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Unit 1 > Unit 1 Deck 1 > Flashcards

Unit 1 Deck 1 Flashcards

1
Q

What is another name for the MTOC? What does it contain?

A

Centrosome, contains 2 centrioles

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2
Q

What is responsible for the shape of the cell? What three parts make it up?

A

Cytoskeleton, made of microtubules, thin filaments (actin), and intermediate filaments

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3
Q

Where are rRNA’s transcribed and processed?

A

Nucleolus

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4
Q

What is an isolate?

A

A strain of bacteria obtained from a specific patient

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5
Q

What is important to know about the 16sRNA gene, 3 facts

A
  1. it is universal to all species
  2. it is unique within each species, but flanked by sequences common to all organisms
  3. used in classification, both broadly, ie bacteria/archaea/eukarya, and specifically for identification of strains and isolates
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6
Q

Where do enteric bacteria live?

A

GI tract

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7
Q

Can generation of diversity be observed?

A

No, this is not observable in human time, but instead 1% per 50 million years. This is not the same as changes in pathogenicity or natural selection. Use rates of 16sRNA gene divergence to measure (graph)

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8
Q

Name three phenotypic changes that prove that natural selection is observable.

A
  1. pathogenicity
  2. host range
  3. drug resistance
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9
Q

Name four minor genetic changes that are observable in “human” time.

A
  1. Point mutation
  2. deletions and duplications
  3. rearrangements
  4. transfers between similar organisms
    * *this is not generation of diversity (no new species), just selection**
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10
Q

What is the date range for the increase in syphilis virulence?

A

1490-1540, endemic syphilis –> yaws – modern syphilis, boiled down to 1-2 nucleotide substitutions

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11
Q

Where did Spanish flu originate and when?

A

1918, Kansas, infected a whopping 1/3 of population, 6% died

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12
Q

What is the date range for the decrease in syphilis virulence?

A

1540-1900 (now endemic), presumable due to continuing mutations

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13
Q

Give two disease examples of a change in host range.

A
  1. AIDS - monkeys

2. SARS - civets/bats

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14
Q

Why is John Snow important?

A

Responsible for the first public health measure to stop the spread of cholera in 1854, London

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15
Q

Name 2 diseases that have been discovered to be due to infections.

A
  1. stomach ulcers - h. pylori

2. cervical cancer - pappilloma virus

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16
Q

What is E.Coli pyr- gal- amp ?

A

E. Coli that cannot make pyrimidine, cannot break down/digest galactose, and is resistant to ampicillin.

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17
Q

What is an R factor?

A

An extrachromosomal element that can encode antibiotic resistance.

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18
Q

Why do humans not have operons?

A

Each human gene has its own regulatory elements. Operons are elements that cover the transcription of multiple related genes.

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19
Q

What is the Ames test and why is it important?

A

The Ames test is a test for mutagenicity, which corresponds, generally, to carcinogenicity. Environmental factors that affect humans also have similar effects on bacteria.

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20
Q

Name two types of DNA that could be taken up by live bacteria in transformation.

A
  1. extrachromosomal DNA

2. Plasmid

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21
Q

What is the most likely fate of transformed DNA once it has been incorporated into a bacterial genome?

A

Digestion by restriction enzymes bc of unusual methylation pattern.

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22
Q

What are three examples of practical medical/laboratory applications of transformation?

A
  1. recombinant hep B vaccine
  2. recombinant insulin
  3. virus vectors for gene therapy
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23
Q

What is the difference between an F+ bacterium and Hfr bacterium?

A

F+ is a male bacterium in which the plasmid has not integrated into the chromosome. Hfr is a male bacterium in which the plasmid is integrated, and stands for “high frequency recombination”

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24
Q

What is the difference between a lytic and a lysogenic phage?

A

Lytic - generalized transduction
Lysogenic - specialized transduction - the virus incorporates itself into the bacterial genome and waits for favorable conditions to lyse the host.

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25
Q

Why is specialized transduction special?

A

Because when the host lyses, the prophage takes with it adjacent DNA from the host chromosome, which can then be incorporated into a new bacterium via either transformation or transduction.

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26
Q

Give four examples of disease where specialized transduction is the mechanism of toxin transfer.

A
  1. Botulism
  2. scarlet fever
  3. cholera
  4. diptheria
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27
Q

What is a compound transposon?

A

A transposon that integrates into a second transposon. If this were later transferred, a new host bacterium could gain double drug resistance from the compound transposon in 1 step.

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28
Q

What is a pathogenicity island?

A

Like an operon, but for pathogenicity. A bacterium has many adjacent genes that all contribute to the pathogenicity of a disease.

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29
Q

Do pathogenicity islands have translocation hardware (like transposons)?

A

Nope, but they can be transferred via the usual ways: transduction, transformation, or conjugation

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30
Q

What do we mean when we say that bacteria are haploid?

A

They only carry 1 copy of their chromosome.

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31
Q

What is an example of extrachromosomal DNA in humans?

A

Mitochondrial DNA, otherwise is not found (no plasmids in humans)

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32
Q

What is the typical size of a plasmid?

A

No bigger than 1-3 genes, in general.

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33
Q

What proportion of our DNA encodes protein?

A

About or less than 10%, proves we are very inefficient, as compared with bacteria who use up to 80% of their genome.

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34
Q

What are the 3 kinds of genes that bacteria have?

A
  1. biosynthetics - make something, ie histidine, his
  2. catabolics - digest something, ie lactase, lac
  3. drug resistance - resists (or digests) an antibiotic, ie chloramphenical, cat
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35
Q

What is an operator? Do humans have them?

A

An operator is a sequence between the promotor and the genes of the operon, only found in bacteria.

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36
Q

What is the function of lactose in the lac operon?

A

This operon is an example of inducible expression. The presence of lactose changes the conformation of the repressor, which then pulls off the operon and RNA polymerase is allowed to do its thing to transcribe the enzymes needed to digest the lactose.

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37
Q

What is the function of tryptophan in the trp operon?

A

This operon is an example of repressible expression. The presence of trp binds TO the repressor to then attach to the operon to stop the bacterium from making its own trp (because it has enough, presumably).

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38
Q

Regulation of lac and trp operaons are what category of bacterial gene regulation? What are the other two categtories?

A

Lac and trp are part of the “nutritional sensing” category, where the presence or absence of a nutrient induces/represses transcription. The other two categories are (1) cell surface sensing, and (2) quorum sensing.

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39
Q

The Ames test uses a point mutation in a bacteria to test carinogenicity. For what biosynthetic gene?

A

Histidine. Do the bacteria go from his- to his?

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40
Q

What did the Griffiths-Avery experiment show?

A

Example of transformation, where the no-capsule live pneumonia picked up the capsule gene from the dead pneumonia and then started making a capsule and killed the mice.

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41
Q

If one was to “transform” bacteria in the lab, what phase would be best for such an experiment?

A

Log phase, because the genetic machinery is all ramped up, the bacteria is happy.

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42
Q

Do bacteria carry enzymes to repair damaged DNA?

A

Yes, but it is limited, because the goal for bacteria is to do things quickly, whereas the goal for humans is to do things accurately.

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43
Q

What is another term for a compound transposon?

A

A composite transposon. Shillitoe uses these terms interchangeably.

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44
Q

What is the ultimate example of multidrug resistance (that could be coded as a pathogenicity island)? What 6 classes of drugs does it resist?

A

MRSA of course! Resists vancomycin A, vancomysin B, penicillin, the aminoglycosides, trimethoprim and methicillin.

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45
Q

Why is methicillin different as an antibiotic?

A

There is no gene to code for its resistance in bacteria. It instead requires a protein receptor on the surface of the bacterial (which is either not present or not functional in MRSA).

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46
Q

What are the 4 parts of Swick’s definition of professionalism?

A
  1. Subordinate your interests to those of your patients
  2. Adhere to high moral and ethical standards
  3. Respond to societal need
  4. Exude humanistic values, ie empathy, altruism, integrity, trustworthiness
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47
Q

What are the three elements in the charter of medical professionalism?

A
  1. Primacy of patient welfare
  2. Patient autonomy
  3. Social justice
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48
Q

What are the core ethics of the medical profession?

A
  1. Place patient interests above one’s own

2. Place society’s interests above those of the medical profession.

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49
Q

What is special about an Hfr cell’s “sexual” activity?

A

The Hfr chromosome and F portion, because incorporated into the same chromosome, all replicates and moves to the F-cell, where the entire chromosome can recombine with the F- in addition to transfer of the F factor.

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50
Q

What size (in Svedbergs) is a bacterial ribosome? A human ribosome?

A

Bacteria - 70S

Humans - 80S

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51
Q

What primarily makes up bacterial cell walls?

A

Peptidoglycan

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52
Q

What is the nucleus “alternative” that bacteria have?

A

Nucleoid - “area” but with no membrane, where the genetic material is stored in the cell

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53
Q

How does staph look under the microscope? Give bacterial shape and appearance.

A

Cocci, clumped characteristic

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54
Q

How does strep look under the microscope? Give bacterial shape and appearance.

A

Cocci, chains

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55
Q

How does neisseria look under the microscope? Give bacterial shape and appearance.

A

Cocci, appear as diplococci

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56
Q

What is an example of bacillus or rod-shaped bacteria?

A

E.Coli, also Pseudomonas

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57
Q

What is an example of a vibrio-shaped bacteria?

A

Vibrio cholera

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58
Q

Why is the spirochete triponema different from other bacteria in its microscopic preparation?

A

Triponema requires darkfield due to its tightly wound corkscrews

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59
Q

What are the 5 steps in gram staining, and the effects of each step?

A
  1. fix (over flame)
  2. stain with CV - all slide turns purple
  3. iodine treatment- gram +’s become permanently purple
  4. alcohol treatment - decolorizes gram -
  5. counterstain with safranin - restains gram - pink
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60
Q

What are the two major characteristics of gram + bacterial cell walls?

A
  1. thick (3 layers) of peptidoglycan

2. no exterior membrane on outside of peptidoglycan

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61
Q

What are the two major characteristics of gram - bacteria?

A
  1. thin (1 layer) of peptidoglycan

2. exterior membrane

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62
Q

In what kind of bacteria can LPS be found? What is LPS?

A

Endotoxin, found in gram - bacteria

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63
Q

What is a major reason why gram - bacteria are harder to treat with antibiotics?

A

Gram -‘s are known to engage in more frequent genetic transfer by plasmid exchange.

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64
Q

In what kind of bacteria can teichoic acid be found? What is teichoic acid?

A

Gram +, endotoxin

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65
Q

What is the most commonly ordered (and one of the cheapest) lab tests ordered?

A

Gram staining! It won’t usually be used for dx, but it is important to know what class of bacteria you are dealing with

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66
Q

Why is LPS so dangerous as an endotoxin?

A

Can cause septic shock, even as components of dead bacteria floating in your system.

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67
Q

What is the glycocalyx of bacteria? Why is it important?

A

Slime layer, important for biofilm formation, and to stay stuck places you want to infect. Glycocalyses also have capsules (sometimes), which resist phagocytosis

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68
Q

What are the differences between pili/fimbrae of gram + and gram - bacteria?

A

Gram - bacteria pili come in many types

Gra + bacteria pili - just recently discovered

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69
Q

Name two virulence factors used by bacteria.

A
  1. Capsule, anthrax, N. meningitidis, klebsiella
  2. Pili/fimbrae, ***E.Coli, if they acquire a pilus, can be very damaging
    - –there are others.
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70
Q

What is the smallest structure visible in light microscopy?

A

Small bacteria, perhaps large viruses

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71
Q

What structure do bacteria use for propulsion?

A

Flagellum

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72
Q

Are the porin proteins of gram + and gram - bacteria the same or different?

A

By definition, they must be different bc of the diff structures of each cell wall

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73
Q

What cleaves peptidoglycan?

A

Lysozyme, found in human tears

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74
Q

What is peptidoglycan made of?

A

crosslinked NAG (n-acetylglucosamine) and NAM (n-acetylmuramic acid)

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75
Q

Name 3 classes of drugs that inhibit peptidoglycan synthesis?

A
  1. Vancomycin
  2. Cephalosporins
  3. Penicillins
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76
Q

What substance makes mycobacterial cell walls unique?

A

Mycolic acid

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77
Q

What is the most toxic part of LPS/LOS endotoxin?

A

Lipid A tail

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78
Q

Name two ways that capsules can help a bacterium evade phagocytosis.

A
  1. The capsule may make the bacteria too big to digest

2. The capsule may cover up epitopes allowing the bacteria to escape immune detection

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79
Q

What kind of pilus is used for attachment?

A

Type I.

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80
Q

Can hundreds of bacteria fit in a human cell?

A

Yes! And sometimes they do!

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81
Q

What kind of pilus is used for propulsion?

A

Type 4.

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82
Q

What kind of pili are used for secretion?

A

Types 3 and 4.

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83
Q

Define an inherited gene complement.

A

Mutation that is transmitted by one or both parents

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84
Q

Define an acquired gene complement.

A

A subset of cells in an individual that arose by clonal propagation from a single mutation in one cell.

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85
Q

What is an inborn error of metabolism?

A

Genetically determined biochemical disorder in which a specific enzyme defect produces a metabolic block. Results in:

  1. accumulation of substrate
  2. deficiency of product
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86
Q

What is the mutation that causes albinism?

A

Mutation of tyrosine oxidase, inability to convert tyrosine to pigment. *NB that albinism can be total or partial

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87
Q

What is the basis for the defects of the 3 hyperphenylalaninemias?

A

Defect in function of phenylalanine hydoxylase which converts phenylalanine to tyrosine.

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88
Q

What is the effect of PKU in cells?

A

Accumulation of phenylalanine, excretion of phenylpyruvic acid (how it is diagnosed in the urine)

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89
Q

Give two clinical examples of phenotypic heterogeneity.

A
  1. Non-PKU hyperphenylalanemia, may be asymptomatic
  2. Variant PKU - between Non-PKU and full blown PKU
    same gene, different phenotype
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90
Q

Why do you add L-Dopa and 5-OH in the treatment of BH4 (tetrahydrobiopterin) deficiency? (as well as BH4 itself)

A

Because BH4 is a cofactor for many pathways, in particular, those involved in neurotransmission.

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91
Q

Why is a somatic cell 2N after S phase?

A

Because there are still only 2 SETS of chromosomes

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92
Q

At what stage of meiosis does reduction division occur?

A

Anaphase I.

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93
Q

What is isomy?

A

The process by which 2 chromosomes from the same source lead to the duplication of 1 chromosome.

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94
Q

What is heterodisomy?

A

The presence of 2 different chromosomes in a pair (that should be identical)

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95
Q

What is the end result for cells that undergo meiotic nondisjunction type I?

A

2 cells have 1 extra chromosome (2 cells with heterodisomy), 2 cells have 1 less chromosome (2 cells with nullisomy)

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96
Q

What is the end result for cells that undergo meiotic nondisjunction type II?

A

2 cells are normal (disomy), 1 cell is heterodisomic (1 extra chromosome) and 1 cell is nullisomic (missing a chromosome)

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97
Q

What is another term for prophase I, where oocytes are arrested in the 3rd month of gestation?

A

Dicytotene

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98
Q

At what stage does an oocyte complete meiosis I?

A

Ovulation

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99
Q

Which strand of DNA serves as the template strand for DNA transcription?

A

Antisense strand

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100
Q

Does a nucleoside contain the base, sugar and phosphate?

A

No! A nucleoside is just the base and sugar.

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101
Q

Where are the sugar and phosphate linkages on a ribose?

A

5’ and 3’ (phosphodiester bond). The base to sugar linkage is at 1’.

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102
Q

What is the general structure of pyrimidine base? What are the pyrimidines?

A

One 6-membered ring. Cytosine, uracil, thymine

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103
Q

What is the general structure of a purine base? What are the purines?

A

An attached 6 membered ring and 5 membered ring. Adenine and Guanine

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104
Q

Is the following a nucleoside, or a nucleoside monophosphate: ADENYLATE

A

nucleoside monophosphate (nmp)

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105
Q

Is the following a nucleoside, or a nucleoside monophosphate: THYMIDINE

A

nucleoside

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106
Q

Is the following a nucleoside, or a nucleoside monophosphate? URIDINE

A

nucleoside

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107
Q

Is the following a nucleoside, or a nucleoside monophosphate: GUANYLATE

A

NMP

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108
Q

Name the structure dCDP.

A

deoxycytidine diphosphate

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109
Q

What is the mechanism of action of AZT?

A

Chain terminator of DNA nucleotides, has affinity for reverse transcriptase, prevents replication of the viral DNA.

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110
Q

Name two situations that can lead to base modifications.

A
  1. Natural occurrence –> important for epigenetic control

2. DNA damage

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111
Q

What are three functions of nucleotides as they are used in cellular function (beyond the central dogma)?

A
  1. cAMP and cGMP are precursors for second messenger systems
  2. CoA is an important coenzyme
  3. ATP and GTP are energy carriers
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112
Q

What is the Chargraff rule?

A

States that in dsDNA, A=T and C=G

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113
Q

What are 3 features of B-DNA?

A
  1. right-handed
  2. 1 turn = 10.5 bp or 34 A (each base pair is 3.4 A)
  3. twisting forms major and minor grooves
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114
Q

What kind of DNA is shorter and appears in dehydrated samples?

A

A-DNA, right-handed, 11bp/turn but 28 A (instead of 34 in B-DNA) per turn –> wider double helix

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115
Q

What kind of DNA is left handed?

A

Z-DNA, 12 bp/turn, repeating unit is 2 bp, instead of 1 in A and B-DNA. Z-DNA can be induced by high salt content, some cations or negative supercoiling

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116
Q

What is Hoogsteen base pairing?

A

Purine bases can sometimes flip to a syn conformation, changing the hydrogen bond partners in the double helix proposal that these modifications add complexity to gene regulation

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117
Q

How does salt bind to DNA?

A

It binds to the phosphate-sugar backbone. More salt content actually stabilizes DNA

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118
Q

Centromeres have more ____ base content, while Telomeres have more ____ base content.

A

A-T, C-G

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119
Q

What happens in low stringency DNA hybridization?

A

Two denatured DNA strands combine, but not perfectly. There may be loops with non-annealed bases. Low stringency DNA hybridization is done below the Tm, while high stringency is done at or very close to the Tm.

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120
Q

What is a nucleosome made of?

A

Eight histone proteins (H2A, H2B, H3 and H4, all times 2), plus the DNA wrapped around 1.65 times, 146 base pairs of DNA per nucleosome!

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121
Q

What is the structure created by the beads on a string of nucleosomes, when they continue to wrap around each other?

A

30-nanometer fiber

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122
Q

Name two essential features of all eukaryotic chromosomes.

A
  1. centromeres

2. telomeres

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123
Q

What is the function of Type I topoisomerase?

A

Cuts 1 strand of DNA

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124
Q

What is the function of Type II topoisomerase?

A

Cuts both strands of DNA

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125
Q

What is the structural feature that renders RNA more vulnerable than DNA to hydrolysis?

A

The 2’ OH. Therefore, in a basic solution, RNA is degraded, while DNA remains stable (if denatured)

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126
Q

What is the main target of antibiotics in bacteria?

A

Bacterial ribosomes

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127
Q

Name two spore-forming bacteria.

A
  1. Bacillus

2. Chlostridium

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128
Q

Name a bacteria that is an obligate aerobe, and requires oxygen to survive?

A

M. tuberculosis.

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129
Q

Name a bacteria that is an obligate anaerobe, and is poisoned by oxygen?

A

C. botulinum.

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130
Q

Name a bacteria that is a facultative anaerobe, and uses oxygen if it’s around, but doesn’t require it to survive.

A

E. Coli

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131
Q

What is the only method of killing off bacterial spores?

A

Autoclave - heat to 121C, or ethylene oxide

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132
Q

What is the behavior of bacteria in the stationary phase?

A

They are only dividing at the rate that other bacteria are dying, steady turbidity

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133
Q

What is the pellicle?

A

Floating garbage visible in the death phase of in vitro bacteria

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134
Q

What is the definition of an obligate aerobe?

A

It has an electron transport chain that ends in oxygen as the recipient.

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135
Q

What powers bacterial flagella?

A

Transmembrane electron gradients

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136
Q

What are three main classes of antibiotics that target bacterial ribosomes?

A
  1. macrolides
  2. tetracyclines
  3. aminoglycosides
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137
Q

What determines a bacteria’s tolerance for oxygen?

A

If it can detoxify oxygen radicals, it contains oxidase, superoxide dismutase, catalase and/or cytochrome

138
Q

What are the requirements for full participation of a bacterium in quorum sensing?

A
  1. produces and secretes inducer
  2. contains receptor for inducer
  3. contains transcriptional activator that responds to inducer
    * *important in biofilms and coordinated expression of toxins**
139
Q

What is the resolution of conventional light microscopy?

A

About 200nm, but can view things as small as 5nm

140
Q

What is fluorescence microscopy?

A

Fluorescence microscopy is a special type of light microscopy that uses fluorescent dyes to detect specific macromolecules within cells.

141
Q

What is the target of indirect immunofluorescence?

A

Used in antibody fluorescence – label secondary antibody to amplify signal

142
Q

What is the resolution of transmission electron microscopy (TEM)?

A

About 2 nm, best for viewing organelles. Dark regions represent areas of e- density

143
Q

How would you identify perioxisomes in tem? Give 3 characteristics.

A
  1. smaller than mitochondria
  2. bigger than lysosomes
  3. may see dark core indicating presence of oxidative enzymes
144
Q

A microorganism is found to be a gram-positive coccus, growing in clumps, catalse-postive, and coagulase-positive. What is it?

A

Staph aureus.

145
Q

Which antibiotic is ALWAYS effective against Group A streptococci?

A

Bacitracin

146
Q

Which is the most likely clinical feature of Group A streptococcal infection?

  1. liver failure 3. anemia
  2. cough 4. spreading infection
A
  1. Spreading infection
147
Q

True or False: Group A strep is negative in the CAMP test, but Group B is positive in the CAMP test.

A

True.

148
Q

True or False: Group A strep is usually resistant to penicillin, but Group B strep is always sensitive to penicillin.

A

False. Group A is usually sensitive to penicillin.

149
Q

True or False: Penumococci are the only streptococci that can be identified by direct examination of gram-stained clinical specimen.

A

True! Because pneumococci are gram-positive diplococci. The rest are all chains.

150
Q

Name the 2 medically relevant neisseria.

A
  1. N. meningitidis

2. N. gonnorhoeae

151
Q

Name the 3 medically relevant staphylococci.

A
  1. S. aureus
  2. S. epidermidis
  3. S. saphrophyticus
152
Q

Name the 5 medically relevant streptococci.

A
  1. Group A
  2. Group B
  3. Pneumococci
  4. Viridans streptococci
  5. Enterococci
153
Q

Name two characteristics of all staphylococci.

A
  1. grow in clumps

2. catalase-positive

154
Q

What does it mean when a staph is catalase positive?

A

It reacts with hydrogen peroxide to produce “fizz” (decomposition of H2O2 to make water and oxygen)

155
Q

Name three characteristics of staph aureus

A
  1. beta-hemolytic
  2. coagulase positive
  3. catalase positive (all staph)
156
Q

Name three virulence factors of staph aureus

A
  1. protein A - binds immunoglobulins
  2. capsule
  3. toxins (ie coaguase, protein A)
157
Q

What is the most common clinical presentation of a staph aureus infection? What is a common method of transmission?

A

Abscesses are common. Transmission is usually by direct contact with infected person/carrier or indirectly by fomities.

158
Q

What kind of hemolysis involvement does staph epidermidis have? Where is it usually found clinically?

A

Non-hemolytic (gamma), found in piercings and catheters bc it likes to form biofilms on plastics and metals.

159
Q

What two kinds of staph infection are coagulase negative?

A
  1. S. epidermidis

2. S. saphrophyticus

160
Q

What are the two main characteristics of streptococci?

A
  1. grow in chains

2. gram positive

161
Q

What major sensitivity do Group A strep have?

A

Bacitracin. Called group A because it reacts to Group A antiserum

162
Q

What major resistivity do Group B strep have?

A

Bacitracin

163
Q

What is the major clinical issue with Group B strep?

A

Found in genital tract of 25% of women, can cause meningitis in babies if transmitted during pregnancy or birth

164
Q

If a coccus stains gram-negative, what genus must it belong to?

A

Neisseria.

165
Q

About how many cocci can fit in a RBC?

A

About 10 because they are each 1 micron in diameter

166
Q

What two cocci are responsible for causing meningitis?

A
  1. Group B strep

2. Neisseria meningitidis

167
Q

What kind of coccus is responsible for endocarditis (and dental caries)?

A

viridians streptococci, 100% of people are carriers!

168
Q

What is the primary virulence factors of viridians streptococci?

A

Sugar-metabolizing enzyme –> can break down to acids and cause dental caries, or can polymerize to sludgy sugars and cause bacteremia/endocarditis

169
Q

What molecule will any enteric cocci be resistant to?

A

Optochin, a bile salt

170
Q

What is the primary virulence factor of pneumococci?

A

Capsule!, 80 types, and the polysaccharide antigen resists long-term or strong immunity on our part. The Quelling reaction used to be used against the pneumococcus capsule

171
Q

In what morphology will beta-hemolytics appear?

A

Chains (streptococci)

172
Q

What is an example of Group A streptococcus?

A

S. pyogenes

173
Q

What are the virulence factors of Group A streptococci (S. pyogenes)?

A
  1. Pili - sticks well to epithelial surfaces
  2. M Protein (immune rxn)
  3. toxins - many!
174
Q

True or False: Group A strep forms blood clots.

A

False! Group A has streptokinase, which breaks down blood clots. It is a beta-hemolytic

175
Q

What are the Lancefield test results of Group A streptococcus?

A

reacts to Group A antiserum

176
Q

What coccus tests positive in the CAMP test?

A

Group B streptococcus (areas on agar of exaggerated hemolysis because of strep and s. aureus)

177
Q

What is the primary virulence factor of group B streptococci?

A

Capsule

178
Q

To what group of antibiotics are group B strep always sensitive?

A

Penicillin

179
Q

To what kind of agar is maltose added to test for neisseria meningitidis?

A

Chocolate agar (blood agar + heat)

180
Q

Name the correct genus and species name for:

A gram + coccus, catalase-positive, coagulase-positive

A

S. Aureus

181
Q

Name the correct genus and species name for:

A gram+ coccus, coagulase -, bacitracin-R

A

Group B strep

182
Q

Name the correct genus and species name for:

A gram - diplococcus, has pili

A

N. gonorrhoeae

183
Q

Name the correct genus and species name for:

A gram - diplococcus, has capsule, ferments maltose

A

N. meningitidis

184
Q

Name the correct genus and species name for:

A coccus, alpha-hemolytic, resistant to optochin

A

Viridians streptococcus

185
Q

Name the correct genus and species name for:

A coccus, beta-hemolytic, positive CAMP test, isolated from neonate autopsy.

A

Group B strep

186
Q

What three intermediate filament proteins make up the nuclear lamina?

A

Lamin A, Lamin B and Lamin C

187
Q

What happens to the lamins during mitosis? Why?

A

They are phosphorylated, which allows their dissassembly and the dissassembly of the nuclear lamina –> vesicularization of the nuclear envelope

188
Q

What can pass through nuclear pores without a NLS?

A

Water, molecules smaller than ~50kDa.

189
Q

About how many nuclear pore channels can a single cell have, on average?

A

3-4,000

190
Q

On what side of the nucleus is Ran-GAP1 found? What reaction does it catalyze?

A

Cytoplasic side; catalyzes RanGTP to RanGDP

191
Q

On what side of the nucleus is Ran-GEF found? What reaction does it catalyze?

A

Nuclear side, catalyzes RanGDP to RanGTP

192
Q

On which side of the nucleus can more RanGTP be found?

A

Nuclear side

193
Q

What amino acids are characteristically found in a NLS?

A

lysine and/or arginine, sometimes a proline

194
Q

Name the steps of importin and Ran translocation.

A
  1. Importin-cargo into nucleus
  2. RanGTP binds to importin-cargo
  3. Cargo is dropped off
  4. Ran-importin exit nucleus
  5. RanGTP is hydrolyzed to RanGDP
195
Q

How does mRNA exit the nucleus?

A

Exportin recognizes the 5’ cap of the mRNA

196
Q

What subunits make up the 45S rRNA large precursor? Which piece is NOT made in the nucleolus?

A

18S becomes small subunit
5.8S, 28S and 5S become large subunit
5S made elsewhere in the nucleus by RNA Pol III

197
Q

What is the fibrillar center of the nucleolus?

A

The area that contains DNA not actively being transcribed

198
Q

What is the dense fibrillar component of the nucleolus?

A

These regions contain rNA actively being transcribed

199
Q

What is the granular component of the nucleolus?

A

Region that contains maturing ribosomal precursors

200
Q

What is satellite DNA?

A

Short, repetitive sequences that centromeres and telomeres

201
Q

What are pseudogenes?

A

Copies of true genes that arose through duplication and became non-functional through genetic drift

202
Q

What is a notable example of repetitive sequences of “junk” DNA?

A

Alu sequences, so named because the area is cut by AluI, Alu repeats make up 5% of the human genome

203
Q

How is histone structure related to epigenetic control?

A

Histone tail post-translational modifications alter the structure (and subsequent function) of chromatin domains

204
Q

What disease is caused by the production of antibodies to self-antigens in the nucleus?

A

SLE

205
Q

What is a cause of spinal muscular atrophy, a pediatric neuromuscular disease?

A

Mutations in the protein SMN (survival of motor neurons) thought to be involved in RNA splicing

206
Q

A loss of function has been described for the gene that encodes the RAN GEF (GTP exchange factor) RCC1. How would you expect this mutation to affect nuceocytoplasmic transport?

A

mRNA export would cease because no Ran-GTP would be made.

207
Q

Stable chromosome maintenance requires which of the following?
Centromeres Telomeres
Origins of replication Exons

A

Centromeres, telomeres and origins of replication

208
Q

What are to functions of the nuclear lamina?

A
  1. Stabilizes nuclear envelope

2. Helps to organize chromosomes

209
Q

What is chromatin made up of?

A

DNA (chromosomes) coated with structural and regulatory proteins. DNA is never naked!

210
Q

What is the main function of the centromere?

A

Assembles kinetochore, segregation of duplicated chromosomes at mitosis and meiosis

211
Q

What sequence does telomerase synthesize?

A

GGGGTTA

212
Q

What charge must histones have in order to properly bind DNA?

A

Positive

213
Q

When does the H1 histone protein become important in chromosome packaging?

A

At the 30nm fiber step, acts as a linker

214
Q

What is an interesting epigenetic fact about histone and chromatin-packing?

A

These tendencies of histone modification and packaging can be inherited.

215
Q

Name two histone tail modifications.

A

Lysine residues can be methylated or acetylated

216
Q

What is important to know about acetylation in histone tails?

A

Locally alters chromatin structure, affecting the access to, or recruiting of, regulatory proteins. Patterns of acetylation are metastable over time, can persist through many cell divisions

217
Q

What percentage of pregnancies result in spontaneous loss?

A

15% of recognized pregnancies, with 80% in the first trimester. 60% of these losses are chromosomal in nature

218
Q

What is the condition associated with trisomy 13?

A

Patau syndrome

219
Q

What is a numerical abnormality in cytogenetics?

A

Change in the total # of chromosomes, a gain or loss

220
Q

What is a structural abnormality in cytogenetics?

A

A change in the size or shape of one or more chromosomes, ie deletion or translocation

221
Q

How is karyotype analysis performed?

A

Chromosomes are arrested at metaphase to analyze size, shape and banding pattern

222
Q

What is the short arm of the chromosome called?

A

P arm

223
Q

What is the long arm of the chromosome called?

A

Q arm

224
Q

What is an acrocentric chromosome?

A

A chromosome that has modified short arms that contain stalks of only rRNA sequences

225
Q

What is the function of telomeres on chromosomes?

A

They cap the DNA (which is sticky) to prevent annealing to maintain normal chromosome structure

226
Q

What is an ideogram?

A

Stained chromosomes in karyotype analysis

227
Q

What kind of stains are used in karyotype analysis?

A

Giemsa or Wright’ stain

228
Q

What are two sources of triploidy?

A
  1. Meiotic nondisjunction

2. Dispermy

229
Q

What is aneuploidy?

A

Gain or loss of chromosomes equaling less than one cplete complement, ie monosomy or trisomy

230
Q

What is 47,XX,+13

A

Trisomy 13 in a female

231
Q

True or False: Aneuploidies are usually inherited

A

No! Aneuploidies are usually due to meiotic or mitotic nondisjunction errors

232
Q

Can mosaicism be inherited?

A

No! It is acquired

233
Q

Name the three viable autosomal trisomies.

A
  1. Down syndrome, trisomy 21
  2. Patau syndome, trisomy 13
  3. Edwards syndrome, trisomy 18
234
Q

What are some features of Patau syndrome?

A
  1. cleft lip and palate
  2. rocker bottom feet
  3. polydactyly
235
Q

What are some features of Edwards syndrome?

A
  1. rocker bottom feet
  2. hand sign (fist)
  3. ventricular septal defect
  4. hypoplasia of muscles
236
Q

What clinical condition is indicated by an individual who is 45,X

A

Turner’s syndrome

237
Q

What clinical condition is indicated by an individual who is 47,XXY

A

Klinefelter’s

238
Q

Mullerian ducts are associated with what sex?

A

Female

239
Q

True or False: It is possible to have a fully functional TDF/SRY and be phenotypically female?

A

True. TDF is not the only sex-determining gene.

240
Q

What is the Lyon hypothesis?

A

One X chromosome is inactivated in all somatic cells of a female. Once established (3-7 days after fertilization), it is permanent. –> dosage compensation, where females and males express the same about of X.

241
Q

What does the Lyon hypothesis suggest about mosaicism?

A

Females are mosaics for somatic traits, depending on which X is inactivated where.

242
Q

Why does non-random X-inactivation occur?

A

If one of the X’s is damaged, it may be preferentially inactivated

243
Q

Give a clinical example of non-random X-inactivation.

A

Duchenne MD. Female carrier for X-linked disease may inactivate a damaged X, leaving her with the only available X, which codes for the mutation in MD.

244
Q

Why is the XIST locus important?

A

Primary X inactivation center on the X chromosome- inactivated by methylation. Process is reversible so the unused X can be passed on.

245
Q

What region of the X chromosome seems to escape X inactivation?

A

Pseudoautosomal region

246
Q

An individual who is 46,XY/47,XY+21 probably had a nondisjunction occur in what kind of cellular division?

A

Mitosis, because meiotic nondisjunction errors typically result in uniform karyoptyes

247
Q

What is the difference between conservative and semiconservative replication?

A

In conservative replication, two new strands are made, leaving the original DNA intact.
In semiconservative replication, one old strand is paired with new.

248
Q

What did the Meselson-Stahl experiment show?

A

It proved that DNA replication is semiconservative by inserting N isotopes into the mixture, and centrifuging after replication. Replication DNA was of hybrid density.

249
Q

Why are there generally two replication forks per origin of DNA synthesis?

A

Because DNA synthesis is bidirectional. Bidirectional synthesis creates a replication bubble.

250
Q

What are the Y-shaped junctions formed by newly synthesized DNA and unsynthesized DNA called?

A

Replication forks – it is also where the leading and lagging strands meet

251
Q

What is the ORC (origin recognition complex)?

A

The ORC is found at the origin of replication in DNA synthesis. It is responsible for the recruitment of other initiation proteins to the origin.

252
Q

What is the enzyme that unwinds the dsDNA, exposing the bases on both sides to serve as templates for hydrogen bond interactions with newly synthesized strands?

A

DNA helicase

253
Q

In DNA replication, what prevents single stranded DNA from re-annealing?

A

ssDNA binding protein

254
Q

What enzyme lays down RNA primer in DNA synthesis, and is only used in DNA synthesis?

A

Primase

255
Q

DNA epsilon polymerase is used for replication of which strand?

A

Leading strand

256
Q

DNA delta polymerase is used for replication of which strand?

A

Lagging strand

257
Q

What are the functions of the sliding clamp (PCNA) and the clamp loader (RF-C) in DNA replication?

A

They keep the DNA polymerase attached to the template and contribute to the high speed at which DNA synthesis can occur.

258
Q

What enzyme eventually removes the RNA primers after DNA replication is complete?

A

RNase

259
Q

What occurs at the E site in DNA replication?

A

Exonucleases proofread the newly synthesized DNA strand

260
Q

With what frequency do errors arise in DNA replication?

A

About 1 per 10,000 (1x10^7) nucleotides

261
Q

What is the process by which DNA replication errors are corrected?

A

DNA mismatch repair, corrects 99% of errors

262
Q

What is one reason why DNA mismatches occur?

A

Newly synthesized DNA has “nicks” in it, where phosphodiester bonds have not finalized or fully come together

263
Q

What is the danger of a DNA mismatch going unfixed?

A

All subsequent DNA synthesis would carry the error (permanent mutation).

264
Q

What is the “mutator phenotype?” Give one clinical example of its presentation

A

Mutator phenotype is when there is a mutation/loss of fx in one of the 7 mismatch repair genes. Can cause a type of colon cancer known as “hereditary non-polyposis colon cancer”- HNPCC

265
Q

What is one major effect of the mutator phenotype?

A

Can cause a snowballing effect of more an more acquired mutations resulting from non-error fixing during DNA replication.

266
Q

Fun fact!!

A

At least 160 proteins are involved in replicating the human genome

267
Q

Fun fact!!

A

At least 40! diseases are caused by aberrant DNA replication. This can include mutations in genes required for DNA snythesis, or mutations in mitochondrial replication, or even DNA viruses!

268
Q

What is “replication stress” in DNA synthesis?

A

Replication forks are vulnerable to:

  1. DNA damage, or
  2. nucleotide starvation
269
Q

What is the worst-case outcome of replication stress due to mutations, drug inhibitions?

A

Replisome destablized
Replication forks unprotected
Accumulation of abnormal replication intermediates…
*double strand breaks

270
Q

What is a clinical application of inducing or creating replication stress?

A

Cancer therapy

271
Q

Defects in the DNA replication protein ATM lead to what clinical manifestation?

A

Ataxia telangiectasia (A-T)

272
Q

Defects in the DNA replication protein lead to what clinical manifestation?

A

Bloom syndrome

273
Q

What is the function of the DNA replication protein ATM?

A

ATM is a protein kinase that regulates p53. When this protein fails to function, p53 builds up in the cell.

274
Q

Name three clinical features of ataxia telangiectasia (A-T)

A
  1. susceptibility to lymphomas
  2. flat red marks on skin from dilation of small vessels
  3. ataxia
275
Q

Name three features (clinical/epigenetic) of Bloom syndrome.

A
  1. susceptibility to cancers
  2. chromosomal alterations, facial telangiectases
  3. sensitivity to mild alkylating agents
276
Q

Name two nucleotide analog chain terminators used in cancer therapy.

A

ddC, ddI

277
Q

Camptothecin is a replication enzyme inhibitor used as a cancer treatment. What does it target?

A

Camptothecin targets topoisomerase I (Top1) and traps is in a cleavage complex

278
Q

Hydroxyurea is replication enzyme inhibitor used as a cancer treatment. What does it target?

A

Depletes cancer of DNA nucleotides. Used for chronic myeloid leukemia

279
Q

5-Fluorouracil (5-FU) is a replication enzyme inhibitor used as a cancer treatment What does it target?

A

5-FU targets thymidine synthetase, depleting amounts of dTTP (affects pyrimidine synthesis)

280
Q

What is a common cause of DNA alkylation leading to disease?

A

Tobacco smoke

281
Q

What is a common cause of the formation of pyrimidine dimers in DNA leading to disease?

A

UV radiation

282
Q

Name three single-strand DNA damage repair methods:

A
  1. BER - base excision repair
  2. NER - nucleotide excision repair
  3. MMR - mismatch repair
283
Q

Name three double-stranded DNA damage repair methods:

A
  1. Homologous recombination
  2. single strand annealing
  3. NHEJ - non-homologous end joining
284
Q

Explain the function of the DNA repair nucleases.

A
  1. DNA repair nucleases recognize the damaged portion of DNA
  2. They they hydrolize the phosphodiester bond that join the damaged nucleotides to the rest of the DNA molecule, leaving a small gap in the DNA helix.
285
Q

Explain the function of DNA polymerase with respect to its activity in DNA repair.

A
  1. DNA polymerase binds the 3’-OH end of the cut DNA strand

2. Fills the gap by making a complementary copy of the information from the template strand

286
Q

In a DNA repair mechanism, after DNA repair nucleases create the nick, and the DNA polymerase fills the gap, what enzyme seals the new base to the helix to complete the repair?

A

DNA ligase

287
Q

What is the major form of dsDNA repairs in humans, despite the occasional minor DNA changes that it produces?

A

NHEJ - non-homologous end joining. Broken DNA bits are assembled and re-annealed and joined.

288
Q

Give 2 clinical and cytogenetic features of Xeroderma Pigmentosum

A
  1. Severe propensity to develop skin cancers (must stay out the sun/ “children of the night”)
  2. Defective NER (nucleotide excision repair) mechanism
289
Q

Name the three basic functions of the medical interview.

A
  1. Build relationship between doctor and patient
  2. To assess diagnose a patient’s problem(s).
  3. To treat a patient’s problem(s).
290
Q

Name the components of the “NURS” model.

A
  1. Naming, “I see you’re upset’
  2. Understanding, “I can understand why you are upset
  3. Respect, “You did the right thing by coming in…
  4. Support
291
Q

What are the whopping TEN components of the health history?

A
  1. Identifying data - source and reliability
  2. Chief Complaint (cc)
  3. HPI
  4. Past medical history (PMI)
  5. Past surgical history (PSH)
  6. Allergies
  7. Current Meds
  8. Personal and social history (SH)
  9. Family history (FH)
  10. Review of systems (ROS)
292
Q

What is the acronym and meaning for evaluating the HPI?

A 
OLDCARTS   OR PQRST (Pallative/provocative, Quality, Radiation, Severity, Temporal)
Onset, context
Location
Duration
Character
Aggravating or associating factors
Relieving or radiating factors
Temporal factors 
Symptom severity
293
Q

Name three components of a PMH

A
  1. Illnesses
  2. Hospitalizations
  3. Accidents
  4. Obgyn hx
  5. Immunizations
  6. Health maintenance/disease prevention
294
Q

What is the mnemonic for OBGYN hx?

A 
TPAL
Term births
Premature births
Abortions/misscarriages
Live births
295
Q

In what section of the medical hx would you write OTC supplements or meds?

A

Put ALL with medications

296
Q

How does a good H&P always begin?

A

Age, gender, cc, most likely dx, also in dx….

297
Q

What is the VITAMIN C mnemonic for differential dx?

A

Vascular-Infection-Trauma-Anatomic-Metabolic-Iatrogenic (or in the blood)-Neoplasm-Collagen vascular

298
Q

What are the three main causes of foodborne illness?

A
  1. Shigella
  2. E. Coli
  3. Salmonella
299
Q

To what phylogenetic grouping does Yersinia belong?

A

Enterobacteriaceae, causes minor foodborne illness

300
Q

Name the 6 opportunistic pathogens, of phylogenetic grouping enterobacteriaceae, for which the aged or immunosuppressed might be at risk?

A
  1. Klebsiella
  2. Proteus
  3. Providencia
  4. Enterobacter
  5. Serratia
  6. Morganella
301
Q

Are enterobacteriaceae gram + or -?

A

gram-negative

302
Q

What is the main clinical obstacle with the treatment of enterobacterial infections?

A

Resistance to antibiotics due to genomic promiscuity/picking up of virulence factors.

303
Q

True or False: Enterobacteriaceae are oxidase (+).

A

False. They are oxidase -, catalase +

–also facultative aerobes, glucose fermenters

304
Q

What is the goal of antimicrobial sensitivity testing?

A

To measure the effectiveness of certain antibiotics on the plates of isolate you have incubated. Areas of antibiotic activity should correspond with associated effectiveness of treatment. Use a table to make sure!

305
Q

What are the two main virulence factors for enterobacteriaceae and why?

A
  1. Attachment pili (type 1) are essential to “hold on” to the gut or urinary tract, where they would otherwise be flushed out
  2. type 3 pili - secretion systems, for adhesion, subverting macrophage attack, and releasing enterotixins
306
Q

Name two enterobacteriaceae that use macrophages as torjan horses for more systemic infection.

A
  1. S. typhi

2. Yersinia enterocolictica

307
Q

What kind of pilus is used my enterobacteriaceae to migrate to the exterior of the gut

A

T3SS, using this bacteria alter macrophages in the Peyer’s patches, then get can hop a ride to the basolateral side of the gut cells.

308
Q

What is Hemolytic-Uremic syndrome?

A

HUS is caused by Shigella and EHEC infections, usually in children, 5-10% mortality, caused by release of the shiga toxin

309
Q

Patients positive for HLA-B27 are at risk for what complication of bacterial infection?

A

Reactive arthritis = arthritis, conjunctivitis, urethritis

after an infection of: shigella, salmonella, yersinia, campylobacter, chlamydia

310
Q

“Can’t see, can’t pee, can’t climb a tree” indicate what dx?

A

Reactive arthritis (Reiter’s syndrome)

311
Q

True or False: Shigella has a very high ID50, meaning it would take many bacteria to make you sick.

A

False. Shigella has a very low ID50. Salmonella has a high ID50.

312
Q

What would you see in a blood smear of a HUS patient? What else is a major symptom?

A

Lysed RBC’s “schistocytes” in blood smear, life-threatning kidney failure
some antibiotics can make it worse

313
Q

What is the bacterial risk associated with stomach stapling (beyond the standard surgical risk)?

A

The neutralization of the stomach, therefore less bacteria are naturally killed off.

314
Q

Why is making a vaccine to salmonella useless?

A

> 2500 serovars, large ID50, bacteremia from it is rare

315
Q

Why would a diabetic be more at risk for UTI’s?

A

Snack service

316
Q

What are the components of phospholipids?

A
  1. fatty acid(s)
  2. glycerol backbone - could also be a related molecule like sphygosine
  3. phosphate group
  4. alcohol
    3&4 = head group
317
Q

What charge does inositol have?

A

No charge, but it is polar. Important in formation of phospholipid head groups

318
Q

Below the Tm of the lipid bilayer, what shape do the membrane phospholipids take on?

A

Gel-like solid, closer packing, limited mobiltiy

319
Q

True or False: Kinks in the lipid bilayer increase membrane fluidity

A

True.

320
Q

How is cholesterol both an increaser and a decreaser (but mostly a decreaser) of membrane fluidity?

A

Cholesterol increases membrane fluidity by preventing close packing due to its size. However it also reduces fluidity because its size and its own lack of flexibility, doe to the lack of an acyl chain.

321
Q

Where on a lipid bilyaer might you see lots of cholesterol?

A

Lipid raft

322
Q

Name 4 ways drugs can get into cells.

A
  1. Passive diffusion
  2. Hijacked transporters
  3. Lipsome delivery
  4. (potential) protein transduction
323
Q

Most cell membranes are about equal parts lipid and protein. Name one major exception to this rule.

A

Myelin - mostly lipid!

324
Q

What are the two components of the fluid mosaic model?

A
  1. Lipid bilayer acts as a solvent for membrane proteins

2. Lateral diffusion is allowed, flip-flopping is not.

325
Q

What molecule, when flipped to the ECM side of the cell, serves as a signal for apoptosis?

A

Phosphatidyl serine

326
Q

True or False: In Turner syndrome, all individuals have at least one cell line with a 45,X chromosome complement.

A

False.

327
Q

XYY males and XXX females are similar in that they:

A

Are usually fertile and phenotypically normal. XXX females may arise as either maternal or paternal meiotic errors.

328
Q

In human females, X-inactivation is a permanent change affecting all cells.

A

False. X-inactivation is permanent in the somatic cells, but all X chromosomes will become active in the germ cells during gametogenesis.

329
Q

A female patient is referred for primary amenorrhea. A full clinical workup reveals no internal female genitalia, testes in the abdominal cavity, and a 46,XY karyotype. The most likely explanation for this is:

A

Androgen receptor defect.

330
Q

The proofreading activity of DNA polymerase involves:

A

3’ to 5’ exonuclease function

331
Q

Homologous recombination is executed by many of the same enzymes that are involved in ________

A

DNA repair.

332
Q

Xeroderma pigmentosum patients lack one or more enzymes required for:

A

Excision repair in DNA

333
Q

True or False: Homologues carry different alleles of the same genes while sister chromatids have the same alleles.

A

TRUE

334
Q

Where does Biosynthesis of glycosaminoglycan chains on proteoglycans occur primarily?

A

Golgi complex

335
Q

What is the site of synthesis of proteins destined for the mitochondrial matrix?

A

Cytosol. Mitochondrial proteins encoded in the nuclear genome are synthesized on free ribosomes in the cytosol and then transported into mitochondria post-translationally

336
Q

What is the function of adaptins?

A

Adaptins bind to clathrin and cargo receptors such as the LDL receptor. Clathrin coats disassemble immediately after the vesicles form without a clear trigger and dynamin is involved in pinching off the necks of the clathrin coated buds. Rabs interact with tethering proteins during vesicle docking.

337
Q

What is a random function of both mitochondria and peroxisomes that is not central to their purposes?

A

Phospholipid synthesis

338
Q

The mitochondrial genome only encodes what kind of RNA?

A

rRNA, tRNA, and a small number of mRNA directly involved in electron transport

339
Q

True or False: A defect in the ER targeting signal sequence of an ER resident protein would result in the protein being secreted from the cell.

A

False. Without an ER targeting signal, the protein would remain in the cytosol.

340
Q

True or False:

SNAREs catalyze the fusion of vesicles with their target membranes.

A

True

Unit 1 (5 decks)

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