The relationship between nucleic acids and proteins Flashcards
Nucleic acids
Nucleic acids are biomolecules that are vital for the continuity of life and are made up of subunits known as nucleotides.
Nucleic acid is a polymer (Monomers build polymers)
Structure of DNA
Nucleotides in DNA are arranged in a double helix. The two strands of DNA are antiparallel and are held together by hydrogen bonds between complementary nitrogenous bases.
5’ to 3’ means: can only add at 3’ end
Messenger RNA
Carries the genetic message from the DNA within the nucleus to the ribosomes, where the message is translated into a particular protein.
→ shorter than DNA
→ Group of three nucleotides in mRNA are a codon
Ribosomal RNA
A stable form of RNA found in ribosome
Transfer RNA
tRNA are molecules that carry amino acids to ribosomes that are free in the cytoplasm, where they are used to construct proteins.
→ An anticodon binds to the complementary codon on mRNA
Degenerative code
Some amino acids can code for more than one codon due to the universal code (same sequence of nucleotides for all organisms)
Genes are more tolerant to mutations
Advantage → Gene manipulation and therapeutic uses (eg: use of CRISPR, bio-tech, insulin being expressed through recombinant plasmid)
Disadvantage → easy for foreign DNA to be incorporated into a genome. (Eg: some viruses are able to hide in the genomes of host cells without being recognised as foreign.
Gene expression
- Transcription
- RNA processing (eukaryotic cells in nucleus)
- Translation
- Post translational modification
Transcription
Initiation - RNA polymerase binds to the promoter region to separate DNA sequence.
Elongation - The polymerase runs in a 3’ to 5’ direction and builds messenger RNA in 5’ to 3’ direction.
Termination - When a stop codon is reached, transcription stops and pre-mRNA molecule is released
RNA processing (eukaryotic cells in nucleus)
Capping: The 5′ end of the pre-mRNA is capped with an altered guanine (G) base which protects the pre-mRNA from enzyme attack and contributes to its stability, helping it attach to the ribosome.
Adding a tail: A poly-adenine (A) tail, with up to 250 A’s, is added at the 3′ end of the pre-mRNA. The poly A tail contributes to the stability of the mRNA and facilitates mRNA export from the nucleus.
Splicing: The regions in the pre-mRNA that correspond to the introns are spliced and the remaining exons are joined together. (done by spliceosomes, which recognise specific base sequences at the ends of the introns)
Alternative splicing of pre-mRNA Sometimes, additional exons are removed by the spliceosomes to add further complexity to RNA processing and gene regulation, enabling one gene to produce a multitude of proteins if required.
Translation
Initiation - Ribosome binds to mature mRNA structure
Elongation - mRNA structure goes through the ribosome and tRNA molecule carries an amino acid complementary to the anticodon creating a polypeptide chain (amino acids form peptide bonds)
Termination - ribosome reads a stop codon and polypeptide chain is released
Post translational modification
Polypeptide chain gets folded in the rough ER (its secondary structure)
The folded protein is transported in a transport vesicle to the Golgi body for final packaging of the protein (completed 3D structure- either at tertiary or quaternary level)
Protein travels in a secretory vesicle to the plasma membrane.
With an input of ATP from the mitochondria, the vesicle fuses with the membrane and the protein leaves the cell by exocytosis.
Exons
Exons contain the instructions that code for the amino acids in the produced protein. They are both transcribed and translated.
Introns
Introns are interrupting segments that separate the exons. They do not contain instructions relating to the protein chain. They are transcribed in the nucleus but are cut out in RNA processing
Promoter
The promoter is where RNA polymerase binds to initiate transcription. Without a functioning promoter region, transcription cannot be properly initiated.
Proteins called transcription factors can bind and regulate the expression of genes.
Also known as TATA box (rich in A and T’s)
Operator
Are the binding sites for repressor proteins. When a repressor binds to the operator, it prevents the RNA polymerase binding to the promoter, and thus transcription cannot be initiated.
Found in prokaryotic genes between the promoter and the gene being transcribed.
RPOS
Regulator, promoter region, operator region, structural genes
Prokaryote
→ Repressor proteins bind to an operator
→ Gene regulation only occurs at transcriptional level
→ Gene regulation only occurs at cytosol
→ Only have exons
→ Structural genes for every operon region
Eukaryotic
→ Regulatory proteins bind in an upstream region
→ Gene regulation occurs at transcriptional level, post-transcriptional modification, translational level
→ Gene regulation occurs at nucleus or cytosol
→ Have exons and introns
→ Have no operator region
Both prokaryotic and eukaryotic
→ Have promoter regions to initiate transcription where RNA polymerase binds to
→ Have structural genes (exons) that code for biological proteins
→ regulation methods (molecules that activate or inhibit gene expression)
Structural genes
Genes that produce proteins that become part of the structure and the functioning of the organism.
Regulatory genes
Genes that produce proteins that control the action of other genes (active or inactive) Many of these act as DNA binding proteins, binding directly to sections on the DNA. Others act as signalling molecules, binding to receptors on the cell surface
Trp operon
Tryptophan is an amino acid that the bacterium Escherichia coli (E. coli) is able to ingest from the surrounding environment. E. coli is able to synthesise tryptophan using enzymes encoded by five genes.
Presence of trp (operator repressor)
- Trp binds to repressor protein causing a configurational change in its shape allowing it to be active
- Repressor can bind to the operator
- Thus, RNA polymerase is unable to bind to the promoter and transcription does not occur as operon is off
Low levels of trp (attenuation)
→ occurs when there is little trp left and is carried by tRNA molecule for translation (attenuation means slowing something down)
1. The ribosome will run past the ‘pause’ and stop when it gets to the stop codon. it now occupies a region of the leader that keeps 1 from binding to 2 and making a loop.
2. Therefore, the RNA polymerase gets further ahead of the ribosome and transcribes 3&4 which bind together forming a loop.
3. This will pull the attenuator away from the DNA.
4. Thus, the RNA polymerase comes off the DNA and does not transcribe the genes of the operon
Absence of trp (attenuation)
- The ribosome translates the mRNA but when it gets to the codons for trp, there is no tRNA with trp.
- The ribosome waits and does not get to the stop codon.
- Thus, the RNA polymerase transcribes domains 2&3 and they stick together creating a loop.
- As 3 is stuck to 2, it can’t stick to 4. Therefore, it does not yank the messenger RNA away from the attenuator.
- The RNA polymerase does not fall off the DNA and continues on transcribing the genes of the operon
Amino acids
The R group variable determines the property of the amino acid (pos/neg charger, hydrophilic/phobic) Interactions between the different R groups determine how folding in the protein occurs.
–> is an amino group, carboxyl group, variable group and hydrogen group
Condensation polymerisation (synthesis) and hydrolysis
The reaction that forms peptide bonds is condensation polymerisation where water is released. The reaction that breaks down peptide bonds is hydrolysis where water is required.
Both requires energy in the form of ATP
Primary protein structures
Specific linear sequence of amino acids in the protein brought together as a polypeptide during translation in the ribosome.
Secondary protein structures
Depending on R group, 3 different folds can occur
Alpha helix: single twisted strand. Help increase SA:V, can stretch / relax and contract - muscle fibres.
Beta-pleated sheets: staggered fold. Can stretch, maintains a structure / appearance surrounding
Random coiling: often the active site of an enzyme allowing a substrate to successfully bind
Tertiary protein structures
The total irregular 3D folding held together by various bonds forming a complex shape. The tertiary structure depends on both the primary and the secondary structures. Bonds include:
hydrogen bonds, ionic attractions between charged R groups, interactions between hydrophobic R groups in the protein interior, covalent disulfide cross links.
These bonds differ in their strength and frequency. Disulfide bridges are the strongest bonds that can form in a tertiary structure.
Quaternary protein structures
Made of more than a single polypeptide chain each with its own primary, secondary and tertiary structure. Those polypeptides are held together by hydrogen bonds and the mutual attraction between polar and amino acid side chains. Has a heavy and light chain
Protome
The complete array of proteins produced by a single cell or organism in a particular environment
Enzyme as catalyst in biochemical pathways
Catalysts are substances that speed up the rate of chemical reactions without the catalyst itself being used up in the reactions.
Ribosome
Site of translation where amino acids join forming a polypeptide chain
Often attached to ER
Rough ER
Consists of a system of membrane bound channels that transport substances within the cell
Through its network of channels the rough ER:
Folds proteins into their correct functional shape/ conformation
Assembles complex proteins by linking together several polypeptide chains eg. haemoglobin protein
Golgi apparatus
Consists of stacks of flattened pockets (cisternae)
As proteins progress through the cisternae of the GA they are modified by enzymes that may add or remove components until the protein is in its mature form
It then packages proteins into vesicles for export from the cell through exocytosis
Vesicles
Secretory vesicles break through GA
Are membrane bound and move to plasma membrane where they fuse with it and discharge protein contents to the exterior through exocytosis
