HL 7.3

· Codon

(tRNA defnition) Each codon has a CCA base sequence at the 3' end that forms the amino acid binding site at the top of the molecule.

· Inorganic prosthetic group

At times, quaternary structures may include an inorganic prosthetic group (these are also called conjugated protein). An example of a conjugated protein is haemoglobin.

· Transcript modification

Changing mRNA prior to translation In eukaryotes, transcription occurs in the nucleus and translation occurs in the cytoplasm at the ribosomes. Due to this compartmentalisation, there is a delay between transcription and translation in eukaryotes while the transcript (mRNA) is modified (splicing, 5- methyl capping and 3'-polyadenylation).

· Hydrophobic interactions

Hydrophobic interactions: the hydrophobic amino acids orient themselves towards the centre of the polypeptide while the hydrophilic amino acids orient themselves outwards. The hydrophobic amino acids are attracted to one another by dispersion forces (Chemistry).

· Ionic bonds

Ionic bonds: attraction between positive and negatively charged variable groups.

· Free ribosome

Proteins are synthesised by free ribosomes will remain in the cell and are generally used in the cytoplasm, mitochondria and chloroplast.

· E site

The E site frees the tRNA, opening the next codon on the mRNA sequence.

· Anticodon

The anticodon loop has 3 nucleotides that form an anticodon to the mRNA codon.

· Peptide bond

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid

· Primary structure

The primary structure of a polypeptide is the sequence and number of amino acids in the chain. The primary structure has amino acids that are linked by covalent peptide bonds. • The polypeptide sequence is linear and can affect all subsequent levels of protein folding due to the interactions between the variable (R) groups of the amino acids. • As there are twenty essential amino acids, these can be arranged in any combination and so this increases the diversity of proteins produced.

· rRNA

type of RNA that combines with proteins to form ribosomes

· Secondary structure

• There are two types of secondary structures: the alpha (α) helix and the beta- pleated (β) sheet. The secondary structures form due to the polar covalent bonds in the backbone, and so this results in hydrogen bonds forming between the carboxyl and amino groups of non-adjacent amino acids. Examples of proteins with secondary structure include: fibrous proteins collagen and keratin, and globular proteins insulin.

· tRNA-activating enzymes

- Each tRNA molecule binds to a specific amino acid in the cytoplasm. This reaction is catalysed by a tRNA-activating enzyme. - The tRNA-activating enzyme is specific to the tRNA molecule and amino acid. - The tRNA-activating enzyme has an active site that binds to both the specific amino acid and tRNA. - This reaction requires energy in the form of ATP.

· Termination of translation steps

9. The process continues until a STOP codon is reached and then elongation stops. The stop codon is located at the 3' terminal of the mRNA sequence. The completed polypeptide is released and the ribosome disassembles into two subunits. All of these elements can be used again. • The stop codon does not recruit a tRNA molecule but recruits a release factor (protein). • The release factor stops translation by breaking the bond between the polypeptide chain and the last tRNA in the P binding site.

· Fibrous protein

A protein that has only a secondary structure; generally insoluble; includes collagens, elastins, and keratins.

· Elongation of the polypeptide steps

A second tRNA molecule will move into the A binding site of the ribosome, the incoming tRNA/anticodon must pair with the mRNA codon. A peptide bond is formed between the amino acid in the A site and the amino acid in the P site, thus linking the new amino acid to the existing chain. The tRNA in the P site is deacylated (no amino acid) and the tRNA in the A site carries the peptide chain. The ribosome translocates, moving the first tRNA into the E site from the P site. This frees the first tRNA and opens up the next codon to be translated at the A site. This process is repeated.

· Alpha helix

A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure.

· charged tRNA

A transfer RNA molecule with an amino acid attached to its 3' end. The amino acid becomes activated from the bond formed between the enzyme and AMP. The activated amino acid can then be coupled to the tRNA molecule by a covalent bond and the AMP is released. The tRNA molecule is "charged" and the energy stored can be used to link the amino acid to the growing polypeptide chain during translation.

· adenosine mono-phosphate

ATPandtheaminoacidareattachedtothe active site of the enzyme, two phosphates are cleaved from the ATP to form adenosine monophosphate (AMP). This forms an amino acid-AMP complex.

· Start codon

AUG codon that signals to ribosomes to begin translation; codes for the first amino acid in a protein

lysosome

An organelle containing digestive enzymes

· Carboxyl group

COOH

· Disulphide bridges

Disulfide bridges: formed between to sulfur atoms.

· Amino group

NH2

· Beta-pleated sheet

One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.

· Anticodon loop

One of three loops on a tRNA which contains the 3 nucleotides that allow it to align specifically with mRNA. Contains the anticodon One loop has 7 unpaired bases and is referred to as the anticodon loop.

· Polysomes

Polysomes (or polyribosomes) are a group of ribosomes that move along a single strand of mRNA. Multiple copies of a polypeptide can be more rapidly synthesised when more than one ribosome moves along the mRNA. Polysomes are visible in electron micrographs of prokaryotes and eukaryotes. Polysomes appear as beads on a string. In prokaryotes, polysomes may form while the mRNA is transcribed from the DNA. The 3' end polysomes will have longer polypeptide chains than those at the 5' end. In eukaryotes, polysomes occur in the cytoplasm and next to the endoplasmic reticulum.

proteins destined for the Golgi apparatus

Proteins destined to the GA is determined by the presence of a signal sequence on the nascent polypeptide chain that is recognised by the signal recognition protein on the endoplasmic reticulum. These proteins will be secreted. The growing polypeptide chain moves into the lumen of the ER as it is created

· Bound ribosome

Proteins synthesised by ribosomes bound to the endoplasmic reticulum (called bound ribosomes) are mostly secreted from the cell or used in lysosomes. • These proteins are destined for use at the Golgi apparatus or plasma membrane.

· Initiator tRNA

Special tRNA that initiates the translation of an mRNA in a ribosome. It always carries the amino acid methionine.

· A site

The A site holds a tRNA carrying the next amino acid to be added to the polypeptide chain during translation.

· P site

The P site holds the tRNA carrying the growing polypeptide chain.

· Initiation + initiation process

The process of initiation requires the assembly of three components to carry out the process: mature mRNA, tRNA and ribosome. Process of initiation: - The small ribosomal subunit binds the 5' end of the mRNA and moves along until it reaches the START codon (AUG) that is nearer the 5' end of the mRNA. - The initiator tRNA carrying the methionine (met) amino acid binds to the start codon on the mRNA with its anticodon by complementary base pairing (UAC). - The large ribosomal subunit binds to the smaller unit, and this locks the initiator tRNA into the P binding site.

· Quaternary structure

The quaternary structure results when more than one polypeptide chain bonds together. At times, quaternary structures may include an inorganic prosthetic group (these are also called conjugated protein). An example of a conjugated protein is haemoglobin . Quaternary structures can be held together by hydrogen bonds, disulfide bridges, and ionic bonds.

· Signal sequence

The sequence within a protein that directs the protein to a particular organelle. Proteins destined to the GA is determined by the presence of a signal sequence on the nascent polypeptide chain that is recognised by the signal recognition protein on the endoplasmic reticulum. These proteins will be secreted.

· Tertiary structure

The tertiary structure refers to the overall 3D shape of the protein. This structure is formed when the polypeptide chain folds up after being formed during translation. It is caused by the interactions between the variable groups of the amino acids in the polypeptide chain and the interaction with the surrounding water medium. The interactions include: ionic bonds, disulphide bridges, hydrophobic interactions and hydrogen bonds being formed. Some examples of proteins with tertiary structures include globular proteins such as enzymes.

· Translation

Translation of the mature mRNA sequence occurs in a 5' to 3' direction in three stages: initiation, elongation and termination.

· Stop codon

UAA, UAG, UGA - stop translation and polypeptide is released

· Conjugated protein

a protein that incorporates one or more non-amino acid units in its structure

· mRNA

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome

· Signal recognition protein

secretory proteins synthesized on membrane bound ribosomes have their signal sequence recognized by this

· Ribosome

site of protein synthesis The structure of ribosomes consists of two subunits, each are made of protein and ribosomal RNA (rRNA). There is a small subunit that binds mRNA on the surface and a larger subunit that has three binding sites for tRNA. The ribosomes have a similar structure between prokaryotes and eukaryotes, except the size of the large subunit differs slightly. Prokaryotes have 70S ribosomes whilst eukaryotes have 80S ribosomes

· Globular proteins

spherical, water-soluble proteins.

· amino acid-AMP complex

tRNA activating enzyme binds ATP to the amino acid, linked by a high energy bond (two P released)

· Splicing

the process of removing introns and reconnecting exons in a pre-mRNA

· tRNA

transfer RNA; type of RNA that carries amino acids to the ribosome The tRNA binding sites are the E site (exit), P site (peptidyl), and A site (aminoacyl). All tRNA molecules have the same basic shape (T-shaped). tRNA have sections that become double stranded by base pairing, and so it creates loops at three locations that differ by the number of nucleotides. One loop has 7 unpaired bases and is referred to as the anticodon loop. The anticodon loop has 3 nucleotides that form an anticodon to the mRNA codon. Each codon has a CCA base sequence at the 3' end that forms the amino acid binding site at the top of the molecule.

· Hydrogen bonds

• Hydrogen bonds: are the attractions between hydrogen and hydroxyl groups.

· Release factor

• The stop codon does not recruit a tRNA molecule but recruits a release factor (protein). • The release factor stops translation by breaking the bond between the polypeptide chain and the last tRNA in the P binding site.