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246 Cards in this Set
- Front
- Back
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Evolutionary genetics
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The study of all levels of genetics as they affect evolutionary processes
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Gene
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a segment of DNA, a place on a chromosome, something that’s is passed from parent to offspring, something that’s is present among individuals in a population
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Genetics
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the study of how this hereditary information is organized, expressed, and inherited
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Model Organism
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is a species that is preeminently suited to the study at hand
• Can be raised easily and inexpensively • It produces large numbers of progeny • Its generation time is short • Genetic variants within the species are readily available for study • It has been the subject of previous studies that have produced relevant background information |
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Molecular Genetics
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the study of the principal molecules of heredity (DNA, RNA, and protein), how they are organized within the cell, and how they interact within the cell
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Population Genetics
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the study of inheritance in populations and how inheritance is affected by external factors, such as natural selection
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Quantitative Genetics
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the study of how multiple genes interact with one another and the environment
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Transmission Genetics
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the study of how genetic material, and the traits encoded by that material, are transmitted from parents to offspring
• Often called classical genetics because it was foundational |
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5´ and 3´ ends
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These are the carbons at the ends of the DNA. DNA polymerases add nucleotides only in the 5’→3’ direction.
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A form (A-DNA)
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Does not exist in living cells—is induced in lab--bases are tilted at about 20 degrees from perpendicular to the axis of the molecule. DNA-RNA hybrids and double-stranded RNA, which do exist in living cells, look like A form DNA
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adenine (A)
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nitrogenous base, purine, deoxyadenosine 5’-monophosphate
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antiparallel conformation
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The conformation of a double-stranded nucleic acid in which the 5’→3’ orientations of the two strands in the double helix run in opposite directions
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B form (B-DNA)
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the most common model for DNA—has bases stacked nearly perpendicular to the axis of the molecule at about a 36 degree angle of rotation for each base pair and with major and minor grooves in a right-handed double helix
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bidirectional replication
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when two replication forks begin in opposite directions from the origin
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cytosine (C)
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nitrogenous base, pyrimidine, deoxycytidine 5’-monophosphate
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D-loop replication
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A mode of replication in which two DNA strands in a circular molecule, separate at an origin of replication and DNA synthesis begins. The newly synthesized strand displaces an old strand and creates a displacement loop.
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deoxyribonucleic acid (DNA)
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the primary carrier of genetic information; a polymer composed of dideoxy nucleotide subunits.
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Deoxyribonucleotide
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when a ribonucleotide does not have an oxygen atom on the 2’ carbon in the ribose sugar
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DNA polymerase
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enzymes which synthesize new strands of DNA. DNA Pol-III synthesizes most of the DNA molecule. DNA polymerases cannot initiate DNA synthesis however.
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guanine (G)
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nitrogenous base, purine, deoxyguanosine 5’-monophosphate
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H form (H-DNA)
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a triple-helical form of DNA. Short sections of B-DNA may rearrange to become H-DNA. May help control the expression of genes
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Helicases
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enzymes which unwind the DNA as the replication fork proceeds along the molecule
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major groove
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the larger of the two grooves in the DNA double helix
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minor groove
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the smaller of the two grooves in the DNA double helix
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nucleic acid
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a nucleotide polymer (RNA or DNA)
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nucleotide
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4 of these subunits make up a DNA molecule. Each nucleotide consists of a five-carbon sugar, deoxyribose, with a nitrogenous base attached to one end and a phosphate group attached to the other.
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phosphodiester bond
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when the phosphate group at the 5’ end of one nucleotide attaches to the 3’ carbon of another nucleotide. There are two ester linkages
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primer
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the segment of RNA which initiates DNA synthesis
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purine
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composed of two rings; a six-membered ring fused with a five-membered ring
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pyrimidine
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have a single six-membered ring in the nitrogenous base
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θ-mode replication
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when replication proceeds bidirectionally in a circular DNA molecule to form a theta-shaped intermediate when replication is partially completed
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replication fork
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the place at which two strands separate
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ribonucleic acid (RNA)
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A nucleic acid composed of ribonucleotides that is similar to DNA
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ribonucleotide
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has an oxygen atom on the 2’ carbon of the ribose sugar
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RNA polymerase
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capable of adding ribonucleotides to a single stranded DNA template that has no nucleotides paired with it
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σ-mode (rolling circle) replication
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a type of replication in which multiple tandem linear copies of a circular molecule are synthesized
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semiconservative DNA replication
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when the two original DNA strands are conserved, each serving as a template on which a new strand forms. The two daughter molecules each contain an original parental strand and a newly synthesized strand
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semidiscontinuous DNA replication
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when one DNA strand is synthesized continuously and the other discontinuously (leading and lagging strands)
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supercoils
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structures that look like knots, but actually represent formation of secondary coils---when tension builds up in the portion of the DNA that is still wound
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telomerase
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enzyme which synthesizes the repeated sequences at the end of a chromosome. Completes the synthesis of DNA.
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thymine (T)
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nitrogenous base, pyrimidine, deoxythymidine 5’-monophosphate
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unidirectional replication
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migration of a replication fork in one direction only from an origin of replication
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uracil (U)
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nitrogenous base unique to RNA (instead of T), pyrimidine
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Z form (Z-DNA)
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double-helix is unusually wound to the left, quite narrow, there are more base pairs per helical turn than in B-DNA. Typical cellular conditions do not favor this, but situations might cause it to appear in segments.
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3´ polyadenylation
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when 100-300 adenine ribonucleotides are added to the 3’ end of the pre-mRNA
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5´ capping
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when a nucleotide with the base 7-methylguanine caps the 5’ end of the pre-mRNA that is being released
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5´ → 3´ direction
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direction which an mRNA is transcribed
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AAUAAA
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the highly conserved consensus sequence 11-30 nucleotides upstream to where the RNA molecules transcribed by RNA polymerase II are usually cleaved
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antisense strand (template strand)
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the DNA strand that serves as the template for transcription and contains the nucleotide sequence complementary to that of the RNA
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CAAT box
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the consensus sequence GGCCAATCT is present in many promoters at about -75 to -80
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central dogma
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defined as “A gene composed of DNA is transcribed into RNA, which is then translated into a polypeptide, which is then processed to become a protein”
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consensus sequences
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the most representative version of a conserved sequence in many genes
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conserved sequences
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regions of DNA that are identical or similar among the promoters studied
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coupled transcription and translation
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translation begins before transcription has terminated
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elongation
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the RNA polymerase extends the RNA chain, which rapidly separates from the DNA, allowing the DNA double-helix to re-form once the RNA polymerase has passed
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enhancer
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additional regions of DNA, usually upstream of the promoter, that influence transcription
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gene
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a segment of DNA that encodes an RNA molecule
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GT–AG rule
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helps to identify introns: GT is on 5’ end and AG is on 3’ end (GU-AG in mRNA)
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hairpin structure
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hairpin forms when complementary nucleotides in the RNA pair with each other to form a double-stranded segment: forms upstream from the consensus sequence UUUUUUA
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initiation
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RNA polymerase binds to DNA at a specific site near the beginning of a gene. After DNA separates, RNA polymerase begins transcription using one of the DNA strands as a template.
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intrinsic termination
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a mechanism in which the nucleotide sequence near the end of the transcribed RNA specified where transcription terminates
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intron
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the removed portions of the pre-mRNA
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exon
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the remaining portions of the pre-mRNA after introns are removed; spliced together to form mature mRNA
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methylation
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the enzyme-catalyzed addition of a methyl group to the nitrogenous base on a nucleotide; some nucleotides in the rRNAs undergo methylation as part of the RNA processing after transcription
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mRNA
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contains information for translation into a protein, sizes and sequences are variable
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NOR (nucleolus organizer region)
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the portion of cellular DNA that contains the tandemly repeated precursor rTNA genes; contained within the nucleolus
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Nucleolus
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helps in rRNA transcription and processing, and synthesis of the ribosomal subunits
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Polypeptide
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linear chain of amino acids
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potential terminators
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sites in a gene that have termination sequences, but do not terminate transcription
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pre-mRNA
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the unprocessed form of the mRNA molecule
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promoter
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where the initiation of transcription begins—marks the beginning of the gene
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protein
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a polypeptide that has assumed its 3-D structure
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rho-dependent termination
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Rho, a protein, interacts with the mRNA and the RNA polymerase at a site called a rho-dependent terminator, causing the RNA polymerase to cease transcription and separate from the DNA
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RNA polymerase
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a class of polymerases which transcribe genes like DNA encoding mRNA
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RNA polymerase I, II, III
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I: transcribes most genes that code for rRNA II: transcribes genes that code fro mRNAs III: transcribes very short genes, including those that code for tRNA and very small rRNAs
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rRNA
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is a structural component of the ribosome, which is the site where the mRNA is translated into a protein
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sense strand (non-template strand)
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the DNA strand that contains the same nucleotide sequence as the RNA
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snRNA
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are involved in eukaryotic mRNA processing
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spliceosome
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a particle, made up of snRNPs, snRNAs, which helps in intron removal from mRNA-encoding genes
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TATA box (Hogness box)
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most eukaryotic mRNA genes have the consensus sequence TATAAAA, a conservedd DNA sequence at about -25 to -30
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termination
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the RNA polymerase reaches the end of the gene, ceases transcribing, and leaves the DNA
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transcription
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the process by which the genetic information is transferred from DNA to RNA
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transcription start point
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the site on the DNA where RNA polymerase adds the first ribonucleotide
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translation
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Polypeptide synthesis in which the amino acid sequence is encoded by a specific RNA sequence
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tRNA
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very small, and carries amino acids to the ribosome for incorporation into the protein
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upstream/downstream
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sites on the DNA. Downstream: the direction of transcription Upstream: opposite direction to transcription
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α helix
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common part of protein secondary structure
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acceptor arm
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forms the part of the tRNA molecule that accepts the amino acid
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amino acid attachment site
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Amino acid attaches to the terminal A on the 2’ or 3’ hydroxyl group
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amino acids
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building blocks of protein. Have a common structure consisting of a central carbon atom with a carboxyl group, an amino acid, and hydrogen atom bound to it
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anticodon
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the center 3 codons on the anticodon arm which lies opposite the acceptor arm in the cloverleaf and consists of a base-paired stem and a loop of seven unpaired nucleotides. The nucleotides in this site pair with 3 codons in mRNA during translation. Written in 3’ to 5’ direction.
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β strand
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linear strand of amino acids. Free to form hydrogen bonds with other amino acids
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β turn
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irregular conformations that serve as bridges between two regular secondary structural conformations
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β-pleated sheet
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formed when beta strands line up side by side and form hydrogen bonds with one another
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charged tRNA
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an amino acid that has its amino acid attached. Has its amino acid attached by a bond between the 2’ or 3’ hydroxyl group on the 3’ end of the tRNA and the carboxyl group of the amino acid
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codon
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Triplet nucleotide combinations. The genetic code has 64.
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cognate tRNAs
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Different tRNAs that carry the same amino acid
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disulfide bond
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the bond formed between the R groups of two cysteines, which stabilizes the tertiary structure of a polypeptide
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enzyme active site
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location in the enzyme where the reaction takes place
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large ribosome subunit
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larger of two subunits that attach to an mRNA during initiation of translation
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peptide bonds
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In translation, amino acids are attached to each other through the formation of these bonds. A peptide bond forms in an enzyme-catalyzed reaction
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polypeptide
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A long chain formed by many amino acids attaching to each other by peptide bonds
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polysome
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when ribosomes and mRNA assemble together
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protein primary structure
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the linear sequence of amino acids attached to each other by peptide bonds
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protein secondary structure
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when polypeptide chains interact with each other: alpha helix, beta strand, beta turn, and the random coil.
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protein tertiary structure
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interactions between the amino acid residues contained in secondary structures causing the polypeptide to fold back on itself; common tertiary interaction is a disulfide bond, beta-pleated sheet
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quaternary structure
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when two or more protein subunits assemble to form the final protein
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R-groups
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the side group of an amino acid that is the only part of the molecule that differs from one amino acid to the next: only 20 different side groups that are utilized in translation
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random coil
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an irregular formation that serves as a bridge between two regular secondary structural conformations (similar to beta-turns)
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reading frame
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initiation codon establishes this reading frame 1) codons in the mRNA do not overlap 2)there are no intervening nucleotides between codons
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ribosome
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composed of rRNA molecules and numerous proteins
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ribosome A site
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aminoacyl or entry site within the ribosome that can hold tRNAs; the ribosome assembles on the mRNA with the A site oriented toward the 3’ end of the mRNA
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ribosome P site
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peptidyl or donor site within the ribosome that can hold tRNAs; the ribosome assembles on the mRNA with the P site toward the 5’ end
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Shine-Dalgarno sequence
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the second conserved sequence, AGGAGG, about seven nucleotides upstream from the initiation codon
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small ribosome subunit
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a smaller subunit of a ribosome, assembled prior to translation
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start codon
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there is an initiation codon somewhere near the 5’ end of the mRNA. It is usually AUG and codes for methionine in eukaryotes and N-formyl methionine in prokaryotes.
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termination codon or stop codon
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3 codons, also called stop codons, that do not specify amino acids and are signals for termination of translation (UAA, UAG, UGA)
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tRNA synthetase
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aka aminoacyl-tRNA synthetase. Is an enzyme which catalyzes the charging of tRNA
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wobble hypothesis
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set of base-pairing rules that explains the pattern of degeneracy in the genetic code. Provides pairing rules for the third nucleotide in a codon with its corresponding nucleotide in the anticodon
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Alkaptonuria
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an inherited disorder which turns urine dark when exposed to the air; has homogentisic acid
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alkylating agent
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adds alkyl groups to several positions on all of the nitrogenous bases of DNA, creating lesions
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AP site
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apurinic or apyrimidinic sites; where a base is missing; they are chemically identical and thus both called AP sites; DNA replication ceases at an AP site
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auxotrophic mutant
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a type of mutation which confers a requirement for supplementation of minimal medium to overcome the effects of the mutation
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β-globin gene
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encodes the protein B-globin, a subunit of adult hemoglobin
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biochemical pathway
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a series of steps through which most compounds in a cell arise; each step is determined and regulated by a specific enzyme
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carcinogen
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cancer-causing agents that mutate certain genes that regulate cell growth and division
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cryptic splice site
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where an intron is removed but is cleaved incorrectly at alternative splice sites; used only when a mutation prevents cleavage of the intron at the correct splice site
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cytosine deamination
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a type of spontaneous lesion in which the amino group on the number 2 carbon of C is removed and a double-bonded oxygen is left in its place
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damaged DNA
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DNA that contains lesions
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deaminating agent
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include bisulfite compounds and nitrous acid; chemical mutagens that express their effects by modifying bases in DNA rather than incorporating themselves into the DNA
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deletion mutation
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point mutation in which one or more nucleotides are deleted from the DNA
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depyrimidination
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a type of chemical alteration that is produce by hydrolysis of the bond between deoxyribose sugar and a pyrimidine base
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end product
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the last intermediate in a pathway
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forward mutation
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a mutation that changes an original, usually functional, form of a gene to a mutant form, in which the DNA sequence differs from the most common sequence; detected as a loss of protein function
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fragile X full mutation
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when the repeated regions expand significantly beyond the premutation size
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fragile X premutation
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repeats ranging from 50 to 230; people with this don’t show symptoms, but descendents of females with the mutation are at high risk
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fragile X syndrome
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a genetic disorder due to expansion of a region in DNA where the trinucleotide sequence CGG is repeated several times in tandem
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frameshift mutation
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deletion and insertion mutations that shift the reading frame
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free radical
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a highly reactive molecule with an unpaired electron; tend to be highly reactive with DNA, attacking and altering bases
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gain-of-function mutations
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mutation that may cause a gene to gain function compared to its previous state, usually by producing greater-than-normal quantity of protein; more rare than loss-of-function mutations
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gene expression
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the process through which the nucleotide sequence of a gene is ultimately manifest in the phenotype of an organism
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genotype
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the underlying genetic constitution that confers the phenotype
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Hb A
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the normal hemoglobin molecule with glutamic acid at position 6 in the Beta-subunits
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Hb S
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the mutant hemoglobin molecule with valine at position 6 in the Beta-subunits
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heme group
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consist of an iron atom surrounded by a protoporphyrin ring; nonprotein substance added to each protein subunit to form the tertiary
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heme pocket
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the pocket in each of the four subunits of the hemoglobin molecule into which oxygen is drawn
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hemoglobin
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a protein essential for the cells of the body to carry out aerobic respiration
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homogentisic acid
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the substance in urine which turns dark in air—in people with alkaptonuria; not degraded by enzymes because they are not present due to a mutation
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Huntington disease
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another disease due to trinucleotide repeat expansion; characterized by progressive neurological degeneration that usually does not begin until after the age of 30
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hydroxylating agent
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adds hydroxyl groups to the bases of nucleotides; a chemical mutagen that causes hydroxyaminocytosine to pair with A instead of G
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imaginal disks
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masses of embryonic tissue that are destined to develop into adult organs in drosophila
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induced mutation
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caused by external agents that chemically alter DNA, usually causing some form of DNA damage
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insertion mutation
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point mutation in which one or more nucleotides are inserted into the DNA
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intercalating agent
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a class of chemical compounds that are similar to the nitrogenous bases in DNA and RNA; these agents insert themselves between the stacked bases in a process called intercalation which causes the DNA molecule to stretch at the insertion point
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ionizing radiation
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high-energy radiation, including protons, neutrons, x-rays, and alpha, beta, gamma rays; mutagenic
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lesion
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chemical modifications of DNA such that it no longer carries one of the four standard bases; not a mutation because it cannot be propagated by DNA replication
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loss-of-function mutation
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mutations that have an effect on a proteins activity to either reduce the proteins ability to function or eliminate its function altogether
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minimal medium
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a medium where neurospora can be grown; composed of sugar, several minerals, and vitamin biotin
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missense mutation
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a mutation that causes an alteration in the amino acid sequence of a gene’s product
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mutagen
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agents that enter the cell and cause mutations (induced mutations)
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mutation hotspots
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certain sites in DNA molecules where insertion and deletion mutations are unusually frequent; short, repeated DNA sequences are present at these sites
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nonionizing radiation
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does not have enough energy to strip electrons from atoms; instead, it causes electrons to assume temporarily higher energy levels within the atom, called excitation; UV radiation is the most important type
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nonsense mutation
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a missense mutation that creates a new termination codon
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one gene-one enzyme
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the idea that each gene produced one enzyme; later modified
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one gene-one polypeptide
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idea that each gene produced one polypeptide; more true than one-gene-one-enzyme
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phenotype
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the outward characteristic that can be measured or observed.
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point mutation
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a change in a single nucleotide or in a few adjacent nucleotides in the DNA; usually affects only one gene
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pyrmidine dimer
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a type of lesion caused by UV light causing covalent bonding between the two adjacent pyrimidines; if left unrepaired, can cause mutations
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reversion
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a second mutation that restore’s the gene’s functions
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same-sense mutation
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a mutation that makes no change in the amino acid sequence; these mutations are also silent mutations
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sickle-cell anemia
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a serious geneteic disorder characterized by weakness, fatigue, heart failure, joint and muscle impairment, abdominal pain and dysfunction, impaired mental function, and eventual death, often during childhood
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silent mutation
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mutations that do not alter protein function
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spontaneous mutation
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naturally occurring mutations due to errors in DNA replication or natural chemical reactions in DNA
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substitution mutation
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most common type of point mutation in which one nucleotide pair is substituted for another.
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suppressor mutation
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a mutation that causes reversion; mutation that produces a separate product that compensates for the lost activity of the first
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tautomeric shift
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when a base temporarily shifts to a less stable form that alters its pairing properties; may cause transitions
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thalassemia
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a genetic disorder caused by a reduction of beta-globin synthesis or the absence of beta-globin.
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transition
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a purine→ purine substitution or pyrimidine → pyrimidine substitution; more frequent than transversions
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transversion
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a purine→ pyrimidine substitution or pyrimidine→ purine substitution
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true breeding
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breed for a trait so that offspring from a plant will all have the same trait as the parent plant
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monohybrid experiments
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experiments in which the two true-breeding parents differ in their phenotypes for only one trait
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parental generation
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varieties that serve as parents for a cross
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F1 generation
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the first-generation progeny of a cross between two true-breeding parents
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Monohybrid
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a hybrid for one trait
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F2 generation
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the progeny of the F1 individuals that have been self-fertilized or crossed with one another
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dominant phenotype
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The phenotype that appeared in the F and in ¾ of the F2 progeny
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recessive phenotype
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the phenotype which was absent from the F1 but reappeared in ¼ of the F2 progeny
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Mendel’s principle of segregation
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because homologous chromosomes segregate from each other during meiosis, alleles at the same locus on homologous chromosomes also segregate from each other, so half the gamest receive one allele and half receive the other
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dihybrid experiments
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experiments in which the original parents differed in two traits but were the same for the other five
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Mendel’s principle of independent assortment
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The inheritance of seed color has no influence on the inheritance of seed shape
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Alleles
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different DNA sequences at the same locus
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Locus
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referring to a gene in terms of its location on a chromosome
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Homozygous
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AA or aa
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Heterozygous
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Aa
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Genotype
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an individual’s genetic composition
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Phenotype
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What we actually see
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Punnett square
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way to predict the outcome of self-fertilization
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monohybrid testcross
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cross between Aa and aa
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parental equivalence
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In the formation of both male and female gametes, segregation of alleles is the same
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trihybrid
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experiments in which the original true-breeding parents differ in three traits
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forked-line method
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an approach that gives the same information as a punnett square
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linked genes
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when genes do not assort independently because they are close together on the same chromosome
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product rule
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when two events are independent of one another, the probability that they will occur together is the product of their individual probabilities
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sum rule
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if two events are mutually exclusive, the probability that one of the two events will occur is the sum of their individual properties
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binomial distribution
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a convenient way to determine certain probabilities
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binomial coefficient
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n!/x!y! portion of the equation
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multinomial distribution
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applied when there are more than two classes into which individuals can fall
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sampling error
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the deviation from expected ratios due to random variation
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chi-square analysis
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compares observed values with hypothesized expected values and determines the probability of observing that outcome under the assumption that the hypothesis is correct
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significant
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.05 is significant
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highly significant
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.01
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type I error
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the erroneous rejection of a correct hypothesis
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multiple alleles
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when more than two alleles for a single locus are present in a population
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incomplete dominance
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when the phenotype of the heterozygote is intermediate between the phenotypes of the two homozygotes
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wild-type alleles
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alleles most often found in nature
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mutant alleles
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deviations from the wild type
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gain-of-function mutation
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a mutation that increases the amount of the gene’s product
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loss-of-function mutation
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results in either an altered product or no product at all
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constitutive mutation
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product is produced constantly
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threshold effects
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For some genes, the normal phenotype is only expressed when a particular threshold level of gene-product function is attained
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codominance
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the distinct expression of both phenotypes in the heterozygotes
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antigens
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substances that interact with antibodies produced by the immune system during an immune reaction
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Bombay phenotype
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people with this phenotype are usually diagnosed as having type O blood because they have neither the A nor the B antigens
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leaky recessive alleles
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an allele that may encode a mutant enzyme that has some function but only a reduced amount
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compound heterozygote
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individuals who are heterozygous for different alleles that confer the same phenotype
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dominance series
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where each allele is dominant over all alleles to its right and recessive to all alleles to its left—> there is potential for this when more than two alleles are present in a population
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lethal alleles
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a mutant allele that eliminates a function essential for survival may kill the organism—often detected as a class of progeny that is absent
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pleiotropy
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the situation in which a single gene influences more than one phenotypic trait
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epistasis
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when one gene in the pathway may influence how another is expressed
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complementary gene action
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the dominant phenotype is encoded by the presence of at least one dominant allele at each locus
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duplicate gene action
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the dominant phenotype is encoded by the presence of at least one dominant allele at either locus
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dominant suppression
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a dominant allele at one locus suppresses the effect of a dominant allele at another locus
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dominant epistasis
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the dominant I allele masks the effect of both alleles at the R locus
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penetrance
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refers to whether the genotype is expressed in the phenotype
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nonpenetrant
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when the phenotypic expression of a particular genotype is lacking under certain conditions
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expressivity
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defines the degree of expression when the genotype is expressed
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modifier genes
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genes that have a minor effect on a phenotype determined by a major groove
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genetic background
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refers to all genes in an individual except the one under study
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DNA markers
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fragments of DNA that can be distinguished from one another because of differences in their nucleotide sequences
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restriction fragment length polymorphisms (RFLPs)
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relies on differences in DNA sequence that affect the position of restriction enzyme recognition sites in the DNA
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tandem nucleotide repeat markers
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a special class of RFLPs based on DNA sequences that are repeated in tandem
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minisatellites
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same thing as VNTRs (below)
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variable number tandem repeats (VNTRs)
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xonaiar od DNA segments of about 10-100 nucleotide pairs that are repeated several times in tandem
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microsatellites (short tandem repeat polymorphisms (STRPs)
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are similar to minisatellites but the repeated segment is shorter, usually consisting of di, tri, or tetranucleotide repeats
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PCR-based markers
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PCR can be used to generate DNA markers for genetic analysis
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random amplified polymorphic DNA (RAPDs)
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is a rapid PCR based DNA marker method to do preliminary DNA sequencing
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