Unit 1 Deck 1 Flashcards
1
Q
What is another name for the MTOC? What does it contain?
A
Centrosome, contains 2 centrioles
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
3
Q
Where are rRNA’s transcribed and processed?
A
Nucleolus
4
Q
What is an isolate?
A
A strain of bacteria obtained from a specific patient
5
Q
What is important to know about the 16sRNA gene, 3 facts
A
- it is universal to all species
- it is unique within each species, but flanked by sequences common to all organisms
- used in classification, both broadly, ie bacteria/archaea/eukarya, and specifically for identification of strains and isolates
6
Q
Where do enteric bacteria live?
A
GI tract
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)
8
Q
Name three phenotypic changes that prove that natural selection is observable.
A
- pathogenicity
- host range
- drug resistance
9
Q
Name four minor genetic changes that are observable in “human” time.
A
- Point mutation
- deletions and duplications
- rearrangements
- transfers between similar organisms
* *this is not generation of diversity (no new species), just selection**
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
11
Q
Where did Spanish flu originate and when?
A
1918, Kansas, infected a whopping 1/3 of population, 6% died
12
Q
What is the date range for the decrease in syphilis virulence?
A
1540-1900 (now endemic), presumable due to continuing mutations
13
Q
Give two disease examples of a change in host range.
A
- AIDS - monkeys
2. SARS - civets/bats
14
Q
Why is John Snow important?
A
Responsible for the first public health measure to stop the spread of cholera in 1854, London
15
Q
Name 2 diseases that have been discovered to be due to infections.
A
- stomach ulcers - h. pylori
2. cervical cancer - pappilloma virus
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.
17
Q
What is an R factor?
A
An extrachromosomal element that can encode antibiotic resistance.
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.
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.
20
Q
Name two types of DNA that could be taken up by live bacteria in transformation.
A
- extrachromosomal DNA
2. Plasmid
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.
22
Q
What are three examples of practical medical/laboratory applications of transformation?
A
- recombinant hep B vaccine
- recombinant insulin
- virus vectors for gene therapy
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”
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.
25
Why is specialized transduction special?
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.
26
Give four examples of disease where specialized transduction is the mechanism of toxin transfer.
1. Botulism
2. scarlet fever
3. cholera
4. diptheria
27
What is a compound transposon?
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.
28
What is a pathogenicity island?
Like an operon, but for pathogenicity. A bacterium has many adjacent genes that all contribute to the pathogenicity of a disease.
29
Do pathogenicity islands have translocation hardware (like transposons)?
Nope, but they can be transferred via the usual ways: transduction, transformation, or conjugation
30
What do we mean when we say that bacteria are haploid?
They only carry 1 copy of their chromosome.
31
What is an example of extrachromosomal DNA in humans?
Mitochondrial DNA, otherwise is not found (no plasmids in humans)
32
What is the typical size of a plasmid?
No bigger than 1-3 genes, in general.
33
What proportion of our DNA encodes protein?
About or less than 10%, proves we are very inefficient, as compared with bacteria who use up to 80% of their genome.
34
What are the 3 kinds of genes that bacteria have?
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
35
What is an operator? Do humans have them?
An operator is a sequence between the promotor and the genes of the operon, only found in bacteria.
36
What is the function of lactose in the lac operon?
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.
37
What is the function of tryptophan in the trp operon?
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).
38
Regulation of lac and trp operaons are what category of bacterial gene regulation? What are the other two categtories?
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.
39
The Ames test uses a point mutation in a bacteria to test carinogenicity. For what biosynthetic gene?
Histidine. Do the bacteria go from his- to his?
40
What did the Griffiths-Avery experiment show?
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.
41
If one was to "transform" bacteria in the lab, what phase would be best for such an experiment?
Log phase, because the genetic machinery is all ramped up, the bacteria is happy.
42
Do bacteria carry enzymes to repair damaged DNA?
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.
43
What is another term for a compound transposon?
A composite transposon. Shillitoe uses these terms interchangeably.
44
What is the ultimate example of multidrug resistance (that could be coded as a pathogenicity island)? What 6 classes of drugs does it resist?
MRSA of course! Resists vancomycin A, vancomysin B, penicillin, the aminoglycosides, trimethoprim and methicillin.
45
Why is methicillin different as an antibiotic?
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).
46
What are the 4 parts of Swick's definition of professionalism?
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
47
What are the three elements in the charter of medical professionalism?
1. Primacy of patient welfare
2. Patient autonomy
3. Social justice
48
What are the core ethics of the medical profession?
1. Place patient interests above one's own
| 2. Place society's interests above those of the medical profession.
49
What is special about an Hfr cell's "sexual" activity?
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.
50
What size (in Svedbergs) is a bacterial ribosome? A human ribosome?
Bacteria - 70S
| Humans - 80S
51
What primarily makes up bacterial cell walls?
Peptidoglycan
52
What is the nucleus "alternative" that bacteria have?
Nucleoid - "area" but with no membrane, where the genetic material is stored in the cell
53
How does staph look under the microscope? Give bacterial shape and appearance.
Cocci, clumped characteristic
54
How does strep look under the microscope? Give bacterial shape and appearance.
Cocci, chains
55
How does neisseria look under the microscope? Give bacterial shape and appearance.
Cocci, appear as diplococci
56
What is an example of bacillus or rod-shaped bacteria?
E.Coli, also Pseudomonas
57
What is an example of a vibrio-shaped bacteria?
Vibrio cholera
58
Why is the spirochete triponema different from other bacteria in its microscopic preparation?
Triponema requires darkfield due to its tightly wound corkscrews
59
What are the 5 steps in gram staining, and the effects of each step?
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
60
What are the two major characteristics of gram + bacterial cell walls?
1. thick (3 layers) of peptidoglycan
| 2. no exterior membrane on outside of peptidoglycan
61
What are the two major characteristics of gram - bacteria?
1. thin (1 layer) of peptidoglycan
| 2. exterior membrane
62
In what kind of bacteria can LPS be found? What is LPS?
Endotoxin, found in gram - bacteria
63
What is a major reason why gram - bacteria are harder to treat with antibiotics?
Gram -'s are known to engage in more frequent genetic transfer by plasmid exchange.
64
In what kind of bacteria can teichoic acid be found? What is teichoic acid?
Gram +, endotoxin
65
What is the most commonly ordered (and one of the cheapest) lab tests ordered?
Gram staining! It won't usually be used for dx, but it is important to know what class of bacteria you are dealing with
66
Why is LPS so dangerous as an endotoxin?
Can cause septic shock, even as components of dead bacteria floating in your system.
67
What is the glycocalyx of bacteria? Why is it important?
Slime layer, important for biofilm formation, and to stay stuck places you want to infect. Glycocalyses also have capsules (sometimes), which resist phagocytosis
68
What are the differences between pili/fimbrae of gram + and gram - bacteria?
Gram - bacteria pili come in many types
| Gra + bacteria pili - just recently discovered
69
Name two virulence factors used by bacteria.
1. Capsule, ***anthrax, N. meningitidis, klebsiella***
2. Pili/fimbrae, ***E.Coli, if they acquire a pilus, can be very damaging
- --there are others.
70
What is the smallest structure visible in light microscopy?
Small bacteria, perhaps large viruses
71
What structure do bacteria use for propulsion?
Flagellum
72
Are the porin proteins of gram + and gram - bacteria the same or different?
By definition, they must be different bc of the diff structures of each cell wall
73
What cleaves peptidoglycan?
Lysozyme, found in human tears
74
What is peptidoglycan made of?
crosslinked NAG (n-acetylglucosamine) and NAM (n-acetylmuramic acid)
75
Name 3 classes of drugs that inhibit peptidoglycan synthesis?
1. Vancomycin
2. Cephalosporins
3. Penicillins
76
What substance makes mycobacterial cell walls unique?
Mycolic acid
77
What is the most toxic part of LPS/LOS endotoxin?
Lipid A tail
78
Name two ways that capsules can help a bacterium evade phagocytosis.
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
79
What kind of pilus is used for attachment?
Type I.
80
Can hundreds of bacteria fit in a human cell?
Yes! And sometimes they do!
81
What kind of pilus is used for propulsion?
Type 4.
82
What kind of pili are used for secretion?
Types 3 and 4.
83
Define an inherited gene complement.
Mutation that is transmitted by one or both parents
84
Define an acquired gene complement.
A subset of cells in an individual that arose by clonal propagation from a single mutation in one cell.
85
What is an inborn error of metabolism?
Genetically determined biochemical disorder in which a specific enzyme defect produces a metabolic block. Results in:
1. accumulation of substrate
2. deficiency of product
86
What is the mutation that causes albinism?
Mutation of tyrosine oxidase, inability to convert tyrosine to pigment. *NB that albinism can be total or partial
87
What is the basis for the defects of the 3 hyperphenylalaninemias?
Defect in function of phenylalanine hydoxylase which converts phenylalanine to tyrosine.
88
What is the effect of PKU in cells?
Accumulation of phenylalanine, excretion of phenylpyruvic acid (how it is diagnosed in the urine)
89
Give two clinical examples of phenotypic heterogeneity.
1. Non-PKU hyperphenylalanemia, may be asymptomatic
2. Variant PKU - between Non-PKU and full blown PKU
same gene, different phenotype
90
Why do you add L-Dopa and 5-OH in the treatment of BH4 (tetrahydrobiopterin) deficiency? (as well as BH4 itself)
Because BH4 is a cofactor for many pathways, in particular, those involved in neurotransmission.
91
Why is a somatic cell 2N after S phase?
Because there are still only 2 SETS of chromosomes
92
At what stage of meiosis does reduction division occur?
Anaphase I.
93
What is isomy?
The process by which 2 chromosomes from the same source lead to the duplication of 1 chromosome.
94
What is heterodisomy?
The presence of 2 different chromosomes in a pair (that should be identical)
95
What is the end result for cells that undergo meiotic nondisjunction type I?
2 cells have 1 extra chromosome (2 cells with *heterodisomy*), 2 cells have 1 less chromosome (2 cells with *nullisomy*)
96
What is the end result for cells that undergo meiotic nondisjunction type II?
2 cells are normal (disomy), 1 cell is heterodisomic (1 extra chromosome) and 1 cell is nullisomic (missing a chromosome)
97
What is another term for prophase I, where oocytes are arrested in the 3rd month of gestation?
Dicytotene
98
At what stage does an oocyte complete meiosis I?
Ovulation
99
Which strand of DNA serves as the template strand for DNA transcription?
Antisense strand
100
Does a nucleoside contain the base, sugar and phosphate?
No! A nucleoside is just the base and sugar.
101
Where are the sugar and phosphate linkages on a ribose?
5' and 3' (phosphodiester bond). The base to sugar linkage is at 1'.
102
What is the general structure of pyrimidine base? What are the pyrimidines?
One 6-membered ring. Cytosine, uracil, thymine
103
What is the general structure of a purine base? What are the purines?
An attached 6 membered ring and 5 membered ring. Adenine and Guanine
104
Is the following a nucleoside, or a nucleoside monophosphate: ADENYLATE
nucleoside monophosphate (nmp)
105
Is the following a nucleoside, or a nucleoside monophosphate: THYMIDINE
nucleoside
106
Is the following a nucleoside, or a nucleoside monophosphate? URIDINE
nucleoside
107
Is the following a nucleoside, or a nucleoside monophosphate: GUANYLATE
NMP
108
Name the structure dCDP.
deoxycytidine diphosphate
109
What is the mechanism of action of AZT?
Chain terminator of DNA nucleotides, has affinity for reverse transcriptase, prevents replication of the viral DNA.
110
Name two situations that can lead to base modifications.
1. Natural occurrence --> important for epigenetic control
| 2. DNA damage
111
What are three functions of nucleotides as they are used in cellular function (beyond the central dogma)?
1. cAMP and cGMP are precursors for second messenger systems
2. CoA is an important coenzyme
3. ATP and GTP are energy carriers
112
What is the Chargraff rule?
States that in dsDNA, A=T and C=G
113
What are 3 features of B-DNA?
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
114
What kind of DNA is shorter and appears in dehydrated samples?
A-DNA, right-handed, 11bp/turn but 28 A (instead of 34 in B-DNA) per turn --> wider double helix
115
What kind of DNA is left handed?
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
116
What is Hoogsteen base pairing?
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**
117
How does salt bind to DNA?
It binds to the phosphate-sugar backbone. More salt content actually stabilizes DNA
118
Centromeres have more ____ base content, while Telomeres have more ____ base content.
A-T, C-G
119
What happens in low stringency DNA hybridization?
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.
120
What is a nucleosome made of?
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!
121
What is the structure created by the beads on a string of nucleosomes, when they continue to wrap around each other?
30-nanometer fiber
122
Name two essential features of all eukaryotic chromosomes.
1. centromeres
| 2. telomeres
123
What is the function of Type I topoisomerase?
Cuts 1 strand of DNA
124
What is the function of Type II topoisomerase?
Cuts both strands of DNA
125
What is the structural feature that renders RNA more vulnerable than DNA to hydrolysis?
The 2' OH. Therefore, in a basic solution, RNA is degraded, while DNA remains stable (if denatured)
126
What is the main target of antibiotics in bacteria?
Bacterial ribosomes
127
Name two spore-forming bacteria.
1. Bacillus
| 2. Chlostridium
128
Name a bacteria that is an obligate aerobe, and requires oxygen to survive?
M. tuberculosis.
129
Name a bacteria that is an obligate anaerobe, and is poisoned by oxygen?
C. botulinum.
130
Name a bacteria that is a facultative anaerobe, and uses oxygen if it's around, but doesn't require it to survive.
E. Coli
131
What is the only method of killing off bacterial spores?
Autoclave - heat to 121C, or ethylene oxide
132
What is the behavior of bacteria in the stationary phase?
They are only dividing at the rate that other bacteria are dying, steady turbidity
133
What is the pellicle?
Floating garbage visible in the death phase of in vitro bacteria
134
What is the definition of an obligate aerobe?
It has an electron transport chain that ends in oxygen as the recipient.
135
What powers bacterial flagella?
Transmembrane electron gradients
136
What are three main classes of antibiotics that target bacterial ribosomes?
1. macrolides
2. tetracyclines
3. aminoglycosides
137
What determines a bacteria's tolerance for oxygen?
If it can detoxify oxygen radicals, it contains oxidase, superoxide dismutase, catalase and/or cytochrome
138
What are the requirements for full participation of a bacterium in quorum sensing?
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
What is the resolution of conventional light microscopy?
About 200nm, but can view things as small as 5nm
140
What is fluorescence microscopy?
Fluorescence microscopy is a special type of light microscopy that uses fluorescent dyes to detect specific macromolecules within cells.
141
What is the target of indirect immunofluorescence?
Used in antibody fluorescence -- label secondary antibody to amplify signal
142
What is the resolution of transmission electron microscopy (TEM)?
About 2 nm, best for viewing organelles. Dark regions represent areas of e- density
143
How would you identify perioxisomes in tem? Give 3 characteristics.
1. smaller than mitochondria
2. bigger than lysosomes
3. may see dark core indicating presence of oxidative enzymes
144
A microorganism is found to be a gram-positive coccus, growing in clumps, catalse-postive, and coagulase-positive. What is it?
Staph aureus.
145
Which antibiotic is ALWAYS effective against Group A streptococci?
Bacitracin
146
Which is the most likely clinical feature of Group A streptococcal infection?
1. liver failure 3. anemia
2. cough 4. spreading infection
4. Spreading infection
147
True or False: Group A strep is negative in the CAMP test, but Group B is positive in the CAMP test.
True.
148
True or False: Group A strep is usually resistant to penicillin, but Group B strep is always sensitive to penicillin.
False. Group A is usually sensitive to penicillin.
149
True or False: Penumococci are the only streptococci that can be identified by direct examination of gram-stained clinical specimen.
True! Because pneumococci are gram-positive diplococci. The rest are all chains.
150
Name the 2 medically relevant neisseria.
1. N. meningitidis
| 2. N. gonnorhoeae
151
Name the 3 medically relevant staphylococci.
1. S. aureus
2. S. epidermidis
3. S. saphrophyticus
152
Name the 5 medically relevant streptococci.
1. Group A
2. Group B
3. Pneumococci
4. Viridans streptococci
5. Enterococci
153
Name two characteristics of all staphylococci.
1. grow in clumps
| 2. catalase-positive
154
What does it mean when a staph is catalase positive?
It reacts with hydrogen peroxide to produce "fizz" (decomposition of H2O2 to make water and oxygen)
155
Name three characteristics of staph aureus
1. beta-hemolytic
2. coagulase positive
3. catalase positive (all staph)
156
Name three virulence factors of staph aureus
1. protein A - binds immunoglobulins
2. capsule
3. toxins (ie coaguase, protein A)
157
What is the most common clinical presentation of a staph aureus infection? What is a common method of transmission?
Abscesses are common. Transmission is usually by direct contact with infected person/carrier or indirectly by fomities.
158
What kind of hemolysis involvement does staph epidermidis have? Where is it usually found clinically?
Non-hemolytic (gamma), found in piercings and catheters bc it likes to form biofilms on plastics and metals.
159
What two kinds of staph infection are coagulase negative?
1. S. epidermidis
| 2. S. saphrophyticus
160
What are the two main characteristics of streptococci?
1. grow in chains
| 2. gram positive
161
What major sensitivity do Group A strep have?
Bacitracin. Called group A because it reacts to Group A antiserum
162
What major resistivity do Group B strep have?
Bacitracin
163
What is the major clinical issue with Group B strep?
Found in genital tract of 25% of women, can cause meningitis in babies if transmitted during pregnancy or birth
164
If a coccus stains gram-negative, what genus must it belong to?
Neisseria.
165
About how many cocci can fit in a RBC?
About 10 because they are each 1 micron in diameter
166
What two cocci are responsible for causing meningitis?
1. Group B strep
| 2. Neisseria meningitidis
167
What kind of coccus is responsible for endocarditis (and dental caries)?
viridians streptococci, 100% of people are carriers!
168
What is the primary virulence factors of viridians streptococci?
Sugar-metabolizing enzyme --> can break down to acids and cause dental caries, or can polymerize to sludgy sugars and cause bacteremia/endocarditis
169
What molecule will any enteric cocci be resistant to?
Optochin, a bile salt
170
What is the primary virulence factor of pneumococci?
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
In what morphology will beta-hemolytics appear?
Chains (streptococci)
172
What is an example of Group A streptococcus?
S. pyogenes
173
What are the virulence factors of Group A streptococci (S. pyogenes)?
1. Pili - sticks well to epithelial surfaces
2. M Protein (immune rxn)
3. toxins - many!
174
True or False: Group A strep forms blood clots.
False! Group A has streptokinase, which breaks down blood clots. It is a beta-hemolytic
175
What are the Lancefield test results of Group A streptococcus?
reacts to Group A antiserum
176
What coccus tests positive in the CAMP test?
Group B streptococcus (areas on agar of exaggerated hemolysis because of strep and s. aureus)
177
What is the primary virulence factor of group B streptococci?
Capsule
178
To what group of antibiotics are group B strep always sensitive?
Penicillin
179
To what kind of agar is maltose added to test for neisseria meningitidis?
Chocolate agar (blood agar + heat)
180
Name the correct genus and species name for:
| A gram + coccus, catalase-positive, coagulase-positive
S. Aureus
181
Name the correct genus and species name for:
| A gram+ coccus, coagulase -, bacitracin-R
Group B strep
182
Name the correct genus and species name for:
| A gram - diplococcus, has pili
N. gonorrhoeae
183
Name the correct genus and species name for:
| A gram - diplococcus, has capsule, ferments maltose
N. meningitidis
184
Name the correct genus and species name for:
| A coccus, alpha-hemolytic, resistant to optochin
Viridians streptococcus
185
Name the correct genus and species name for:
| A coccus, beta-hemolytic, positive CAMP test, isolated from neonate autopsy.
Group B strep
186
What three intermediate filament proteins make up the nuclear lamina?
Lamin A, Lamin B and Lamin C
187
What happens to the lamins during mitosis? Why?
They are phosphorylated, which allows their dissassembly and the dissassembly of the nuclear lamina --> vesicularization of the nuclear envelope
188
What can pass through nuclear pores without a NLS?
Water, molecules smaller than ~50kDa.
189
About how many nuclear pore channels can a single cell have, on average?
3-4,000
190
On what side of the nucleus is Ran-GAP1 found? What reaction does it catalyze?
Cytoplasic side; catalyzes RanGTP to RanGDP
191
On what side of the nucleus is Ran-GEF found? What reaction does it catalyze?
Nuclear side, catalyzes RanGDP to RanGTP
192
On which side of the nucleus can more RanGTP be found?
Nuclear side
193
What amino acids are characteristically found in a NLS?
lysine and/or arginine, sometimes a proline
194
Name the steps of importin and Ran translocation.
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
How does mRNA exit the nucleus?
Exportin recognizes the 5' cap of the mRNA
196
What subunits make up the 45S rRNA large precursor? Which piece is NOT made in the nucleolus?
18S becomes small subunit
5.8S, 28S and 5S become large subunit
5S made elsewhere in the nucleus by RNA Pol III
197
What is the fibrillar center of the nucleolus?
The area that contains DNA not actively being transcribed
198
What is the dense fibrillar component of the nucleolus?
These regions contain rNA actively being transcribed
199
What is the granular component of the nucleolus?
Region that contains maturing ribosomal precursors
200
What is satellite DNA?
Short, repetitive sequences that centromeres and telomeres
201
What are pseudogenes?
Copies of true genes that arose through duplication and became non-functional through genetic drift
202
What is a notable example of repetitive sequences of "junk" DNA?
Alu sequences, so named because the area is cut by AluI, Alu repeats make up 5% of the human genome
203
How is histone structure related to epigenetic control?
Histone tail post-translational modifications alter the structure (and subsequent function) of chromatin domains
204
What disease is caused by the production of antibodies to self-antigens in the nucleus?
SLE
205
What is a cause of spinal muscular atrophy, a pediatric neuromuscular disease?
Mutations in the protein SMN (survival of motor neurons) thought to be involved in RNA splicing
206
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?
mRNA export would cease because no Ran-GTP would be made.
207
Stable chromosome maintenance requires which of the following?
Centromeres Telomeres
Origins of replication Exons
Centromeres, telomeres and origins of replication
208
What are to functions of the nuclear lamina?
1. Stabilizes nuclear envelope
| 2. Helps to organize chromosomes
209
What is chromatin made up of?
DNA (chromosomes) coated with structural and regulatory proteins. DNA is never naked!
210
What is the main function of the centromere?
Assembles kinetochore, segregation of duplicated chromosomes at mitosis and meiosis
211
What sequence does telomerase synthesize?
GGGGTTA
212
What charge must histones have in order to properly bind DNA?
Positive
213
When does the H1 histone protein become important in chromosome packaging?
At the 30nm fiber step, acts as a linker
214
What is an interesting epigenetic fact about histone and chromatin-packing?
These tendencies of histone modification and packaging can be inherited.
215
Name two histone tail modifications.
Lysine residues can be methylated or acetylated
216
What is important to know about acetylation in histone tails?
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
What percentage of pregnancies result in spontaneous loss?
15% of recognized pregnancies, with 80% in the first trimester. 60% of these losses are chromosomal in nature
218
What is the condition associated with trisomy 13?
Patau syndrome
219
What is a numerical abnormality in cytogenetics?
Change in the total # of chromosomes, a gain or loss
220
What is a structural abnormality in cytogenetics?
A change in the size or shape of one or more chromosomes, ie deletion or translocation
221
How is karyotype analysis performed?
Chromosomes are arrested at metaphase to analyze size, shape and banding pattern
222
What is the short arm of the chromosome called?
P arm
223
What is the long arm of the chromosome called?
Q arm
224
What is an acrocentric chromosome?
A chromosome that has modified short arms that contain stalks of only rRNA sequences
225
What is the function of telomeres on chromosomes?
They cap the DNA (which is sticky) to prevent annealing to maintain normal chromosome structure
226
What is an ideogram?
Stained chromosomes in karyotype analysis
227
What kind of stains are used in karyotype analysis?
Giemsa or Wright' stain
228
What are two sources of triploidy?
1. Meiotic nondisjunction
| 2. Dispermy
229
What is aneuploidy?
Gain or loss of chromosomes equaling less than one cplete complement, ie monosomy or trisomy
230
What is 47,XX,+13
Trisomy 13 in a female
231
True or False: Aneuploidies are usually inherited
No! Aneuploidies are usually due to meiotic or mitotic nondisjunction errors
232
Can mosaicism be inherited?
No! It is acquired
233
Name the three viable autosomal trisomies.
1. Down syndrome, trisomy 21
2. Patau syndome, trisomy 13
3. Edwards syndrome, trisomy 18
234
What are some features of Patau syndrome?
1. cleft lip and palate
2. rocker bottom feet
3. polydactyly
235
What are some features of Edwards syndrome?
1. rocker bottom feet
1. hand sign (fist)
3. ventricular septal defect
4. hypoplasia of muscles
236
What clinical condition is indicated by an individual who is 45,X
Turner's syndrome
237
What clinical condition is indicated by an individual who is 47,XXY
Klinefelter's
238
Mullerian ducts are associated with what sex?
Female
239
True or False: It is possible to have a fully functional TDF/SRY and be phenotypically female?
True. TDF is not the only sex-determining gene.
240
What is the Lyon hypothesis?
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
What does the Lyon hypothesis suggest about mosaicism?
Females are mosaics for somatic traits, depending on which X is inactivated where.
242
Why does non-random X-inactivation occur?
If one of the X's is damaged, it may be preferentially inactivated
243
Give a clinical example of non-random X-inactivation.
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
Why is the XIST locus important?
Primary X inactivation center on the X chromosome- inactivated by methylation. Process is reversible so the unused X can be passed on.
245
What region of the X chromosome seems to escape X inactivation?
Pseudoautosomal region
246
An individual who is 46,XY/47,XY+21 probably had a nondisjunction occur in what kind of cellular division?
Mitosis, because meiotic nondisjunction errors typically result in uniform karyoptyes
247
What is the difference between conservative and semiconservative replication?
In conservative replication, two new strands are made, leaving the original DNA intact.
In semiconservative replication, one old strand is paired with new.
248
What did the Meselson-Stahl experiment show?
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
Why are there generally two replication forks per origin of DNA synthesis?
Because DNA synthesis is bidirectional. Bidirectional synthesis creates a replication bubble.
250
What are the Y-shaped junctions formed by newly synthesized DNA and unsynthesized DNA called?
Replication forks -- it is also where the leading and lagging strands meet
251
What is the ORC (origin recognition complex)?
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
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?
DNA helicase
253
In DNA replication, what prevents single stranded DNA from re-annealing?
ssDNA binding protein
254
What enzyme lays down RNA primer in DNA synthesis, and is only used in DNA synthesis?
Primase
255
DNA epsilon polymerase is used for replication of which strand?
Leading strand
256
DNA delta polymerase is used for replication of which strand?
Lagging strand
257
What are the functions of the sliding clamp (PCNA) and the clamp loader (RF-C) in DNA replication?
They keep the DNA polymerase attached to the template and contribute to the high speed at which DNA synthesis can occur.
258
What enzyme eventually removes the RNA primers after DNA replication is complete?
RNase
259
What occurs at the E site in DNA replication?
Exonucleases proofread the newly synthesized DNA strand
260
With what frequency do errors arise in DNA replication?
About 1 per 10,000 (1x10^7) nucleotides
261
What is the process by which DNA replication errors are corrected?
DNA mismatch repair, corrects 99% of errors
262
What is one reason why DNA mismatches occur?
Newly synthesized DNA has "nicks" in it, where phosphodiester bonds have not finalized or fully come together
263
What is the danger of a DNA mismatch going unfixed?
All subsequent DNA synthesis would carry the error (permanent mutation).
264
What is the "mutator phenotype?" Give one clinical example of its presentation
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
What is one major effect of the mutator phenotype?
Can cause a snowballing effect of more an more acquired mutations resulting from non-error fixing during DNA replication.
266
Fun fact!!
At least 160 proteins are involved in replicating the human genome
267
Fun fact!!
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
What is "replication stress" in DNA synthesis?
Replication forks are vulnerable to:
1. DNA damage, or
2. nucleotide starvation
269
What is the worst-case outcome of replication stress due to mutations, drug inhibitions?
Replisome destablized
Replication forks unprotected
Accumulation of abnormal replication intermediates...
***double strand breaks**
270
What is a clinical application of *inducing or creating* replication stress?
Cancer therapy
271
Defects in the DNA replication protein ATM lead to what clinical manifestation?
Ataxia telangiectasia (A-T)
272
Defects in the DNA replication protein lead to what clinical manifestation?
Bloom syndrome
273
What is the function of the DNA replication protein ATM?
ATM is a protein kinase that regulates p53. When this protein fails to function, p53 builds up in the cell.
274
Name three clinical features of ataxia telangiectasia (A-T)
1. susceptibility to lymphomas
2. flat red marks on skin from dilation of small vessels
3. ataxia
275
Name three features (clinical/epigenetic) of Bloom syndrome.
1. susceptibility to cancers
2. chromosomal alterations, facial telangiectases
3. sensitivity to mild alkylating agents
276
Name two nucleotide analog chain terminators used in cancer therapy.
ddC, ddI
277
Camptothecin is a replication enzyme inhibitor used as a cancer treatment. What does it target?
Camptothecin targets topoisomerase I (Top1) and traps is in a cleavage complex
278
Hydroxyurea is replication enzyme inhibitor used as a cancer treatment. What does it target?
Depletes cancer of DNA nucleotides. Used for chronic myeloid leukemia
279
5-Fluorouracil (5-FU) is a replication enzyme inhibitor used as a cancer treatment What does it target?
5-FU targets thymidine synthetase, depleting amounts of dTTP (affects pyrimidine synthesis)
280
What is a common cause of DNA alkylation leading to disease?
Tobacco smoke
281
What is a common cause of the formation of pyrimidine dimers in DNA leading to disease?
UV radiation
282
Name three single-strand DNA damage repair methods:
1. BER - base excision repair
2. NER - nucleotide excision repair
3. MMR - mismatch repair
283
Name three double-stranded DNA damage repair methods:
1. Homologous recombination
2. single strand annealing
3. NHEJ - non-homologous end joining
284
Explain the function of the DNA repair nucleases.
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
Explain the function of DNA polymerase with respect to its activity in DNA repair.
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
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?
DNA ligase
287
What is the major form of dsDNA repairs in humans, despite the occasional minor DNA changes that it produces?
NHEJ - non-homologous end joining. Broken DNA bits are assembled and re-annealed and joined.
288
Give 2 clinical and cytogenetic features of Xeroderma Pigmentosum
1. Severe propensity to develop skin cancers (must stay out the sun/ "children of the night")
1. Defective NER (nucleotide excision repair) mechanism
289
Name the three basic functions of the medical interview.
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
Name the components of the "NURS" model.
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
What are the whopping TEN components of the health history?
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
What is the acronym and meaning for evaluating the HPI?
```
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
Name three components of a PMH
1. Illnesses
2. Hospitalizations
3. Accidents
4. Obgyn hx
5. Immunizations
6. Health maintenance/disease prevention
294
What is the mnemonic for OBGYN hx?
```
TPAL
Term births
Premature births
Abortions/misscarriages
Live births
```
295
In what section of the medical hx would you write OTC supplements or meds?
Put ALL with medications
296
How does a good H&P always begin?
Age, gender, cc, most likely dx, also in dx....
297
What is the VITAMIN C mnemonic for differential dx?
Vascular-Infection-Trauma-Anatomic-Metabolic-Iatrogenic (or in the blood)-Neoplasm-Collagen vascular
298
What are the three main causes of foodborne illness?
1. Shigella
2. E. Coli
3. Salmonella
299
To what phylogenetic grouping does Yersinia belong?
Enterobacteriaceae, causes minor foodborne illness
300
Name the 6 opportunistic pathogens, of phylogenetic grouping enterobacteriaceae, for which the aged or immunosuppressed might be at risk?
1. Klebsiella
2. Proteus
3. Providencia
4. Enterobacter
5. Serratia
6. Morganella
301
Are enterobacteriaceae gram + or -?
gram-negative
302
What is the main clinical obstacle with the treatment of enterobacterial infections?
Resistance to antibiotics due to genomic promiscuity/picking up of virulence factors.
303
True or False: Enterobacteriaceae are oxidase (+).
False. They are oxidase -, *catalase* +
| --also facultative aerobes, glucose fermenters
304
What is the goal of antimicrobial sensitivity testing?
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
What are the two main virulence factors for enterobacteriaceae and why?
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
Name two enterobacteriaceae that use macrophages as torjan horses for more systemic infection.
1. S. typhi
| 2. Yersinia enterocolictica
307
What kind of pilus is used my enterobacteriaceae to migrate to the *exterior* of the gut
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
What is Hemolytic-Uremic syndrome?
HUS is caused by Shigella and EHEC infections, usually in children, 5-10% mortality, caused by release of the shiga toxin
309
Patients positive for HLA-B27 are at risk for what complication of bacterial infection?
Reactive arthritis = arthritis, conjunctivitis, urethritis
| after an infection of: shigella, salmonella, yersinia, campylobacter, chlamydia
310
"Can't see, can't pee, can't climb a tree" indicate what dx?
Reactive arthritis (Reiter's syndrome)
311
True or False: Shigella has a very high ID50, meaning it would take many bacteria to make you sick.
False. Shigella has a very low ID50. *Salmonella* has a high ID50.
312
What would you see in a blood smear of a HUS patient? What else is a major symptom?
Lysed RBC's "schistocytes" in blood smear, life-threatning kidney failure
**some antibiotics can make it worse**
313
What is the bacterial risk associated with stomach stapling (beyond the standard surgical risk)?
The neutralization of the stomach, therefore less bacteria are naturally killed off.
314
Why is making a vaccine to salmonella useless?
>2500 serovars, large ID50, bacteremia from it is rare
315
Why would a diabetic be more at risk for UTI's?
Snack service
316
What are the components of phospholipids?
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
What charge does inositol have?
No charge, but it is polar. Important in formation of phospholipid head groups
318
Below the Tm of the lipid bilayer, what shape do the membrane phospholipids take on?
Gel-like solid, closer packing, limited mobiltiy
319
True or False: Kinks in the lipid bilayer increase membrane fluidity
True.
320
How is cholesterol both an increaser and a decreaser (but mostly a decreaser) of membrane fluidity?
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
Where on a lipid bilyaer might you see lots of cholesterol?
Lipid raft
322
Name 4 ways drugs can get into cells.
1. Passive diffusion
2. Hijacked transporters
3. Lipsome delivery
4. (potential) protein transduction
323
Most cell membranes are about equal parts lipid and protein. Name one major exception to this rule.
Myelin - mostly lipid!
324
What are the two components of the fluid mosaic model?
1. Lipid bilayer acts as a solvent for membrane proteins
| 2. Lateral diffusion is allowed, flip-flopping is not.
325
What molecule, when flipped to the ECM side of the cell, serves as a signal for apoptosis?
Phosphatidyl serine
326
True or False: In Turner syndrome, all individuals have at least one cell line with a 45,X chromosome complement.
False.
327
XYY males and XXX females are similar in that they:
Are usually fertile and phenotypically normal. XXX females may arise as either maternal or paternal meiotic errors.
328
In human females, X-inactivation is a permanent change affecting all cells.
False. X-inactivation is permanent in the somatic cells, but all X chromosomes will become active in the germ cells during gametogenesis.
329
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:
Androgen receptor defect.
330
The proofreading activity of DNA polymerase involves:
3' to 5' exonuclease function
331
Homologous recombination is executed by many of the same enzymes that are involved in ________
DNA repair.
332
Xeroderma pigmentosum patients lack one or more enzymes required for:
Excision repair in DNA
333
True or False: Homologues carry different alleles of the same genes while sister chromatids have the same alleles.
TRUE
334
Where does Biosynthesis of glycosaminoglycan chains on proteoglycans occur primarily?
Golgi complex
335
What is the site of synthesis of proteins destined for the mitochondrial matrix?
Cytosol. Mitochondrial proteins encoded in the nuclear genome are synthesized on free ribosomes in the cytosol and then transported into mitochondria post-translationally
336
What is the function of adaptins?
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
What is a random function of both mitochondria and peroxisomes that is not central to their purposes?
Phospholipid synthesis
338
The mitochondrial genome only encodes what kind of RNA?
rRNA, tRNA, and a small number of mRNA directly involved in electron transport
339
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.
False. Without an ER targeting signal, the protein would remain in the cytosol.
340
True or False:
| SNAREs catalyze the fusion of vesicles with their target membranes.
True
