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Biology > Biological Molecules - Proteins > Flashcards

Biological Molecules - Proteins Flashcards

1
Q

What are the monomer units of proteins?

A

Polypeptides are composed of long chains of amino acid monomer units. One or more polypeptides can be combined to form functional proteins.

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2
Q

What evidence do amino acids provide for evolution?

A

The fact that the same 20 amino acids occur in all living organisms provides indirect evidence for evolution.

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3
Q

Amino acids are amphoteric. What does this mean?

A

They have basic and acidic properties. Amino group acts as a base. The carboxyl group acts as an acid.

In a neutral aqueous solution, they exist as dipolar ions (zuritterions).

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4
Q

What does dipeptide mean?

A

Two amino acids join together by a condensation reaction.

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5
Q

What does polypeptide mean?

A

More than two amino acids join together by a condensation reaction.

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6
Q

Every amino acid has a central carbon atom to which are attached four different chemical groups. What are they?

A
  • amino group (-NH2)
  • carboxyl group (-COOH)
  • hydrogen atom (-H)
  • R (side) group
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7
Q

What is an amino group?

A

A basic group from which the amino part of the name amino acid is derived.

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8
Q

What is a carboxyl group?

A

An acidic group which gives the amino acid the acid part of its name.

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9
Q

What is an R (side) group?

A

A variety of different chemical groups. Each amino acid has a different R group. These 20 naturally occurring amino acids differ only in their R (side) group.

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10
Q

What happens when the pH of the solution that the amino acid is in is decreased?

A

If the pH is decreased, the amino acids become positively charged. The negative oxygen reacts with the excess hydrogen ions in the solution. This gets rid of the negative charge, leaving only the positive nitrogen ion.

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11
Q

What happens when the pH of the solution that the amino acid is in is increased?

A

If the pH is increased, the amino acids become negatively charged. This is because if the solution is alkaline, nitrogen donates its extra hydrogen atom. This gets rid of the positive charge, leaving only the negative oxygen ion.

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12
Q

What is the isoelectric point?

A

The pH at which the amino acid is neutral.

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13
Q

What is a pH buffer?

A

A pH buffer regulates the pH and keeps it neutral. This is vital in order to stop enzymes denaturing. Therefore amino acids act as buffers.

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14
Q

What determines the properties of an amino acid?

A

the R group

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15
Q

What are the properties of a simple hydrocarbon chain?

A

Non-polar and hydrophobic.

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16
Q

What are the properties of a polar hydrocarbon chain?

A

Polar and hydrophilic.

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17
Q

What are the properties of the second carboxyl group?

A

Negatively charged and acidic.

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18
Q

What are the properties of the second amino group?

A

Positively charged and basic.

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19
Q

What is a peptide bond?

A

Proteins are made of many amino acids which are joined together by peptide bonds. These are formed by a condensation reaction between the carboxyl group of one amino acid and the amino group of another. The peptide bond can be broken by hydrolysis.

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20
Q

Where does hydrolysis occur?

A

Hydrolysis occurs in the digestion of proteins in the stomach.

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21
Q

Where will hydrogen bonds form?

A

Due to unequal sharing of electrons, hydrogen bonds will form between:

  • NH groups and C=C groups
  • OH groups on R-groups
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22
Q

Where will ionic bonds form?

A

In aqueous solution, ionic bonds can be formed between charged R groups. A negatively charged carboxyl group will form an ionic bond with a positively charged amino group.

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23
Q

Where will disulphide bridges form?

A

Only occurs between the sulphonyl groups of two cysteine amino acids.

Interchain bond = between two different polypeptide chains
Intrachain bond = between the same polypeptide chain

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24
Q

What levels can protein structure be organised into?

A
  • primary structure
  • secondary structure
  • tertiary structure
  • quaternary structure
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25
Q

What is polymerisation?

A

Through a series of condensation reactions, many amino acid monomers can be joined together in a process called polymerisation. The resulting chain of many hundreds of amino acids is called a polypeptide.

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26
Q

What is the primary structure of proteins?

A

The number and sequence of amino acids in a polypeptide chain forms the primary structure of any protein. The DNA code carries the information that determines the sequence of amino acids and therefore the sequence is specific for each protein. Due to the different properties of each amino acid, the sequence will determine its shape and therefore its function.

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27
Q

How many types of primary protein structure are there?

A

As polypeptides have many (usually hundreds) of the 20 naturally occurring amino acids joined in different sequences, there is an almost limitless number of possible combinations, and therefore types, of primary protein structure.

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28
Q

What determines the ultimate shape and therefore function of a protein?

A

The primary structure of a protein. A change in just a single amino acid in this primary sequence can lead to a change in the shape of the protein and may stop it carrying out its function. Therefore a protein’s shape is very specific to its function.

29
Q

Is a single polypeptide chain or a number of polypeptide chains more common?

A

A simple protein may consist of a single polypeptide chain. More commonly however, a protein is made up of a number of polypeptide chains.

30
Q

What is the secondary structure of proteins?

A

The linked amino acids that make up a polypeptide possess both -NH and -C=O groups on either side of every peptide bond. The -NH group has an overall positive charge while the -C=O group has an overall negative charge. These two groups therefore readily form weak hydrogen bonds. This causes the long polypeptide chain to be twisted into a 3D shape, such as an alpha helix or a beta pleated sheet.

31
Q

What is the tertiary structure of proteins?

A

The alpha helices or the beta pleated sheets of the secondary protein structure can be twisted and folded even more to give the complex, and often specific, 3D structure of each protein (the tertiary structure).

32
Q

What is the shape of the tertiary structure determined by?

A

This shape is determined by hydrophilic acids shielding hydrophobic amino acids in aqueous solution.

33
Q

How is the tertiary structure maintained?

A

This structure is maintained by a number of different bonds. Where the bonds occur depends on the primary structure of the protein.

34
Q

What bonds maintain the tertiary structure?

A
  • Disulphide bridge = which are fairly strong and therefore not easily broken.
  • Ionic bonds = which are formed between any carboxyl and amino groups that are not involved in forming peptide bonds. They are weaker than disulphide bonds and are easily broken by changes in pH.
  • Hydrogen bonds = which are numerous but easily broken.
35
Q

What plays the most important role in the function of a protein?

A

It is the 3D shape of a protein that is important when it comes to how it functions. It makes each protein distinctive and allows it to recognise, and be recognised by, other molecules. It can then interact with them in a very specific way.

36
Q

What is the quaternary structure of proteins?

A

Large proteins often form complex molecules containing a number of individual polypeptide chains that are linked in various ways. Often these protein complexes will also have a non-protein component called a prosthetic group associated with the molecules. Although the 3D structure is important to how a protein functions, it is the sequence of amino acids (primary structure) that determines the 3D shape in the first place.

37
Q

Give an example of non-protein (prosthetic) group.

A

Haemoglobin consists of four polypeptide chains. Each chain has an iron-containing haem group.

38
Q

What is a fibrous protein?

A
  • Regular, repetitive sequences of amino acids.
  • Insoluble, strong, long, thin and tough.
  • Quarternary structure (multiple polypeptide chains).
  • Lots of bonding between polypeptides.
  • e.g. Collagen = provides mechanical strength and rigidity in artery walls, tendons, bones and cartilage, triple helix.
39
Q

What is a globular protein?

A
  • Rolled into a spherical shape with hydrophilic groups pushed outside and hydrophobic R groups turned inwards.
  • Have an outside and an inside.
  • Quarternary structure.
  • Soluble in water and easily transported in fluid.
  • e.g. Haemoglobin = 4 polypeptide chains (2 alpha and 2 beta globin chains) and 4 haem groups (one per polypeptide).
  • e.g. Enzymes = soluble, complex 3D shape.
  • e.g. Insulin = 2 polypeptide chains joined by a single disulphide bridge.
40
Q

Describe the test for proteins.

A

The most reliable protein test is the Biuret test, which detected peptide bonds.

  1. Place a sample of the solution to be tested in a test tube and add an equal volume of sodium hydroxide solution at room temperature.
  2. Add a few drops of very dilute copper (II) sulphate solution (Biuret reagent) and mix gently.
  3. A purple coloration indicates the presence of peptide bonds and hence a protein. If no protein is present, the solution remains blue.
41
Q

What is a protein?

A

A polymer which is made up of amino acids linked by peptide bonds. May also contain prosthetic groups as part of its quaternary structure.

42
Q

What is an amino acid?

A

A monomer which makes up proteins. Has a central carbon atom which is bonded to a carboxylic acid group, an amino group, a hydrogen atom and an R group.

43
Q

What is an amino group?

A

The -NH2 group of an amino acid.

44
Q

What is a carboxyl group?

A

The -COOH group of an amino acid.

45
Q

Where is condensation used?

A

in many synthetic processes

46
Q

Where is hydrolysis used?

A

in digestion

47
Q

The polypeptide with its specific sequence of amino acids is called the ‘primary structure of the protein.’ What is the sequence of amino acids in the polypeptide governed by?

A

It is governed by the sequence of codons in the gene that assembles that polypeptide by using the messenger RNA/transfer RNA/ribosome mechanism.

48
Q

The secondary structure of proteins is a characteristic of what type of proteins?

A

fibrous type structural proteins

49
Q

The tertiary structure of proteins is a characteristic of what type of proteins?

A

globular type proteins, such as enzymes and antibodies

50
Q

In addition to being classed as fibrous or globular forms according to their 3D structure, what else can proteins be classed as?

A

simple or conjugated

51
Q

What are simple proteins?

A

Simple proteins only contain amino acids in their structure and exist as several different types, such as albumins, globulins and scleroproteins.

52
Q

What are conjugated proteins?

A

Conjugated proteins contain amino acids in nucleoproteins, phosphoric acid in phosphoproteins and lipids in lipoproteins. Haemoglobin is a conjugated protein consisting of four globular polypeptides each of which contains a porphyrin ring which also contains iron. (contain a non-polypeptide group)

53
Q

What does the pH measure?

A

The pH measures the hydrogen ion concentration of the medium in which the amino acid or protein is.

54
Q

What does the hydrogen ion concentration affect?

A

The hydrogen ion concentration will affect how the amino acids and proteins ionise. In a high hydrogen ion concentration, the amino acids will be predominately positively charged cations. In a lower hydrogen ion concentration, the amino acids will be predominately negatively charged anions.

55
Q

How do charges on a protein resulting from the pH effect have an influence on its behaviour?

A
  • The charges on the active sites of an enzyme may affect the capability of the enzyme to join with its specific substrate. This is why enzymes tend to work best at specific pHs.
  • At the iso-electric point, the protein carries equal numbers of opposite charges. Opposite charges attract which may make the protein molecules clump together and precipitate. At other pHs, the protein only carries like charges. These repel molecules from each other and thus may increase the solubility.
  • At extremes of pH, the protein molecules may carry huge numbers of like charges as reactions 1 and 2 go almost to completion. These charges may exert a large repulsive force which breaks apart the hydrogen and ionic bonds holding the 3D structure together. The 3D structure therefore breaks apart and the protein is denatured since its structure and functional ability is lost.
56
Q

What is denaturation?

A

Denaturation is the loss of function of a protein caused by a loss of structure. Another agent of denaturation may be heat. This can disrupt the hydrogen and ionic bonds, thus causing the 3D structure to unravel. Most proteins denature around 45 degrees. Sulphur bonds are more stable to heat and thus proteins with many such bonds can withstand higher temperatures, e.g. enzymes in bacteria which live in hot springs and ribonuclease in saliva.

57
Q

What are examples of structural proteins?

A

Many structural proteins belong to the class of scleroproteins. Examples are;

  • collagen: found as strong non-elastic, white fibres in tendons, cartilage and bone.
  • elastin: found as yellow elastic fibres in ligaments and joint capsules.
  • keratin: found as a horny impermeable protein in skin, hair, feathers, nails and hooves.

Other structural proteins are the lipoproteins of cell membranes, viral coat proteins, fibroin found as spider silk and cocoon silk, selerotin found in insect exoskeletons, and mucoproteins found in lubricating joint (synovial) fluid.

58
Q

What are examples of enzymes?

A

Hydrolases such as:
- amylases, proteases and lipases used in digestion

Oxido-reductases such as:
- the dehydrogenases used in the metabolic cycles

Ligases which:
- enable molecules to be bonded together using the energy from ATP

59
Q

What are examples of hormones?

A

Some hormones are protein in nature, such as somatotropin - pituitary growth hormone and insulin which regulates blood glucose concentrations.

60
Q

What are examples of buffers?

A

Many amino acids and proteins have buffering ability and thus reduce pH change within the organism. A classic example is haemoglobin which can react with the hydrogen ions forming reduced haemoglobin. This buffers the blood between pH 7.2 and 7.6.

61
Q

What forms a waterproof hard layer on skin surface?

A

keratin

62
Q

What enables joint capsules to stretch?

A

elastin

63
Q

What forms strong fibres in muscle tendons?

A

collagen

64
Q

What can join molecules using energy from ATP?

A

ligase (enzyme)

65
Q

What bonds are present in the primary structure?

A
  • peptide bonds
66
Q

What bonds are present in the secondary structure?

A
  • peptide bonds

- hydrogen bonds

67
Q

What bonds are present in the tertiary structure?

A
  • peptide bonds
  • hydrogen bonds
  • ionic bonds
  • disulphide bridges
68
Q

What bonds are present in the quarternary structure?

A
  • peptide bonds
  • hydrogen bonds
  • ionic bonds
  • disulphide bridges

Biology (67 decks)

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