Block One Lecture 12
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What does _(insert structure below here)_ refer to?
- primary structure
- primary: actual sequence of amino acids
- secondary: refers to the first signs of 3D structure-- alpha helix and beta pleated sheets
- tertiary: refers to the interaction between sheets and helices
- quaternary: interaction of peptide subunits
Explain in depth tertiary structure
- increases the complexity of 3D structure
- hydrogen, ionic, and disulfide bonds
- hydrophobic interactions
Explain quaternary structure in detail.
interaction of peptide subunits: same bond types in tertiary structure/ not all proteins have quaternary structure
What is mutation?
It may be __(3)__.
change in genetic materia
neutral, beneficial, or harmful
agent that causes mutations
occur in the absence of a mutagen
base: change in one base (aka: point mutation)
missense: result in change of amino acid
nonsense: result in a nonsense codon
frameshift: insertion or deletion of one or more nucleotide pairs
What can ionizing radiation do? What can repair this?
causes the formation of ions that can react with nucleotides and the deoxyribose-phosphate backbone
nucleotide excision repair
What does UV radiation do? What helps this?
- causes thymine dimers
Explain in detail UV radiation.
1) exposure causes adjacent thymies to become cross linkd, forming a thymine dimer and disrupting their normal base pairing
2) an enzyme cuts out and removes the damaged DNA
3) DNA pol fills the gap by synthesizing new DNA, using the intact strand as a template
4) DNA ligase seals the remaining gap by joining hte old and new DNA
Frequency of mutation
1) spontaneous mutation rate: 1 in 10^9 replicated base pairs or 1 in 10^6 replicated genes
mutagens increase to 10^-5 or 10^-3 per replicated gene
Positive (direct) selection versus negative (indirect) selection
Positive: detects mutant cells because they grow or appear different
Negative: detects mutant cells because they do not grow
Explain replica plating.
1) A sterile velvet is pressed on the grown colonies on the master plate which has the medium containing (a particular nutrient such as histidine)
2) cells from each colony are transferred from the velvet to new plates (one that has the nutrient and one that does not)
3) the plates are incubated
4) growth on the plates is compared. A colony that grows on teh medium with the nutrient (such as histidine) but could not grow on the medium without histidine is an auxotrophic (histidine-requiring mutant)
What is the Ames Test?
uses bacteria as carcinogen indicators
1. Based on observation that exposure of mutant bacteria to mutagenic substances may cause new mutations that reverse the effect of the original mutation: reversions
Explain the procedure of the Ames Test.
an experimental sample with the suspected mutagen is placed on a medium lacking the histidine. Then, after incubation, the experimental plate is compared to the control plate
vertical gene transfer
horizontal gene transfer
occurs during reproduction between generations of cells
transfer of genes between cells of the same generation
Explain the Griffith experiment.
He took four rats:
1) First rat: injected living encapsulated bacteria into to--> mouse died--> isolated the bacteria and cultured it only to find colonies of encapsulated bacteria
2) second rat: injected living nonencapsulated bacteria into it--> mouse remained healthy--> isolated it and cultured finding a few colonies of nonencapsulated bacteria; phagocytosis destroyed nonencapsulated bactera
3) third rat: heat-killed encapsulated bactera were injected into it--> mouse remained healthy--> isolation resulted in a culture with no colonies
4) fourth rat: injected living nonencapsulated and heat killed encapsulated bacteria into the mouse--> mouse died--> colonies of encapsulated bacteria were isolated from the dead mouse--> transformation had occurred
Genetic material is taken from the environment
It has to be a critical mass.
Signle stranded exogenous DNA is taken up. RecA and associated proteins will help with homologous recombination and repair of DNA
How do gram positive and engative recombine?
Gram p: transformasome
Gram n: pilus/ sex pilus
a phage infects the donor bacterial cell
phage DNA and proteins are made and hte bacterial chromosome is broken down into pieces
occassionally dring phage assembly, pieces of bacterial DNA are packaged in a phage capsid. Then, the donor cell lyses and releases phage particles containing bacterial DNA
a phage carrying bacterial DNA infects a new host cell, the recipient cell
recombination can occur, producing a recombinant cell with a genotype different from both the donor and recipient cell
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