Proteins Flashcards
1
Q
What is the role of DNA/genes in terms of proteins?
A
- DNA codes for proteins
- A gene is a stretch of DNA that codes for proteins
- The sole purpose of the genetic code of the cell’s DNA is to contain the code for making proteins
- DNA replication and control of gene expression is carried out by proteins (DNA is not a protein)
2
Q
What elements are found in protein?
A
Carbon, hydrogen, oxygen, nitrogen and sulfur
3
Q
How many different amino acids are there and what makes them differ between eachother?
A
- 20 different amino acids
- Different R-groups result in different amino acids
4
Q
How many amino acids are non-essential, essential and conditionally essential? And why?
A
- 5 are non-essential => this is because our bodies are able to make them from other amino acids
- 9 are essential => this is because they can only be obtained from what we eat
- 6 are conditionally essential => this is because they are only needed by infants and growing children
5
Q
What are the different roles of proteins?
A
- Enzymes
- Membrane protein
- Antibodies
- Filamentous
- Buffers
- Fibrous
- Transport
- Regulatory
- Hormones + receptors
- Storage for growth
6
Q
What is the role of enzymes?
A
Catalyse reactions which enable metabolism and therefore life to take place
7
Q
What is the role of membrane proteins?
A
Transmembrane proteins such as carrier proteins or ion channels allow transport of substances into and out of the cells and organelles
8
Q
What is the role of antibodies?
A
To recognise foreign antigens and allow the immune system to attack and destroy these
9
Q
What is the role of filamentous proteins?
A
- Found in muscle and tissue as well as the cytoskeleton (microfilament, intermediate filaments, microtubules)
- Allow movement within tissues and cells
10
Q
What is the role of buffers?
A
Soluble proteins in the blood which help stabalise the pH of blood
11
Q
What is the role of fibrous proteins?
A
- Protein found in structural tissue such as hair, skin, nails, tendons, bone etc
- Allow for strength and where required, felixibility
- Includes collagen, elastin and keratin
12
Q
What is the role of transport proteins?
A
To carry molecules e.g. haemoglobin carries oxygen around the body
13
Q
What is the role of regulatory proteins?
A
Allow for control of gene expression
14
Q
What is the role of hormones and receptors?
A
Cell signalliing involves both hormones (some of which are proteins e.g. insulin) and cell surface receptor proteins (these are often glycoproteins)
15
Q
What is the role of proteins in storage for growth?
A
Proteins found in seeds, milk and eggs
16
Q
Draw an amino acid
A
Answer on revision card
17
Q
Draw an amino acid free in solution. What is it called?
A
Drawing on revision card
- The become a zwitterion
18
Q
What is a polypeptide?
A
A sequence of amino acids joined by peptide bonds
19
Q
Draw two amino acids forming a dipeptide
A
Answer on revision card
20
Q
What is the method for chromatography?
A
- Draw a horizontal pencil line on the chromatography paper about 2 cm from the bottom of the paper
- Put a small and concentrated spot of each sample on the pencil line and make sure they are evenly spaced out
- Allow each spot to dry before labelling them with pencil
- Tape the top of the paper to a pencil so you can suspend it from the top of a beaker
- Place the pencil on the rim of the beaker and observe the distance from the bottom of the paper to the bottom of the beaker before you put any water in the beaker
- Put enough water in the beaker (about 1cm depth of water) to be sure not to let the samples immerse in the water
- Lower the paper horizontally into the water and allow the water to absrob up the paper
- Take the paper out before the waterfront reaches the top so you can measure where the solvent front is
- Trace the solvent with a pencil line
21
Q
How do you calculate the Rf?
A
Rf = distance travelled by component/distance travelled by solvent
22
Q
What is the primary (1°) structure of protein?
A
- The sequence of amino acids in the polypeptide chain joined together by peptide bonds
- It is determined by the genetic code on the DNA/gene or the base sequence of the DNA
- The particuar amino acids in the sequence will influence how the polypeptide folds to give the the protein’s final shape
- This in turn determines its function
23
Q
What bonds are involved in the primary structure of a protein?
A
Only peptide bonds
24
Q
What is the secondary (2°) structure of protein?
A
- Intial local folding of polypeptide chain
- 2 regular shapes form between parts of polypeptide chain which are close to each other
- Hydrogen bonds may form within the amino acid chain, pulling it into a coil shape called an alpha helix
- Hydrogen bonds may also form between polypeptide chains that lie parallel to one another forming a pleated sheet called beta pleated sheet
- These shapes form due to hydrogen bonds between the carboxyl group (slightly electronegative) and the amine group (slightly electropositive) of the peptide bonds of amino acids
25
What bonds are involved in the secondary structure of a protein?
Bonds in the secondary structure include peptide bonds and hydrogen bonds
26
What is the tertiary (3°) structure of protein?
- The further folding of a polypeptide chain to give the final 3 dimensional structure of the protein
- The coiling/folding of sections of proteins into their secondary structures brings R-groups of different amino acids closer together so they are close enough to interact and further folding of these sections occur
27
What interactions between the R-groups occur in a tertiary (3°) structure of protein?
- Ionic bonds => these are stronger than hydrogen bonds and form between oppositely charged R-groups
- Hydrophobic interactions => weak interactions between non polar R-groups
- Hydrogen bonds => this bond occurs between polar/hydrophilic R -groups. These are the weakest of the bonds formed. They are easily broken by an increase in temperature or change in pH
- Disulfide bond/sulfur bridges => these are covalent disulphide bonds which occus between R-groups that contain sulfur atoms. These are the strongest of the bonds. They cannot be broken by increase in temperature or change in pH.
28
Where do hydrophobic interactions occur?
- In the interior of proteins (hydrophobic environment) where it is not in contact with water
- Parts of membrane proteins in contact with the phospholipid bilayer
29
What is significant about the disulphide bond?
- This bond is very significant in protein structure as it gives increased stability to proteins
- Found in proteins in thermophilic bacteria
30
What is the quaternary (4°) structure of protein?
- The association of 2 or more polypeptide chains to form subunits
- The interactions between the subunits are the same in the tertiary structure except that they are between different protein molecules
- Many proteins require a quaternary (4°) structure to be functional e.g. haemoglobin and all fibrous proteins
31
What are the types of proteins?
Globular and fribrous proteins
32
What is a globular protein?
A compact, water soluble and roughly spherical looking protein
33
How is a globular protein formed?
- They form when proteins fold into their tertiary structure in such a way that the hydrophobic R-groups on the amino acids are kept away from the aqueous environment
- The hydrophilic R-groups are on the outside of the protein
- This means that the protein is soluble in water
34
Why is it important for globular proteins to be soluble?
- They are essential for regulating many of the processes necessary for life
- These include processes such as chemical reactions, immunity, muscle contraction etc
35
What are some examples of globular proteins?
- Haemoglobin
- Insulin
- Myglobin
- Amylase
- Catalase
36
What is a conjugated protein? What are some examples of a conjugated protein?
- Conjugated proteis are globular proteins that contain a non-protein component called a prosethetic group
- Proteins without prosthetic groups are called simple proteins
37
What are the different types of prosthetic groups?
- Lipids or carbohydrates can combine with proteins forming lipoproteins or glycoproteins
- Metal ions and molecules derived from vitamins also form prosthetic groups
- Haem groups are examples of prosthetic groups
38
What is haemoglobin? What is formed from and how does it work?
- The red,oxyegn carrying pigment found in red blood cells
- It has a quaternary structure formed of 2 alpha subunits and 2 beta subunits
- Each subunit contains a prosthetic non protein part called the haem group
- The iron ion present in the haem groups are each able to combine reversibly with an oxygen molecule
- The binding of oxygen changes the shape of the haemoglobin
- This is what enables haemoglobin to transport oxygen around the body
39
What is denaturation? And why does it occur?
Denaturation is the loss of the exact 3D structure of a protein, however the primary structure remains intact
Occurs because of:
- Rise in temperature above optimum breaks hydrogen bonds
- Change in pH, breaks ionic and hydrogen bonds
40
What is a fibrous protein? And how are they formed?
- Long chain structural proteins which make up hair, skin, bone, tendons, ligaments etc
- It is integral to lots of tissues such as alveoli and blood vessels
- Fibrous proteins are formed from long, insoluble molecules. This is due to the presence of a high proportion of amino acids with hydrophobic R-groups in their primary structures.
- They contain a
limited range of amino acids, usually with small R-groups.
- The amino acid sequence in the primary structure is usually quite repetitive.
- This leads to very organised structures reflected in the roles fibrous proteins often have. Keratin, elastin, and collagen are examples of
fibrous proteins.
- Fibrous proteins tend to make strong, long, stable molecules which are not
folded into complex three-dimensional shapes like globular proteins and do not get denatured as readily
41
Where is keratin found?
Hair, nails and skin
42
What amino acids are present in keratin?
It has a large proportion of the sulfur-containing amino acids such as cysteine
43
Explain the property of keratin in terms of its structure.
- The many sulfur-containing amino acids results in many strong disulfide bonds (disulfide bridges) forming strong, inflexible and insoluble materials
- The degree of disulfide bonds determines the flexibility e.g. hair contains fewer bonds making it more flexible than nails which contain more bonds
- The unpleasent smell produced when hair or skin is burnt is due to the prescence of relatively large quantities of sulfur in these proteins
44
Where is elastin found?
- Elastic fibres
- Protein fibres
- Alveoli
- Walls of blood vessels (veins & arteries)
- Ligaments
- Ear cartilage
45
What is the property of keratin?
- Strong
- Inflexible
- Resistent to scratching and tearing
46
Explain the property of elastin in terms of its structure.
- Elastic fibres give these structures the flexibility to expand when needed, but also return to their normal size
- Elastin is a quaternary protein made by linking many soluble tropoelastin protein molecules to make a very large, insoluble and stable, cross-linked structure
- Elastin is formed when multiple tropoelastin molecules aggregate via interactions between the hydrophobic areas
47
What is elastin mainly formed of?
Tropoelastin molecules
48
What are the properties of elastin?
- Stretchy
- Recoils
- Flexible
49
Where is collagen found?
- Skin muscles
- Bones
- Tendons
- Ligaments
- Nervous system
50
Explain the property of collagen in terms of its structure.
- Collagen molecules have three polypeptide chains wound around each other in a triple helix structure to form a tough, strong rope-like structure
- Many hydrogen bonds form between the polypeptide chains forming long quaternary proteins with staggered ends
- Collagen also contains high proportions of the amino acids proline and hydroxyproline. The R-groups in these amino acids repel each other and this adds to the stability of collagen
51
What are the main amino acids present in collagen?
- Glycine
- Proline
- Hydroxyproline
52
What is the property of collagen?
- Remains soft and felxible under low stress
- Resists stretching
- Rigid
53
What is the sequence of globular and fibrous proteins?
Globular - irregular amino acid sequence
Fibrous - repetitive amino acid sequence
54
What is TLC?
- Thin layer chromatography is a technique used to seperate the individual components of a mixture
- The technique can be used to separate and identify a mixture of amino acids in solution
55
How do you test for proteins?
- Firstly, a sample of the solution is placed in a test tube and then an equal volume of NaOH is added to make the solution alkaline
- Use a pippette and holding the tube at a 45 angle carefully allow 1cm3 of biuret reagant [dilute copper (II) sulfate solution] to slide down the side of the tube
- Shake carefully and gently mix the test tube
56
What can be used as a stationary phase for TLC?
Silica gel
57
What enzyme catalyses the formation of peptide bonds?
Peptidyl transferase
