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1.1 - Molecular Biology > Proteins > Flashcards

Proteins Flashcards

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1
Q

What are the 4 elements which proteins ALWAYS contain

A
  1. Carbon
  2. Hydrogen
  3. Oxygen
  4. Nitrogen
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2
Q

What are the 2 other elements which some proteins MIGHT ALSO contain

A
  1. Sulphur
  2. Phosphorus
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3
Q

What is the sub unit of a protein

A

an amino acid

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4
Q

What is a chain of amino acids called

A

polypeptide chain of amino amino acids

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5
Q

What is the structure of an amino acid?

A

All Amino Acids have the same basic structure, attached to a carbon there is :

  1. An amino group - NH2 at one end of the terminal - The N Terminal
  2. A carboxyl group - COOH at the other end of the terminal - The C Terminal
  3. A hyrdrogen atom
  4. The R group (which is different in each amino acid)
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6
Q

How many amino acids are used to make up proteins?

A

20 different amino acids are used to make up proteins

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7
Q

What is the shape of a protein determined by?

A

The specific sequence of Amino Acids in the polypeptide chain (Primary Structure)

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8
Q

How many different types of proteins are there?

A

There are thousands of different types of protein and their shape is determined by the specific sequence of Amino acids

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9
Q

What are the 7 biological activities proteins are involved in

A
  1. Enzymes are biological catalysts which speed up the rate of reaction
  2. Carrier proteins transport materials across cell membranes
    • Cell membrane (phospholipid bilayer with carrier proteins)
  3. Antibodies defend the body against disease causing microbes
  4. Structural proteins support cells and tissues
  5. Hormones transmit information
  6. Contractile proteins such as ACTIN and MYOSIN bring about contraction in muscle
  7. Transport proteins such as haemoglobin carry oxygen.
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10
Q

Atom structure, Polymer, # Amino Acids, # Proteins

What is a protein longer answer

A

A protein is composed of the elements:

  • Carbon
  • Hydrogen
  • Oxygen
  • Nitrogen
  • &…may also contain Sulpher/Phosphorus

A protein is:

  • A polymer
  • Made up of monomers, called Amino Acids
  • Which are organised in linear chains, called polypeptides

There are approximately 20 amino acids used to make up proteins.

There are thousands of different types of proteins and their shape is determined by the specific sequence of amino acids in the chain

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11
Q

What is the name given to to a molecule such as an Amino Acid which can act as an acid or a base

A

amphoteric

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12
Q

What is the structure of an Amino Acid

Draw it…

A
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13
Q

How are proteins able to resist pH changes

A

When an Amino Acid forms a protein there is still an Amino Group at one end and a carboxyl group at the other end.

The protein can therefore accept or give up hydrogen ions just like an Amino Acid

This gives the protein the ability to resist changes in pH and act as a buffer

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14
Q

What is the name given to an Amino Acid which has both a positive and negative charge at a pH7

A

zwitterion

ZWITT ER ION

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15
Q

Describe how a regular amino acid transforms into a zwitterion

A
  • At Ph7, the Ph of the cell….
  • The Amino Acid gains an H and becomes +vly charged.
  • The carboxyl group is acidic and at pH7 , it loses an H becoming negativly charged
  • So….At pH7 there is a positevly charged side and a negativly charged side
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16
Q

Draw an amino acid as a zwitterion

A
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17
Q

What is a peptide bond?

A

The chemical bond formed by a condensation reaction between the amino acid group of one amino acid and the carboxyl group of another amino acid

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18
Q

How does a peptide bond form?

A
  • A protein is a linear sequence of amino acids
  • A condensation reaction occurs between the amino group of of one amino acid and the carboxyl group of another amino acid
  • Resulting in the loss of a molecule of water
  • The chemical bond that forms as a result of this process is called a PEPTIDE BOND
  • When 2 amino acids are joined together by a peptide bond they are called a DIPEPTIDE
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19
Q

What is the primary structure of an Amino Acid?

A

The primary structure of an amino acid is…. the sequence of amino acids in the polypeptide chain

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20
Q

What does the primary structure determine?

A

The primary structure determines the shape and therefore function of the protein

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21
Q

What determines the composition of the primary structure itself?

A

The composition of the primary structure is determined by the base sequence of amino acids in one strand of the DNA molecule

22
Q

What is the role of the primary structure? - Longer Answer

A

The primary structure of an amino acid is…. the sequence of amino acids in the polypeptide chain

It is determined by the base sequence of one strand of a DNA molecule

The primary structure determines the shape and therefore function of the protein

23
Q

What is the secondary structure?

A

The shape that polypeptide chains form as a result of hydrogen bonding, between the =O on -CO groups and the -H on NH groups, in the peptide bonds along the chain

e.g. A spiral alpha helix or a less common Beta pleated sheet

24
Q

What are two types of secondary structure

A
  1. Alpha helix
    • e.g. Keratin
  2. Beta pleated sheet (Less common)
    • e.g. Fibroin, in silk, has a high proption of Beta pleated sheet
25
Q

What is formed… when the alpha helix of the secondary protein structure is folded and twisted into a more complex compact 3d Structure

A

A tertiary structure

26
Q

What is tertiary structure

A

The tertiary structure of a protein

is the complex three dimensional shape the molecule takes

when the polypeptide alpha helix twists and folds around itself

27
Q

How is the tertiary structure formed?

A

A tertiary structure is formed when…

The alpha helix, a secondary protein structure, is folded and twisted into a more complex, compact, 3d structure

28
Q

4 bonds

How is the shape of a tertiary structure maintained

A

The shape of the tertiary structure is maintained by the following bonds.

  1. Hydrogen bonds
  2. ionic bonds
  3. Covalent bonds
  4. disulphide bonds
  5. hydrophobic interactions
29
Q

How does a hydrogen bond support the structure of a protein

A

Hydrogen bonds are found between hydrogen atoms and some oxygen and nitrogen atoms in the polypeptide chain

The hydrogen atoms have a small negative charge and the oxygen and nitrogen atoms have a small positive charge

The opposite charges attract

Although the bonds are weak, because they are large in number the molecules three dimensional shape is maintained

30
Q

How does an Ionic bond support the structure of a protein

A

An ionic bond is found between any charged groups that are not joined together by a peptide bond

These iconic bonds are stronger than hydrogen bonds but they can be broken by changes in pH and temperature

31
Q

How does an disulfide bond support the structure of a protein

A

Some amino acids e.g. Cystein and methionine…. contain sulfur atoms

Disulfide bonds can occur between sulfur atoms which are close to each other

These sulfer bonds are very strong and can be found in e.g. Keratin and Collagen

32
Q

How does the a hydrophobic effect also influence protein structure

A

When globular proteins are in solution their hydrophobic groups point inwards away from the water.

33
Q

what is this

A

troppocollagen

34
Q

What is a quarternary structure?

QUARTER NARY

A

Some polypeptide chains do not function unless they are joined to other polypeptide chains.

e.g. Insulin has 2 polypeptide chains

Sometime they may also be associated with non protein groups, forming large, complex molecules

e.g. Haemoglobin

HAEM O GLOBIN

35
Q

What is denaturation

De nat u ration

A

The permanent loss in shape of a molecule?

36
Q

What 4 things can cause denaturation

A

Changes in temperature and pH

Heavy metal ions

Organic Solvents

37
Q

How might denaturation be caused by a rise in temperature

A

The molecule starts to vibrate as the temperature rises

The bonds are broken by this vibration

Changing the shape and therefore function of the molecule which can be permanent

38
Q

What are the specific changes which Denaturation cause

A

Denaturation influences the tertiary and quartenary structure of the molecule

However

It does not influence the primary or secondary structure.

39
Q

What are the names given to the two broad groups of proteins based upon their 3 dimensional shape…

A
  1. Globular
  2. Fibrous
40
Q

What is the structure of a globular protein

A

A global protein is a….

  • Compact molecule
  • Containing highly twisted polypeptide chains
  • which roll up into a spherical molecule

The molecule is water soluable because as the protein rolls up….

  • The hydrophobic R group of amino acids point inwards to the centre of the molecule
  • Whilst the hydrophilic R group of amino acids are on the outside of the molecule
41
Q

What is the function of globular proteins

A

Globular proteins are less stable than fibrous molecules and are soluable in water

They tend to be involved in metabolic reactions and include e.g. Enzymes, Antibodies and Hormones.

42
Q

How does a protein form?

A

When one polypeptide chain bonds with other polypeptide chains, it forms a protein containing thousands of amino acids

43
Q

What is a specific example of a globular protein

A

Haemoglobin

44
Q

What is the chemical structure of haemoglobin

A

Haemoglobin has

  • 4 polypeptide chains
  • which are joined together by Disulfide bonds
  • At the centre of each polypeptide chain is an iron containing group called haem
  • Each of these Haem groups has an iron ion Fe2+
  • As each Iron ion can bind with one molecule of oxygen (O2), there are 4 molecules of oxygen
  • This is an example of a non protein prosthetic group
  • This protein combines with the prosthetic group forming a cojugated protein.
45
Q

What is the metabolic function of haemoglobin

HAEM O GLOBIN

A

Haemoglobin picks up O2 in the lungs forming oxyhaemoglobin

Oxyhaemoglobin is broken down (dissacociates) in the tissues giving up its oxygen, and then reverts back to haemoglobin.

46
Q

What are the properties of a fibrous protein

A

A fibrous protein has

  • long, thin molecules which are
  • insoluble in water
  • and are very strong and tough.

e.g. Collagen

47
Q

What is the structure of a fibrous protein

A

Fibrous proteins have polypeptide chains laid down in parallel chains, linked together to form lon fibres or sheets

e.g. Collagen

A single collagen fibre contains three polypeptide chains, which are individually twisted in the form of a helix, and twisted around each other collectively to form a triple helix.

Hydrogen bonds hold the three polypeptide chains in place.

48
Q

What are the differences between a fibrous protein and a globular protein

A

Fibrous Protein Globular Protein

Stable structure Relatively unstable structure

Insoluable in H20 Soluable in H2O

Support structure Metabolic processes

Long polypeptide chains Spherical ball

Collagen and bone Enzymes, hormones, antibodies

49
Q

what is the test for protein

A

biuret test

50
Q

What are the 3 steps involved in a Biuret test?

A

To test for protein

  1. Add a few drops of biuret reagent (Sodium hydroxide and copper sulphate
  2. Sodium Hydroxide reacts with the copper sulphate is added to form blue copper hydroxide
  3. The copper hydroxide reacts with the peptide bonds present in the protein to form a purple biuret

The more concentrated the protein the darker purple the mixture

51
Q

In chemical terms what is a buffer

A

A buffer is an element which can act as both a base or an acid

1.1 - Molecular Biology (11 decks)

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