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Biology AOS1 -Nucleic Acids and Protein roles - Coggle Diagram
Biology AOS1 -Nucleic Acids and Protein roles
2B - Nucleic Acids
Encode instructions for the synthesis of proteins
Nucleoties consist of a pentose (5 carbon) sugar, a nitrogen containing base and one or more phosphate groups.
5' prime end is where the 5th carbon is
Nucleotides can only be added to the 3' end
RNA
mRNA
Carries a copy of the genetic code fron the DNA in the nucleis to the ribosome
tRNA
Carries amino acids from the cell cytoplasm to the ribosome, and pairs with the complimentary code carried by the mRNA
rRna
Comprises 60% of the ribosome structure the other 40 is proteins
2C - Genes
2D - Gene Expression
Genetic code and protein synthesis
A cell produces proteins by reading and interpreting the information within the genes of DNS (This is known as gene expression)
Protein synthesis occurs through - Transcription, RNA processing, Translation.
the steps in protein synthesis is possible because genes follow the genetic code which is a set of rules by which information is encoded in genetic material.
The genetic code has a non-overlapping triplet nature, universal and degenerate.
Non-overlapping triplet nature - nucleic acids are read in successive sets of three nucleotides. Each nucleotide is only part of one codon.
Universal - The same nucleic acid sequence codes for the same amino acids in all living things
Degenerate - A single amino acid can be coded for by more than one codon
Gene expression
Transcription
What?
Creation of a pre-mRNA molecule from genetic information found in dna
Why?
DNA is large and cannot leave the nucleus, so transcription is important as it creates a smaller molecule thar is able to leave the nucleus and spread the code for a protein around the cell
Initiation
Activation of transcription: Proteins called transcription factors bind to the promoter region to activate transcription.
With the help of these factors, RNA polymerase binds to the promoter region.
This then signels for the weak hydrogen bonds between two DNA strands to break
The result is the bases of each strand being ecposed. The DNA helix is unwound and unzipped and the RNA is then able to start transcribing
2A- Protein structure and function
Definitions
Protein - A biomacromeleculemade of amino shapes folded into a 3D shape.
Polypeptide - A long chain of amino acids. Proteins can be made out of one or many
Proteome - All the proteins that are expressed by a cell or an organism at a given time.
Protein Diversity - The folding of a protein into a woeking tertiary or quarterly structure. This depends on its primary structure
Functions of proteins
Enzymes
Transport
Structure
Hormones - e.g insulin
Defense
Storage
Amino acid structure
The chemical structure is composed of a central carbon aton, a carbocyl group (COOH), an amino group (NH2), an R-group and a hygrogen atom.
Protein structure
Secondary Structure
Tertiary Structure
Quaternary structure
When 2 or more Tertiary structures bond together - Is functional
2 or more polypeptide chains each with their own structure held together by hydrogen bonds
The bonds form and fold together to create a more 3D shape
chaperone proteins bring them together and are held by hydrogen bonds.
When a polypeptide coils and folds by forming hydrogen bonds between amino acids. Structures include - Alpha Helix, Beta pleted folds, Random coils
Formed by condensation polymerisation reaction
The sequence amino acids form peptide bons between the amino acids and carboxyl group.
opposites attract
2E - Gene Regulation
Why
Energy conservation and produce the appropriate proteins ( Even though every somatic cell is identical not all cells express the same genes)
Structural Genes
A segment of DNA that doesn't code for regulatory proteins, but instead code for structural or functional proteins.
Regulatory genes
A segment DNA responsible for producing regulatory proteins that control the expression of other genes.
Regulatory genes can turn gene expression off or on, aswell as increase and decrease the rate of gene expression by promoting or hindering transcripton.
repressor proteins
Proteins which inhibit or decrease the expression of STRUCTURAL GENES
Activator proteins
Can initiate or increase the expression of structural genes.
Prokaryote
Operons are found in prokaryotic genes
A cluster of linked genes that share a common promoter and operator and are transcribed at the same time.
Operators
Operators are always located downstream of the genes promoter region, they can be used as a binding site for repressor or activator proteins, which are produced by regulatory genes, and control gene expression.
The trp operon contains a series of fenes that are involved in the production of the amino acid
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. It is composed of a series of structural genes which are controlled by a common promoter and operator.
The entire TRP is monited by a regulator upstream
2F - Protein Secretory Pathway
PSP - The protein secrarory pathway incolves various organelles that produce, fold, modify and package proteins, eventually exporting them from the cell via the process of exocytosis.
Many of the proteins produced by cells do not actually remain in the cell that produced them. Instead, they are often exported out of the cell so that they can be used somewher else in the body.
Export of waste products to ensure that toxins do not build up within the intracellular enviroment.
Exocytosis
exocytosis is the process by which the contents of a vesicle are released from the cell
Bulk transport
Exoctosis is a form of bulk transpoert which allows for the movement of large substances, such as proteins out of the cell.
Bulk transport is a form of active transport, and therefore, the process of exocytosis requires the input of energy.
Ecocytosis is possible due to the fluid nature od the plasma membrane which allows it to fuse with the vesicle.
Stages
A vesicle containing secretory products is transported to the plasma membrane
The membrane of the vesicle fuses with the plasma membrane
secratory products are released from the cell into the extracellular enviroment
Organelles (directly) involved and their functions
Ribosome
The ribosomes are the sites of protein synthesis. They assemble the polypeptide chains from amino acidsby translating mRNA.
Rough endoplasmic reticulum
If a protein is destined to be secreted, the ribosomes synthesising it is usually attached to the rough endoplasmic reticulum rather than being free in the cytosol.
The enviroment inside the rough endoplasmic reticulum allows for the correct folding of newly formed polypeptide chains befote being passed to the gogi apparatus.
Transport Vesicle
Golgi apparatus
Secretory vesicle
Chapter 3 - Enzymes
Enzymes speed up biochemical reactions by lowering the activation energy required to initiate a given reaction
Enzymes are organic (i.e carbon based) catalysts. This means that they speed up, or cataluse, chemiocal reactions that would normally take much longer to occur
How do enzymes catalyse reactions
enzymes bind(through a conformational change) to a molecule called a substrate (which is the name given to the reactant undergoing an enzyme facilitated reaction)
Conformational change basically means that even though the enzymes are pretty much the right shape they change ever so slightly to be the perfect shape.
Upon bonding, the substrare undergoes a chemical reachtion and form a product(s), which then leaves the ebzyme
3/.The enxyme remains unchanged from the reaction and is now free to cataluyse further reations
Induced fit model
Each enzymes has an active site. The active site is a pocket like area of the enzymes rertiary structure where the substate binds to.
Due to the compatability of the complex three-dimensional structures , we say that the active site and substrate are complimentary in shape.
When a substrate binds to an enzymes active site, together they form an enzyme-substrate complex.
Upon binding, the active site undergoes a conformational change to accommodate the substrare, and the substrate undergoes a small change in turn.
Enzymes generally are written ending in 'ase'
Activation energy
Every chemical reaction requires and input of energy to start. This initial requiremement is the activation energy.
Definition
The minimum amount if energy required to energise aroms or molecules to a stare where they can underfo a chemical transformation.
Its the hurdle that reactants need to get over to start a chemical reaction.
All reactions have an activation energy, regardless if they are anabolic or catabolic.
anabolic
catabolyc
Enzymes reduce the activation energy needed in chemical reactions by bringing the reactants closer to the state they need to be in order to react.
They reduce the size of the hurdle which means the reactions can occur at a quicker rate.
Enzymes are capable of catalysing reactions continuously, and fluentlhy 'team up' to woek in chains of reactions.
Biochemical pathway
In a biochemical pathway, one enzyme will function to catalyse a substrate into a product which will then become the substrate of a second enzyme.
Enzymes are specific to their substrate, so enzymes must function in pathways to reach the desired outcome
Factors that affect enzymes
Temperature
There is not a specific temperature for all enzymes - tempreture effects can be optimal, too hot, too cold
When temperature increases enzymes and substrated move faster and collide with eachother more frequentlu, allowing reactions to occur faster.
When temperature increases, molecules have a greater kinetic energy and collide more frequently
Enzymes can be denatured under certain condition including, if the temperature goes beyond its optimal point. Denaturation causes a conformational change in the active site of an enzyme causing the substrate to no longer fit. THIS IS IRREVERSABLE
When Enzyme activity is reduced the enzyme and substrate molecules move slower and collide less frequently. When it becomes too cold enzymes experience little to no activity and can freeze. THIS IS REVERSABLE
The tollerance range refers to the wide range of a given condition that an enzyme can function under. Outside this range the enzyme is inactive.
The optimal temperature is a narrow range where the enzyme functions its best.
pH
Enzymes have optimal pHs where they function best
The pH of different enzymes vary greatly depending on where the enzymes are located
Denaturation occurs at both extremes when it comes to pH. When it increases or decreases towards its tollerance range limits enzyme activity decreases until denaturation occurs.
concentration
Competetive inhibition
Conmpetative inhabition
non competative inhabition
Coenzymes
Coenzymes assist enzymes in catalysing reactions. They bind to the active site to share energy.
4A -
Restriction endonucleases
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4B - CRSPR - CAS 9
Exposure 1
The bacteriophage injects its DNA into a bacterium, which identifies that the viral dna is a foreighn substance.
Cas1 and Cas 2 are enxymes that cut a short section of the viral DNA (typically 30 nucleotides long). This is known as a protospacer.
The protospacer is introduced to the bacterium's CRISPR gene and becomes a spacer.
Expression 2
4E recombination and transormation
Purpose
To genitacally modify bacteria to produce human proteins has revolutionised modern medicine and Agriculture.
Definition
Plasmid DNA -
Antibiotic Seletion
Transformed
Insulin
Insulin is an important hormone that regulates our blood glucose. Without insulin our glucose can't get out of the blood and into the cells.
Plasmid vectors are produced with amp(r), lacZ and BamHI restriction site.
Insulin A and B subunit genes cut and ligagted to form recombinant plasmids
Recombination
Transformation
