D1.2 - PROTEIN SYNTHESIS

list and describe a few examples of proteins

collagen: structural protein found in skin, muscles, bones, tendons, ligaments, blood vessels etc. it is the most abundant protein by mass in the body

insulin: signalling protein (hormone) that makes cells absorb sugar from the blood

hemoglobin: transport protein found in RBC that carries oxygen throughout the body

trypsin: an enzyme that catalyses a chemical reaction

describe the process of transcription

• occurs in nucleus for eukaryotic cells / nucleoid region (cytoplasm) in prokaryotic cells

• RNA polymerase is an enzyme seperates DNA strands along a gene (only occurs on one of the DNA strands)

• RNA nucleotides form complementary base pairs with one DNA strand (template) by hydrogen bonding:

  • A-U, T-A, G-C, C-G

• RNA polymerase moves along the DNA in a 5’ → 3’ direction antiparallel to the DNA template and covalently bonds w the RNA nucleotides into a single strand

• at the end of the gene, RNA polymerase releases the RNA, and the DNA returns to its original double helix structure

  • DNA is very stable (base sequence does not change) and is unaffected by transcription

• RNA produced has a base sequence based on the DNA sequence

  • mRNA IS BEING SYNTHESISED IN A 5’ TO 3’ DIRECTION - ANTIPARALLEL TO DNA TEMPLATE

describe gene expression

refers to how active a gene is and how often it is transcribed and translated

• genes can be “on” or “off”

• genes can have a range of expression

  • frequent, sometimes, seldom, as needed, never

✓ transcription → gene expressed

✕ transcription → gene not expressed

gene - sequence of DNA that codes for a protein

explain transcription using the diagram provided

• occurs in the nucleus (euk) or cytoplasm (prok)

• DNA double helix strands are separated by RNA polymerase

• a gene is transcribed

• RNA polymerase enzyme responsible for transcription

  • enzyme covalently bonds RNA nucleotides together

• DNA is unchanged and returns back to double helix structure

• complementary base pairing between newly synthesised RNA strand and DNA template strand

describe the structure of a protein

• proteins are polypeptides and are composed of amino acids (polymers)

  • monomer: amino acid

  • polymer: polypeptide

    • “polypeptide” used during translation bc it hasn’t folded up into a fully functioning protein yet

• amino acids are held together by peptide bonds

• 20 kinds of amino acids are used

list and outline the 3 kinds of RNA

mRNA: messenger RNA that contains the code for building protein

tRNA: transfer RNA that brings amino acids to the ribosome

rRNA: ribosomal RNA is part of the ribosome itself

describe the function of mRNA

Messenger RNA (mRNA) carries the genetic code that determines the order of amino acids in a polypeptide sequence

describe the function of tRNA

Transfer RNA (tRNA) is responsible for transporting amino acids to the ribosome according to the mRNA sequence

describe the function and structure of a ribosome

• composed of rRNA and protein with a complex, globular shape separated into a large and small subunit and are complex macromolecular machines, they consist of 2 distinct subunits

large subunit: 3 binding sites for tRNAs (E, P, A), but only 2 tRNA molecules can bind simultaneously at a time, creates peptide bonds between amino acids

small subunit: binds to the mRNA and decodes the genetic message

describe the function of rRNA

ribosomes are composed of both ribosomal RNA (which contributes to the catalytic activity) and protein (which provides structural stability)

describe codon and anticodon

codon: a sequence of three mRNA bases that codes for a specific amino acid or a stop signal during protein synthesis

anticodon: a sequence of three nucleotides in tRNA that is complementary to a specific codon in mRNA

describe the function of codons and anticodons

codon function: codons which are read by the ribosome during the translation process which instructs the ribosome to start the creation of a polypeptide sequence, add a specific amino acid to the growing polypeptide chain, or to stop the creation of the polypeptide sequence

anticodon function: anticodons are a sequence of 3 tRNA bases that are complementary to a codon which carries the appropriate amino acid to be condensed onto the growing polypeptide chain during translation

HOW TO REMEMBER TRANSLATION EASILY: Mr Cat App

• MR: Messenger RNA binds to the Ribosome (via the small subunit)

• CAT: Codons (on mRNA) are recognised by complementary Anticodons on Transfer RNA

• APP: Amino acids are joined by the ribosome via Peptide bonds to form Polypeptides

what is a genetic code

the genetic code is a set of rules by which information encoded within mRNA sequences are converted into amino acid sequences (polypeptides) by living cells

• represented by a table that identifies the corresponding amino acid for each codon combination (64 codon possibilities)

what are the two key features of genetic code

• it is universal and it has degeneracy

  • universal: genetic code is universal as almost every living organism uses the same code (there are a few rare and minor exceptions)

  • degenerate: as the genetic code has around only 20 amino acids but 64 different codon combinations, more than one codon may code for a single amino acid

outline transcription and translation and describe the directionality

transcription is the process by which a gene sequence is copied into a complementary RNA sequence by RNA polymerase

translation is the process

explain the initiation process of transcription

• promoter Binding and transcription factors: RNA polymerase binds to a specific region of the DNA known as the promoter with the help of transcription factors which are proteins as they guide the enzyme onto the promoter region which is located upstream of the gene to be transcribed

• DNA strand separation: RNA polymerase unwinds and separates the DNA double helix, creating a transcription bubble which exposes the template strand of DNA that will be used for the synthesis of RNA

• Free RNA nucleotides within the cell line up opposite their complementary base partner

• RNA polymerase covalently binds the RNA nucleotides together via condensation reactions (forming phosphodiester bonds)

• The 5’-phosphate is linked to the 3’-end of the growing mRNA strand, hence transcription occurs in a 5’ → 3’ direction

explain the elongation process of transcription

• RNA synthesis: RNA polymerase synthesises a single strand of RNA by adding ribonucleotides that are complementary to the DNA template strand which occurs in the 5' to 3' direction.

• Base Pairing:

  • adenine (A) - uracil (U)

  • thymine (T) - adenine (A)

  • guanine (G) - cytosine (C)

  • cytosine (C) - guanine (G)

explain the termination process of transcription

• termination signals: RNA polymerase continues elongation until it reaches a specific sequence of nucleotides that signals the end of the gene (termination site)

• release of RNA: once the RNA polymerase reaches a termination signal, the newly synthesised mRNA strand is released from the RNA polymerase and DNA template

explain what post transcriptional RNA modification is in eukaryotes and why they are essential

post transcriptional RNA modifications are crucial steps that occur after the initial synthesis of pre mRNA and before it is translated into protein

• ensure the stability, transport, and proper function of the mRNA

explain post transcriptional RNA modifications in eukaryotes

• capping: addition of methyl group at 5’-end

  • provides protection and allows transcript to be recognised by the ribosome

    protecting mRNA from degradation

• polyadenylation: addition of long chain of adenine at 3’-end (poly-A-tail)

  • improves stability of RNA and facilitates export

  • protecting mRNA from degradation

• splicing: removal of non coding sequence (introns) and splicing together of coding sequences (exons) to form a continuous coding sequence

  • intron(thrown out/recycled): non-coding sequences of DNA within genes transcribed into RNA (doesn’t code for amino acids; have other functions)

  • exon(expressed, actually used to build protein): coding sequences of DNA or RNA within genes transcribed into RNA

what are non-coding DNA

• sequences that do not code for a protein which only occur in around 1.5% of a DNA sequence

  • regulatory regions: enhancer and silencer regions where activator and repressor proteins bind to help or hinder initiation

explain the the initiation process of translation

• ribosomal assembly: the small subunit of the ribosome binds to the 5’ end to the 3’ end of the mRNA and slides across the molecule (in a 5’ to 3’ direction) until it reaches a start codon (AUG)

• tRNA binding: the initiator tRNA carrying the amino acid methionine, recognises the start codon and binds to it by its anticodon (UAC)

• large subunit joining: the large ribosomal subunit then attaches to the small ribosomal subunit to form a functional ribosome, creating the A (aminoacyl), P (peptidyl), and E (exit) sites

explain the the elongation process of translation

• aminoacyl-tRNA binding: an aminoacyl-tRNA (charged tRNA carrying an amino acid) enters the ribosome and binds to the A site where its anticodon binds with corresponding codon on the mRNA

• peptide bond formation: the amino acid in the a site is transferred into the growing polypeptide held in the P site where the ribosomal enzyme catalyses the formation of a peptide bond between the amino acid in the A site and the growing chain in the P site

• translocation: as the ribosome slides along the mRNA by one codon, it shifts the tRNA holding the polypeptide chain that was in the A site into the P site and the tRNA with no amino acid into the E site where it exits the ribosome. after this happens, this opens the A site for a new tRNA with a new amino acid to bind to the A site and continue the elongation process

explain the the termination process of translation

• stop codon recognition: when the ribosome reaches a stop codon (UAA, UAG, or UGA) on the mRNA, there is no corresponding tRNA

• release factor binding: a release factor binds to the stop codon, prompting the ribosome to add a water molecule instead of an amino acid, which releases the polypeptide chain

• disassembly: the ribosomal subunits, mRNA, and release factor disassemble, completing the translation process releasing all the enzymes involved

explain the modification of polypeptides into their functional state

• proteins are modified after translation for functional state

  • formation of disulphite bridge between cysteine residues

  • conjugation with inorganic cofactors (haeme group)

use insulin as an example and explain the modification of its polypeptides into its functional state

• pre-insulin modified into insulin

  • pre-insulin consists of: signal sequence, A chain, B chain and C-peptide

    • signal sequence in preproinsulin is removed in the rER

    • proinsulin folds: the A chain and B chain of the preproinsulin are linked by disulphite bridges

    • converted into proinsulin

    • proinsulin is transported into the golgi complex where the c-peptide is removed

    • results in (mature) insulin which is then packaged into secretory vesicles

explain how proteasomes help recycle amino acids

• proteasomes: they are complex structures within a cell that degrade uneeded proteins by breaking the peptide bonds within proteins

  • they help regulate protein expression levels and recycle amino acids

  • by controlling breakdown and synthesis of proteins, proteasome plays an important role in sustaining functional proteome

what is alternative splicing

• regulatory mechanism in gene expression that allows a single gene to produce multiple mRNA variants

  • different arrangement of exons spliced together to produce a variety of proteins

explain how alternative splicing of exons are able to produce variants of a protein from a single gene

by selectively removing certain exons from polypeptides from a single gene sequence, cells can produce variants of proteins that may have different functional roles or regulatory mechanisms