Both are 5-carbon pentose sugars. Deoxyribose (DNA): missing the 2'-OH group (has only H at 2' position) -> makes DNA more stable. Ribose (RNA): has a hydroxyl group (OH) at the 2' position -> makes RNA less stable, more reactive, and susceptible to hydrolysis. The 2'-OH is why RNA is single-stranded and DNA is double-stranded
In DNA: adenine (A) pairs with thymine (T) via 2 hydrogen bonds; guanine (G) pairs with cytosine (C) via 3 hydrogen bonds. In RNA: adenine pairs with uracil (U); guanine pairs with cytosine. These rules are complementary: if one strand is 5'-ATGC-3', the other is 3'-TACG-5'. Chargaff's rules: [A]=[T] and [G]=[C] in double-stranded DNA
Each strand of the original DNA molecule serves as a template for a new strand. Result: each new DNA molecule consists of one original (parental) strand and one newly synthesized strand. Predicted by Watson and Crick; proven by Meselson-Stahl experiment (1958). Conservative and dispersive replication were ruled out
Enzyme that unwinds and separates the two DNA strands at the replication fork. Breaks hydrogen bonds between base pairs. Creates positive supercoiling ahead of the fork (relieved by topoisomerase). Moves at ~1000 nucleotides/second in prokaryotes. Forms the replication bubble (bidirectional replication in eukaryotes)
Enzyme that synthesizes new DNA strands by adding nucleotides in the 5' -> 3' direction. Requires a free 3'-OH group (needs a primer). Prokaryotes: DNA Pol III (main synthesis), DNA Pol I (primer removal/fill-in), DNA Pol II (repair). Eukaryotes: Pol alpha, delta, epsilon. All move 5' -> 3' only
Enzyme that joins Okazaki fragments on the lagging strand by forming phosphodiester bonds. Seals the gaps between short newly synthesized DNA segments. Uses ATP to catalyze the bond formation. Also used in DNA repair (joining patches of newly synthesized DNA) and in recombinant DNA technology
Leading strand: synthesized continuously in the 5' -> 3' direction toward the replication fork. Lagging strand: synthesized discontinuously away from the fork, in short Okazaki fragments (~1000 nt in prokaryotes, ~200 nt in eukaryotes). Both require primers. Primase synthesizes RNA primers (~10 nt); DNA Pol I (prokaryotes) removes primers and fills gaps
Enzyme that synthesizes RNA from a DNA template (transcription). Prokaryotes: one RNA polymerase (core enzyme + sigma factor for initiation). Eukaryotes: three types - Pol I (rRNA), Pol II (mRNA, snRNA), Pol III (tRNA, 5S rRNA). Transcribes 5' -> 3' following base pairing rules (A -> U in RNA). Does not require a primer
5' cap: 7-methylguanosine in a 5' -> 5' triphosphate linkage added co-transcriptionally. Poly-A tail: ~200 adenine residues added post-transcriptionally by poly-A polymerase. Both modifications are added to the pre-mRNA while it is being transcribed. Both are essential for mRNA stability, processing, and translation efficiency. Degraded together in mRNA turnover
Introns: non-coding sequences removed from pre-mRNA by splicing. Exons: coding sequences that remain in mature mRNA and are translated. Some introns are self-splicing (ribozymes). Alternative splicing: different combinations of exons can be included in mature mRNA -> one gene -> multiple proteins. Prokaryotes have very few/nol introns
Eukaryotic pre-mRNA undergoes three major modifications before leaving the nucleus: 1) 5' methylguanosine cap (7-methylguanosine added to 5' end; protects mRNA, aids ribosome binding, prevents degradation). 2) 3' poly-A tail (~50-250 adenine residues; protects 3' end, aids export, extends half-life). 3) RNA splicing (introns removed, exons joined)
The three tRNA binding sites on the ribosome. A site (aminoacyl): incoming charged tRNA enters here. P site (peptidyl): holds the tRNA attached to the growing polypeptide chain. E site (exit): empty tRNA exits here after donating its amino acid. The ribosome moves 5' -> 3' along the mRNA; tRNAs move A -> P -> E
Codon: 3-nucleotide sequence on mRNA; each codon specifies one amino acid (64 codons -> 20 amino acids + 3 stop codons + 1 start codon). Anticodon: 3-nucleotide sequence on tRNA; complementary and antiparallel to the mRNA codon. Wobble: the 3rd position of the anticodon can pair with more than one codon (explains degeneracy)
tRNA (transfer RNA) brings amino acids to the ribosome during translation. Each tRNA has an anticodon that matches an mRNA codon, and a 3' end where its specific amino acid attaches (aminoacylation by aminoacyl-tRNA synthetase). ~45 different tRNAs in humans; wobble allows fewer tRNAs than codons
Heritable changes in gene expression without changes to the DNA sequence itself. Mechanisms: DNA methylation (silences genes, especially on inactive X chromosome), histone modification (acetylation opens chromatin -> up transcription; methylation can activate or repress). Epigenetic marks can be passed to daughter cells during cell division and sometimes to offspring
The operon model (Jacob & Monod, 1961) explains prokaryotic gene regulation. An operon = promoter + operator + genes + regulatory gene. lac operon (inducible): lactose removes the repressor -> genes for lactose metabolism are expressed. trp operon (repressible): tryptophan acts as a corepressor -> turns off genes when tryptophan is abundant
Proteins that regulate transcription by binding to DNA. General TFs: required for RNA polymerase to bind (eukaryotes). Specific TFs: bind enhancers/silencers (can be thousands of bases away; loop DNA to reach promoter). Activators up transcription; repressors down transcription. Combinatorial regulation: different combinations of TFs in different cell types
Different cell types express different subsets of genes, despite having identical genomes. Determined by: transcription factor combinations, chromatin accessibility, DNA methylation, post-transcriptional regulation. Allows cell differentiation and specialization during development. Housekeeping genes are expressed in all cells
DNA sequences upstream of a gene where RNA polymerase and transcription factors assemble to initiate transcription. In eukaryotes: TATA box (~25-35 bp upstream of TSS), Initiator, CpG islands. In prokaryotes: -10 (Pribnow box) and -35 sequences. Core promoter: minimal sequence needed for basal transcription
Totipotent: cells that can give rise to any cell type, including the placenta (zygote, early blastomeres). Pluripotent: cells that can give rise to all cell types of the body but not the placenta (embryonic stem cells). Multipotent: differentiated cells that can give rise to multiple cell types within one lineage (e.g., hematopoietic stem cells -> all blood cell types)
A single nucleotide substitution in DNA. Types: transitions (purine -> purine or pyrimidine -> pyrimidine) and transversions (purine -> pyrimidine or vice versa). Effects depend on location: promoter mutations (change regulation), coding mutations (change amino acid), splice site mutations (skip exon/intron inclusion). Silent mutations may have no phenotypic effect due to codon degeneracy
Insertion or deletion of nucleotides not in multiples of 3. Shifts the reading frame -> all codons downstream are changed. Usually produces a completely different amino acid sequence from the mutation point onward and often introduces a premature stop codon -> truncated protein. More severe than point mutations
Silent mutation: nucleotide change but the same amino acid is coded (due to codon degeneracy); no phenotypic effect. Missense mutation: a different amino acid is substituted; protein function may be altered (e.g., sickle cell: Glu -> Val). Nonsense mutation: a stop codon is created; premature termination -> truncated, usually nonfunctional protein
A technique to separate DNA fragments (or proteins) by size using an electric field through a gel matrix (agarose for DNA). DNA is negatively charged (phosphate backbone) -> moves toward the positive electrode. Smaller fragments move faster/longer distance. Used in DNA fingerprinting, genetic disease diagnosis, forensic science
An in vitro method to amplify specific DNA sequences exponentially. Components: DNA template, two primers (flank target region), DNA polymerase (heat-stable Taq), dNTPs, Mg2+. Steps (thermal cycling): denaturation (94 degrees C) -> annealing (primer binding) -> extension (72 degrees C). Can amplify from a single DNA molecule. Applications: forensics, medical diagnosis, ancient DNA, gene cloning
The uptake of foreign DNA by a bacterial cell. In nature: competence factors allow DNA uptake. In the lab: using calcium chloride + heat shock or electroporation. Recombinant plasmids (with genes of interest + antibiotic resistance marker) are introduced. Transformed cells are selected using antibiotics. Used in gene cloning and production of recombinant proteins (e.g., insulin)
Bacterial enzymes that cut DNA at specific sequences (usually 4-8 bp palindromes). Type II restriction enzymes are used in molecular biology. Create either sticky ends (overhanging, complementary) or blunt ends. Named after the bacterial species (e.g., EcoRI from E. coli). Essential tools for recombinant DNA technology
A revolutionary gene-editing technology adapted from bacterial immune systems. CRISPR = Clustered Regularly Interspaced Short Palindromic Repeats. gRNA (guide RNA) directs Cas9 to a specific genomic location. Cas9 creates a double-strand break. The cell's repair mechanisms (NHEJ - error-prone -> knockout; HDR - precise editing) modify the gene. Nobel Prize 2020 (Doudna & Charpentier). Applications: gene therapy, agriculture, disease research
Creating genetically identical organisms or DNA sequences. Gene cloning: inserting a gene into a vector (plasmid) and replicating in bacteria. Organismal cloning: creating an organism genetically identical to another. Somatic cell nuclear transfer (SCNT): nucleus from a somatic cell -> enucleated egg -> embryo -> Dolly the sheep (1996). Therapeutic cloning: creating embryonic stem cells from a patient's own DNA
Both are 5-carbon pentose sugars. Deoxyribose (DNA): missing the 2'-OH group (has only H at 2' position) -> makes DNA more stable. Ribose (RNA): has a hydroxyl group (OH) at the 2' position -> makes RNA less stable, more reactive, and susceptible to hydrolysis. The 2'-OH is why RNA is single-stranded and DNA is double-stranded
In DNA: adenine (A) pairs with thymine (T) via 2 hydrogen bonds; guanine (G) pairs with cytosine (C) via 3 hydrogen bonds. In RNA: adenine pairs with uracil (U); guanine pairs with cytosine. These rules are complementary: if one strand is 5'-ATGC-3', the other is 3'-TACG-5'. Chargaff's rules: [A]=[T] and [G]=[C] in double-stranded DNA
Each strand of the original DNA molecule serves as a template for a new strand. Result: each new DNA molecule consists of one original (parental) strand and one newly synthesized strand. Predicted by Watson and Crick; proven by Meselson-Stahl experiment (1958). Conservative and dispersive replication were ruled out
Enzyme that unwinds and separates the two DNA strands at the replication fork. Breaks hydrogen bonds between base pairs. Creates positive supercoiling ahead of the fork (relieved by topoisomerase). Moves at ~1000 nucleotides/second in prokaryotes. Forms the replication bubble (bidirectional replication in eukaryotes)
Enzyme that synthesizes new DNA strands by adding nucleotides in the 5' -> 3' direction. Requires a free 3'-OH group (needs a primer). Prokaryotes: DNA Pol III (main synthesis), DNA Pol I (primer removal/fill-in), DNA Pol II (repair). Eukaryotes: Pol alpha, delta, epsilon. All move 5' -> 3' only
Enzyme that joins Okazaki fragments on the lagging strand by forming phosphodiester bonds. Seals the gaps between short newly synthesized DNA segments. Uses ATP to catalyze the bond formation. Also used in DNA repair (joining patches of newly synthesized DNA) and in recombinant DNA technology
Leading strand: synthesized continuously in the 5' -> 3' direction toward the replication fork. Lagging strand: synthesized discontinuously away from the fork, in short Okazaki fragments (~1000 nt in prokaryotes, ~200 nt in eukaryotes). Both require primers. Primase synthesizes RNA primers (~10 nt); DNA Pol I (prokaryotes) removes primers and fills gaps
Enzyme that synthesizes RNA from a DNA template (transcription). Prokaryotes: one RNA polymerase (core enzyme + sigma factor for initiation). Eukaryotes: three types - Pol I (rRNA), Pol II (mRNA, snRNA), Pol III (tRNA, 5S rRNA). Transcribes 5' -> 3' following base pairing rules (A -> U in RNA). Does not require a primer
5' cap: 7-methylguanosine in a 5' -> 5' triphosphate linkage added co-transcriptionally. Poly-A tail: ~200 adenine residues added post-transcriptionally by poly-A polymerase. Both modifications are added to the pre-mRNA while it is being transcribed. Both are essential for mRNA stability, processing, and translation efficiency. Degraded together in mRNA turnover
Introns: non-coding sequences removed from pre-mRNA by splicing. Exons: coding sequences that remain in mature mRNA and are translated. Some introns are self-splicing (ribozymes). Alternative splicing: different combinations of exons can be included in mature mRNA -> one gene -> multiple proteins. Prokaryotes have very few/nol introns
Eukaryotic pre-mRNA undergoes three major modifications before leaving the nucleus: 1) 5' methylguanosine cap (7-methylguanosine added to 5' end; protects mRNA, aids ribosome binding, prevents degradation). 2) 3' poly-A tail (~50-250 adenine residues; protects 3' end, aids export, extends half-life). 3) RNA splicing (introns removed, exons joined)
The three tRNA binding sites on the ribosome. A site (aminoacyl): incoming charged tRNA enters here. P site (peptidyl): holds the tRNA attached to the growing polypeptide chain. E site (exit): empty tRNA exits here after donating its amino acid. The ribosome moves 5' -> 3' along the mRNA; tRNAs move A -> P -> E
Codon: 3-nucleotide sequence on mRNA; each codon specifies one amino acid (64 codons -> 20 amino acids + 3 stop codons + 1 start codon). Anticodon: 3-nucleotide sequence on tRNA; complementary and antiparallel to the mRNA codon. Wobble: the 3rd position of the anticodon can pair with more than one codon (explains degeneracy)
tRNA (transfer RNA) brings amino acids to the ribosome during translation. Each tRNA has an anticodon that matches an mRNA codon, and a 3' end where its specific amino acid attaches (aminoacylation by aminoacyl-tRNA synthetase). ~45 different tRNAs in humans; wobble allows fewer tRNAs than codons
Heritable changes in gene expression without changes to the DNA sequence itself. Mechanisms: DNA methylation (silences genes, especially on inactive X chromosome), histone modification (acetylation opens chromatin -> up transcription; methylation can activate or repress). Epigenetic marks can be passed to daughter cells during cell division and sometimes to offspring
The operon model (Jacob & Monod, 1961) explains prokaryotic gene regulation. An operon = promoter + operator + genes + regulatory gene. lac operon (inducible): lactose removes the repressor -> genes for lactose metabolism are expressed. trp operon (repressible): tryptophan acts as a corepressor -> turns off genes when tryptophan is abundant
Proteins that regulate transcription by binding to DNA. General TFs: required for RNA polymerase to bind (eukaryotes). Specific TFs: bind enhancers/silencers (can be thousands of bases away; loop DNA to reach promoter). Activators up transcription; repressors down transcription. Combinatorial regulation: different combinations of TFs in different cell types
Different cell types express different subsets of genes, despite having identical genomes. Determined by: transcription factor combinations, chromatin accessibility, DNA methylation, post-transcriptional regulation. Allows cell differentiation and specialization during development. Housekeeping genes are expressed in all cells
DNA sequences upstream of a gene where RNA polymerase and transcription factors assemble to initiate transcription. In eukaryotes: TATA box (~25-35 bp upstream of TSS), Initiator, CpG islands. In prokaryotes: -10 (Pribnow box) and -35 sequences. Core promoter: minimal sequence needed for basal transcription
Totipotent: cells that can give rise to any cell type, including the placenta (zygote, early blastomeres). Pluripotent: cells that can give rise to all cell types of the body but not the placenta (embryonic stem cells). Multipotent: differentiated cells that can give rise to multiple cell types within one lineage (e.g., hematopoietic stem cells -> all blood cell types)
A single nucleotide substitution in DNA. Types: transitions (purine -> purine or pyrimidine -> pyrimidine) and transversions (purine -> pyrimidine or vice versa). Effects depend on location: promoter mutations (change regulation), coding mutations (change amino acid), splice site mutations (skip exon/intron inclusion). Silent mutations may have no phenotypic effect due to codon degeneracy
Insertion or deletion of nucleotides not in multiples of 3. Shifts the reading frame -> all codons downstream are changed. Usually produces a completely different amino acid sequence from the mutation point onward and often introduces a premature stop codon -> truncated protein. More severe than point mutations
Silent mutation: nucleotide change but the same amino acid is coded (due to codon degeneracy); no phenotypic effect. Missense mutation: a different amino acid is substituted; protein function may be altered (e.g., sickle cell: Glu -> Val). Nonsense mutation: a stop codon is created; premature termination -> truncated, usually nonfunctional protein
A technique to separate DNA fragments (or proteins) by size using an electric field through a gel matrix (agarose for DNA). DNA is negatively charged (phosphate backbone) -> moves toward the positive electrode. Smaller fragments move faster/longer distance. Used in DNA fingerprinting, genetic disease diagnosis, forensic science
An in vitro method to amplify specific DNA sequences exponentially. Components: DNA template, two primers (flank target region), DNA polymerase (heat-stable Taq), dNTPs, Mg2+. Steps (thermal cycling): denaturation (94 degrees C) -> annealing (primer binding) -> extension (72 degrees C). Can amplify from a single DNA molecule. Applications: forensics, medical diagnosis, ancient DNA, gene cloning
The uptake of foreign DNA by a bacterial cell. In nature: competence factors allow DNA uptake. In the lab: using calcium chloride + heat shock or electroporation. Recombinant plasmids (with genes of interest + antibiotic resistance marker) are introduced. Transformed cells are selected using antibiotics. Used in gene cloning and production of recombinant proteins (e.g., insulin)
Bacterial enzymes that cut DNA at specific sequences (usually 4-8 bp palindromes). Type II restriction enzymes are used in molecular biology. Create either sticky ends (overhanging, complementary) or blunt ends. Named after the bacterial species (e.g., EcoRI from E. coli). Essential tools for recombinant DNA technology
A revolutionary gene-editing technology adapted from bacterial immune systems. CRISPR = Clustered Regularly Interspaced Short Palindromic Repeats. gRNA (guide RNA) directs Cas9 to a specific genomic location. Cas9 creates a double-strand break. The cell's repair mechanisms (NHEJ - error-prone -> knockout; HDR - precise editing) modify the gene. Nobel Prize 2020 (Doudna & Charpentier). Applications: gene therapy, agriculture, disease research
Creating genetically identical organisms or DNA sequences. Gene cloning: inserting a gene into a vector (plasmid) and replicating in bacteria. Organismal cloning: creating an organism genetically identical to another. Somatic cell nuclear transfer (SCNT): nucleus from a somatic cell -> enucleated egg -> embryo -> Dolly the sheep (1996). Therapeutic cloning: creating embryonic stem cells from a patient's own DNA