Biological Molecules : Proteins

Question 1

What is haemoglobin?

Answer 1

A protein. This means that haemoglobin is made up of amino acids like all proteins

Question 2

What are amino acids and what is the polymer made from amino acids?

Answer 2

Monomers.

The polymer made from amino acids is a polypeptide chain and the folded polypeptide chain or chains makes the protein

Question 3

What is the basic structure of every amino acid?

Answer 3

An amine group (left side) NH2

R group or side chain (this is variable function group ) MIDDLE

Carboxylic acid group COOH (right Hand side)

Question 4

What protein are red blood cells packed with?

Answer 4

Haemoglobin

It’s important because it carries oxygen around the body where it is needed

Question 5

What are some R groups like?

Answer 5

Some R groups carry a charge (some are positively charged and some are negatively charged

Some ARE POLAR (so have a slightly positive charge and others a slight negative charge

SOMe have NO CHARGE and are NON-POLAR

Question 6

WHAT is the function group (R group) like?

Answer 6

It is variable

Question 7

Whats a peptide bond?

Answer 7

The bond formed when amino acids are brought close together and bonded together

Question 8

Condensation reaction

Answer 8

As a pep[tide bond is formed, one hydrogen atom and one oxygen atom from one amino acid and one hydrogen atom from the other join together to form a water molecule

Peptide bond (covalent) is formed
Water eliminated (released)

Question 9

Hydrolysis reaction

Answer 9

Peptide bond (covalent) broken
Water used up

Question 10

What do two amino acids joined together result in?

Answer 10

A dipeptide molecule

Question 11

Whats a polypeptide ?

Answer 11

On ribosomes, a long chain of amino acids is formed all linked together by peptide bonds

Question 12

What are the four levels of protein organisation?

Answer 12

• primary
• secondary
• tertiary
• quaternary

Question 13

Many proteins are just a single polypeptide chain. However a haemoglobin molecule is made of…

Answer 13

Four polypeptide chains all wound around each other in a very precise pattern

Question 14

What are the two of the polypeptide chains in haemoglobin molecules (and the two others)?

Answer 14

Two of the polypeptide chains are identical and called alpha chains (a chains)

Two are identical and are called beta chains

Each of the chains is made up of 141 amino acids

Question 15

Why do a chains differ from b chains?

Answer 15

Although they are the same length, they have a different primary structure

(Same size and length, different sequences)

Question 16

Explain primary structure

Answer 16

The primary structure of a protein is the exact sequence of amino acids in the polypeptide chain

(Different amino acids can be represented by one letter or three letter abbreviations)

Question 17

Explain the secondary structure

Answer 17

The secondary structure of a protein describes the coiling and folding of the polypeptide chain into :

• an alpha helix(singular) or helices (plural)
• beta pleated sheets

Question 18

What bonds occur in secondary structure?

Answer 18

Weak hydrogen bonds between the amine and carboxylic groups from between different parts of the chain to stabilise it

(Hydrogen bonding in the secondary structure does not involve the R groups

Question 19

Explain tertiary structure

Answer 19

Further folding of the polypeptide chain which gives a specific 3 dimensional shape. (Makes more of a spherical shape)

Further folding of the polypeptide chan; the secondary structure alpha helix and beta pleated sheets are incorporated into the tertiary structure

Question 20

What are the different types of bonds that the shape in the tertiary structure is stabilised by?

Answer 20

• weak hydrogen bonds: wherever slightly positive charged groups are found close to slightly negatively charged groups, hydrogen bonds form. This includes R groups
• DISULPHIDE BONDS: strong bonds between two cysteine molecules (amino acids with sulphur R groups)
• IONIC BONDS: (opposite charges) R groups sometimes carry a charge, either +ve or -ve. Where oppositely charged amino acids are found close to each other, an ionic bond forms
• HYDROPHOBIC AND HYDROPHILIC INTERACTIONS: (wants to be in the middle inside) In a water based environment, hydrophobic amino acids (with nonpolar R groups) will be most stable if they are held together with water excluded (hydrophobic amino acids and hydrophilic amino acids)
  In general, when polypeptide chain is folded, the hydrophobic amino acids are on the inside therefore keeping them away from the water based solvent

Question 21

Explain quaternary structure

Answer 21

Some proteins have more than one polypeptide chain; these have quaternary structure. This is the way the polypeptide chains fit together (these chains are held together by hydrogen or ionic bonds involving the R groups)

Question 22

What are prosthetic groups in the quaternary structure?

Answer 22

Some proteins have non protein prosthetic groups attached. In the case of haemoglobin there are 4 haem groups associated with the quaternary structure

Question 23

Whats a conjugated protein?

Answer 23

Haemoglobin is an example and its because it has a prosthetic group

Question 24

How is a primary structure of a protein determined ?

Answer 24

The DNA contains genes - sequences of nucleotide bases (A T G C) which when read in triplet code, determine which amino acids should be added during translation at the ribosomes

The gene is transmitted as mRNA which leaves the nucleus and travels to a ribosome

Question 25

How might a change in the primary structure lead to a change in the tertiary structure?

Answer 25

If changes are made in the primary structure which lead t different intramolecular bonds than the tertiary structure is changed

Question 26

Folded=

Answer 26

Beta pleated sheets

Question 27

Coiled =

Answer 27

Alpha helix

Question 28

In which organelle does the secondary structure process occur?

Answer 28

Inside the cistern are of the rough Endoplasmic reticulum

Question 29

Where in the cell would the addition of a prosthetic group occur?

Answer 29

Inside the Golgi apparatus

Question 30

Whats the method for the biuret test for proteins, polypeptides and peptides

Answer 30

1. Label the test tubes with the food materials that your plan to test for protein.
2. Add 2cm3 of the test solution to a test tube. (or use dispatcher two add 1 cm depth of finely chopped up or ground material., then add 2cm3 of distilled water, put the clean bong in and shake it carefully, at least 10 times)
3. Add 10 drops of biuret reagent to the test solution. You may get clearer results if you tilt test tube at 45° and roll the reagent down the glass. Do not shake the test tube..
4. Observe the test solution for a purple/violet or blue colour. Record your observations and deductions from the biuret test in a suitable table.

Question 31

Give possible results of the biuret test

Answer 31

• Violet purple colour is a positive result. It confirmed the presence of proteins.
  The purple/violet colour is due to the presence of two or more peptide bonds in a compound . Proteins polypeptides, and most part peptides should give positive results.
• A blue colour is a negative result
  It confirms the absence of proteins or a concentration that is below the level of sensitivity of a biuret test

Question 32

Give two differences between the secondary and tertiary structures of a protein

Answer 32

• tertiary structure can be stabilised by hydrophobic and hydrophilic interactions
• tertiary structure gives the polypeptide chain its 3 dimensional shape

Question 33

Whats a globular protein?

Answer 33

Haemoglobin is an example of a globular protein. It’s three-dimensional structure is essentially a ball shape. Enzymes are also globular proteins as are hormones such as insulin. They tend to have biochemical functions

globular proteins are usually soluble in water . This is because they are folded, say that amino acids with hydrophilic R groups are on the outside. Is solubility allows them to be stable in the cytoplasm and blood plasma.

Question 34

Fibrous proteins

Answer 34

In fibrous proteins, the polypeptide join together to form, long, fibres or sheets
These proteins are strong and insoluble in water
They tend to have structural functions, for example keratin, which makes up hair skin and nails over elastin fibres in the blood vessel walls and in alveoli

Question 35

Collagen

Answer 35

Collagen is an example of a fibrous protein. It’s found in skin, bone, cartilage, teeth, tendons, and muscles and ligaments and walls of blood cells. It gives great toughness to the structures.

Question 36

Structure of collagen

Answer 36

The quaternary structure of collagen is three polypeptide chains. The three identical polypeptide chains in a molecule of collagen, wind around each other to form a triple helix.

In the primary structure, every third amino acid is glycine . The sequences of a polypeptide is a staggered, so that guy seen as always found every position along the triple helix.. this allows the free polypeptides to pack closely together to form many hydrogen bonds along the whole length.

The helices are arranged, so they overlap without any lines of weakness where the collagen fibres my break, if pulled very hard. The mini cross-links and hydrogen bonds within the triple helices give collagen is great strength

Question 37

Collagen doesnt show a secondary, tertiary and quaternary structure in the same way as globular proteins like haemoglobin. Therefore..

Answer 37

The triple helix is a left-handed helix (an a helix has a right hand turn) and there is no further folding to get a complex 3-D tertiary shape

Question 38

What is elastin

Answer 38

A fibrous protein found in elastic fibres ( along with small protein fibres). Elastic fibres are present in the walls of blood vessels and an alveoli of the lungs- they give me structures the flexibility to expand when needed, but also return to their normal size

Question 39

What is keratin

Answer 39

Group of fibrous protein is present in hair, skin and nails. It has a large proportion of the sulphur containing amino acid., cysteine. This results in many disulphide bridges (forming strong, inflexible, and insoluble materials)

Question 40

What is denaturation of proteins caused by

Answer 40

It is caused by :
- temperature
- change in pH

Question 41

What is the temperature in the denaturation of proteins

Answer 41

The tertiary structure of a globular protein is held together, mostly by fairly weak bonds, such as hydrogen bonds. So when the temperature increases the molecules vibrate more.

If a protein vibrates too much, it’ll break some of these weak bones and the shape of a molecule change, so the protein is denatured

Different proteins denature at different temperatures, but most protein is the nature of temperatures are in 45°C

Question 42

What is changing pH in the denaturation of proteins?

Answer 42

Hydrogen bonds depend on very weak attraction between a slightly positive charged hydrogen and a slightly negative charge oxygen in different parts of the protein molecule. Ionic bonds also depend on opposite charges for bonding. These bonds can be broken by changes in the pH. (The concentration of hydrogen ions)

The concentration of hydrogen ion surrounding the party increases or decrease is this affects charges holding together the folds of a globular protein. When these bonds break, the proteins becomes denatured.

Question 43

What is paper chromatography used for

Answer 43

A technique used for the separation & identification of relatively small molecules or ion by a moving solvent on sheets or strips of absorbant paper (chromatography paper)

Question 44

What happens as the solvent moves up the paper

Answer 44

If fervent molecules move at different with the smallest molecules moving the fastest

This technique is used to separate small molecules such as amino acids, small peptides and sugars

Question 45

What are the three factors that affect the rate at which a particular molecule travels up the paper

Answer 45

1. The size of the molecule
   The smaller, the molecule, the faster it can travel
   Larger molecules are more likely to get trapped in the cellulose fibres of the paper
   Also large amount of some more mass in Bedford to overcome more gravitational force to ascend the paper
2. The solubility of a molecule in the solvent being used.
   The greater the solubility ( the greater, the degree, that the molecule can dissolved in a solvent) the faster, it can travel
3. The polarity of a molecule.
   When using paper, nonpolar molecules travel up the paper more quickly . This is because cellulose is polar in nature, so polar molecules are attracted to and interact with the silos people, and therefore when using thin-layer chromatography gels which are not polar the polarity of the molecule has no effect.

Question 46

why is achieving maximum resolution important?

Answer 46

Because the biochemist knows the properties of a different molecules, and this can inform the choices of solvent and medium

Question 47

What name is given to the line at the base of the paper where the mixture is loaded?

Answer 47

The origin

Question 48

Why should the line be ruled in pencil?

Answer 48

Because the inconsolable in money, solvents, and the ink pigments would contaminate the results. Graphite is insoluble and will not contaminate the results.

Question 49

What is the solvent front?

Answer 49

The farthest point that the solvent reaches

Question 50

What is the RF value?

Answer 50

It is used to describe the ratio proportion of a distance travelled compared to the solvent front

Question 51

Why is it often necessary to use a locating Regent?

Answer 51

Because the spots are colours and cannot be seen on the paper

The locating Regent makes them visible

Question 52

And why do we measure to the centre of the spots?

Answer 52

Because within any sport, there will be molecules which travelled faster than average and molecules, which travel slower than average

By taking the centre of the sport, you can measure the mean value distance travelled by molecules

Question 53

How might the other two amino acids be identified when the mixture of unknown amino acids are seen to contain for different amino acids?

Answer 53

If not amino acids known standards were run alongside the mixture of unknown, then it would be possible to find matches for the remaining spots

Question 54

What is the advantage of two way chromatography of a one-way chromatography?

Answer 54

Better resolution of two types of molecule can be achieved. If two molecules are similar in size, polarity insolubility in the first solvent than the RF value will be very similar and spots will overlap.. but by changing the solvent it should be possible to separate the molecules, and the rate of travel in the second solvent will defer, and the RF values will be less similar than before

Two-way chromatography provides better separation of substances that behave in a similar fashion in the first solvent and a second run in a different solve it resolves to very close spots more clearly

Question 55

why must a different solvent based for the second run

Answer 55

Because if the same solvent is used, as in the first run done, the RF, values of the two molecules would remain very similar. They were not properly resolved in the first one, so they won’t be properly resolved in the second one is the solvent remains the same.

The molecules are obviously similar in size and polarity, and therefore interaction with the medium . So the third factor which affects the rate of chromatography, the solubility in a particular solvent has to be used to achieve resolution.