definitions Flashcards
Organic Molecule
Contain C and H.
Proteome
Complete set of proteins expressed by the organism at a certain point in time.
Primary Structure
Linear sequence of amino acids in the polypeptide chain.
Secondary Structure
Folding/coiling of regions of the polypeptide chain.
Tertiary Structures
Folding/coiling of the entire polypeptide chain, resulting in its 3D structure.
Quaternary Structure
2 or more polypeptide chains joined together to form a single functional protein.
Chaperonins
Proteins that assist with the folding of other proteins.
Fibrous Proteins
Elongated and insoluble.
E.g. Catalase
Globular Proteins
Folded and coiled into a spherical tertiary and/or quaternary structure. Generally soluble.
E.g. Collagen
Denaturisation
Process of altering hydrogen bonds, disulphide bridges, that create the tertiary structure.
Usually loss of function.
Cofactors
Non-biological compounds that assist with protein folding and function.
Condensation Polymerisation
Reaction during which nucleotides link together.
Gene
Region of DNA that contains information to produce a protein.
Genome
Complete set of genes in an organism.
mRNA
Carries copy of DNA from nucleus to ribosomes.
rRNA
rRNA and proteins make up ribosomes.
tRNA
Transfers amino acids from cytoplasm to ribosomes.
Ribosomes
Organelles that make proteins based on mRNA instructions.
Codon
Triplet of nucleotides.
Degenerate
More than 1 codon can code for the same amino acid
RNA Polymerase
Synthesises RNA by transcription of genes.
Promoter
Binding region for RNA polymerase.
Exons
Sections of gene that codes for protein
Introns
Sections of gene that does not code for protein.
Transcription
Production of mRNA from DNA in nucleus.
Initiation:
Transcription factors join to RNA polymerase.
RNA polymerase recognises it, attaching and unzipping the DNA molecule by breaking hydrogen bonds.
Elongation:
RNA polymerase moves along, creating a transcription bubble. It moves from 3’-5’on the DNA and creates the mRNA prime from the 5’-3’ direction.
Termination:
Transcription ends when RNA polymerase reaches the termination codon and detaches.
The DNA molecule reforms.
RNA Processing
5’ cap added to 5’ end.
Poly-A tail added to 3’ end.
Splicing removes introns and joins exons together.
Alternative Splicing
mRNA can be spliced in many ways as some exons may be removed.
Translation
Codons on mRNA translated into amino acid sequence by ribosomes.
Initiation:
Ribosome attaches to 5’ end of mRNA strand, moving along until it reaches the start codon.
tRNA binds joins to start codon, attaching to complementary bases.
Elongation:
Complementary tRNA molecules adds specific amino acids to the growing polypeptide chain via condensation polymerisation.
Termination:
When stop codon reached, polypeptide chain released into the cytoplasm or rough endoplasmic reticulum.
Regulatory Genes
Code for transcription factors that control rate of expression for other genes.
Structural Genes
Code for proteins that are not involved in gene regulation.
Operon
Unit of DNA, consisting of regulated clusters of related genes.
Enzyme
Organic catalysts that increase the rate of metabolic reactions by lowering the activation energy.
Active Site
Part of enzyme formed by tertiary folding that interacts with specific substrate to catalyse a specific reaction.
Lock and Key Model
Substrate has a complementary shape to active site.
Induced Fit Model
Substrate binds to active site and creates a ‘conformational change’ of active site so they fir better.
Catabolic Reactions
Substrates broken down and energy released.
Anabolic Reactions
Require input of energy to produce larger molecules from smaller substrates.
Reversible Inhibition
Bonds between inhibitor and enzyme weak and can be easily broken.
Irreversible Inhibition
Bonds between inhibitor and enzyme are strong and can’t be broken.
Competitive Inhibition
Shape of inhibitor is complementary to shape of active site, blocking substrate from binding.
Non-competitive Inhibition
Inhibitor binds to an allosteric site, changing the shape of the enzyme’s active site.
Coenzymes
Non-protein, organic cofactors.
Cytokines
involved in communication between immune cells.
Apoptosis
Programmed cell death.
Vector
Organism that spreads disease to others but is not affected by it.
Virus
Highly infectious pathogen that infects living cells and uses the cell’s metabolic machinery to replicate.
Prion
Misfolded proteins that have pathogenic properties.
Bacteria
Unicellular prokaryotes that can have pathogenic properties.
Antigen
Specific group of molecules that can induce an immune response.
Self-Antigen
Displayed by cells of organism.
Non-self-Antigen
Not displayed by cells of organism.
Foreign material provoking an immune response.
First Line of defence
Physical, chemical microbiological barriers that provide innate resistance.
Innate Immune Response
Non-specific, fast acting response against pathogens that have entered the organism.
Leukocytes
White Blood cells
Phagocytes
Leukocytes that engulf and breakdown pathogens via phagocytosis.
Complement Proteins
Proteins that circulate in the blood and create pores in pathogen’s membrane, enhancing phagocytosis.
Opsonisation
Tagging of antigens, attracting phagocytes to pathogen.
Interferons
Cytokines that are produced by host cell infected by virus. Activates nearby cells to increase resistance and create antiviral proteins.
Inflammation
Accumulation of fluid, plasma proteins and leukocytes that occurs when tissue is damages or infected.
Fever
Increase in body temperature to create unfavourable environment for pathogen.
Adaptive Immunity
Specific, slower response against pathogens.
Results in immunological memory.
Immunological Memory
Ability to remember antigens after primary exposure to create more effective secondary response upon re infection.
Lymphocytes
White Blood Cells that are specific for adaptive immune response.
Humoral Immunity
Antibodies produced by b cells secreted into bloodstream.
Cell-Mediated Immunity
Action of T lymphocytes and phagocytes.
Clonal Expansion
After clonal selection, specific lymphocyte will proliferate and differentiate.
Plasma Cells
Specialise in antibody production
Memory B Lymphocytes
Can divide and give rise to plasma cells upon secondary exposure to pathogen.
Antibody/Immunoglobin
Protein produced by plasma cells as part of the humoral immune response
Neutralisation
Binding to pathogens and toxins to inhibit their action.
Agglutination
Bind to antigens, forming inactivated clumps that enhance phagocytosis.
T helper Cells
Promote inflammation and activates B cells and macrophages.
Cytotoxic T cells
Recognise/kill foreign/infected host cells by releasing perforins, which lyses cell, or initiates apoptosis.
Antigen-Presenting Cells
Cells that have specialised function to display antigens on MHC class-II proteins.
MHC-I
Communicate with cytotoxic t cells about proteins being produced in each cell.
Located on every nucleated cell
MHC-II
Only present in APCs.
Lymphatic System
Network of tubes that drains lymph from body tissues
Lymph
Fluid in tissues
Lymph Nodes
Contain lymphocytes that filters the lymph for antigens and pathogens.
Active Immunity
Protection provided by individual’s own adaptive immune response.
Passive Immunity
Protection provided through the transfer of antibodies produced by another organism.
Attenuated Vaccines (Viruses)
Vaccines that contain microbes that has been weakened.
Inactivated Vaccines (Bacteria)
Contain microbes that have been inactivated.
Requires booster shots.
Subunit Vaccines
Vaccines that do not contain live microbes.
E.g. only antigens injected.
Require multiple doses.
Toxoid Vaccines
Use toxins to stimulate response.
Herd Immunity
Phenomenon in which a sufficient number of people in a population need to be vaccinated in order to significantly reduce the chances of the disease spreading throughout the population.
Essential for Protection of those who can’t be vaccinated.
Allergens
Non-pathogenic substances that invoke an immune response.
Autoimmune Disease
When lymphocytes recognise self-antigens as non-self and results in an adaptive immune response directed against them.
Antigenic Drift
Small mutations in the genes of a virus that leads to changes to surface proteins of the virus.
Antigenic Shift
Major mutations in the genes of a virus that leads to the creation of new subtypes.
Chemotherapy
Administration of drugs that are cytotoxic to cells that multiply rapidly.
Immunotherapy
Any treatment that harnesses the immune system of a patient to fight diseases.
Monoclonal antibodies
Antibodies produced by single clone of B cell in culture to produce a large volume of the clone.
Alleles
Variations of a gene
Species
Group of organisms that can interbreed to produce viable and fertile offspring.
Gene pool
Sum of alleles possessed by individuals in the population.
Mutation
Changes in the DNA sequence due to chance events.
Point Mutation
Mutation that adds/removes/changes a single nucleotide in the DNA sequence.
1 nucleotide replaced with another.
Altered codon still codes for the same amino acid due to degeneracy of genetic code.
Missense mutation
Altered codon codes for another amino acid.
Nonsense mutation
Altered codon becomes a stop codon, likely resulting in the production of a truncated protein.
Frameshift Mutation
One/two nucleotides are added/removed altering sequence of all codons following the insertion/deletion.
Block mutation
Mutation that affects large segments of chromosomes.
Duplication Mutation
Replication of section of chromosome.
Deletion Mutation
Deletion of segment of chromosome
Inversion
Section of chromosome detaches, rotates 180o, then reattaches.
Translocation
Segment of chromosome exchanged with another segment.
Aneuploidy
Presence of abnormal number of a particular chromosome.
Polyploidy
Condition that results from cells containing more than 2 times the haploid number of chromosomes.
Gene Flow
Changes in the gene pool of a population due to the migration of individuals
Genetic Drift
Allele frequencies change randomly overtime due to chance events.
Bottleneck Effect
When population size is drastically reduced due to a random chance event.
Founder effect
When a small group of organisms in a population break away from the original population to start their own.
Fossils
Preserved remains of previously living organisms or their traces.
Impression Fossils (Mould fossil)
When organism decays, leaving impression of organism’s surface.
Cast Fossils
Impression fossils that have been filled with foreign material.
Mineralised Fossil
Impression fossils that have been filled with minerals.
Trace Fossil
Preserved evidence of organism’s activity or behaviour
Transitional Fossils
Show features of both ancestral species it originated from and the descendent species that is evolving into.
Law of superposition
Lowest stratum is the oldest, above strata get progressively younger.
Index Fossil
A fossil used as a basis of comparison to determine the relative ages of other organisms.
Must be:
Abundant (Big population size)
Widespread (occupies different locations)
Short-lived (If long-lived, leads to greater uncertainty due to organism occupying several strata/layers)
Easily identifiable
Carbon-14 Dating
Calculating the amount of C-14 in proportion to C-14 in the organism.
Half-life: 5730 years
Only valid for 50,000 years.
Argon-Potassium Dating
Calculating the amount of Ar-14 in igneous rock near organism.
Half Life: 1.25 billion years
Only valid for more than 500,000 years.
Divergent Evolution
When a species becomes more phenotypically different due to their exposure to different selection pressures.
Evident by homologous structures
Convergent Evolution
When dissimilar species become phenotypically similar due to their exposure to similar selection pressures.
Evident by analogous structures.
Homologous Structures
Features with same morphology but can have different functions.
Analogous Structures
Features with different morphology but similar structures.
Vestigial Structures
Structures that had a purpose in the ancestral species by serves little to no purpose in the current descendent species.
Molecular Homology
Comparing DNA/protein sequences between species to determine their evolutionary relationships.
Molecular Clock
The usage of the assumption that DNA accumulates mutations at a constant rate to determine approximately how long ago species diverged from a common ancestor.
Primate
Order including apes and old-world monkeys (no prehensile tail).
Features:
Opposable thumbs
Flattened nails
Stereoscopic vision
Longer gestational period
Hominoid
Superfamily including all extant apes, their extinct ape ancestors, and gibbons.
Hominid
Family including all extant apes and their extinct ape ancestors.
Features:
No tails.
Molars have 5 cusps.
Flattened rib cage
Partially/fully erect posture.
Locomotion by brachiation (Climbing from branch to branch), knuckle-walking or bipedalism.
Hominin
Tribe including all extant members of the homo genus and their extinct, bipedal ancestors.
Australopithecus afarensis/africanus
- First bipedal ape/hominin.
- Evolved in Africa.
Homo habilis
Made the first tools
Homo erectus
- First to use fire
- First to expand out of Africa
- More systematic hunting
Trends overtime
- Pelvis became wider and more bowl-shaped to support more weight.
- Larger cranial capacity.
- Reduced brow ridge.
- Flatter face
- Spine became S-shaped
- Increased Valgus angle between knees to bring knees under body for support.
- Reduced jaw size due to cooking.
- Arms got shorter, legs got longer.
- More centralised Foramen magnum
Cultural Evolution
Accumulation of knowledge passed onto the next generation by verbal, written or symbolic communication.
Multiregional Evolution Model
Homo erectus migrated across Africa, Asia and Europe.
Isolation of populations resulted in divergence of gene pools, but some gene flow occurred, resulting in evolution of all groups.
Out of Africa Model
After Homo erectus left, Homo sapiens evolved and spread, displacing older populations.
Polymerases
Enzymes that catalyse the formation of polymers of nucleic acids.
Polymerase Chain Reaction
Process used to amplify (make multiple copies of) target sequences of DNA.
Denaturation: heated to 94oc to break hydrogen bonds
Annealing: cooled to 55oc, to allow primers to bind/anneal to the ends of template strands.
Extension: heated to 72oc, to allow Taq polymerase to create new double-strands from 3’-5’ direction.
Repeat
Gel Electrophoresis:
Process of separating DNA fragments based on size.
1. Agarose + buffer solution prepared and placed into chamber.
2. Wells made at negative end.
3. DNA samples loaded into wells.
4. DNA ladder is added.
5. Power attached.
6. Small fragments move faster/further, bigger fragments move slower/shorter.
7. Fragments detected by applying a stain.
Plasmids
Small circular DNA molecules found in bacteria
Restriction Enzymes (Endonucleases)
Enzymes that cut DNA into smaller fragments at specific recognition/restriction sites.
Ligases
Group of enzymes that joins fragments of DNA/RNA by forming phosphodiester bonds.
Recombinant DNA
DNA from 2 different sources joined together.
Heat Shock
Placing bacterial cells and recombinant plasmids in ice-cold solution, then increasing temperature to disrupt the plasma membrane.
Electroporation
Mixture of bacterial cells and plasmids subjected to an electric shock to disrupt plasma membrane.
DNA Profiling
Comparing non-coding sections of DNA of individuals.
Issues:
- Wrongly identifying person.
- Person can be forced to give DNA sample
- Storing DNA may be seen an unethical.
Short Tandem Repeats
Repeating sequence of 2-6 nucleotides. Number of repeats vary amongst individuals, and so is used during DNA profiling.
Genetically Modified Organism
Any organism in which DNA has been artificially modified.
Transgenic Organism
Any organism in which foreign DNA has been introduced into their genome.
Emerging Diseases
Previously unrecognised diseases that have rapidly increased in incidence and virulence over time.
Virulence
Ability of the pathogen to cause disease.
Epidemic
Sudden increase of cases in a population at a particular time.
Pandemic
Spread of disease over various regions of the world at a given time
