-layer:
- mobile phase = liquid solvent (ethanol, water, etc)
- stationary phase = thin (0.1-0.3mm) layer of solid such as silica gel on a glass or plastic plate.

45
Q

What are the key basic principles of chromatography?

A
  • mobile phase moves through or over the stationary phase
  • the components in the mixture spend different amounts of time in each phase
  • the components that spend longer in the mobile phase travel further and faster
  • the time spent in different phases is what separates the components in the mixture
46
Q

What is an Rf value?

A

The ratio of the distance travelled by the spot to the distance travelled by the solvent.

47
Q

How are Rf values calculated?

A

distance travelled by spot / distance travelled by solvent

48
Q

How can amino acids be identified on a chromatogram?

A

Once the paper is dry, it must be sprayed with ninhydrin reagent and gently supplied with heat.

Biology Module 2 (8 decks)

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