Amino acids and proteins

Question 1

Define

• amino acids
• peptides
• proteins

Answer 1

• Proteins are large molecules found in every cell in the body. It is made up of amino acids
• Amino acids are the basic structural units of proteins
• Peptide is a chain of amino acids

Question 2

Understand the basic structure of an amino acid

Answer 2

• Amino group

• A carboxylic acid group
• Hydrogen atom
• Distinctive R group (side chain) bonded to a carbon atom. What differentiates one amino acid from the other is the R group

Question 3

How are peptide bonds formed?

Answer 3

• When the carboxylic acid group of one amino acid joins with the amine group of a second amino group, a peptide bond is formed.
• Upon the joining of two amino acids, water is released as a product. This is known as a condensation reaction, or dehydration synthesis.

Question 4

Outline the process of proteins synthesis

Answer 4

Central dogma is known as the flow of the cycle.
DNA –> RNA –> Protein
General rule

There are two steps:
Transcription
* In transcription, the DNA double helix unwinds.
RNA polymerase attaches the exposed DNA strand.
* The RNA polymerase moves along the DNA strand, making up a complementary RNA strand as it moves along
* The RNA is modified/bases added or deleted
* mRNA then moves out of the nucleus into the cytoplasm. There it goes into the Ribosome.

Translation

• Ribosomes have two subunits.
• At the smaller sub unit, mRNA is read and “translated”. tRNA comes and matches its anti-codon to the codon at the mRNA. It is read 3 bases at a time.
• At the larger sub unit, the amino acids on the tRNA is released, and amino acids join up in peptide bonds.

Question 5

Discuss the variety of proteins functions (7)

Answer 5

• Enzymes and hormones: biological catalysts for metabolism. Hormones help regulate activities, e.g. regulating blood glucose
• Antibodies and compliment system: Involved in immune system to defend against antigens.
• Structural and mechanical support: Helps give strength and flexibility to body structures.
• Carriers and transport nutrients: Transportation of oxygen
• Fluid balance: ensure that body fluids are evenly distributed in blood and within cells
• Acid-Base balance: help keep the pH of body fluids within a tight range
* Energy: gives calories, can be used as energy when necessary

Question 6

Differentiate the four levels of a protein structure: primary, secondary, tertiary, and quaternary structure

Answer 6

Primary structure:

• Describes the unique order in which amino acids are linked together to form a protein
• Proteins are constructed from a set of 20 amino acids.

Secondary structure:

• Refers to the coiling or folding of a polypeptide chain that gives the protein its 3-D shape
• There are two types of structures: Alpha helix which resembles a coiled string and Alpha pleated sheet, which is folded or pleated
• This is due to the way the peptide chains join up with each other and thus from the backbone.

Tertiary structure:
* Refers to the comprehensive 3-D structure of the polypeptide chain, due to side chain interactions between two R groups of amino acids

Quaternary structure:

• While many proteins are made up of a single polypeptide chains thus having 3 structures only, there are some which are made up of multiple polypeptide chains
• When these chains join together, they give the protein its quaternary structure.

Question 7

What does Vmax and Km stand for?

Answer 7

Vmax (maximum velocity) = The rate at which saturation point is achieved

Km (Michaels constant) = the affinity a substrate has for the enzyme. The higher the Km the lower the affinity. The lower the Km the higher the affinity

• The reaction rate will approach Vmax more quickly at a lower substrate concentration
• A small Km indicates that the enzyme requires only a small amount of substrate to become saturated. Hence, the maximum velocity is reached at relatively low substrate concentrations.
* A large Km indicates the need for high substrate concentrations to achieve maximum reaction velocity