U6 - Expression & Regulation Cram

"X-ray crystallography (Franklin, 1950s)"

"Technique used by Rosalind Franklin to image DNA. Her results showed DNA has a regular, repetitive pattern consistent with a helix."

"Chargaff's Rules"

"For all species: A = T and C = G. Adenine pairs with thymine, cytosine pairs with guanine. Applies to DNA base composition."

"Purines"

"Nucleotides with a double ring structure: adenine and guanine."

"Pyrimidines"

"Nucleotides with a single ring structure: cytosine, thymine (DNA), and uracil (RNA)."

"Hydrogen bonds in A-T base pair"

"Two hydrogen bonds hold adenine and thymine together."

"Hydrogen bonds in C-G base pair"

"Three hydrogen bonds hold cytosine and guanine together."

"Watson-Crick model of DNA"

"First 3D double helix model of DNA, combining Franklin's helix shape data and Chargaff's base pairing rules."

"DNA backbone"

"Sugar-phosphate backbone. Nucleotide bases are found in the center, pairing between the two strands."

"Antiparallel strands"

"The two DNA strands run in opposite directions: one 5' to 3', the other 3' to 5'. The 5' end has a free phosphate group; the 3' end has a free hydroxyl group."

"What is the primary function of DNA?"

"DNA is the primary source of heritable genetic information, storing and transmitting information across generations. RNA serves this role in some viruses."

"Eukaryotic DNA location and chromosome shape"

"Eukaryotic DNA is in the nucleus. Chromosomes are linear."

"Prokaryotic DNA location and chromosome shape"

"Prokaryotic DNA is in the nucleoid region. Chromosomes are circular."

"Plasmids"

"Small, circular DNA molecules separate from the main chromosome. Found primarily in prokaryotes. Replicate independently and carry genes useful in specific environments but not required for basic survival."

"What happens when a gene of interest is inserted into a plasmid?"

"A recombinant plasmid is formed. When inserted back into bacteria, the bacteria express the inserted gene."

"Horizontal gene transfer via plasmids"

"Bacteria can exchange plasmid DNA with neighboring cells. Recipient bacteria can then express the acquired genes, aiding survival."

"RNA vs. DNA: strand structure"

"RNA is single stranded. DNA is double stranded."

"RNA vs. DNA: base pairing rules"

"RNA: A=U, C=G. DNA: A=T, C=G."

"RNA vs. DNA: full names"

"RNA = ribonucleic acid. DNA = deoxyribonucleic acid."

"When does DNA replication occur?"

"During the S phase of the cell cycle."

"Conservative model of replication"

"The parental double strand directs synthesis of an entirely new double strand. The original strands are fully conserved together in one molecule."

"Semi-conservative model of replication"

"Each parental strand serves as a template. After one round, each daughter molecule contains one parental strand and one new strand."

"Dispersive model of replication"

"Parental DNA is broken up and distributed randomly between daughter molecules, which contain a mix of parental and new DNA."

"Meselson-Stahl experiment"

"Used heavy (15N) and light (14N) nitrogen isotopes in bacteria to test replication models. Results (Gen 1: 100% hybrid; Gen 2: 50% hybrid, 50% light) supported semi-conservative replication."

"Give an example of semi-conservative replication proportions across generations."

"Gen 1: 100% hybrid. Gen 2: 50% hybrid, 50% light. Gen 3: 25% hybrid, 75% light. Gen 4: 12% hybrid, 88% light."

"Origin of replication"

"Site on the chromosome where DNA replication begins. Proteins attach here and open the DNA to form a replication fork."

"Helicase"

"Enzyme that unwinds the DNA double helix at the replication fork."

"Single-strand binding proteins (SSBPs)"

"Proteins that bind to separated DNA strands to prevent them from re-bonding during replication."

"Topoisomerase"

"Enzyme that relieves strain ahead of the replication fork by relaxing supercoiling."

"Primase"

"Enzyme that adds short RNA primers to the parental DNA strand, providing a 3' end for DNA polymerase to extend from."

"Why are RNA primers needed in DNA replication?"

"DNA polymerase can only add nucleotides to an existing strand. Primers provide the initial 3' hydroxyl group that DNA polymerase needs to start synthesis."

"DNA Polymerase III (prokaryotes)"

"Main replicative polymerase. Reads the template strand 3' to 5' and synthesizes new DNA 5' to 3'."

"Leading strand synthesis"

"Synthesized continuously toward the replication fork. Requires only one primer. DNA polymerase moves in the same direction as fork progression."

"Lagging strand synthesis"

"Synthesized discontinuously, away from the replication fork. Requires many primers. Produced as short Okazaki fragments."

"Okazaki fragments"

"Short segments of DNA synthesized on the lagging strand. Later joined into a continuous strand by DNA ligase."

"DNA Polymerase I (prokaryotes)"

"Replaces RNA primer nucleotides with DNA nucleotides after Okazaki fragments are formed."

"DNA ligase"

"Joins Okazaki fragments by forming phosphodiester bonds, creating a continuous lagging strand."

"Why do linear chromosomes have a 5' end replication problem?"

"DNA polymerase can only add to a 3' end, so the 5' end of the lagging strand cannot be completed. Without a fix, chromosomes would shorten with each replication."

"Telomeres"

"Repeating non-coding nucleotide sequences at the ends of linear chromosomes. They form a cap that postpones erosion of coding sequences."

"Telomerase"

"Enzyme that adds telomere repeats to chromosome ends, counteracting shortening over successive replications."

"DNA proofreading"

"DNA polymerase checks each added nucleotide during synthesis. Incorrectly paired nucleotides are removed and replaced."

"Mismatch repair"

"Post-replication repair process. Enzymes identify and replace incorrectly paired nucleotides that escaped proofreading."

"Nucleotide excision repair"

"If DNA segments are damaged, nucleases remove the affected nucleotides, and DNA polymerase plus ligase replace them."

"Gene expression"

"The process by which DNA directs protein synthesis. Consists of two stages: transcription and translation."

"Transcription"

"Synthesis of RNA using a DNA template. Occurs in the nucleus (eukaryotes) or cytoplasm (prokaryotes). The template strand is read 3' to 5'; mRNA is built 5' to 3'."

"Translation"

"Synthesis of a polypeptide using mRNA as a template. Occurs at ribosomes in the cytoplasm. Converts a nucleotide sequence into an amino acid sequence."

"mRNA (messenger RNA)"

"Synthesized during transcription. Carries the coding sequence from the nucleus to ribosomes in the cytoplasm."

"tRNA (transfer RNA)"

"Carries a specific amino acid. Has an anticodon that base-pairs with the complementary mRNA codon. Key player in translation."

"Anticodon"

"A three-nucleotide sequence on tRNA that is complementary and antiparallel to the corresponding mRNA codon."

"rRNA (ribosomal RNA)"

"Component of ribosomes. Helps catalyze peptide bond formation between amino acids during translation."

"Template strand"

"The DNA strand transcribed during transcription. Also called the noncoding, minus, or antisense strand. mRNA is complementary and antiparallel to it."

"Base-pairing rules during transcription"

"A (DNA) pairs with U (RNA). T (DNA) pairs with A (RNA). C pairs with G. G pairs with C."

"Give an example of transcription: DNA template 3'-ATACGCAAT-5'"

"mRNA produced: 5'-UAUGCGUUA-3'. Codons UAU, GCG, UUA code for Tyr, Ala, Leu."

"Codon"

"A group of three mRNA nucleotides that codes for one amino acid or a stop signal."

"Codon count breakdown"

"64 total codons: 61 code for amino acids, 3 are stop codons. Start codon is AUG (codes for methionine)."

"Start codon"

"AUG. Codes for methionine. Marks the beginning of translation."

"Stop codons"

"Three codons (UAA, UAG, UGA) that do not code for amino acids. Signal termination of translation."

"Genetic code: universality"

"The genetic code is universal across all life. Supports the concept of common ancestry."

"Redundancy in the genetic code"

"Most amino acids are coded by more than one codon. This means many point mutations are silent."

"Reading frame"

"The specific grouping of codons on mRNA that must be maintained for correct protein synthesis. A shift by even one nucleotide changes every downstream codon."

"Give an example of reading frame shift."

"Correct: THE FAT CAT ATE THE RAT. Shifted by 1: HEF ATC ATA TET HER AT. Completely different meaning, illustrating why frameshift mutations are so disruptive."

"RNA polymerase"

"Enzyme that transcribes DNA into RNA. Reads the template strand 3' to 5' and builds RNA 5' to 3'."

"Promoter region"

"A specific DNA sequence upstream of a gene where RNA polymerase (and transcription factors) bind to initiate transcription."

"TATA box"

"A sequence commonly found in eukaryotic promoter regions. Helps position RNA polymerase for transcription initiation."

"Transcription factors (eukaryotes)"

"Proteins that must bind the promoter before RNA polymerase can bind and initiate transcription in eukaryotes."

"Sigma factor (prokaryotes)"

"A small protein subunit that binds RNA polymerase and allows it to recognize and bind a specific promoter in prokaryotes."

"Transcription bubble"

"The locally unwound region of DNA formed when RNA polymerase binds and separates the strands, exposing the template for transcription."

"Transcription elongation"

"RNA polymerase moves downstream along the template strand (3' to 5'), adding complementary RNA nucleotides to the 3' end of the growing mRNA (5' to 3'). DNA re-forms behind it."

"Transcription termination (prokaryotes)"

"RNA polymerase transcribes a termination sequence, causing it to detach. mRNA is released directly and proceeds to translation with no processing needed."

"Polyadenylation signal sequence (eukaryotes)"

"DNA sequence transcribed by RNA polymerase. Produces AAUAAA in the RNA, which triggers enzymatic cleavage and release of pre-mRNA from RNA polymerase."

"What three modifications must eukaryotic pre-mRNA undergo before translation?"

"1. 5' cap (modified guanine nucleotide). 2. Poly-A tail (50-250 adenine nucleotides at 3' end). 3. RNA splicing (introns removed, exons joined)."

"5' cap function"

"Modified guanine nucleotide added to the 5' end of pre-mRNA. Aids ribosome recognition and protects mRNA from degradation."

"Poly-A tail function"

"50-250 adenine nucleotides added to the 3' end of pre-mRNA. Stabilizes mRNA, aids nuclear export, and protects from degradation."

"RNA splicing"

"Removal of introns from pre-mRNA and joining of exons to produce mature mRNA."

"Introns"

"Non-coding intervening sequences in pre-mRNA. Removed during RNA splicing. Do not code for amino acids."

"Exons"

"Coding sequences in pre-mRNA that are retained and joined after splicing. Code for amino acids."

"Alternative splicing"

"Different combinations of exons from the same pre-mRNA are joined, allowing one gene to produce multiple different polypeptides."

"Mature mRNA"

"Pre-mRNA after all three modifications (5' cap, Poly-A tail, splicing). Leaves the nucleus and is translated at ribosomes."

"Aminoacyl-tRNA synthetase"

"Enzyme that attaches the correct amino acid to its corresponding tRNA. Produces charged tRNA."

"Charged tRNA"

"A tRNA molecule carrying its specific amino acid, ready to participate in translation."

"Ribosome structure"

"Two subunits: small and large. Prokaryotes: 30S (small), 50S (large). Eukaryotes: 40S (small), 60S (large). The large subunit has A, P, and E sites."

"A site (ribosome)"

"Aminoacyl site. Holds the incoming charged tRNA carrying the next amino acid."

"P site (ribosome)"

"Peptidyl site. Holds the tRNA carrying the growing polypeptide chain."

"E site (ribosome)"

"Exit site. The tRNA that has donated its amino acid exits the ribosome from here."

"Translation initiation"

"Small ribosomal subunit binds mRNA. Charged tRNA carrying methionine binds the start codon AUG. Large subunit joins. Met-tRNA goes to the P site. All other tRNAs enter at the A site."

"Translation elongation: 3 steps"

"1. Codon recognition: charged tRNA anticodon matches mRNA codon at A site. 2. Peptide bond formation: polypeptide transfers to A-site tRNA. 3. Translocation: A-site tRNA moves to P site, P-site tRNA moves to E site, A site opens for next tRNA."

"Translation termination"

"A stop codon reaches the A site. A release factor binds, hydrolyzes the bond holding the polypeptide to the P-site tRNA. Polypeptide is released. Ribosome disassembles."

"Primary protein structure"

"The linear chain of amino acids linked by peptide bonds. Determined entirely by the gene sequence."

"Secondary protein structure"

"Local coils and folds (alpha helices, beta sheets) stabilized by hydrogen bonds between backbone atoms."

"Tertiary protein structure"

"Overall 3D shape of a single polypeptide, determined by side-chain (R-group) interactions."

"Quaternary protein structure"

"The assembly of two or more polypeptide chains interacting to form a functional protein complex."

"Chaperone proteins"

"Proteins that assist other polypeptides in folding correctly. Some polypeptides cannot reach functional conformation without them."

"Retroviruses and reverse transcription"

"Retroviruses (e.g., HIV) carry RNA as their genome. Reverse transcriptase converts viral RNA into DNA, which integrates into the host genome and is used as a template for RNA production during replication."

"Reverse transcriptase"

"Enzyme used by retroviruses to synthesize DNA from an RNA template, reversing the normal flow of genetic information (RNA to DNA)."

"Gene expression and phenotype"

"The combination of which genes are expressed and at what level determines cell phenotype. Not all genes are expressed in every cell. Environment can also affect phenotype."

"Give an example of same DNA producing different cell types."

"Neurons and muscle cells have identical DNA but express different sets of genes, producing neuron-specific or muscle-specific proteins."

"Variable expressivity"

"The same disease-causing genotype produces different severity of symptoms in different individuals."

"Constitutively expressed genes"

"Genes transcribed at all times regardless of conditions. Provide a continuous supply of essential products (e.g., housekeeping genes for glycolysis)."

"Inducible genes"

"Genes whose transcription can be switched on or off in response to environmental or internal signals (e.g., rice pathogen-defense genes)."

"Why must cells regulate gene expression?"

"To save energy and resources, respond to environmental changes, and in eukaryotes, maintain different specialized cell types."

"Operon"

"A cluster of related bacterial genes controlled by a single promoter, transcribed together as a unit. Components: promoter, operator, structural genes."