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DNA and Proteins
Stage 2 Biology - topic 1: DNA and proteins
| Term | Definition |
|---|---|
| Biotechnology | The modification of living organisms for human purposes, also called genetic engineering |
| Genetic code | The set of rules used by living cells to translate information encoded within genetic material into proteins |
| Plasmids | Simple loops of DNA in bacteria containing a couple of genes, separate from the large circular chromosome |
| Viruses | Non-living infectious agents containing DNA or RNA that can invade cells and make the cells express the genes on the viral DNA/RNA |
| DNA Probe | A short strand of DNA or RNA with a base sequence complementary to the target gene, used for locating specific genes |
| Restriction enzymes | Enzymes derived from bacteria that cut DNA at specific recognition sequences, often used to isolate genes of interest |
| Eco R1 | An example of a restriction enzyme, with the recognition sequence GAATTC |
| Sticky end | The little piece of single-stranded DNA left by the cut from a restriction enzyme. It's ready to bind with other sticky ends cut with the same restriction enzyme |
| Bacterial transformation | The process by which bacteria take up external DNA, often used to introduce new genes into bacteria |
| Electroporation | A method of introducing DNA into cells by applying an electric field, increasing the permeability of the cell membrane |
| Microinjection | A method of introducing DNA directly into the nucleus of a cell, often used in embryos to create transgenic organisms |
| Agrobacterium tumefaciens (Agrobacterium) | A soil bacterium that can infect plants and insert its Ti plasmid DNA into plant cells |
| Ti plasmid | Tumor-inducing plasmid found in Agrobacterium tumefaciens, used for introducing genes into plants |
| CRISPR-Cas9 | A bacterial immune system that can be repurposed for precise gene editing in other organisms |
| Cas9 | An enzyme produced by bacteria in the CRISPR system that cuts DNA at a specific location guided by RNA |
| Guide RNA | RNA that binds to Cas9 and leads it to the complementary sequence of a target DNA for cutting |
| De novo proteins | New proteins designed and created from scratch using computational methods and gene synthesis |
| Transgenic | term used to refer to an organism that contains genes from other organisms |
| Target gene | A gene intentionally inserted into a different organism |
| DNA hybridisation of a probe | Combination of separated DNA strands with the probe, by binding it to the complementary bases on one of the strands. |
| recognition sequence | A specific sequence of nucleotides at which a restriction enzyme cleaves a DNA molecule |
| DNA ligase | an enzyme that joins DNA fragments by making bonds between the sugar and phosphate in the sugar-phosphate backbone after the bases have bound complementary to one another with hydrogen bonds |
| Heat shock | Cells are heated to disrupt the cell membrane and allow plasmids to enter |
| Transformation | process in which one strain of bacteria is changed by a gene or genes from another organism |
| DNA Extraction | Cell membrane broken down by detergents. Protease removes the proteins associated with DNA. Ethanol makes DNA precipitate. Centrifuging concentrates the DNA. |
| PCR | polymerase chain reaction |
| Denaturation (PCR) | the first step of PCR when the DNA sample is heated to 94 to separate strands as hydrogen bonds |
| PCR in order | Denaturation. Anealing. Elongation. |
| Annealing (PCR) | DNA primers attach to opposite ends of the target sequence in the DNA at 40-60 degrees |
| Elongation (PCR) | A heat-tolerant DNA polymerase (Taq) copies the strands at 72 degrees |
| PCR Ingredients | DNA, primers, free nucleotides, Taq Polymerase |
| Taq polymerase | A DNA synthesis enzyme that can withstand the high temperatures of PCR |
| Primer | A short segment of DNA that acts as the starting point for a new strand |
| 92 degrees | Denaturation in PCR |
| 40-60 degrees | Annealing in PCR |
| 72 degrees | Elongation in PCR |
| DNA amplification | Creation of many copies of a segment of DNA by the polymerase chain reaction |
| Gel Electrophoresis | A method for separation and analysis of biomacromolecules and their fragments, based on their size and charge. Smaller fragments travel further in a set time |
| Agarose gel | preferred gel for DNA electrophoresis |
| Negative charge | Used to separate DNA strands in gel electrophoresis |
| DNA Amplification | Creation of many copies of a segment of DNA by the polymerase chain reaction |
| Restriction enzyme | Enzyme that cuts DNA at a specific sequence of nucleotides |
| Relationship between DNA fragment size and distance moved in Gel electrophoresis | Small pieces travel faster and so go further in the same amount of time as the large pieces, spreading out |
| Chain termination method | method of DNA sequencing using labeled dideoxynucleotides to terminate DNA replication; it is also called the dideoxy method or the Sanger method |
| Sanger sequencing | Dideoxynucleotides halt DNA polymerization at each base, generating sequences of various lengths that encompass the entire original sequence. Terminated fragments are electrophoresed and the original sequence can be deduced. |
| Dideoxynucleotide | type of nucleotide used during DNA sequencing to terminate synthesis. *Special* ATGC with different coloured flourescent tags on each base type |
| capillary tube | A thin tube used for gel electrophoresis when sequencing DNA |
| Electropherogram | 4 colour data printout of the Sanger sequence with the fluorescent dyes |
| DNA sequencing | Determining the exact order of the base pairs in a segment of DNA. |
| short tandem repeats (STRs) | sections of a chromosome in which DNA sequences are repeated e.g.GATAGATAGATAGATA is 4 repeats of GATA Used to make DNA "fingerprints" |
| DNA fingerprint | a representation of parts of an individual's DNA that can be used to identify a person or sample of tissue or fluid |
| locus (pl. loci) | Location of a gene or short tandem repeat (STR) on a chromosome |
| DNA profile | A distinctive pattern of DNA fragments (e.g. STRs) that can be used to match a biological sample to an individual |
| Economic issues of collecting genetic information | - Cost of storing and securing DNA database is high - Genetic testing can be expensive for patients |
| Cultural issues of collecting genetic information | - May result in discrimination - Some cultures or religious groups may see it as unnatural |
| Ethical issues of collecting genetic information | - Data privacy: Employers and insurers could use to discriminate - If you find out you have a rare genetic disorder, are you obliged to tell relatives? |
| Differentiation | process in which cells become specialized in structure and function |
| gene expression | process by which a gene produces its product and the product carries out its function |
| Transcription factor | A regulatory protein that binds to DNA and affects transcription of specific genes. |
| stem cell | unspecialized cell that can give rise to one or more types of specialized cells |
| Genotype | genetic makeup of an organism |
| Phenotype | the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment. |
| hormones | chemical messengers that are manufactured by the endocrine glands, travel through the bloodstream, and affect other tissues |
| promotor region | portion of a gene that signals for RNA polymerase to start transcription |
| Methylation | addition of a methyl group to cytosine |
| epigenetics | the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself. |
| epigenome | The genome-wide distribution of epigenetic marks. |
| substitution mutation | Mutation in which a single base is replaced, potentially altering the gene product. |
| deletion mutation | a mutation in which one or more pairs of nucleotides are removed from a gene, causing a frame shift |
| insertion mutation | a mutation in which one or more nucleotides are added to a gene, causing a frame shift |
| frame shift | a genetic mutation caused by a deletion or insertion in a DNA sequence that shifts the way the sequence is read |
| mutagen | A chemical or physical agent that interacts with DNA and causes a mutation. AKA mutagenic chemical |
| ionizing radiation | may cause mutation e.g x-rays and UV |
| high temperatures (effect on DNA) | may cause mutation |
| viruses (effect on DNA) | may cause mutations |
| Mutagenic chemical (example) | cigarette smoke |
| Trisomy 21 | Also called Down Syndrome. Caused by an extra chromosome 21. |
| Polypeptide | A polymer (chain) of many amino acids linked together by peptide bonds. |
| Primary Structure | The first level of protein structure; the specific sequence of amino acids making up a polypeptide chain. |
| Secondary Structure | The second level of protein structure; the regular local patterns of alpha helix or Beta sheets of a polypeptide chain. |
| Tertiary Structure | The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the amino acids making up the chain. |
| Quaternary Structure | The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits. |
| Alpha Helix | the spiral shape resulting from the coiling of a polypeptide in a protein's secondary structure |
| Beta Pleated Sheet | sheet-like secondary structure of proteins |
| Haemoglobin structure | large, globular protein made of four polypeptide chains, |
| Enzyme | A type of protein that speeds up (catalyses) a chemical reaction in a living thing |
| Receptor proteins | Proteins that transmit information in and out of cells. They bind complementary to signalling molecules like hormones |
| Hormone | Chemical messengers, often proteins, that bind complementary with receptors |
| hormone-receptor complex | a hormone bound to a receptor molecule |
| active site | a region on an enzyme that binds to a substrate during a reaction. |
| Substrate | reactant of an enzyme-catalyzed reaction |
| Product | A substance produced in a chemical reaction |
| Antibody | A molecule produced by the body that binds complementary to part of an invading virus or bacteria (antigen) and inactivates it |
| Complementary | Having a shape that fits with another molecule e.g active site of enzyme with a substrate, hormone with a receptor, antibody with an antigen |
| ase | ends names of enzymes |
| synthesis reaction | an enzyme reaction in which two or more substances combine to form a new compound |
| breakdown reaction | an enzyme reaction when one reactant breaks down to form two or more products |
| lock-and-key model | The model of the enzyme that shows the substrate fitting perfectly into the active site |
| Induced fit model | Change in the shape of an enzyme's active site that enhances the fit between the active site and its substrate(s) |
| Denaturation | loss of normal shape of a protein due to heat or other factor |
| optimal temperature | Temperature at which an enzyme works the best |
| optimal pH | pH at which an enzyme works best |
| mutation | a random error in a gene that leads to loss of function in a protein because it is not the correct shape |
| competitive inhibitor | A substance that competes with substrate for active site because it has the same shape as the substrate |
| non-competitive inhibitor | A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing its shape so that it no longer binds to the substrate |
| feedback inhibition | A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway |
| enzyme concentration | The greater concentration of the enzyme the greater the rate of reaction |
| substrate concentration | enzyme activity increases with this; more collision between substrate molecules and the enzyme |
| enzyme saturation | A point of substrate concentration at which all enzymes are engaged, and adding more substrate will not increase reaction rate. |
| activation energy | Energy needed to get a reaction started |
| How enzymes lower activation energy | Straining bonds in reactants to make it easier to achieve transition state - Positioning reactants together to facilitate bonding |
| Chromosomes | a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes. |
| Translation | Process by which mRNA is decoded and a protein is produced |
| Transcription | (genetics) the organic process whereby the DNA sequence in a gene is copied into mRNA |
| Protein | An organic compound that is made of one or more chains of amino acids |
| DNA | deoxyribonucleic acid, a self-replicating material present in nearly all living organisms as the main constituent of chromosomes. It is the carrier of genetic information. |
| Ribosome | Cytoplasmic organelles at which proteins are synthesized. |
| amino acids | building blocks of proteins |
| Polypeptide | A polymer (chain) of many amino acids linked together by peptide bonds. |
| Nucleotide | monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base |
| Cytosine | The base that pairs with Guanine |
| Guanine | The base that pairs with Cytosine |
| Thymine | The base that pairs with Adenine in DNA |
| Adenine | The base that pairs with Thymine in DNA |
| Uracil | Nitrogen base that pairs with adenine in RNA. |
| Ribose | A five-carbon sugar present in RNA |
| Deoxyribose | A five-carbon sugar that is a component of DNA nucleotides |
| nitrogenous base | A molecule found in DNA and RNA that encodes genetic information in cells. |
| complementary base pairing | In DNA, T pairs with A; G pairs with C; RNA, U pairs with A and G pairs with C |
| double helix | Shape of DNA |
| Gene | A segment of DNA on a chromosome that codes for a specific trait |
| Introns | Noncoding segments of nucleic acid that lie between coding sequences. |
| Exons | Coding segments of eukaryotic DNA. |
| Splicing | removal of introns and rejoining of exons |
| mRNA | messenger RNA |
| mature mRNA | mRNA after splicing has occurred |
| nuclear pores | small holes in the nuclear membrane |
| rRNA | ribosomal RNA |
| tRNA | transfer RNA; type of RNA that carries amino acids to the ribosome |
| protein synthesis | the formation of proteins by using information contained in DNA and carried by mRNA |
| Codon | A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid |
| Anticodon | group of three bases on a tRNA molecule that are complementary to an mRNA codon |
| Triplet | group of three bases on the template strand of DNA that are complementary to the triplet that occurs on mRNA |
| AUG | start codon (methionine) |
| 5' to 3' | The direction that polymerase adds free nucleotides to a growing chain |
| Circular Chromosome | Form of chromosome present in prokaryotes (e.g. bacteria) |
| Linear Chromosomes | Form of chromosome present in eukaryotes |
| Hydrogen bonds | The form of bond between complementary bases |
| Phosphate group | Binds with a sugar to make the backbone of DNA |
| Sugar-phosphate backbone | The alternating chain of sugar and phosphate to which the DNA and RNA nitrogenous bases are attached |
| Antiparallel | The opposite arrangement of the sugar-phosphate backbones in a DNA double helix. |
| Histone | protein molecule around which DNA is tightly coiled in chromatin |
| Unbound DNA | DNA in prokaryotes that is not wound around histones |
| cytosol | liquid portion of cytoplasm |
| Replication | Copying process by which a cell duplicates its DNA |
| Semi-conservative | Each half of an original DNA molecule serves as a template for a new strand, and the two new DNA molecules each have one old and one new strand. |
| Helicase | An enzyme that untwists the double helix of DNA at the replication forks. |
| DNA polymerase | Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule |
| RNA polymerase | enzyme that links together the growing chain of RNA nucleotides during transcription using a DNA strand as a template |
| Protein Synthesis | the formation of proteins by using information contained in DNA and carried by mRNA (Transcription + Splicing + Translation) |
| Amino acid | Building blocks of protein |
| 64 | number of possible codons |
| 20 | number of amino acids |
| degenerate code | multiple codons encode a single amino acid |
Created by:
justineforrest
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