Proteins

Proteins

1. An amino group
2. A carboxyl group
3. An "R group"

• There are 20 different "R groups" that can be attached to the amino acid.
• This diversity in possible R-groups is what leads to the diverse array of proteins within a cell, each with its own particular structure and function.
• Interactions between R-groups give proteins their overall 3-dimensional structure.
• Different R-groups have different biochemical properties:
• Some are hydrophobic;
• Others are positively charged;
• Or negatively charged;
• Some are "special cases."

• Amino acids are joined together by a dehydration / condensation reaction in order to form a peptide bond.
• The peptide bond forms between the carboxyl group of one amino acid and the amino group of the other amino acid.
• Once amino acids are joined together into a long chain, a repeating backbone of N-C-C atoms forms. Each individual "N-C-C" is one amino acid in the chain.
• The amino group of the first amino acid in the chain is on one end, while the carboxyl group of the last amino acid is on the other end of the chain.
• The end with the amino group is called the N-terminus, while the end with the carboxyl group is called the C-terminus.

Functions of Proteins

1. Enzymes - catalyze (increase the speed of) reactions. Example: breakdown of lactose during digestion is carried out by the enzyme lactase.
2. Transportation - proteins can shuttle things around/in/out of the cell. Example: ion channels allow for electrolytes to enter and leave cells.
3. Support - maintaining cell structure. Example: cytoskeleton of cells.
4. Signaling - communication between different parts of the cell or the entire body. Example: insulin is a short protein (peptide) hormone that facilitates glucose entry into certain cells.
5. Movement - movement of things in the cell or movement of the cell itself (e.g. cilia or flagella). Example: the airways keep themselves clean from pollution by moving cilia.
6. Defense - proteins that are active in the immune system. Example: antibodies are proteins.

Protein Folding

• This shape is dictated by the sequence of amino acids and the chemical interactions between their side groups, resulting in secondary, tertiary or quaternary structures.
• Protein folding can occur naturally as proteins are produced in the cell or they may require assistance from other proteins called chaperones. Example: antibodies fold in a such a way that pockets form where antigens can fit in and bind.

Denaturation

• When proteins lose their natural shape they are said to be denatured.
• Note that in this case the actual protein sequence does not change.
• Proteins can be denatured by:
• Changes in pH
• High temperatures
• Chemicals

The Four Levels of Protein Structure

• Primary Structure: the sequence of amino acids.
• Secondary Structure: hydrogen bonding between backbone atoms, leading to the formation of alpha-helices or beta-sheets.
• Tertiary Structure: interactions between R groups (e.g. hydrogen bonds, Van der Waals interactions).
• Quaternary Structure: interactions between two or more fully folded proteins.

Protein Production

From a Gene to a Protein

• Genes are coded for in the DNA by nucleic acids
• DNA is transcribed into a single stranded RNA message (mRNA)
• Transcription = the process of complimentary base pairing RNA nucleic acids with DNA
• RNA is then translated by ribosomes into a polypeptide chain which spontaneously folds into a functional protein

Translation

• messenger RNA (mRNA) is recognized by ribosomes
• In prokaryotes this happens immediately after transcription
• In eukaryotes RNA needs to be shuttled from the nucleus to the cytoplasm before this happens
• Ribosomes read the RNA in 3 nucleotide chunks known as codons
• transfer RNA (tRNA) is recruited by the ribosome that contains the correct anti-codon to base-pair with the mRNA
• tRNAs carry specific amino acids based on which anti-codon it possesses
• This allows the ribosome to know exactly which tRNA to call
• The ribosome forms a peptide bond between amino acids
• The process is repeated until a STOP codon is read which tells the ribosome to stop translation