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BIO 2200 > BIO 2200 Exam 3 > Flashcards

BIO 2200 Exam 3 Flashcards

1
Q

What is a mutation?

A

Inheritable change in DNA nucleic acid sequence of the genome.

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2
Q

What is a silent mutation?

A

change in the DNA sequence but not in the protein sequence, same amino acid is inserted since the code is degenerated

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3
Q

What is a nonsense mutation?

A

conversion of an amino acid codon to a stop codon

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4
Q

What is a missense mutation?

A

change of the codon from one amino acid to another

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5
Q

What are microdeletions and microinsertions?

A

Microdeletions are removals of one or more bases while microinsertions are insertions of one or more extra bases

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6
Q

What are insertional mutations cause by?

A

By transposons, which are DNA that are able to hop around the chromosome on their own.

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7
Q

What is a point mutation and what are the three types?

A

Point mutations are changes in a single base pair and the three types are silent, nonsense, and missense.

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8
Q

What are reversions?

A

Mutations that restore the wild-type phenotype in a cell that has previously been mutated.

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9
Q

What are true reverants or first-site revertants?

A

the original phenotype of the cell is restored. The original is replaced and the gene is the same as it was before the mutation occurred.

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10
Q

What are Pseudorevertants or second-site revertants (Suppression mutations)?

A

A second mutation occurs in different place that compensates for the effect of the original mutation. Genotype of the revertant is not the same as the wild-type even though the phenotype is.

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11
Q

What are auxotrophs?

A

Mutants that have mutations in the genes involved in nutrition and need supplementary organic nutrient growth medium.

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12
Q

What are phototrophs?

A

Cells that are nutritionally wild-type and do not need nutrient other than the primary carbon source.

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13
Q

What are the mutation rates for DNA? for RNA?

A

for DNA it is 10-6 to 10-7 per kilobase per single round; for RNA, it is 1000 times higher than DNA -about 10-4 per base per single round of replication because RNA repair function does not exist

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14
Q

What are chemical mutagens?

A

chemicals that cause mutations

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15
Q

What is site directed mutagenesis?

A

These mutations are not naturally occurring, they are placed in a specific place in the gene by a researcher. A small portion of the gene can be chemically synthesized and mutations can be placed at whatever locations you want. This mutated piece of DNA can then be used to replace the wild type segment in the gene and you now have a gene carrying the mutation in the specific place where you wanted it.

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16
Q

What are biological mutagens?

A

Some pieces of DNA are able to hop around the chromosome on their own (transposons). When they hop, they often hop into the middle of a gene. Many of these are quite large and when they insert into a gene they completely disrupt it. These are what cause the formation of multicolored corn and they are used extensively in research.

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17
Q

What is the SOS response?

A

Repair system in bacteria for damaged DNA. The damaged base or bases are removed and new bases are put in but the new bases can be anything because the template is not read by the repair enzyme. There is a 1 in 4 chances of putting in the same base pair

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18
Q

What is the Ames test?

A

use bacteria to screen for cancer causing agents

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19
Q

What are the three types of genetic exchange in bacteria?

A

transformation, transduction, and conjugation

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20
Q

What is transformation?

A

DNA present in the surrounding medium passes through the cell membrane and becomes integrated into the bacterial genome.

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21
Q

What is transduction?

A

DNA from the chromosome of a phage infected bacterium is accidentally encapsidated instead of the viral DNA and when this virus particle attaches to another bacterium and injects this host DNA it becomes integrated into the bacterial chromosome.

22
Q

What are the two types of conjugation?

A

Plasmid transfer (Plasmid carries genes necessary for its transfer) and Chromosome Transfer (A conjugative plasmid integrates into the chromosome and when it tries to conjugate it attempts to transfer the entire chromosome).

23
Q

What are the 5 steps of molecular cloning?

A
  1. Isolation and fragmentation of DNA source
  2. Joining DNA fragments to cloning vector
  3. Placing cloned DNA into host organism
  4. Detection of cloned DNA
  5. Amplification of DNA/host organism
24
Q

What is electrophoresis of DNA?

A

It is the process of separating DNA fragments in an agarose gel. When a current is applied, the DNA migrates towards the positive electrode (DNA has a negative charge). The smaller the fragment, the faster it moves.

25
Q

What is a vector? What are expression vectors and shuttle vectors?

A

A vector is a bacteriophage, plasmid, or other agent that transfers genetic material form one cell to another. Expression Vectors are used to get the protein expressed from the cloned DNA. Shuttle Vectors are vectors that can stably replicate in two or more unrelated host organisms

26
Q

How do you clone with Lambda?

A

The COS sites are recognized by phage enzymes and the DNA spontaneously assembles in vitro. This way, you have a ready-made delivery system to get large pieces of DNA into a cell. It is very difficult to get pieces of DNA as big as 50 KB into cells. Since viruses have solved this problem, they are natural vectors for cloning DNA.

27
Q

What is a cosmid? What are the advantages?

A

If you take the COS site of the lambda genome and clone it into a plasmid cloning vector like pBR322, you get a cosmid. Therefore, any DNA put in the cosmid will be packaged in vitro and easily introduced into the host. The major advantage of cosmids is that they do not have any of the lambda genes except the COS site and can therefore package very large amounts of DNA.

28
Q

Why is E. coli a good host for cloning vectors?

A

Most thoroughly understood organism in the world. Gut organism potential pathogen. Makes endotoxins. Strains used today get around all of these things so is still the organism of choice.

29
Q

Why are eukaryotes used as host for cloning vectors and what are some you might use?

A

Mainly for expression and study of eukaryotic genes. Some you might use are yeast, mammalian cells, or insect cells.

30
Q

What are the 6 steps to Sanger Sequencing?

A
  1. Use a radioactive primer.
  2. Add polymerase and a mixture of dNTPs for DNA synthesis.
  3. Divide the reaction into 4 tubes. Add one ddNTP (ddATP, ddCTP, ddGTP or ddTTP) to each tube.
  4. Polymerase adds nucleotides to the primer. When a ddNTP is incorporated into the growing chain, that chain is terminated. This produces a fragment of DNA corresponding to each nucleotide in the DNA sequence.
  5. Run gel with each of the four reactions (acrylamide-similar to agarose but much firmer)
  6. Read sequence.
31
Q

What is metagenomics?

A

The genomic analysis of all of the genomes of all of the organisms inhabiting a particular environment. The metagenome is the total gene content of all of the organisms inhabiting a particular environment.

32
Q

What is Transcriptome Analysis?

A

Study of all the transcripts (mRNA) produced by an organism at any given time or condition. DNA microarray technology is the main tool for this analysis.

33
Q

What is Proteome Analysis (proteomics)?

A

Study of all the proteins produced by an organisms at any given time or condition. Two-dimensional gel electrophoresis and mass spectrometry are the main tools. The proteome is all of the proteins produced in a cell or tissue or organism.

34
Q

What is structural genomics?

A

the large-scale determination of the 3D molecular structures of all of the proteins in a proteome.

35
Q

What are the two types of metabolites?

A
  1. Primary Metabolites: produced during early (primary) growth phase.
  2. Secondary Metabolites: Produced near the stationary phase at the end of log phase
36
Q

What are 5 characteristics of secondary metabolites?

A
  1. The metabolite is not formed by all of the organisms.
  2. Not essential for growth and reproduction.
  3. Production depends upon growth conditions.
  4. Usually produced in groups of related compounds.
  5. Can manipulate the cell and growth conditions get overproduction of the secondary metabolite.
37
Q

What are the two vitamins discussed in this chapter?

A

B12-cyanocobalamine contains cobalt and is produced only by bacteria (certain strains of Propionibacterium and Pseudomonas). Riboflavin is synthesized b several types of microorganisms including bacteria, yeast and other fungi.

38
Q

What is the most common amino acid?

A

Most common is glutamic acid, which is a flavor enhancer.

39
Q

What is somatotropin?

A

A protein; Injecting somatotropin in mature cows stimulates milk production and prevents death of mammary cells.

40
Q

How are viruses used in gene therapy?

A

Parts of a pathogen are cloned in viruses that very immunogenic and used to make a vaccine instead of the whole virus or organism. This is much safer and more effective than injecting the killed or inactivated pathogen.

41
Q

What are the two models of endosymbiosis?

A
  1. Nucleated cells arose from the Archaea as the genome grew in size and then acquired the mitochondrial ancestor and then after that some cells acquired chloroplasts and evolved into plants
  2. Hydrogen Hypothesis: the Archaea first picked up the endosymbiant that was to be the mitochondria and then later they developed the nucleus. The bacterial cell produced hydrogen and consumed oxygen and the archael cell consumed the hydrogen as an energy source. Some of these nucleated cells then picked up the progenitor of chloroplasts and the plant line were born.
42
Q

What is the concept of natural selection?

A

Charles Darwin proposed that all species of life have evolved over time from common ancestors, through the process called natural selection. Adaptive mutations improve fitness of an organism, increasing its survival compared to competing organisms.

43
Q

What are molecular clocks? What is the most widely used one?

A

These are certain genes and proteins that are used to measure evolutionary change. Major assumption of this approach is that nucleotide changes occur at a constant rate and are usually neutral and random. The most widely used molecular clocks are small subunit ribosomal RNA genes.

44
Q

What is sequence alignment?

A

This involves aligning the sequence of interest with sequences from homologous genes from other strains or species.

45
Q

What is a phylogenetic tree?

A

Graphic illustration of the relationships among sequences. Composed of nodes and branches.

46
Q

What are the three methods of the polyphasic approach to taxonomy?

A
  1. Phenotypic analysis: examines the morphological, metabolic, physiological, and chemical characters of the cell.
  2. Genotypic analysis: DNA profiling, hybridization, multilocus sequencing, GC ratio analysis.
  3. Phylogenetic analysis
47
Q

What are three characteristics of the nucleus?

A

o Nucleus contains chromosomes. DNA is wound around histones and packed into nucleosomes to form chromatin. They are visible under light microscope without staining.
o Enclosed by two membranes: Outer membrane and Inner membrane. Nuclear pores allow proteins and nucleic acids to be transported in or out of nucleus.
o Within the nucleus is the nucleolus – the site of ribosomal RNA synthesis

48
Q

What are three characteristics of the mitochondrion?

A

o Location of respiration and oxidative phosphorylation.
o Over 1,000 per animal cell, surrounded by two membranes. Folded internal membrane called cristae.
o Bacterial dimensions (rod or spherical).

49
Q

What are three characteristics of chloroplasts?

A

o Contains chlorophyll, found in phototrophic eukaryotes (plant, algae or protists). Size, shape, and number of chloroplasts vary.
oHas an outer and inner membrane. Lumen of the chloroplast is called the stroma, with flattened membrane discs thylakoids (no cristae).
o Stroma contains large amounts of Rubisco, key enzyme in Calvin cycle, which converts CO2 from the atmosphere into glucose.

50
Q

What are two characteristics of the Endoplasmic reticulum?

A

o There are two types of ER (smooth and rough). Rough ER contains attached ribosomes, while smooth ER does not.
o Smooth ER participates in the synthesis of lipids, and rough ER is a major producer of glycoproteins.

51
Q

What is the Golgi complex?

A

stacks of membrane distinct from, but functioning in concert with, the ER. Modifies products of the ER destined for secretion.

52
Q

What are three parts of the cytoskeleton?

A

o Microtubules: 25 nm in diameter composed of a- and b- tubulin. Function in maintaining cell shape, in motility, in chromosome movement, and in movement of organelles.
o Microfilaments: 7 nm in diameter, polymers of actin. Function in maintaining cell shape, motility by pseudopodia, and cell division.
o Intermediate filaments: 8–12 nm in diameter, containing keratin proteins. Function in maintaining cell shape and positioning of organelles in cell

BIO 2200 (2 decks)

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