Topic 2: Proteins

Question 1

CFTR Protein

1. What type of protein is it?
2. Where is it found?
3. What does it do?

Answer 1

1. A CHANNEL PROTEIN
2. In CELL MEMBRANE OF MUCUS PRODUCING CELLS lining the respiratory, digestive and reproductive systems
3. Transports CHLORIDE IONS (Cl-)

NOTE: In people with CF – the CFTR protein doesn’t work or is not present – this causes the symptoms of the disease

Question 2

Proteins are ________.

1. Name the monomers (smaller units) that proteins are made from
2. Name the 4 elements that all proteins are made from + another 1 that some of proteins contain

Answer 2

polymers

1. AMINO ACIDS
2. Carbon, hydrogen, oxygen + nitrogen
3. SOME proteins contain sulphur

Question 3

Key Summary
(Proteins) How do you draw a generalised amino acid?

Answer 3

..................H
...................|
.HOOC -- C -- NH^2
...................|
..................R

NOTE: dots are there so it displays properly

Question 4

Key Summary
(Proteins) Describe the structure of an amino acid.
(5 points)

Answer 4

1. Central carbon atom with 4 groups bonded to it
2. H/hydrogen atom (on top)
3. R/residual group (at the bottom)
4. NH2/amino group (to the right)
5. COOH/carboxyl group (to the left)

Question 5

Key Summary
(Proteins) How do amino acids join to form a {dipeptide / polypeptide}
(3 steps)

Answer 5

1. A peptide bond JOINS the amino acids together
2. A CONDENSATION REACTION occurs BETWEEN THE AMINO GROUP OF ONE AMINO ACID AND THE CARBOXYL GROUP of another.
3. A molecule of WATER is lost for each bond that forms (from OH of COOH and H of NH2 group) – so water is produced

Read the question
Dipeptide = 2 amino acids join
Polypeptide = many amino acids join

Question 6

How does a polypeptide form? (1 point)

Answer 6

1. A polypeptide forms when many amino acids joined by peptide bonds, forming a long chain

Question 7

How do proteins form? (start from after the polypeptide chain has been formed) (1 point)

Answer 7

1. A protein forms when a polypeptide chain is FOLDED, held together by BONDS (other than peptide bonds) into a more 3 dimensional (3D) shape, which can perform a specific function

Question 8

Key Summary:
(Proteins) Primary Structure definition
(1 point)

Answer 8

1. Primary structure is the SPECIFIC SEQUENCE of amino acids in a polypeptide chain, joined by PEPTIDE BONDS in CONDENSATION REACTIONS.

Question 9

Secondary structure summary:

1. name the type of bond
2. groups bond forms between…
3. two main types of secondary structure?

Answer 9

1. Hydrogen bond
2. The slightly positive H atom of N-H group of a peptide bond, and the slightly negative O atom of a C=O group of another peptide bond
3. Alpha helix and beta pleated sheet

Question 10

Tertiary structure summary

1. types of bonds (3 types)
2. bonds form between

Answer 10

1. Ionic, hydrogen, disulphide

2. R groups

Question 11

Where do hydrogen bonds form? (Tertiary structure)

1 point

Answer 11

1. forms between a slightly positive atom (eg. H of O-H group) in the R group of one amino acid and the slightly negative atom (eg. O of C=O group) of an R group in another amino acid

Question 12

Where do Ionic bonds form? (Tertiary structure)

1 point

Answer 12

1. forms between a POSITIVELY CHARGED R GROUP and a NEGATIVELY CHARGED R GROUP

Question 13

Where do disulphide {bond/bridge} form? (Tertiary structure)

1 point

Answer 13

1. forms between an R GROUP CONTAINING AN S-H GROUP and another R GROUP CONTAINING AN S-H GROUP

Question 14

What interactions help the polypeptide fold into its tertiary structure? (2 points)

Answer 14

1. Amino acids with {hydrophobic/non-polar} R groups move to the centre of the protein
2. Amino acids with {hydrophilic/polar} R groups move to the outside (surface) of the protein

NOTE: Amino acids that were distant in the primary structure may now become very close to each other after the folding has taken place

Question 15

What protein structures (2 structures) are hydrogen bonds involved in?

Do they form in the same groups? (1 point)

Answer 15

BOTH secondary and tertiary structure

1. they form between different groups

Question 16

Quaternary structure definition? (1 point)

3 types of bond formed?

2 Examples of quaternary structures?

Answer 16

1. Definition: The three-dimensional arrangement of MORE THAN ONE polypeptide chain
2. hydrogen,
3. ionic,
4. disulphide

Examples:
1. Haemoglobin – has 4 polypeptide chains
2. Collagen – has 3 polypeptide chains
Note: So proteins only have quaternary structure if they have more than one polypeptide chain

Question 17

Key Summary:

Describe how a protein forms (for fibrous and then globular)

(2 steps + 1 for fibrous and 1 for globular)

Answer 17

For every protein:

1. Primary structure is the SPECIFIC of amino acids in a polypeptide chain, joined by PEPTIDE BONDS in CONDENSATION REACTION
2. PPROTEIN FOLDS INTO A SPECIFIC 3D SHAPE

Then:

3. If fibrous – may have {secondary structure/hydrogen bonds} (read question), but no tertiary structure
   Note: Collagen has primary and quaternary
4. If globular – {secondary and tertiary structure (enzymes) /ionic, disulphide, hydrogen bonds}
   May have quaternary structure e.g. insulin, haemoglobin

Question 18

Key Summary: How is the primary structure important in determining the final 3D structure and function of the protein?
(4 points)

Answer 18

1. Primary structure - sequence of amino acids in polypeptide chain, determines position of amino acid R GROUPS
2. Bonds - IONIC, DISULPHIDE and HYDROGEN, form between the R groups
3. The bonds that form determine {HOW A POLYPEPTIDE FOLDS into a specific 3D shape/tertiary structure}, forming a protein
4. SPECIFIC 3D SHAPE allows protein to have specific properties e.g. be soluble and carry out a specific function
   (read question if for a specific protein and state function e.g. enzyme - determines the shape of the active site to catalyse reaction, haemoglobin – to bind oxygen)

Question 19

Explain how a {dipeptide / polypeptide} is broken down

4 steps

Answer 19

1. HYDROLISIS reaction
2. A molecule of WATER is required for each bond broken
3. PEPTIDE BOND(S) broken
4. Amino acids are released

Question 20

Protein molecules can be divided into two basic types, ________ proteins and ________ proteins

Answer 20

globular

fibrous

Question 21

Many proteins contain only _____ _____ and no other chemical groups, but:

__________ _________ have another chemical (prosthetic) group associated with their _________ chain(s).

Give 3 examples of conjugated proteins

Answer 21

amino acids

Conjugated proteins

polypeptide

Examples;

1. Myoglobin and haemoglobin - polypeptide chains are associated with an iron-containing group.
2. Glycoproteins – the prosthetic group is made of carbohydrate
3. Lipoproteins – proteins conjugated with lipids

Question 22

Key Summary: Describe the molecular structure of a fibrous protein (5 points)

Answer 22

1. Contain long linear polypeptide chains made up of many amino acids
2. Contain repetitive sequences of amino acids
3. Have little or no tertiary structure
4. Have hydrophobic R groups on outside of the protein
5. If more than one polypeptide chain - chains lie parallel to each other with cross links (bonds) holding chains together

Question 23

The three-dimensional shapes of globular proteins are critical to their roles in binding to other substances

Key Summary: Describe the molecular structure of a globular protein
(3 points)

Answer 23

1. Contain polypeptide chains of amino acids joined by peptide bonds, folded into a compact, spherical shape
2. Have tertiary structure held by ionic, disulphide or hydrogen bonds (some may have quaternary structure)
3. Many hydrophilic side chains (R groups) on the outside of the protein

NOTE: Read the question if for a specific named protein e.g. enzymes have an active site, haemoglobin is {quaternary/4 polypeptide chains}

Question 24

Key Summary: Give similarities of fibrous and globular proteins
(2 similarities)

Answer 24

Similarities:

1. Both made of amino acids, joined by peptide bonds to form polypeptide chains
2. Both contain hydrogen bonds

Question 25

Key Summary: Give differences of fibrous and globular proteins (4 differences)

Answer 25

Differences: 1. Fibrous proteins have LITTLE OR NO TERTIARY STRUCTURE, globular proteins have TERTIARY + SOMETIMES QUATERNARY structure 2. Fibrous proteins have REPETITIVE SEQUENCES OF AMINO ACIDS, globular proteins do not 3. Fibrous proteins consist of LONG LINEAR POLYPEPTIDE CHAINS of amino acids, globular proteins are SPHERICAL IN SHAPE 4. Fibrous proteins have amino acids with HYDROPHOBIC R GROUPS ON THEIR OUTSIDE, globular proteins have amino acids with HYDROPHILIC R GROUPS ON THEIR OUTSIDE

Question 26

Key Summary: Properties of fibrous proteins (2 properties for fibrous)

Answer 26

Fibrous proteins: 1. Insolubility in water 2. Strength

Question 27

Key Summary: Properties of globular proteins (1 property for globular)

Answer 27

Globular proteins: 1. Insolubility in water due to hydrophilic side chains (R groups) on the outside of the protein 

Question 28

Key Summary: Give examples of fibrous proteins proteins (4 examples fibrous)

Answer 28

Fibrous proteins: 1. Collagen 2. Fibrin 3. Keratin 4. Myosin

Question 29

Key Summary: Give examples of globular proteins (4 examples globular)

Answer 29

Globular proteins: (Important in metabolic reactions) 1. Haemoglobin 2. Enzymes (e.g. thromboplastin, thrombin, DNA polymerase) 3. Some hormones e.g. insulin 4. Antibodies and plasma proteins

Question 30

1. function of collagen (1 function) | 2. Key properties (2 properties)

Answer 30

1. Strength in skin, bones, tendons, artery walls | 2. Strength, insolubility

Question 31

Key Summary: Describe the structure of collagen (6 points)

Answer 31

1. FIBROUS PROTEIN - MADE OF LONG POLYPEPTIDE CHAINS of amino acids joined by peptide bonds 2. CONTAINS REPETITIVE SEQUENCES OF AMINO ACIDS 3. HYDROPHOBIC AMINO ACIDS ON THE OUTSIDE of the protein 4. QUATERNARY STRUCTURE - 3 POLYPEPTIDE CHAINS 5. TRIPLE HELIX - 3 POLYPEPTIDE CHAINS wind around each other and are held together with hydrogen bonds 6 .Collagen molecules are staggered in a collagen fibril to prevent weak points along the length of the molecule with cross-links between molecules

Question 32

Key Summary: How the structure of collagen relates to its function. (4 points)

Answer 32

1. Made of hundreds of amino acids (large) and has many amino acids with hydrophobic R groups - makes it INSOLUBLE IN WATER 2. Many small R groups - SO THE TRIPLE HELIX CAN FORM 3. TRIPLE HELIX (3 long polypeptide chains tightly coiled around each other) with MANY REPEATING SEQUENCES OF AMINO ACIDS - for high (tensile) STRENGTH 4. When collagen molecules form collagen fibrils, molecules are staggered to prevent weak points – gives high tensile STRENGTH and FLEXIBILTIY, WITHOUT STRETCHING, required for support in tissues - skin, bones, tendons, artery walls

Question 33

State the function of haemoglobin (1 point)

Answer 33

1. Binds oxygen in red blood cells for oxygen transport

Question 34

Key Summary: Describe the structure of haemoglobin | 4 points

Answer 34

1. GLOBULAR PROTEIN – 4 polypeptide chains are folded into a COMPACT, SPHERICAL 3D SHAPE – secondary and tertiary structure 2. QUATERNARY STRUCTURE - CONTAINS 4 POLYPEPTIDE CHAINS 3. Many HYDROPHILIC R GROUPS on the outside of the protein 4. CONJUGATED PROTEIN - each polypeptide chain is associated with an iron containing haem group

Question 35

Key Summary: How the structure of haemoglobin relates to its function. (3 points)

Answer 35

1. Bonds (eg. ionic) between R groups determine folding which determines GLOBULAR 3D structure with SPHERICAL shape - ALLOWS MORE HAEMOGLOBIN TO FIT INSIDE EACH RED BLOOD CELL 2. 4 polypeptide chains each join with haem group forming a CONUGATED PROTEIN - precise 3D structure allows haem group of each polypeptide chain to be HELD IN THE CORRECT POSITION TO BIND ONE MOLECULE OF OXYGEN 3. HYDROPHILIC R GROUPS ON THE OUTSIDE ALLOW HAEMOGLOBIN TO BE SOLUBLE to allow oxygen transport in red blood cells from lung alveoli to tissues

Question 36

How is a secondary structure formed (1 point) and name the type of bond {involved/formed} (1 type of bond)

Answer 36

1. Formed when amino acids interact to form an alpha helix or a beta pleated sheet. 1. Hydrogen bond

Question 37

Define Tertiary structure (2 points) and name the 3 types of bond formed.

Answer 37

1. Further folding of the secondary structure into a {precise/specific} 3D shape. 2. Held together by bonds between amino acid R groups. 1. Hydrogen 2. Ionic 3. Disulphide