Proteins B1.2

• What are amino acids?

  Amino acids are the building blocks of proteins, each with a central carbon atom (alpha carbon) that is covalently bonded to four other atoms.
• What are the four other atoms/groups bonded to the carbon backbone?

  The nitrogen of an Amino Group (-NH₂): A nitrogen-containing functional group that acts as a base- accepts one proton

  The carbon of a Carboxyl Group (-COOH): A functional group that acts as an acid- donates one proton

  A R Group (Side Chain): A variable group that determines the properties and identity of the amino acid. It can be anything.

  A hydrogen atom
• What does amphiprotic mean and why are amino acids amphiprotic?

  Amino acids are amphiprotic, meaning that they can accept or donate protons (Amino group accepts, carboxyl group donates)
• What is a dipeptide?

  Dipeptide: Two amino acids joined by a single peptide bond, formed through condensation reactions, in which a water molecule is removed. They are a type of oligopeptide.
• What is an oligopeptide?

  Oligopeptide: Short chain of less than 20 amino acids linked by peptide bonds. Oligopeptides include dipeptides, tripeptides (three amino acids), and other small peptides.
• What is a polypeptide?

  Polypeptide: Long chain of more than 20 amino acids linked by peptide bonds. Polypeptides fold into specific three-dimensional structures to form functional proteins.
• What is a peptide bond?

  Peptide bonds are formed through condensation reactions (water added), where amino acids are connected via the carboxyl and the amine groups (-COOH) and (-NH2). This reaction (condensation reaction) is catalysed in cells by ribosomes, and is a directional process, meaning that the amine group of a free amino acid is linked to the carboxyl at the end of the chain. The bond is always the same, no matter what the R-group is. It creates a C-N link.
• Where does polypeptide formation occur?

  Polypeptide formation occurs in ribosomes, which are found in two locations:

  Free ribosomes in the cytoplasm - Synthesize proteins used within the cell.

  Ribosomes attached to the rough endoplasmic reticulum (rER) - Synthesize proteins for secretion or use in membranes.

  Polypeptides are synthesized during translation, where mRNA directs the ribosome to assemble amino acids in the correct order using tRNA and peptide bond formation.
• How do animals obtain amino acids?

  Animals obtain amino acids from their food. They need twenty different ones for their ribosomes to make polypeptides.
• How do plants obtain amino acids?

  Plants can make twenty different amino acids through photosynthesis, and through the use of inorganic nitrogen sources such as nitrates or ammonium ions from the soil, which their ribosomes may use to make polypeptides. The sources of nitrogen are used as organic molecules through metabolic pathways like the nitrogen assimilation pathway.
• What are essential amino acids?

  Essential amino acids: Amino acids that cannot be made (synthesised) by humans, so must be obtained through diet. Humans have nine essential amino acids (the rest are non-essential)
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  Histidine

  Isoleucine

  Valine

  Leucine

  Methionine

  Phenylalanine

  Threonine

  Tryptophan

  Lysine
• What are non-essential amino acids?


  Non-essential amino acids: Amino acids that the body can make (synthesise) from other molecules, so they do not need to be consumed in the diet. They may be made through metabolic pathways that transform amino acids from essential to non-essential. Humans have eleven
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  Alanine

  Arginine (conditionally)

  Asparagine

  Aspartic acid

  Cysteine (conditionally)

  Glutamic acid

  Glutamine (conditionally)

  Proline

  Serine

  Tyrosine (conditionally)

  Glycine
• What is a conditionally essential amino acid?

  Conditionally essential amino acids become conditionally essential under specific conditions, such as illness, injury, or infancy, when the body cannot produce enough of them.
• What are the implications of a vegan diet in regards to amino acids?

  Many plant-based protein sources are incomplete proteins, meaning they lack one or more essential amino acids. For example:

  Legumes (e.g., beans, lentils) are low in methionine.

  Grains (e.g., rice, wheat) are low in lysine.

  Vegans must combine different plant protein sources (complementary proteins) to ensure they obtain all essential amino acids. For example:

  Rice and beans together provide all essential amino acids.

  Hummus (chickpeas) and whole wheat bread also form a complete protein.

  Some plant proteins, like soy and quinoa, are complete proteins and provide all essential amino acids.

  Ensuring variety in a vegan diet is crucial to avoid deficiencies, particularly in amino acids like lysine, methionine, and tryptophan, which are less abundant in plant-based foods.
• How are amino acids formed?

  Amino acids are all linked by ribosomes, one at a time, to form polypeptides. The ribosomes are able to form peptide bonds between any pair of amino acids, meaning that all sequences are possible. These sequences are not random- they are formed using instructions in the form of genetic code. This genetic code includes all twenty amino acids.
• How many possible sequences of polypeptides are there?

  For a dipeptide, both amino acids in the dipeptide may be any out of twenty. Therefore, there are 20 x 20 possible sequences, or 20^2. For a tripeptide, there are 20 x 20 x 20 possible sequences, or 20 ^3, and so on. Therefore, for polypeptides, the number of possible sequences is 20^n with n being the number of amino acids in the chain. This number, n, may be anything from 20 to 10,000.
• What is a proteome?

  Because of the large number of amino acids in a polypeptide, the number of possible sequences is effectively infinite. Only an extremely small proportion of all possible sequences are made by an organism, and this is known as the organism's proteome.
• What are some examples of polypeptides?

  Beta-endorphin, secreted by the pituitary gland has 31 amino acids. It is a pain killer.

  Insulin, secreted by the pancreas, has two short polypeptides, one with 21 amino acids, and the other with 20. It uses glucose for energy.

  Alpha amylase, secreted by the salivary glands, has 496 amino acids alongside one sodium and one chloride atom. It digests starch.

  Titin is part of the muscle structure and has 34,350 amino acids. It provides structure and flexibility.
• How are DNA base sequences diverse?

  The limitless diversity of DNA base sequences arises due to the vast number of possible combinations of nucleotide bases (adenine, thymine, cytosine, and guanine). This diversity is essential for genetic variation among organisms. The four bases follow complementary base pairing (A-T and C-G) in the double helix.

  DNA sequences can be any length, and each nucleotide position in a sequence has four possible bases. The number of possible sequences grows exponentially as the length increases. For a sequence of n bases, the number of combinations is 4^n.

  The limitless diversity of DNA sequences allows for genetic variation, which is critical for evolution and natural selection. Mutations and genetic recombination increases diversity.
• What is denaturation?


  Denaturation is the process by which a protein loses its three-dimensional shape due to the disruption of weak bonds (such as hydrogen bonds, ionic bonds, and hydrophobic interactions), leading to a loss of function. It does not involve the breaking of peptide bonds, so the primary structure remains intact, but the secondary, tertiary, and quaternary structures are affected.

  Denaturation is permanent. A soluble protein may denature and form an insoluble protein- which then forms a precipitate. This is because the hydrophobic R-groups in the centre of the molecule have undergone a conformational change and are now exposed to the water.
• How does heat affect proteins?

  Heat may cause denaturation as it causes vibrations between the molecule that can break intermolecular bonds or interactions. Proteins vary in their heat tolerance depending on their environments. For example, DNA polymerase from Thermus aquaticus works best at 80 degrees celsius and is commonly used in biotechnology. When eggs are heated, dissolved proteins in the yolk and the white denature and become insoluble, therefore solidifying.

  Increased kinetic energy breaks weak bonds (hydrogen bonds, ionic bonds), altering the secondary and tertiary structure.

  The protein loses its shape, and enzymes lose their active site specificity (substrates can no longer bind).

  If the temperature exceeds the protein's tolerance range, denaturation is irreversible.
• How do low temperatures affect proteins?

  Molecular motion slows down, reducing enzyme-substrate collisions.

  The protein retains its structure but functions inefficiently.
• How do pH extremes affect proteins?

  pH extremes, be that alkaline or acidic, cause denaturation. This is because positive and negative charges on the R-groups are altered, breaking ionic bonds within the protein or causing new ionic bonds to form. However, some proteins, such as pepsin which has optimum pH of 1.5, are specialised to withstand extreme ph.
• How does low pH affect proteins?

  Excess H⁺ ions disrupt ionic bonds between positively and negatively charged R-groups.

  This alters the tertiary structure, potentially leading to denaturation.

  Example: Enzymes like amylase in the mouth function at neutral pH, while pepsin in the stomach requires low pH (around 2).
• How does high pH affect proteins?

  Excess OH⁻ ions interfere with ionic bonds in a similar way, leading to protein unfolding.

  Loss of the active site shape in enzymes results in reduced or no function.
• What is insulin?

  Insulin has two short polypeptides, one with 21 amino acids, and the other with 20. that are responsible for the uptake of glucose into cells. They reduce glucose concentration in the blood, and are secreted by beta cells in the pancreas. Body cells have special receptors for insulin to which the hormone binds.
• What are digestive enzymes?

  Enzymes in the digestive tract break down macromolecules (lipids, proteins, carbohydrates) into their monomers. Thy include: Lipase (produced by pancreas and released in small intestine, breaking down fats) Pepsin (produced in stomach, breaks down polypeptides) Amylase (in salivary glands, mouth and by pancreas, breaking down starch).
• What is keratin

  Keratin is a fibrous protein composed of two polypeptide chains. Equipped with high tensile strength it is found in hair, nails, claws and hooves as a structural component and building block.
• What are collagens?

  Collagens are proteins in the cells which form the dermis of skin. They are rope-like, fibrous proteins with three polypeptides wound together, forming a mesh of fibres in skin and blood vessel walls that resist tearing. They are also a structural component in teeth, bones and tendons
• What is rhodopsin?

  Rhodopsin is found in the retina of the eye. They are light sensitive pigment of rod cells in the retina, that change the eye's shape in the response to absorbing photons of light. The change in shape causes a nerve impulse to be sent to the brain.
• What are immunoglobins?

  Immunoglobins are also called antibodies in the immune/defence system. They are produced by white blood cells (B-cells) and function by binding to antigens (foreign proteins structures) on bacteria or pathogens.
• What is haemoglobin?

  Haemoglobin is a protein composed of 4 polypeptides (2 alpha and 2 beta globin chains) which is found in red blood cells. It's main function is to transport oxygen around the body.
• What is titin?

  Titin is part of the muscle structure and has 34,350 amino acids. It provides structure and flexibility.
• What is alpha amylase?

  Alpha amylase, secreted by the salivary glands, has 496 amino acids alongside one sodium and one chloride atom. It digests starch.
• What is beta endorphin?

  Beta-endorphin, secreted by the pituitary gland has 31 amino acids. It is a pain killer.