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Alfred Hershey and Martha Chase

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-Figured out DNA was the basis of genetic material -Used bacteriophages, viruses that infect bacteria

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James Watson and Francis Crick

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-Structure of DNA -Used X-ray crystallography

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X-ray crystallography

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-Process used to visualize molecules three-dimensionally

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4 Major features of DNA

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1. DNA is a double helix 2. Sugar (deoxyribose) attached to a nitrogen base 3. A to T, G to C 4. Antiparallel

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Double helix

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-Side of sugar-phosphate components, with rungs of nitrogenous bases

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Antiparallel

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-Left side runs 5' to 3' while the opposite strand runs 3' to 5'

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Replication

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-Making of DNA from an existing DNA strand

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DNA polymerases

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-Catalyzes the elongation of new DNA at the replication fork

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Leading strand

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-DNA replication occurs continuously along the 5' to 3' strand

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Lagging strand

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-Runs 3' to 5' is copied in series of segments

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Okazaki fragments

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-Lagging strand is synthesized in separate pieces

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DNA ligase

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-Sealed together DNA

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Accuracy of DNA replication

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1. Specificity of base pairing 2. Mismatch repair 3. Nucleotide excision REPAIR

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Mismatch repair

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-Special repair enzymes fix incorrectly paired nucleotides

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Nucleotide excision repair

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-Incorrectly placed nucleotides are excised or removed by nucleases, and the gap left over filled in with the correct nucleotides

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Nucleases

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-Enzymes that remove incorrectly placed nucleotides

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Telomeres

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-Short, repetitive nucleotide sequences

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Chromatin

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-DNA and proteins packed together

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Euchromatin

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-Chromatin is in highly extended form

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Heterochromatin

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-Condensed chromatin

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Gene expression

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-Process by which DNA directs the synthesis of proteins

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One gene-one polypeptide hypothesis

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-Each gene codes for a polypeptide which can be a protein

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Transcription

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-Synthesis of RNA using DNA as a template

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Messanger RNA (mRNA)

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-Produced during transcription -Carries the genetic message of DNA to the protein-making machinery of the cell in the cytoplasm, the ribosome

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RNA processing

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-Turns pre-mRNA to mRNA

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Translation

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-Production of a polypeptide chain and are written as a series of three-nucleotide groups, called triplet code

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Template strand

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-Only one strand of the DNA is transcribed

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Codons

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-mRNA base triplets

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RNA polymerase

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-An enzyme that separates the two DNA strands and connects the RNA nucleotides as they base-pair along the DNA template strand

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Promoter

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-DNA sequence at which RNA polymerase attaches

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Terminator

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-DNA sequence that signals the end of transcription

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Transcription unit

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-Entire stretch of DNA that is transcribed into an RNA molecule

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3 main stages of Transcriptopn

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1. Initiation 2. Elongation 3. Terminatin

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Initiation

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-RNA polymerase recognizes and binds to the promoter

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Transcription factors

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-Assist the binding of RNA polymerase to the promoter and the initiation of transcription

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Transcription initiation complex

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-Whole complex of RNA polymerase II and transcription factors

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Elongation

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-RNA polymerase moves along the DNA untwisting the double helix -RNA nucleotides added to the 3' end -Double helix re-forms, with the new RNA molecule strangling away from the DNA template

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Termination

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-After RNA polymerase transcribes a terminator sequence in the DNA, the RNA transcript is released, and the polymerase detaches

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Key post-transcriptional modifications

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-5' cap -poly- A tail

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RNA Splicing

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-Large portions of the newly synthesized RNA strand are removed

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Introns

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-Sections of the mRNA that are spliced out

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Exons

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-Sections that remain and subsequently spliced together by a spliceosome

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Small nuclear RNA (snRNA)

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-Catalyzes the excision of the introns and joining of the exons

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Ribozyme

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-When RNA serves as a catalyst

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tRNA

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-Transferring amino acids from a pool of amino acids in the cell's cytoplasm to a ribosome

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Anticodon

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-A nucleotide triplet allows it to pair specifically with a complementary codon on the mRNA

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Codon

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-An mRNA triplet -64 different codon

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rRNA

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-Complexes with proteins to form the two subunits that form ribosomes

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Wobble

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-Relaxation of base-pairing rules

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P site

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-Holds the tRNA that carries the growing polypeptide chain

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A site

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-Holds the tRNA that carries the amino acid that will be added to the chain next

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E site

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-Exit site for tRNA

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3 stages of Translation

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1. Initiation 2. Elongation 3. Termination

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Initiation (Translation)

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...

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Elongation (Translation)

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1. Codon recognition 2. Peptide bond formation 3. Translocation

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Termination (Translation)

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-A stop codon in the mRNA is reached and translation stops -Release factor binds to the stop codon and the polypeptide is freed from the ribosome

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Signal peptide

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-Sequence of the leading 20 or so amino acids directing proteins to their final destination

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Mutation

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-Alterations in the genetic material of the cell

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Point mutation

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-Alterations of just one base pair of a gene

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Nucleotide-pair substitution

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-Replacement of one nucleotide and its partner with another pair of nucleotides

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Missense mutations

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-Substitutions that enable the codon to still code for an amino acid, may not be correct one

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Nonsense mutations

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-Substitutions that change a regular amino acid codon into a stop codon, ceasing translation

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Insertions

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-Additions of nucleotide pairs in a gene

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Deletions

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-Losses of nucleotide pairs in a gene

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Frameshift mutation

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-Causes the mRNA to be read incorrectly

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Mutagens

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-Substances or forces that interact with DNA in ways that cause mutations

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Operon

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-Genes are often clustered into units

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Operator

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-Controls the access of RNA polymerase to the genes -Found within the promoter site or between the promoter and the protein coding genes of the operon

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Promoter of operon

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-Where RNA polymerase attaches

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Genes of the operon

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-Entire stretch of DNA required for all the enzymes produced by the operon

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Regulatory genes

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-Produce repressor proteins that may bind to the operator site

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Repressible operon

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-Normally on but can be inhibited -Normally anabolic, building an essential organic molecule

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Corepressor

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-Binds to the repressor protein, activating it

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Inducible operon

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-Normally off but can be activated -Normally catabolic, breaking down food molecules for energy

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Inducer

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-A specific small molecule binds to and inactivates the repressor protein

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Differential gene expression

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-Expression of different genes by cells with the same genome

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DNA methylation

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-Addition of methyl groups to NA -Causes DNA to be more tightly packed, reducing gene expression

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Histone acetylation

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-Acetyl groups are added to amino acids of histone proteins, making the chromatin less tightly packed and encouraging transcription

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Epigenetic inheritance

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-Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence

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Transcription initiation

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-Control point in gene expression -DNA control elements that bind transcription factors are involved in regulation

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Transcription initiation complex

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-Enhances gene expression

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Enhancer regions

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-DNA sequences from the gene

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Activators

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-Proteins that bind DNA sequences to the promoter region

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micro RNAs (miRNA)

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-Bind to mRNA and degrade the mRNA or bind to mRNA and block its translation

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small interfering RNAs (siRNAs)

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-Bind to mRNA and degrade the mRNA or bind to mRNA and block its translation

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Zygote transformations

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1. Cell division 2. Cell differentiation 3. Morphogenesis

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Cell division

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-Series of mitotic divisions that increases the number of cells

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Cell differentiation

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-Process by which cells become specialized in structure and finction

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Morphogenesis

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-Gives an organism its shape

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Cytoplasmic determinants

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-Maternal substances in the egg that influence the course of early development

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Cell-cell signals

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-Result from induction

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Induction

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-Molecules produced by one cell influencing neighboring cells, causing cells to differentiates

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Determination

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-A series of events that lead to observable differentiation of a cell -Caused by cell-cell signals and is irreversible

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Pattern formation

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-Set up the body plan and is a result of cytoplasmic determinants and inductive signals

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Morphogens

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-Plays a role in establishing differing features

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Homeotic genes

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-Master control genes that control pattern formation

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Oncogenes

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-Cancer-causing genes

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Proto-oncogenes

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-Genes that code for proteins that are responsible for normal cell growth

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Cancer

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-Caused by a mutation in a gene whose products normally inhibit cell division

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Tumor-suppressor genes

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-Genes that inhibit cell division

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p53 gene

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-Tumor-suppressor gene

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Apoptosis

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-Cell programed death

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Capsid

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-Protein shell that surrounds the genetic material

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Viral envelopes

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-Surround the capsid and aid the viruses in infecting their hosts

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Bacteriophages or Phages

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-Viruses that infect bacterial cells

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Host range

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-Viruses can infect only a very limited variety of hosts

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Lytic cycle

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-Ends in the death of the host cell by rupturing it (lysis) -Bacteriophage injects its DNA into a host cell and takes over the host cell's machinery to synthesize new copies of the viral DNA

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Lysogenic cycle

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-Bacteriophage's DNA becomes incorporated into the host cell's DNA and is replicated along with the host cell's genome

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Prophage

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-Viral DNA

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Retroviruses

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-RNA viruses that use reverse transcriptase to transcribe DNA from an RNA template

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Viroids

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-Circular RNA molecules several hundred nucleotides in length that infect plants -Causes errors in plant growth

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Prions

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-Misfolded, infectious proteins that cause the misfolding of normal proteins they contact in various animal species

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Genetic engineering

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-Process of manipulating genes and genomes

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Biotechnology

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-Process of manipulating organisms or their components for the purpose of making useful products

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Recombinant DNA

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-DNA that has been artificially made, using DNA from different sources

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Gene cloning

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-Process by which scientists can produce multiple copies of specific segments of DNA that they can work with in the lab

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Restriction enzymes

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-Used to cut strands of DNA

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Restriction sites

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-Specific locations where DNA is cut

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Restriction fragments

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-A set of DNA molecules after they have been cut by restriction enzymes

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Sticky ends

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-Single-stranded end

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Cloning vector

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-Carries the DNA sequence to be cloned and is often a bacterial plasmid

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Nucleic acid hybridization

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-Used to find the gene

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Genomic library

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-Set of thousands of recombinant plasmid clones, each of which has a piece of the original genome being studied

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cDNA library

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-Made up of complementary DNA made from mRNA transcribed by reverse transcriptase

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PCR

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-Method used to amplify a particular piece of DNA without the use of cells -Used to amplify DNA when the source is impure or scanty

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Gel electrophoresis

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-Lab technique used to separate macromoleculees

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Microarray assays

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-Genome-wide studies

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Restriction fragment length polymorphisms (RELPs)

answer

-Result from small differences in DNA and can be detected by electrophoresis -Allows for diagnosis of disease and answers paternity and identity questions

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Nuclear transplantation

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-Nucleus of an egg is removed and replaced with the diploid nucleus of a body cell

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Stem cells

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-Goal of human cloning

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Embryonic stem cells

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-Pluripotent, which means capable of differentiating into many different cell types -Use them for the repair of damaged or diseased organisms

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Uses of DNA tech

answer

1. Diagnosis of disease 2. Gene therapy 3. The production of pharmaceuticals 4. Forensic applications 5. Environmental cleanup 6. Agricultural applications -GM organisms

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Bioinformatics

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-Use of computers, software, and mathematical models to process and integrate the incredible volume of data from these sequencing projetcs

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Proteomics

answer

-Protein interactions are analyzed

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Systems biology

answer

-Aims to model the behavior of entire biological systems and is enhanced by bioinformatics

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Repetitive DNA

answer

-Sequences that are present in multiple copies in the genome

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Transposable elements

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-Repetitive DNA -Move from one location to another in the genome with the aid of transposase

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Transposons

answer

-Moves by means of a DNA intermediate

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Retrotransposons

answer

-Move by means of a RNA intermediate, and leave a copy at the original site -Involves reverse transcriptase

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Multigene families

answer

-Collections of two or more identical or very similar genes

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Evo-devo

answer

-A field of biology that compares developmental processes to understand how they may have evolved and how changes can modify existing organismal features or lead to new ones

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Homeotic genes

answer

-Master regulatory genes that control placement and spatial organization of body parts by controlling the developmental fate of groups of cells

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Homeobox

answer

-Widely conserved 180-nucleotide sequence found with homeotic genes -Found in many genes

Topic 5: Molecular Genetics

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