Chapter 2.3 Flashcards
Amino acid
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)
Proteins
- 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
Proteins are extremely important in cells. why?
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)
polypeptide.
When many amino acids are bonded together by peptide bonds the molecule formed
During hydrolysis reactions polypeptides
are broken down to amino acids when the addition of water breaks the peptide bonds
In order to form a peptide bond
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
Proteins: Structures
- 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
Primary structure of protein
- 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)
The secondary structure of a protein occurs
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
how can the hydrogen bonds in the secondary structure be broken
by high temperatures and pH changes
The secondary structure only relates to
hydrogen bonds forming between the amino group and the carboxyl group (the ‘protein backbone’)
Most fibrous proteins have
secondary structures (e.g. collagen and keratin)
Tertiary structure
-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
tertiary structured proteins are the following bonds
- Strong covalent disulphide
- Weak hydrophobic interactions
- Weak hydrogen
- Ionic
The α-helix (secondary structure)
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)
The β-pleated sheet (secondary structure)
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
quaternary structure
- 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
Disulphide
- 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
Hydrogen
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
Ionic
- 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
A polypeptide chain will fold differently due to the interactions. The three-dimensional configuration that forms is called
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
The arrangements of the R groups is important to the functioning of haemoglobin
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)
Summary of bonds in proteins table
Haemoglobin
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)
haemoglobin Function
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
prosthetic
a permanent non-protein part of a protein eg: haem group in haemoglobin
prosthetic haem
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)
Hydrophobic interactions
Hydrophobic interactions form between the non-polar (hydrophobic) R groups within the interior of proteins
Collagen
is the most common structural protein found in vertebrates
collagen overview
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
Structure of collagen
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
In vertebrates it is the component of connective tissue which forms: (collagen)
- Tendons
- Cartilage
- Ligaments
- Bones
- Teeth
- Skin
- Walls of blood vessels
- Cornea of the eye
–Collagen is an insoluble fibrous protein
Function of collagen
- 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)
The collagen molecules are positioned in the fibrils so that
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
collagen fibrils
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
glycine
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
Comparison between Collagen & Haemoglobin Table
condensation reaction
water is released
Globular proteins
are compact, roughly spherical (circular) in shape and soluble in water
-Globular proteins form a spherical shape when folding into their tertiary structure
Globular protein features
- 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
Globular proteins form a spherical shape when folding into their tertiary structure because
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
Fibrous protein
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
Comparison of Globular & Fibrous Tertiary Proteins Table
