Micro Chapter 8 Lecture

  1. what is genetics
    the study of genes: what they are, how they are replicated, how they carry information, and how they're expressed.
  2. what is a gene
    a length of DNA that encodes the instructions for making RNA
  3. define DNA
    deoxyribonucleotides that are linked together
  4. what is a chromosome
    a DNA structure that carries hereditary information (a gene)
  5. what is a genome? what is it made up of?
    the entire genetic complement of an organism

    it is made up of chromosomes and plasmids
  6. what are nucleotides made up of?
    a nitrogenous base, deoxyribose, and a phosphate group
  7. genotype vs phenotype
    genotype- an organisms genetic makeup 

    phenotype- the physical or physiological expression
  8. what are plasmids?
    • small pieces of DNA that replicate independently because they carry their own information
    • - they aren't essential for normal microbial growth, replication, or reproduction
    • -they do provide survival advantages
  9. what are the 4 types of plasmids?
    • 1. Fertility (F) factors: conjugation pili
    • 2. Resisitance (R) factors: beta lactamase
    • 3. Bacteriocin factors: E. coli colicins 
    • 4. Virulence plasmids: ex. salmonella modulates immune system to keep it from being killed

    *HUMANS DO NOT HAVE PLASMIDS but other Eukaryotes can
  10. explain the genome characteristics of prokaryotes vs eukaryotes
    • prokaryotes
    • complexity: simple
    • genome includes: chromosomal DNA and plasmids
    • chromosomes: few, usually unicellular and haploid (one copy)
    • location of chromosomes: nucleoid region
    • DNA organization: histone-like proteins

    • eukaryotes
    • complexity: complex
    • genome includes: chromosomal dna, dna in mitochondria/chloroplasts, and plasmids
    • chromosomes: many, nuclear chromosomes are linear and diploid (2 copies)
    • location of chromosomes: nucleus
    • DNA organization: histones
  11. what are histones? euchromatin vs heterochromatin
    organizational proteins

    euchromatin- loose, allow the gene to be expressed

    heterochromatin- tight, do not allow the gene to be expressed
  12. define genetic replication, recombination, and expression
    replication- genetic information vertically transferred between generations of cells 

    recombination- genetic information transferred between cells of the same generation 

    expression- genetic info in the cell produce proteins needed for cell function
  13. DNA strand characteristics
    • -sugar phosphate backbone (phosphodiester bonds)
    • -strands are held together by the hydrogen bonds between the base pairs (AT, GC)
    • -the double helix is due to the nucleoproteins
    • -strands are anti-parallel and complementary to each other
  14. which nucleotides are pyrimidines and which are purines?
    • purines- AT
    • pyrimidines-GC
  15. describe nucleotide structure? how do nucleotides connect? how do you stop the chain?
    nucleotides have a 3' and a 5' end. the 3' end must be available with the hydroxyl (-OH) group present to add new nucleotides. 

    if the 3' hydroxyl isn't present, the chain stops.
  16. in which direction is DNA built? why?
    5' to 3' because it starts at the 5' phosphate of one nucleotide to the 3' hydroxyl of the next nucleotide (they are linked together by phosphodiester bonds)
  17. where does replication begin? how? what are the rest of the steps?
    at the origin of replication. 

    -the DNA strand's hydrogen bonds are broken by helicase at the replication fork. SSBs (single-stranded binding proteins) help keep the stands separated until they're copied. 

    • -leading strand: DNA polymerase adds complementary bases 5' to 3'
    • -lagging strand: RNA primase lays down RNA primer in short segments. DNA polymerase III lays new DNA behind it in okazaki fragments. DNA polymerase I then replaces the RNA fragments with DNA and ligase links the okazaki fragments together.

    *dna replication is bi-directional (replication bubble)
  18. why is DNA replication considered semi conservative? why is that important? what else helps?
    -each new "daughter" helix of DNA contains an original strand of DNA and a new strand of DNA. 

    • -this helps DNA have high fidelity because complements to the original strands are being replicated. 
    • -DNA polymerase acts as a proof-reader
  19. list the "players" of DNA replication, the template and the product
    players: dNTPs (ATGC), origin, helicase, SSBs, RNA primase, DNA polymerase III and I, Okazaki fragments, and ligase

    • -DNA
    • -DNA
  20. what is DNA methylation and why is it important?
    -dna methylation is when a methyl group (CH3) is added to an adenine or cytosine

    -it plays a role in many processes:
  21. what is transcription? what is translation?
    -making an RNA copy of DNA 

    -making a protein from RNA transcription (protein synthesis)
  22. what is the "central dogma" of genetics?
    DNA is transcripted into RNA 

    RNA is translated into proteins (polypeptides)
  23. what are the 4 types of RNA transcribed from DNA?
    • RNA primer
    • mRNA
    • tRNA 
    • rRNA
  24. what are the 3 steps of RNA transcription? explain
    • initiation- when RNA polymerase binds to the promoter, the DNA strand begins to unwind
    • (prokaryotes use signma factors, eukaryotes use transcription factors)

    elongation- RNA synthesizes a new strand by adding free complementary nucleotides (AUGC) to the template DNA strand. After the DNA has been transcribed, it rewinds

    termination- when the mRNA reaches a termination sequence, the strand is let go. We have a completed strand of mRNA
  25. what are the players, template, and product of transcription?
    you start with DNA

    players involved are: RNA polymerase, promoter, rNTP (nucleotides), and termination sequence

    you end with mRNA
  26. how is RNA polymerase different from DNA polymerase?
    • -RNA polymerase doesn't need a primer or helicase
    • -Uracil is used in place of thymine
    • -rNTPs are used instead of dNTPs
    • -RNA polymerase isn't as good at proof reading as dna polymerase. it has a low fidelity=more mutations

    *this is why HIV and influenza is constantly mutating and changing
  27. How is transcription is eukaryotes different than transcription in prokaryotes?
    • -in eukaryotes, transcription occurs in the nucleus (mainly), the mitochondria, and chloroplasts 
    • -it uses 3 types of polymerases with transcription factors (instead of polymerase and sigma factors) 
    • -mRNA is transcribed in the nucleus, before translation. in eukaryotes it is not simultaneous (in prokaryotes transcription and translation happens at the same time in the cytoplasm)
  28. where does transcription and translation happen in eukaryotes vs prokaryotes?
    • eukaryotes
    • transcription-nucleus, mito and chloroplasts
    • translation- cytoplasm

    • prokaryotes
    • transcription- cytoplasm
    • translation- cytoplasm
  29. why do eukaryotes transcribe and translate separately? 

    what is the process that happens between these points? benefit? explain
    for eukaryotes the region of DNA/RNA genes that code for proteins contains extrons (protein coding) and introns (non coding). So, the mRNA has to be processed before it leaves the nucleus and is transcribed. 

    • alternative splicing- new combinations of exons
    • spliceosomes run across the mRNA strand, removing the introns creating just a full strand of RNA with coding exons to be read by the ribosome
  30. why is the genetic code considered universal translation?
    it is used for EVERYTHING, even viruses
  31. what are the universal start and stop codons? state their names? 
    -when answering on the exam, how should you indicate the start and stop codons when writing the code?
    • start: AUG (methionine) 
    • stop: UAA or UAG (tyrosine)

    • start: don't write "start", write methionine
    • stop: don't write stop, leave empty (or should we write serine)? 

    • *this completed code is the strand of protein 
    • *the 3rd letter is the wobble position
  32. what are the players, instructions, and product of translation? 

    task of players?
    • mRNA- gives the instructions to make the protein
    • tRNA- amino acid carrier 
    • ribosomes- amino acid barriers, protein factories 
    • amino acids- protein parts; monomers
    • GTP- energy 

    • you start with mRNA nucleotides that give instruction 
    • you end with proteins/amino acids
  33. what are the steps in translation?
    initiation- the ribosome attaches to the mRNA and the tRNA helps it read and look for a start codon

    elongation- as the codons are read, peptide bonds join them together to make a protein/amino acid. each peptide costs 1 GTP. this is why translation is considered high energy. 

    termination- when the ribosome and tRNA read the stop codon, the termination factors remove the peptide from the mRNA strand and ribosome
  34. why is gene expression regulated?

    name the 2 methods this is done?
    protein synthesis requires a lot of energy. 75% of genes are making proteins all the time for cellular life processes. 

    the other 25% is regulated and made only when the cell needs it to conserve energy

    • pre-transcriptional control
    • translational control
  35. what is pre-transcriptional regulation? explain mechanisms.
    it is when the cell controls gene expression by regulating the amount of mRNA from a specific gene/enzyme is made 

    repression- it responds when there is too much final product in the pathway, and it works to turn the gene off 

    induction- when there is too little of the gene, the inducible enzymes are turned on and more genes are expressed
  36. what are some examples of pre-transcriptional regulation?
    • operons
    • quorum sensing
    • epigenetic control (DNA methylation)
    • recruitment of transcriptional factors
  37. how can you turn genes off epigenetically through pre-transcriptional regaulation?
    heavily methylated genes are turned of
  38. how can you turn genes off through quorum sensing in pre-transcriptional regulation?
    when there is a change in the density of the population, bacteria can tell each other when to stop and start synthesizing to increase their chances of survival
  39. what is the operon? what are they made up of?
    -the functional unit of genes (mainly prokaryotes)

    -1 operator (regulates like a stop like), 1 promoter, and structural genes

    *the combination of the 3 is the Lac operon
  40. what is the difference between the inducible Lactose operon and the repressible Tryptophan/Arginine operon?
    -inducible: genes are turned off until they are needed and turned on 

    -repressible: genes are turned on until they are not longer needed and turned off
  41. explain how tryptophan can act as a repressor?
    one of the genes that gets transcribed then translated is tryptophan. when it is made in excess, it binds to the repressor protein. then the repressor protein binds to the operator, which blocks RNA polymerase from synthesizing tryptophan.
  42. what is post-transcriptional control/regulation?


    describe how it works
    instead of regulating how much of an mRNA is made, it regulates how often the mRNA is made into a protein (it affects how readily ribosomes are to read the mRNA)

    it allows fine control and can protect proteins from making viruses

    siRNA (silence) binds to the mRNA that carries gene that it doesn't want to be expressed. the antisenseRNA (RISC) breaks down the mRNA complex and no protein is made because the ribosomes aren't able to respond to it
  43. what are some examples of translational regulation?
    • ribosome recruiting to mRNA 
    • controlling mRNA stability
    • riboswitches
    • eukaryotes can control RNA processing and nuclear export
  44. what is a mutation?
    a permanent change in the nucleotide sequence. it can be spontaneous and is usually harmful
  45. explain the difference between somatic mutations and germ-line mutations?
    • somatic- they happen in body cells and are not heritable 
    • ex. cancer

    germ line mutation- they happen in reproductive cells (egg or sperm/from mom or dad) and are heritable
  46. what are the two types of mutations? explain.
    point mutation- a change in the nucleotide base at a specific location in gene, leads to codon change, leads to mRNA change, leads to change in amino acid, therefore a change in the protein

    Frameshift mutation- there is an addition (insertion) or subtraction (deletion) of a nucleotide base from a gene sequence. the gene's reading frame is altered. (1 codon=3 nucleotides)
  47. what is a silent point mutation
    silent mutations- they change the nucleotide sequence, but do not change the amino acid sequence (missense mutation=aa change)Â
  48. what are some of the phenotypic effects of point mutations? meaning, what are their expressions?
    -there could be no effect if the new protein works like the original (silent mutation) 

    -there could be a good effect if the new protein works better than the original (rare) 

    -the new protein could work worse than the original, or not work at all. (most common)
  49. what are the differences between a spontaneous mutation and an induced mutation? explain.
    spontaneous- these happen in the absence of DNA altering agents. they happen during replication due to base pairing mistakes 

    induced- happen when DNA-altering agents are involved=mutagens
  50. explain the 5 different types of mutagens that cause induced mutations
    ultraviolet (UV) lights- causes thyamines to be inserted, so base pairing is prevented  during replication. this leads to gaps in the DNA. transcription is stopped, and no protein is made

    x-rays, gamma rays- generates free radicals that are highly energetic. they cause DNA strands to break leading to chromosome fragmentation 

    chemical mutagens- they change nucleotide sequences by inserting base analogues 

    frame shift mutagens- they are flat nucleotides that slip between bases, causing base pairs to be displaced so the DNA unwinds

    base-altering chemicals- they deaminate and remove amino groups (NH2) from the nitrogenous bases AGC.
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Micro Chapter 8 Lecture