Biology Exam Revision

DNA

Two polypeptide nucleotide strands that are double stranded.

Antiparallel

Refers to the orientation of the two strands of DNA.

Phosphate group

5' end of a DNA strand.

Sugar group tail end

3' end of a DNA strand.

Template strand

DNA acts as a template that is complementary to the coding strand, containing coded information to synthesize proteins.

RNA

Single stranded, has nitrogenous bases, carries genetic information for protein synthesis.

mRNA

Takes genetic code transcribed from DNA to ribosome.

rRNA

Located in ribosome.

tRNA

Carries specific amino acids to ribosome to build protein.

Nucleic acids

Information molecules that carry genetic information.

Nucleotide

Monomer that makes up nucleic acid (polymer).

Hydrogen bonds

Form between nitrogenous bases in double stranded DNA.

Phosphodiester bonds

Form between phosphate and pentose sugar of two different nucleotides, to form a single strand.

Peptide bond

Form between amino acids.

Gene expression

Involves genes undergoing transcription and translation to produce proteins which shape characteristics of organism.

Structural genes

Involved in structure or function.

Regulatory genes

Control the activity of other genes, often code for repressor proteins which bind to promoter region and prevent transcription.

Gene structure

Includes a promoter at the start, introns that are spliced out, exons that are coding segments of DNA, and an operator region in prokaryotes as a regulatory mechanism.

Transcription

Creation of complementary messenger RNA from DNA in the nucleus.

RNA processing

Involves removal of introns, alternative splicing, addition of Poly A tail and Methyl cap, resulting in final mRNA.

Translation

Building of polypeptide chains from amino acids guided by sequence of codons in mRNA.

Stop codon

A sequence of nucleotides that signals the end of protein synthesis.

Amino acid structure

Composed of an amino/amine group, a carboxyl group, and a side chain with an R group (variable).

Proteins

Required for cell function and structure, existing in globular (3D rounded shape) and fibrous (long structure) forms.

Proteome

Set of proteins produced by an organism.

Primary structure

Sequence of amino acids in a polypeptide chain.

Secondary structure

Folding formed by hydrogen bonds between atoms in a polypeptide chain, causing the chain to coil and pleat.

Alpha helix

A type of secondary structure that provides elasticity.

Beta pleated

A type of secondary structure that is not elastic but strong.

Random coils

A type of secondary structure that contributes to protein diversity.

Tertiary structure

Overall 3D folding of a protein resulting from secondary structure undergoing further folding held together by various bonds between the R groups.

Quaternary folding

The joining together of two or more polypeptide chains.

Denatured protein

A protein that loses its shape and becomes non-functional, often irreversibly.

Cells

Smallest functioning unit of life.

Organelles

Specialized structures within a cell that perform specific functions.

Mitochondria

Site of aerobic respiration.

Chloroplast

Site of photosynthesis.

Ribosome

Site of protein synthesis.

RER (Rough Endoplasmic Reticulum)

Site of protein folding and packaging into vesicles.

Golgi apparatus

Site of protein modification (addition of carbohydrates) and packaging into secretory vesicles.

Lysosome

Site of lipid synthesis.

Transport vesicle

Moves substances from the RER to the Golgi apparatus.

Secretory vesicles

Transport substances to be excreted from the cell, made of a phospholipid bilayer.

Gene regulation

The process that starts or stops transcription and translation of proteins.

Operon

A group of structural genes with related functions usually encoded together in the genome in a block called an operon and transcribed together under the control of a single promoter or operator region.

Trp operon

Found in E. coli bacteria, these genes code for enzymes to make the amino acid tryptophan, used in protein synthesis.

Repressor Protein

A protein that binds to the operator region to prevent RNA polymerase from binding to the promoter, inhibiting transcription when activated by high tryptophan.

Attenuation

The process where high tryptophan levels lead to simultaneous transcription and translation, causing a terminator hairpin to form and RNA polymerase to detach, stopping transcription.

Anti terminator

Allows RNA polymerase to continue, prevents detachment

Selective breeding

Breeding organisms with favourable traits to increase chances of offspring possessing these traits

Genetically modified organism

Organisms whose genome has been altered using genetic engineering techniques - Faster, success rate varies

Transgenic organism

Type of GMO that has DNA inserted from another species

CRISPR Cas-9

Used to delete, repair, mutate DNA

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)

Separates spaces (stored bacteriophage sequences from previous encounters)

Cas9

Enzyme that cuts DNA

gRNA

Allows CRISPR-Cas9 to identify specific DNA sequence in genome (by being complementary to specific sequences of DNA, and is transcribed from CRISPR region)

Cas9-gRNA complex

Finds and attaches to specific target

Process (in DNA technology)

1. sgRNA is produced that is complementary to gene of interest 2. Bind sgRNA to Cas9 3. sgRNA will guide Cas9 to gene of interest 4. sgRNA binds to complementary DNA then Cas9 will bind to PAM sequence 5. Cas9 cuts DNA of interest

Restrictive enzymes

Cut DNA at specific recognition sequence

Palindromic recognition

Reads same running 3' to 5' as it does 5' to 3'

Sticky ends

Overhang of one of DNA strands, generally preferred by scientists as easier to combine DNA from different sources (fragments naturally anneal due to hydrogen bonds of complementary strands)

Blunt ends

No overhang

Ligase

Enzyme that forms phosphodiester bonds so that fragments are joined permanently

Polymerase

Enzyme that adds nucleotides and copies whole genes

PCR

Semi conservative process that copies small amounts of DNA quickly

Primer

Short single stranded sequence of DNA complementary to part of target DNA, that binds to section of DNA that polymerase than attaches to (provides starting point)

Taq polymerase

Type of DNA polymerase that binds to the primer, synthesizes the new DNA strand, and can survive in high temperatures

Denaturation

DNA is heated to 95 degrees to separate strands

Annealing

DNA cooled to 55 degrees. Short DNA primers anneal to both strands of DNA (3' ends)

Extension

Temperature increased to 73 degrees. Taq polymerase attached to primer and brings in free DNA nucleotides according to base pairing rule. Reads 3' to 5', makes new DNA 5' to 3'.

Reverse transcriptase

Converts RNA into DNA which is inserted into host cell genome.

Gel electrophoresis

Separates DNA fragments based on size and charge - DNA samples are loaded into well at top of gel, electric current applied. DNA negatively charged so moves towards positive terminal. Shorter fragments move faster (further). Each band contains fragments of same length. Bands are compared to DNA ladder to estimate unknown fragment length.

DNA profiling

Distinguishes individuals based on variable (non coding) regions in DNA. Short tandem repeats (STRs) are areas of 2-6 repeating bases on chromosomes that are used for profiling.

Plasmid

Small circular extrachromosomal (separate from chromosome) DNA molecule naturally occurring in bacteria.

Recombinant insulin production

1. Amplify gene of interest (through PCR) 2. Create a recombinant plasmid (cut gene of interest with restriction enzymes and cut plasmid with same restriction enzymes before inserting gene of interest + combine using ligase) 3. Transformation: uptake of foreign DNA into bacteria - Calcium chloride: Makes membrane positively charged to DNA is attracted - Heat shock: Opens pores in bacterial plasma.

Screening and selection

Bacteria are placed in agar plate with bacteria that plasmid should be resistance to if it has the antibiotic resistance gene (bacteria not containing plasmid is killed)

Recombinant insulin

Required by diabetics to lower blood glucose concentration

Cost effective recombinant insulin

High purity, not many ethical issues compared to extracting from animals

Reporter gene

Expression of this gene signals successful uptake of plasmid, specifically if gene is expressed (indicates functional protein - successful transcription and translation)

Beta galactosidase as a reporter gene

When bacteria with functioning beta gal is exposed to X gal, it turns blue

Non-functioning beta galactosidase

When bacteria with non functioning beta gal is exposed to X gal, it will turn white

Scenario 1

IF bacteria NEVER gets a plasmid, it will simply die to the ampicillin as it doesn't have the resistance gene

Scenario 2

IF bacteria contains a non recombinant plasmid (doesn't contain gene of interest), it will turn blue

Scenario 3

IF bacteria contains a recombinant plasmid, where desired gene is inserted NEXT to beta gal. gene, it will turn blue

Scenario 4

IF bacteria contains a recombinant plasmid (does contain gene of interest) where the desired gene is inserted WITHIN the beta gal. gene, it will turn white

Classic blue white screening

Shows that gene is successfully inserted; doesn't necessarily confirm correct protein folding

Functional protein indication

Scenario 2: blue colony indicates a functional protein as beta galactosidase would make a fusion protein with insulin, so if it is expressed than insulin is expressed (as they under the same promoter)

Process to create recombinant insulin

Steps to create insulin alpha and beta gene by PCR (or extract genes from cell) and remove introns

Restriction enzyme use

Cut insulin alpha gene with restriction enzyme

Plasmid A

Cut plasmid A containing an antibiotic resistance gene and beta galactosidase gene with the same restriction enzyme (so that they can bind together)

Combining genes

Combine insulin alpha gene and plasmid (they will bind) and add DNA ligase to form phosphodiester bonds between insulin and plasmid DNA backbones

Transformation

Place recombinant insulin alpha plasmid into bacteria A using transformation (heat shock method)

Selection of transformed bacteria

Select the successfully transformed bacteria using antibiotics and use blue white screening to identify blue colonies containing insulin A gene

Repeat for insulin Beta gene

Repeat steps 2-5 for the insulin Beta gene, with plasmid B and bacteria B

Insulin A and B proteins

Proteins produced by bacteria through binary fission, which are purified and combined to create functional insulin.

Consequence based approach

An ethical approach where actions are evaluated based on the best possible outcomes for the most people, regardless of whether the action is right or wrong.

Duty/rules based approach

An ethical approach where individuals have an obligation to follow rules, regardless of the consequences.

Virtue based approach

An ethical approach that considers the virtues or morals of the person carrying out the action.

Integrity

An ethical principle involving actions that reflect truth and trustworthiness.

Justice

An ethical principle involving actions that ensure fairness.