Chapter 2.3

Question 1

Amino acid

Answer 1

are the monomers of proteins

• There are 20 amino acids found in proteins common to all living organisms
• The general structure of all amino acids is a central carbon atom bonded to:

–An amine group -NH2

–A carboxylic acid group -COOH

–A hydrogen atom

–An R group (which is how each amino acid differs and why amino acid properties differ e.g. whether they are acidic or basic or whether they are polar or non-polar)

Question 2

Proteins

Answer 2

• are polymers (and macromolecules) made of monomers called amino acids
• The sequence, type and number of the amino acids within a protein determines its shape and therefore its function
• Proteins are extremely important in cells

Question 3

Proteins are extremely important in cells. why?

Answer 3

because they form all of the following:

• Enzymes
• Cell membrane proteins (eg. carrier)
• Hormones
• Immunoproteins (eg. immunoglobulins)
• Transport proteins (eg. haemoglobin)
• Structural proteins (eg. keratin, collagen)
• Contractile proteins (eg. myosin)

Question 4

polypeptide.

Answer 4

When many amino acids are bonded together by peptide bonds the molecule formed

Question 5

During hydrolysis reactions polypeptides

Answer 5

are broken down to amino acids when the addition of water breaks the peptide bonds

Question 6

In order to form a peptide bond

Answer 6

a hydroxyl (-OH) is lost from a carboxylic group of one amino acid and a hydrogen atom is lost from an amine group of another amino acid

• The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid
• This is a condensation reaction so water is released. The resulting molecule is a dipeptide -When many amino acids are bonded together by peptide bonds the molecule formed is called a polypeptide.
• A protein may have only one polypeptide chain or it may have multiple chains interacting with each other

Question 7

Proteins: Structures

Answer 7

• There are four levels of structure in proteins, three are related to a single polypeptide chain and the fourth level relates to a protein that has two or more polypeptide chains
• Polypeptide or protein molecules can have anywhere from 3 amino acids (Glutathione) to more than 34,000 amino acids (Titan) bonded together in chains

Question 8

Primary structure of protein

Answer 8

• The sequence of amino acids bonded by covalent peptide bonds is the primary structure of a protein
• DNA of a cell determines the primary structure of a protein by instructing the cell to add certain amino acids in specific quantities in a certain sequence. This affects the shape and therefore the function of the protein
• The primary structure is specific for each protein (one alteration in the sequence of amino acids can affect the function of the protein)

Question 9

The secondary structure of a protein occurs

Answer 9

when the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds

-There are two shapes that can form within proteins due to the hydrogen bonds:

–α-helix

–β-pleated sheet Hydrogen bonds can be broken by high temperatures and pH changes

Question 10

how can the hydrogen bonds in the secondary structure be broken

Answer 10

by high temperatures and pH changes

Question 11

The secondary structure only relates to

Answer 11

hydrogen bonds forming between the amino group and the carboxyl group (the ‘protein backbone’)

Question 12

Most fibrous proteins have

Answer 12

secondary structures (e.g. collagen and keratin)

Question 13

Tertiary structure

Answer 13

-Further conformational change of the secondary structure leads to additional bonds forming between the R groups (side chains) -The additional bonds are:

—Hydrogen (these are between R groups)

—Disulphide (only occurs between cysteine amino acids) —Ionic (occurs between charged R groups)

—Weak hydrophobic interactions (between non-polar R groups) This structure is common in globular proteins

Question 14

tertiary structured proteins are the following bonds

Answer 14

• Strong covalent disulphide
• Weak hydrophobic interactions
• Weak hydrogen
• Ionic

Question 15

The α-helix (secondary structure)

Answer 15

shape occurs when the hydrogen bonds form between every fourth peptide bond (between the oxygen of the carboxyl group and the hydrogen of the amine group)

Question 16

The β-pleated sheet (secondary structure)

Answer 16

shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds

Question 17

quaternary structure

Answer 17

• Occurs in proteins that have more than one polypeptide chain working together as a functional macromolecule, for example, haemoglobin
• Each polypeptide chain in the quaternary structure is referred to as a subunit of the protein

Question 18

Disulphide

Answer 18

• Disulphide bonds are strong covalent bonds that form between two cysteine R groups (as this is the only amino acid with a sulphur atom)
• These bonds are the strongest within a protein, but occur less frequently, and help stabilise the proteins
• These are also known as disulphide bridges Can be broken by oxidation -Disulphide bonds are common in proteins secreted from cells eg. insulin

Question 19

Hydrogen

Answer 19

Hydrogen bonds form between strongly polar R groups. These are the weakest bonds that form but the most common as they form between a wide variety of R groups

Question 20

Ionic

Answer 20

• Ionic bonds form between positively (amine group -NH3+) and negatively charged (carboxylic acid -COO–) R groups
• Ionic bonds are stronger than hydrogen bonds but they are not common
• The bonds are broken by pH changes

Question 21

A polypeptide chain will fold differently due to the interactions. The three-dimensional configuration that forms is called

Answer 21

tertiary structure of a protein

-Each of the twenty amino acids that make up proteins has a unique R group and therefore many different interactions can occur creating a vast range of protein configurations and therefore functions

Question 22

The arrangements of the R groups is important to the functioning of haemoglobin

Answer 22

If changes occur to the sequence of amino acids in the subunits this can result in the properties of haemoglobin changing.

-This is what happens to cause sickle cell anaemia (where base substitution results in the amino acid valine (non-polar) replacing glutamic acid (polar) making haemoglobin less soluble)

Question 23

Summary of bonds in proteins table

Answer 23

Question 24

Haemoglobin

Answer 24

is a globular protein which is an oxygen-carrying pigment found in vast quantities in red blood cells

• It has a quaternary structure as there are four polypeptide chains.
• These chains or subunits are globin proteins (two α–globins and two β–globins) and each subunit has a prosthetic haem group
• The four globin subunits are held together by disulphide bonds and arranged so that their hydrophobic R groups are facing inwards (helping preserve the three-dimensional spherical shape) and the hydrophilic R groups are facing outwards (helping maintain its solubility)

Question 25

haemoglobin Function

Answer 25

is responsible for binding oxygen in the lung and transporting the oxygen to tissue to be used in aerobic metabolic pathways - As oxygen is not very soluble in water and haemoglobin is, oxygen can be carried more efficiently around the body when bound to the haemoglobin - The presence of the haem group (and Fe2+) enables small molecules like oxygen to be bound more easily because as each oxygen molecule binds it alters the quaternary structure (due to alterations in the tertiary structure) of the protein which causes haemoglobin to have a higher affinity for the subsequent oxygen molecules and they bind more easily - The existence of the iron II ion (Fe2+) in the prosthetic haem group also allows oxygen to reversibly bind as none of the amino acids that make up the polypeptide chains in haemoglobin are well suited to binding with oxygen

Question 26

prosthetic

Answer 26

a permanent non-protein part of a protein eg: haem group in haemoglobin

Question 27

prosthetic haem

Answer 27

group contains an iron II ion (Fe2+) which is able to reversibly combine with an oxygen molecule forming oxyhaemoglobin and results in the haemoglobin appearing bright red -Each haemoglobin with the four haem groups can therefore carry four oxygen molecules (eight oxygen atoms)

Question 28

Hydrophobic interactions

Answer 28

Hydrophobic interactions form between the non-polar (hydrophobic) R groups within the interior of proteins

Question 29

Collagen

Answer 29

is the most common structural protein found in vertebrates

Question 30

collagen overview

Answer 30

Collagen is a fibrous structural protein that is formed by triple helices collagen molecules arranging into collagen fibrils and finally into collagen fibres which have high tensile strength

Question 31

Structure of collagen

Answer 31

is formed from three polypeptide chains closely held together by hydrogen bonds to form a triple helix (known as tropocollagen) - Each polypeptide chain is a helix shape (but not α-helix as the chain is not as tightly wound) and contains about 1000 amino acids with glycine, proline and hydroxyproline being the most common - In the primary structure of collagen almost every third amino acid is glycine

Question 32

In vertebrates it is the component of connective tissue which forms: (collagen)

Answer 32

- Tendons - Cartilage - Ligaments - Bones - Teeth - Skin - Walls of blood vessels - Cornea of the eye **--Collagen is an insoluble fibrous protein**

Question 33

Function of collagen

Answer 33

- Flexible structural protein forming connective tissues - The presence of the many hydrogen bonds within the triple helix structure of collagen results in great tensile strength. This enables collagen to be able to withstand large pulling forces without stretching or breaking - The staggered ends of the collagen molecules within the fibrils provide strength - Collagen is a stable protein due to the high proportion of proline and hydroxyproline amino acids result in more stability as their R groups repel each other - Length of collagen molecules means they take too long to dissolve in water (collagen is therefore insoluble in water)

Question 34

The collagen molecules are positioned in the fibrils so that

Answer 34

there are staggered ends (this gives the striated effect seen in electron micrographs) - When many fibrils are arranged together they form collagen fibres - Collagen fibres are positioned so that they are lined up with the forces they are withstanding

Question 35

collagen fibrils

Answer 35

Covalent bonds also form cross-links between R groups of amino acids in interacting triple helices when they are arranged parallel to each other. The cross-links hold the collagen molecules together called fibrils

Question 36

glycine

Answer 36

This is the smallest amino acid with a R group that contains a single hydrogen atom ---Glycine tends to be found on the inside of the polypeptide chains allowing the three chains to be arranged closely together forming a tight triple helix structure

Question 37

Comparison between Collagen & Haemoglobin Table

Answer 37

Question 38

condensation reaction

Answer 38

water is released

Question 39

Globular proteins

Answer 39

are compact, roughly spherical (circular) in shape and soluble in water -Globular proteins form a spherical shape when folding into their tertiary structure

Question 40

Globular protein features

Answer 40

- This orientation(non-polar and polar groups) enables globular proteins to be (generally) soluble in water as the water molecules can surround the polar hydrophilic R groups - The solubility of globular proteins in water means they play important physiological roles as they can be easily transported around organisms and be involved in metabolic reactions - The folding of the protein due to the interactions between the R groups results in globular proteins having specific shapes. This also enables globular proteins to play physiological roles, for example, enzymes can catalyse specific reactions and immunoglobulins can respond to specific antigens - Some globular proteins are conjugated proteins that contain a prosthetic group eg. haemoglobin which contains the prosthetic group called haem

Question 41

Globular proteins form a spherical shape when folding into their tertiary structure because

Answer 41

their non-polar hydrophobic R groups are orientated towards the centre of the protein away from the aqueous surroundings and --their polar hydrophilic R groups orientate themselves on the outside of the protein

Question 42

Fibrous protein

Answer 42

are long strands of polypeptide chains that have cross-linkages due to hydrogen bonds -They have little or no tertiary structure - Due to the large number of hydrophobic R groups fibrous proteins are insoluble in water - Fibrous proteins have a limited number of amino acids with the sequence usually being highly repetitive - The highly repetitive sequence creates very organised structures that are strong and this along with their insolubility property, makes fibrous proteins very suitable for structural roles, for example, keratin that makes up hair, nails, horns and feathers and collagen which is a connective tissue found in skin, tendons and ligaments

Question 43

Comparison of Globular & Fibrous Tertiary Proteins Table

Answer 43