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Cell Physiology (Fall) > Nilson > Flashcards

Nilson Flashcards

1
Q

Diagnosing osteosarcomas

A

Classic “sunburst” appearance in radiographs. Frequent pulmonary metastasis.

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2
Q

Normal canine karyotype

A

38 pairs of short acrocentric autosomes and one pair of sex chromosomes

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3
Q

Canine OSA karyotype

A

Chaotic: hyperploidy or hypoploidy, many metacentric chromosomes, telomere fusions and interstitial telomere signals.

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4
Q

What is the pattern between species and autosomal chromosome number?

A

There is no real pattern. Varies widely across species.

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5
Q

Name the three steps to compile a basic chromosome

A
  1. Naked DNA wraps around histones (circular proteins).
  2. Histones aggregate into a line.
  3. Aggregate chain wraps around a chromatin fiber in large loops (like flower petals) to form the chromosome.
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6
Q

Telomere

A

Repeating sequence that protects the end of the chromosome. Non coding.

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7
Q

Origin of replication

A

Site on the chromosome where replication will begin. Forms bubbles during replication.

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8
Q

Centromere

A

Can be acrocentric or telocentric, the area that binds two sister chromosomes together and assists in their separation during cell division

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9
Q

Kinetochore

A

Protein that forms around the centromere to help with the attachment of microtubules to the centromere.

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10
Q

Daughter chromatid

A

Newly produced genetic material

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11
Q

Aneuploidy

A

Description for hyperploidy, hypoploidy, or chromosome breakage

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12
Q

What causes hypo- or hyper-ploidy?

A

Lack of centromeres (unsure what causes this) leads to random segregation of the chromosomes during cell division.

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13
Q

What causes chromosome breakage?

A

Multiple centromeres, which can then be pulled in different directions. Often happens because of telomeric region end joining.

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14
Q

Okazaki fragment

A

Fragments (approximately 150 nts) built along the lagging strand during DNA replication (as the bubble opens exposing dan from 3’ to 5’, small fragments built from 5’ to 3’ along it)

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15
Q

How do you recognize newly formed DNA strands?

A

Will have small nicks in it from areas where Okazaki fragments have not yet been joined together by DNA ligase.

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16
Q

What causes the end of replication problem?

A

Since DNA cannot be added to the 5’ end, Okazaki fragments will always leave a 3’ overhang on the newly replicated DNA (there is not an exact primer for the end of the strands). As DNA is replicated, this overhang will lead to the shortening of the chromosome.

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17
Q

What solves the end of replication problem?

A

Telomerase
Adds a G rich non-coding sequence to the end of chromosomes as new genetic material is created. This protects the DNA - the end is still shortened but the chromosome loses nothing of value and new sections of telomere can be added on. There will still always be a small 3’ overhang on the telomere.

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18
Q

Telomerase binding proteins

A

Bind to the G rich regions of the telomere. Shelters the end of the chromosome and prevents non-homologous end joining that can create multiple centromeres. Because of the overhang, something will always be trying to “fix” those ends - this prevents.

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19
Q

Goldilocks Principle for Telomeres

A

Don’t want it to be too long or too short! Problems can develop either way.

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20
Q

Interstitial telomere

A

If telomerase binding proteins don’t function as they should, telomere ends will be joined by non-homologous end joining. Leads to a chromosome with telomeric DNA in the center and two centromeres, so future breakage.

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21
Q

Metacentric Robertsonian translocation

A

Normal centrosome is acrocentric. Centrosomes can split and reform one large chromosome with a metacentric chromosome. Other (smaller) parts of the chromosome is then lost.

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22
Q

Marker for canine OSA

A

Interstitial telomere sequences

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23
Q

Why does speed of the telomerase matter?

A

Determines cell life. Slows over the course of the cell life - if it slows enough then the cell can die or problems related to aging will arise.

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24
Q

Acrocentric chromosome

A

Centromere is further towards one end of the chromosome than the other. Normal.

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25
Metacentric chromosome
Centromere is in the center of the chromosome. Abnormal, often caused by metacentric Robertsonian translocation.
26
Telocentric chromosome
Centromere is very near to the end of the chromosome. Normal.
27
Spontaneous Lymphoma
One of most common canine neoplasms. Many features common to human lymphoma.
28
Normal rate of mutation
Normally between 10^-6 and 10^-11 mutations per round of replication - VERY RARE but still can occur.
29
Silent mutation
No change in the amino acid structure of any proteins.
30
Frame Shift mutation
Usually from an addition or deletion of a nt - causes a completely different aa sequence to be created.
31
Truncation mutation
Single aa mutation or frame shift mutation causing an early stop codon and so a shorter than normal protein
32
Transition mutation
Single nucleotide from purine to other purine; or pyrimidine to other pyrimidine.
33
Transversion mutation
Single nucleotide from purine to pyrimidine or vice versa.
34
DNA microsatellite
Easily mutated portion of DNA often used as polymorphic gene markers.
35
"Slippage" in DNA microsatellite
CA repeats (or CAG or CGG triple nucleotide sequences) which DNA polymerase is prone to make errors with. Causes an increase or decrease in gene length at these areas.
36
What are some diseases associated with DNA slippage?
Muscular dystrophy, fragile X syndrome, Huntington's disease
37
How do mutations in DNA replication become permanent?
Can see a change (kink) in initial replication. If not proof-read, it will become permanent by the second round of replication.
38
What percentage of cells will be mutated if a mutation is not proof-read?
1/4 of cells from the initial normal cell that began replication.
39
What causes tumor growth?
If a mutation gives the new cell a selective growth advantage, such as the deletion of a tumor suppression gene.
40
Mismatch Repair type of damage
Replication errors
41
Nucleotide Excision repair type of damage
Pyrimidine Dimer or a bulky adduct (ie estrogen) added to a base
42
Mismatch Repair enzymes
MSH, MLH, PMS
43
Nucleotide Excision repair enzymes
XPC, XPA, XPD, ERCCI-XPF, and XPG
44
Double-strand break repair type of damage
Double strand breaks | Caused by multiple centromeres, UV/ionizing radiation, or chemotherapeutic agents.
45
Double-strand break enzymes
Recombination repair: RecA and RecB | NHEJ (non homologous end joining): Ku70/80, DNA-PKcS, Artemis, Ligase IV, Cernunnos-XLF, XRCC4
46
What would a mismatch error look like in a double strand (daughter and original strands)?
A bulge | No hydrogen bond between the two bases so not holding to each other tightly
47
How is a mismatch error repaired?
Enzyme (MSH,MLH,PMS) identifies the daughter strand by nicks in the DNA. Enzymes create new nicks on either side of the error just on the daughter DNA. Normal polymerase and ligase can then fill the gap.
48
Non-synthesis errors
To non-replicating DNA Hydrolytic damage (normal under certain physiological conditions) Exposure to UV light Ionizing radiation or chemotherapeutic agents (introduces double strand breaks)
49
Clastogens
Agents that can cause DNA breakage
50
Hydrolytic Damage Repair Enzyme
Glyosylase | Removes just the base that has become deaminated. Gap will be filled by polymerase and then joined by ligase.
51
Hydrolytic Damage
Base becomes deaminated by normal hydrolytic damage in the system.
52
OxoG
Failsafe for Hydrolytic Damage. Binds to the deaminated base (A G base only) and will stay until fixed by Glyosylase. Or, if replication occurs with the error, will stay until a C is placed underneath and then can later be cleaved out and replaced.
53
Non-homologous end joining after damage
Brings double stranded breaks back together, but there is NO TEMPLATE involved in this. Must trim the ends before reattachment and so leaves out a few bases, but still better than free floating DNA in the cell.
54
Non-homologous end joining in the normal cell
Helps in variable RNA splicing | Common in B and T cell immune cells (light chains and heavy chains)
55
Enzyme process in NHEJ
1. Ku70/80 binds and clips ends of the broken strands 2. DNA-PKcS and Artemis bind 3. Ligase IV, Cernunnos-XLF, and XRCC4 bind and join the two ends.
56
Diseases caused by deficiencies in NHEJ enzymes
Lymphoproliferative diseases (Ataxia telangiectasia, AT-like syndrome, Nijmegen Breakage Syndrome)
57
Is lymphoma in golden retrievers genetic or breed-related.
Genetic, not breed related. Dogs with lymphoma had deficiencies in DNA repair (more susceptible to clastogens because they cannot repair DNA after)
58
Muscular dystrophy
Genetic disease caused by a truncated dystrophin protein (from a frame shift mutation)
59
Dystrophin
``` Massive protein (79 exons) found in skeletal and cardiac muscle. Role is mechanical stability during muscle contraction by connecting the contractile apparatus to the sarcolemma of the muscle cell. Actin binding domain, many identical rod domains and sarcolemma binding domain. ```
60
Protein splicing
Exon combination, gets rid of non-coding introns. | pre- mRNA to final coding product mature mRNA.
61
Alternative splicing
Normal in mRNA - variation in exons (ie 1235 vs 2345). More genetic variation without more genetic material.
62
Signals for exon/intron splicing
5' end of the exon: CAG sequence 3' end of intron rich in G,U,A Branch site signaled by A in center of the intron 5' end of intron: CAG
63
SNURPs
Small NUclear Ribosomal Proteins Abbreviated as "U" proteins Contain RNA sequence to bind around the intron and exon junction.
64
Spliceosomes
Complex of SNURPs, which are held together by H-bonds. Assist in the formation of an intron lariat and binding of exons.
65
Transesterification reactions
Two reactions aided by the spliceosome. 1. Branch site attacks 5' end of the exon and creates the lariat loop. 2. Now free 5' end of the exon attacks and binds the 3' end of the next exon. Intron lariat released.
66
Intron lariat
Section of intron that has been released after protein splicing - shaped like a lasso with beginning of the intron attached to the branch site of the intron.
67
ESEs
Exonic splice enhancer sequences Protect exons and increase the efficiency of the splicing event Covers exons so that protein is spliced perfectly. Also helps identify introns by flanking them.
68
AONs
antisense oligonucleotides artificially designed bind to a region usually bound by ESEs, and causes the whole area to be cut out by spliceosomes.
69
What do AONs do to the frame of the protein?
Can cause a frame shift mutation.
70
Why might AONs help with MD?
Hopefully will be able to shift the protein back into the correct frame, only missing a few exons.
71
Morpholino
Similar to a nucleotide but less reactive. Ribose ring of DNA is replaced by a morpholine ring which does not have any free phosphate groups and so is not charged. Purpose: not as easily degraded and easier diffusion through non-polar cell membranes.
72
How are we going to get the AON into the cell?
Attach to a cargo protein that is carried into the cell via receptor-mediated endocytosis.
73
Why use beagles in genetics studies?
Easier to breed and to handle in research situations.
74
What was the effect of morpholine-AONs on MDs in beagles?
Therapeutic levels of dystrophin in 5-22 weeks and eventual long-term remission of MD.
75
Why is more research needed to develop an MD therapy?
Dystrophin mutations are very breed specific. Need more testing for various breeds and possibly for human therapy.
76
Vitamin D resistant rickets
Body cannot use vitamin D. Bones cannot take up calcium without Vitamin D absorption. Hereditary - can be autosomal or X-linked. Caused by single nucleotide polymorphism causing a frame shift and very truncated protein.
77
What are the two sources of Vitamin D?
UV light absorption by skin (only in some species - not in the dog or the cat) Dietary sources
78
What organs does Vitamin D have to pass through in order to become activated?
Skin to circulation Food to intestine to circulation Then must go through the liver and then the kidney to become activated.
79
What is the active form of Vitamin D?
1-alpha-25(OH)2-D3 | Called calciferol
80
What two structures does calciferol effect the most?
Immune cells: Induces differentiation | Bone: Increases bone mineralization by facilitating calcium uptake
81
How many genes does calciferol regulate?
HUNDREDS (200 - 300 in most species)
82
What are some elements of eukaryotic genes?
``` Insulator Distal enhancer upstream enhancer silencer proximal promoter elements TATA box! downstream enhancer ```
83
Where on the eukaryotic gene does the core promoter bind?
Upstream enhancer
84
What is the function of the TATA box?
For accurate transcription, need a definitive, foolproof starting point for RNA polymerase.
85
Trans activator
Protein with a DNA binding domain that binds to a cis DNA sequence to control gene expression.
86
Cis acting element
DNA sequences in the vicinity of the structural portion of a gene that are REQUIRED for gene expression. Where Trans activators bind.
87
Transcription factor
Factors (often trans activators) that turn genes on or off to a certain degree. MANY factors for every gene.
88
Nuclear receptors
Transcription factors that use zinc fingers to bind response elements in the promoter regulatory regions of genes.
89
zinc fingers
Amino acid chain with two "fingers" organized around zinc molecules Proximal (P) and Distal (D)boxes D box recognizes a specific DNA sequence by fitting into a DNA grove P box fits more tightly into grooves of helix shape and holds on tightly
90
Type I Nuclear receptors
holds loosely to the DNA
91
Type II Nuclear receptors
holds DNA unless it is allosterically changed to release the strand.
92
What type of Nuclear receptor is Vitamin D receptor?
Type II - needs an allosteric change to activate.
93
Vitamin D receptor
A heterodimeric nuclear receptor | Will relieve transcriptional repression (activate) when allosterically activated by calciferol.
94
"Tying up" in horses
Muscle trauma after a workout without a cool-down period. Can be caused by two diseases (PSSM or RER). Causes horses that are large in front and small in back and have elevated plasma creatinine kinase (muscle damage indicator).
95
PSSM
Polysaccharide Storage Myopathy (very common in draft horses)
96
RER
Recurrent Exertional Rhabdomyolysis (common in warm-blooded horses)
97
miRNA
micro RNAs Small non-coding RNA In humans: at least 10 with significant roles in muscle development, maintenance, and repair.
98
Where do we find the genetic material for miRNAs?
In Pol-II transcription areas (same areas of the transcription of mRNA). Can be in introns or in complete non-coding area.
99
5' end specialization of mRNA
Methylated linkage cap
100
3' end specialization of mRNA
Poly-A tail
101
Stem-loops
Areas of mRNA that create miRNA | mRNA single strand areas that fold over on themselves to create (imperfect) W-C binding
102
pri-miRNA
Stands for primary. | Single stranded section of mRNA that forms stem-loops.
103
Guide pri-miRNA
Will eventually be saved as the functional area Opposite code as target mRNA Sometimes can be passenger or guide (both sides functional)
104
Passenger pri-miRNA
Similar code to target mRNA | can also be guide in some cases (both sides functional)
105
DROSHA
Enzyme in the nucleus Processes pri-miRNA to pre-miRNA by cutting stem-loop from other sections of single stranded mRNA pre-miRNA then transported to the cytoplasm
106
Dicer
Enzyme in the cytoplasm that cleaves BASED ON LENGTH NOT ON SEQUENCE Processes pre-miRNA to mature miRNA by cutting off a 24 nt strand. Length is measured by the shape of the enzyme - PAZ domain holds RNA and 'handle' cleaves it.
107
RISC complex
Binds to mature miRNA in the cytoplasm. Helps guide miRNA to the target there and keep it there (since usually not a perfect fit) at least as long as it takes to block translation of the target.
108
How would we identify pri-miRNA?
Stem loops | Usually approximately 74 nt to be a good candidate for DROSHA
109
What do the clips of Dicer and Drosha have in common?
Both asymmetrical.
110
What is the relationship between miRNAs and PSSM and RER?
Each disease has a miRNA that is significantly more expressed.
111
How could we create a marker for PSSM or RER?
Some miRNAs leak into the bloodstream at high amounts. May be able to use this as a susceptibility marker for tying up.
112
Which X chromosome is inactivated during X inactivation?
Random.
113
At which stage does X-inactivation occur?
the 32-64 cell stage. Causes the patches seen on calico cats - different sections have different X chromosomes inactivated.
114
XIC
X inactivation center. Central locus for x-inactivation.
115
Xist and Tsix
Both non-coding RNAs encoded on opposing strands of DNA in the X-chromosome. Code for miRNAs that coat the strand to inactivate and then recruit other factors to modify and condense the chromosome to inactivate it.

Cell Physiology (Fall) (3 decks)

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