Biological Molecules : Proteins Flashcards
What is haemoglobin?
A protein. This means that haemoglobin is made up of amino acids like all proteins
What are amino acids and what is the polymer made from amino acids?
Monomers.
The polymer made from amino acids is a polypeptide chain and the folded polypeptide chain or chains makes the protein
What is the basic structure of every amino acid?
An amine group (left side) NH2
R group or side chain (this is variable function group ) MIDDLE
Carboxylic acid group COOH (right Hand side)
What protein are red blood cells packed with?
Haemoglobin
It’s important because it carries oxygen around the body where it is needed
What are some R groups like?
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
WHAT is the function group (R group) like?
It is variable
Whats a peptide bond?
The bond formed when amino acids are brought close together and bonded together
Condensation reaction
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)
Hydrolysis reaction
Peptide bond (covalent) broken
Water used up
What do two amino acids joined together result in?
A dipeptide molecule
Whats a polypeptide ?
On ribosomes, a long chain of amino acids is formed all linked together by peptide bonds
What are the four levels of protein organisation?
- primary
- secondary
- tertiary
- quaternary
Many proteins are just a single polypeptide chain. However a haemoglobin molecule is made of…
Four polypeptide chains all wound around each other in a very precise pattern
What are the two of the polypeptide chains in haemoglobin molecules (and the two others)?
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
Why do a chains differ from b chains?
Although they are the same length, they have a different primary structure
(Same size and length, different sequences)
Explain primary structure
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)
Explain the secondary structure
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
What bonds occur in secondary structure?
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
Explain tertiary structure
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
What are the different types of bonds that the shape in the tertiary structure is stabilised by?
- 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
Explain quaternary structure
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)
What are prosthetic groups in the quaternary structure?
Some proteins have non protein prosthetic groups attached. In the case of haemoglobin there are 4 haem groups associated with the quaternary structure
Whats a conjugated protein?
Haemoglobin is an example and its because it has a prosthetic group
How is a primary structure of a protein determined ?
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
How might a change in the primary structure lead to a change in the tertiary structure?
If changes are made in the primary structure which lead t different intramolecular bonds than the tertiary structure is changed
Folded=
Beta pleated sheets
Coiled =
Alpha helix
In which organelle does the secondary structure process occur?
Inside the cistern are of the rough Endoplasmic reticulum
Where in the cell would the addition of a prosthetic group occur?
Inside the Golgi apparatus
Whats the method for the biuret test for proteins, polypeptides and peptides
- Label the test tubes with the food materials that your plan to test for protein.
- 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)
- 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..
- Observe the test solution for a purple/violet or blue colour. Record your observations and deductions from the biuret test in a suitable table.
Give possible results of the biuret test
- 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
Give two differences between the secondary and tertiary structures of a protein
- tertiary structure can be stabilised by hydrophobic and hydrophilic interactions
- tertiary structure gives the polypeptide chain its 3 dimensional shape
Whats a globular protein?
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.
Fibrous proteins
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
Collagen
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.
Structure of collagen
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
Collagen doesnt show a secondary, tertiary and quaternary structure in the same way as globular proteins like haemoglobin. Therefore..
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
What is elastin
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
What is keratin
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)
What is denaturation of proteins caused by
It is caused by :
- temperature
- change in pH
What is the temperature in the denaturation of proteins
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
What is changing pH in the denaturation of proteins?
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.
What is paper chromatography used for
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)
What happens as the solvent moves up the paper
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
What are the three factors that affect the rate at which a particular molecule travels up the paper
- 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 - 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 - 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.
why is achieving maximum resolution important?
Because the biochemist knows the properties of a different molecules, and this can inform the choices of solvent and medium
What name is given to the line at the base of the paper where the mixture is loaded?
The origin
Why should the line be ruled in pencil?
Because the inconsolable in money, solvents, and the ink pigments would contaminate the results. Graphite is insoluble and will not contaminate the results.
What is the solvent front?
The farthest point that the solvent reaches
What is the RF value?
It is used to describe the ratio proportion of a distance travelled compared to the solvent front
Why is it often necessary to use a locating Regent?
Because the spots are colours and cannot be seen on the paper
The locating Regent makes them visible
And why do we measure to the centre of the spots?
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
How might the other two amino acids be identified when the mixture of unknown amino acids are seen to contain for different amino acids?
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
What is the advantage of two way chromatography of a one-way chromatography?
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
why must a different solvent based for the second run
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.
