My Flashcards

Proteins

Macromolecules of 1 or more polypeptide chains folded and coiled together into a specific shape

Proteome

All the proteins expressed by a cell or organism at a given time

Primary Structure

The specific sequence of amino acids in a polypeptide chain

Secondary Structure

The folding and coiling of a polypeptide chain, resulting in the formation of alpha helices and beta pleated sheets.

Tertiary Structure

The overall functioning 3D shape of a protein. It is formed when secondary structures further fold by forming interactions and bonds between amino acids and R-Variable groups of different structures.

Quaternary Structure

The protein structure formed when 2 or more polypeptide chains with tertiary structures are bonded together to form one functional protein.

Gene

A section of DNA that stores genetic information to make a specific protein

Genome

The complete set of DNA in an organism at a specific time

mRNA

Carries genetic information from the nucleus to the ribosomes for protein synthesis

tRNA

Delivers specific amino acids to the ribosomes after recognising specific nucleotide sequences on mRNA

rRNA

Serves as the main structural component of ribosomes within cells

Universality

The idea that nearly all organisms use the same codons to encode for the same amino acids

Unambigious

The idea that each codon can only code for 1 specific amino acid

Degenerate

The idea that multiple codons can code for the same amino acid

Non-Overlapping

The idea that adjacent codons are read independently in groups of 3 nucelotides

Promoter Region

Region that serves as the binding site for RNA polymerase, the enzyme responsible for initiating transcription

Introns

Regions of non-coding DNA

Exons

Regions of coding DNA

Operator Region

The binding site for transcription factors, which are proteins that can regulate the expression of a gene

Gene Expression

The process by which the genetic information stored within a gene is used to produce a protein

Transcription (short)

The process where a sequence of DNA is used as a template to create a complementary sequence of pre-mRNA

Transcription (long)

Transcription occurs at the nucleus and begins when the RNA polymerase binds to the promoter region of a DNA sequence. This breaks the hydrogen bonds between opposite nucleotides, causing the DNA double helix to unwind and unzip. RNA Polymerase then moves along the template strand of DNA, reading the sequence in a 3' - 5' direction, and uses the free-floating RNA nucleotides to produce a complementary 5' - 3' pre-mRNA strand. Transcription stops when the termination sequence is read, causing the RNA polymerase to detach and release the pre-mRNA molecule.

Translation (short)

The process where mRNA is read to produce a corresponding sequence of amino acids to form a polypeptide

Translation (long)

Translation begins with the binding of a mRNA molecule to a ribosome, with the reading of the start codon initiating translation. tRNA molecules with complementary anticodons delivers specific corresponding amino acids to the ribosome. Adjacent amino acids are then joined together with peptide bonds to form a growing polypeptide chain. Translation ends when a stop codon is recognised, causing the ribosome to release the polypeptide chain into either the cytosol or endoplasmic reticulum.

RNA Processing

RNA processing is the process in which a pre-mRNA molecule is converted into a mature mRNA strand in order to leave the nucleus and be converted into a protein. RNA processing involves the removal of introns, splicing together of exons, and the addition of a poly-A tail to the 3' end and methyl-G cap to the 5' end, allowing for the formation of many different proteins from a single gene.

Gene Regulation

The control of gene expression either by inhibiting or activating transcription.

Structural Genes

Segments of DNA that encodes for proteins that are involved in the structure or functioning of the cell

Regulatory Genes

Segments of DNA that encode for proteins that regulate the expression of other structural genes

Trp Operon

A series of genes within E.Coli that encode for the production of the amino acid tryptophan.

Trp Repression

Trp Repression involves the use of a repressor protein to regulate the expression of trp structural genes. When tryptophan levels are high, tryptophan molecules bind to the trp repressor protein, inducing a conformational change that converts the protein into its active form. The active repressor protein will then bind to the operator region as a result, physically preventing the RNA Polymerase from transcribing the trp structural genes and hence, limiting the amount of tryptophan present in the cell. On the other hand, when tryptophan levels are low, tryptophan is not available to bind to and activate the repressor protein, meaning that the RNA Polymerase can transcribe the trp structural genes, allowing for an increase in the amount of tryptophan present.

Attenuation

Attenuation involves the use of folding in mRNA to regulate the expression of trp structural genes. In attenuation, RNA polymerase begins transcription, producing a growing mRNA strand that a ribosome begins translating simultaneously. When tryptophan levels are high, the ribosome does not have to pause at the 2 adjacent tryptophan codons that are part of the attenuator sequence in the leader region because the tRNA molecules carrying tryptophan arrives quickly. This leads to the formation of a terminator hair pin loop, which causes the ribosome to detach from the mRNA molecule. RNA polymerase will also detach from the template strand as a result, causing transcription of the trp operon to stop, meaning the tryptophan structural genes are not expressed. On the other hand, when tryptophan levels are low, the ribosome translating the mRNA will pause at the tryptophan codons in the leader region and waits for the arrival of the tRNA molecules carrying tryptophan. By pausing, an anti-terminator hairpin loop is formed instead, meaning that the ribosome will not detach, allowing for the transcription to continue and the 5 structural genes to be expressed.

Operon

A group of functionally related structural genes that share a common promoter and operator region and are regulated by the same regulatory gene

Ribosomes

The place where translation occurs, meaning that they are the site of protein synthesis

Rough Endoplasmic Reticulum

The place where polypeptide chains are folded into proteins, before being packaged into transport vesicles.

Golgi Apparatus

Modifies and packages proteins so that they are able to be packaged into secretory vesicles

Protein Secretory Pathway

The polypeptide chains for the proteins are synthesised at the ribosomes attached to the rough endoplasmic reticulum. In the endoplasmic reticulum, the polypeptide chains are then folded into proteins before being transported to the Golgi Apparatus in transport vesicles. At the Golgi Apparatus, the proteins are modified and are then packaged into secretory vesicles. The protein is then exported from the cell through exocytosis, which involves the fusion of the secretory vesicle with the plasma membrane, leading to the release of the protein into the extracellular environment.

Endonuclease

Enzymes that catalyses the cleavage of phosphodiester bonds within RNA or DNA

Ligases

Enzymes that joins fragments of DNA or RNA together by catalysing the formation of phosphodiester bonds between them

Polymerase

Enzymes that catalyses the formation of polymers from monomers

Restriction Enzymes

A type of endonuclease that cuts the nucleic acid strands at a specific recognition site.

Sticky Ends

The result of a staggered cut through DNA by an endonuclease, forming overhanging nucleotides

Blunt Ends

The result of a straight cut through DNA by an endonuclease, forming no overhanging nucleotides

Primers

Short, single stranded sections of nucleic acids that acts as a starting point for polymerases to attach.

Protospacer

Short sequences of DNA extracted from the bacteriophage DNA by the endonucleases Cas1 and Cas2, which are then incorporated into the bacterium's CRISPR gene as spacers.

CRISPR

Short, clustered repeats of DNA found in prokaryotes which protect them against viral invasion

PAM Sequence

A sequence of 2-6 nucleotides that the Cas1-Cas2 complex and Cas9 proteins are able to constantly recognise and are only present in non-self DNA.

CRISPR-Cas9 in Bacteria

Bacterias use the CRISPR-Cas9 system as a defence mechanism to protect themselves against viral attacks from bacteriophages. When a bacteriophage invades a bacterium, a Cas1-Cas2 complex cuts out a protospacer, a short section of the viral DNA, by recognising a PAM sequence. The protospacer is then introduced into the bacterium's CRISPR gene as a spacer, with repeated segments separating the spacers from each other in the CRISPR gene. The spacers is then transcribed along with half a palindrome from the repeat either side of it to produce guide RNA (gRNA). The gRNA will then bind to the Cas9 endonuclease to form the CRISPR-Cas9 complex. The CRISPR-Cas9 complex will then scans to cell to find the specific PAM sequence, which are only present in non-self DNA. Upon recognition, Cas9 unwinds and unzips the DNA, allowing the gRNA to align with the DNA. If DNA complementary to the gRNA is present, it will bind to the DNA, causing the Cas9 enzyme to cleave the phosphodiester bond, forming a blunt ends.

CRISPR-Cas9 in Gene Editing

To use CRISPR-Cas9 for gene editing, synthetic guide RNA (sgRNA) with a complementary spacer to the target DNA is created in a lab. A Cas9 enzyme with an appropriate target PAM sequence is then chosen and is added to a mixture of sgRNA to form the CRISPR-Cas9 complex, which are then injected into cells. In the cell, the Cas9 searches for the target PAM sequence and when it recognizes, it causes the DNA to unwind and unzip, allowing sgRNA to align with the adjacent DNA and if complementary, bind to the sequence, signalling Cas9 to create a blunt cut at 2 places, removing the target gene. Scientists can also inject sequences of DNA in hopes that the cell will ligate the sequence into the gap.

Taq Polymerase

A heat-resistant DNA polymerase enzyme that is used in PCR due to its extremely high optimal temperature

Polymerase Chain Reaction (short)

A DNA manipulation technique used to amplify a specific DNA sequence.

Polymerase Chain Reaction (long)

To begin the polymerase chain reaction (PCR), the DNA sample, Taq polymerase, DNA nucleotides, forward primers and reverse primers are mixed into a solution, which is placed in a thermal cycler. The first step of PCR is denaturation, in which the DNA sample mixture is heated to 94C to break the hydrogen bonds between complementary DNA strands, separating the 2 strands. The next step is annealing, where the mixture is cooled to approximately 55C to allow primers to anneal to complementary sequences on the DNA strands. The last step is elongation, where the mixture is heated to 72C, the optimal temperature of Taq polymerase. Taq polymerase will attach to the primers and uses them as a starting point to synthesise a new complementary strand of DNA. The cycle is then repeated multiple times to produce more copies, doubling the copies of DNA each time.

Gel Electrophoresis (short)

A DNA manipulation technique used to separate DNA fragments based on their molecular size

Gel Electrophoresis (long)

To begin gel electrophoresis, the standard ladder and DNA fragments are loaded into separate wells of a prepared agarose gel, which is immersed in a buffer solution rich in ions that helps it to conduct the electric current. The electric current is then passed through the gel via electrodes, where the negative electrode is positioned near the side of the wells and the positive electrode is positioned on the opposite side furthest from the wells. The negatively charged DNA fragments migrate through the pores of the gel from the negative electrode towards the positive electrode. The shorter fragments will move more easily through the pores and hence move faster and migrates further than longer fragments. After a period of time, the electric current is then switched off and the DNA fragments will settle into bands, which can be made visible under a UV light via staining.

Plasmids

Small, circular loops of DNA separate from the chromosome found in bacteria

Recombinant Plasmids

Plasmids that are edited to incorporate a gene of interest

Vector

A means of introducing foreign DNA into an organism.

Bacterial Transformation

The process in which bacteria takes up foreign DNA from their environment.

Insulin

The hormone responsible for regulating blood glucose levels

Diabetes

A disease where the body can't properly produce or respond to insulin, requiring insulin to be artificially administered into the body.

Gene of Interest

A gene that scientists want to be expressed in recombinant bacteria

Making Recombinant Plasmids

To make a recombinant plasmids, the gene of interest is cut out and isolated using a sticky end restriction enzyme. The same restriction enzyme is then used again to cut the selected plasmid open so that the plasmid vector and gene of interest have complementary sticky ends. The two are then joined together using ligase, which catalyses the formation of a phosphodiester bonds between the DNA fragment and the plasmid, creating a recombinant plasmid.

Reporter Gene

A gene with an easily identifiable phenotype so that we can identify whether a plasmid has taken up the gene of interest.

Heat Shock

In heat shock, the bacterial cells and recombinant plasmids are incubated in an ice cold calcium chloride solution, which increases the permeability of the bacterial cell's plasma membrane. Temperature is then rapidly, distrupting the plasma membrane and increasing the chances that the bacteria uptakes the plasmid, The temperature is then colled down to return the plasma membrane to its previous state.

electroploration

In electroporation, an electric current is briefly passed through a solution of bacterial cells and recombinant plasmids, distrupting the plasma membrane and increases the chances that the bacteria uptakes the recombinant plasmids.

Making Insulin

- Plasmid vector with ampicillin resistance gene, tetracycline resistance gene, BamHI and EcoRI recognition site is selected
- Subunit genes A and B are isolated using BamHI. BamHI is used again to cut open the plasmid vector so they have complementary sticky ends. They are then joined together with DNA ligase to make recombinant plasmids for each subunit gene.
- Recombinant plasmids are added to a solution of E.Coli and some of the bacteria cells take up the recombinant plasmid
- Bacteria cells are cultured on agar plates containing ampicillin, with the surviving ones being transformed bacteria
- Transformed bacteria cells are spread onto agar plates containing tetracycline, with the ones that don't survive containing the recombinant plasmids
- Recombinant plasmids are then collected, cut open using EcoRI and have a lacZ gene inserted,which is the gene that encodes B-galacotoise, the protein that forms a fusion protein with insulin subunits to protect it from enzyme digest.
- Recombinant plasmids containing the lacZ gene are added to another solution of E.Coli and some of the bacteria cells take up the recombinant plasmids
- Insulin subunits are extracted from the fusion protein and is isolated and purified. The 2 insulin chains are then mixed together, causing the formation of disulphide bonds between them, making human insulin.

Genetic Engineering

The alteration of an organism's genome using genetic recombination technologies

GMO

An organism that has had its genome altered using genetic engineering

Host Organism

The organisms that receives the altered genes

Cisgenic Organisms

GMOs that has genes from the same species inserted into its genome

Transgenic Organisms

GMOs that has genes from a different species inserted into its genome

Photosynthesis

The chemical process plants use to convert light into chemical energy

Photosynthesis Equation

6CO2 + 12H2O → C6H12O6 + 6O2 + 6H2O

Light-Dependent Stage

The stage where light energy splits water molecules into oxygen and hydrogen inside the thylakoid stage

Inputs, Outputs and Location of LD stage

Inputs - 12H2O, 12NADP+, 18ADP + Pi, Outputs - 6O2, 12NADPH, 18ATP, Location - Thylakoid

ATP

A high energy molecule that breaks down to provide energy to power cellular processes

NADPH

A coenzyme that carries electrons and protons, collecting and shuttling them at high energy.

Light-Independent Stage

The stage where carbon dioxide is used to form glucose in the stroma.

Inputs, Outputs and Location of LI stage

Inputs - 6CO2, 18ATP, 12NADPH, Outputs - C6H12O6, 18ADP + Pi, 12NADP+, 6H2O, Location - Stroma

Rubisco

The enzyme responsible for the initial carbon fixation reaction in the light-independent stage of photosynthesis

Photorespiration

A wasteful process that is initiated when rubisco binds to the oxygen

C3

Plants with no adaptation used to minimise photorespiration

C4 Plants

Plants that minimise photorespiration by separating the light-independent stage over space, with the initial carbon fixation happening in a mesophyll cell while the rest of the process occurs in a bundle-sheath cell.

CAM Plants

Plants that minimise photorespiration by separating the light-independent stage over time. The initial carbon fixation occurs at night, and the contents are stored in vacuoles before being released at a controlled rate during the day to undergo the rest of the Calvin Cycle.

Cellular Respiration

The process by which an organism breaks down glucose into usable energy in the form of ATP to power metabolic reactions

Aerobic Cellular Respiration Equation

C6H12O6 + 6O2 → 6CO2 + 6H2O + 30/32ATP

Inputs, Outputs and Location of Glycolysis

Input - C6H12O6, 2ADP + Pi, 2NAD+, Output - 2 pyruvate, 2ATP, 2NADH, Location - Cytosol

Inputs, Outputs and Location of Kreb's Cycle

Input - 2 acetyl-CoA, 2ADP + Pi, 6NAD+, 2FAD, Output - 4CO2, 2ATP, 6NADH, 2FADH2, Location - Mitochondrial Matrix

Input - 6O2, 26 or 28 ADP + Pi, 10NADH, 2FADH2, Output - 6H2O, 10NAD+, 2FAD, 26 or 28ATP, Location - Cristae

Lactic Acid Fermentation Equation

Glucose + NADH → 2 Lactic Acid + NAD+

Alcohol Fermentation

Glucose + NADH → 2 Ethanol + 2CO2 + NAD+

Renewable

A resource that can be produced at a faster rate than it is used

Carbon Neutral

A resource that has no net release of CO2 into the atmosphere

Bioethanol Production

To make bioethanol, the biomass is first broken down into starch so that its surface area is increased. Enzymes will then break down the starch and convert them into glucose via hydrolysis. Yeast will then be added and produces ethanol through anaerobic fermentation, which will then by dehydrated and purified to create liquid bioethanol.

Pathogens

Agents that cause disease

Antigens

Molecules that can be recognised by the immune system

DIsease

Distruptions or interruptions of the organism's functioning

Self Antigens

Antigens located on the surface of cells that mark it so that the immune system doesn't attack it

Non-Self Antigens

Antigens that indicate the cell is foreign, causing the immune system to attempt to eliminate it

Cellular Pathogens

Pathogens that have a cellular structure and are living organisms

Non-Cellular Pathogens

Pathogens that lack a cellular structure and are non-living organisms