Week 6 Flashcards

1
Q

Descriptions of the Abdomen

A

Flat
Scaphoid
Rounded
Protuberant

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2
Q

9 regions of Abdomen

A

Upper
1) R Hypochondriac
2) Epigastric
3) L Hypogastric
Middle
4) R Lumbar
5) Umbilical
6) L Lumbar
Lower
7) R Iliac/Inguinal
8) Hypogastic/Suprapubic
9) L Ilian/Inguinal

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3
Q

4 Quadrants of Abdomen

A

RUQ
RLQ
LUQ
LLQ

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4
Q

Organs located in R Hypochondriac Region:

A

Liver
Gallbladder
R Kidney
Hepatic Flexure of LI

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5
Q

Organs located in L Hypochondriac Region:

A

Stomach
Liver (tip)
Spleen
Pancreas (tail of)
L Kidney
Splenic Flexure of LI

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6
Q

Organs located in Epigastric region:

A

Abdominal esophagus
Stomach
Pancreas
SI
Liver
Galbladder
R/L Kidneys
R/L Adrenal Glands

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7
Q

Organs located in R Lumbar region:

A

Liver
Gallbladder
R Kidney
Ascending colon
SI

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8
Q

Organs located in Umbilical region:

A

Stomach
Pancreas
Transverse colon
SI
R/L Kidneys

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9
Q

Organs located in L Lumbar region:

A

L Kidney
Descending Colon
SI

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10
Q

Organs located in R Iliac/Inguinal region:

A

SI
Appendix
Cecum
Ascending Colon
R ovary and uterine tube

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11
Q

Organs located in Hypogastric/Suprapubic:

A

SI
Sigmoid Colon
Rectum
Bladder
Uterus/Ovaries/Uterine tubes
Prostate/Seminal Vesicles/Vas deferens

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12
Q

Organs located in L Iliac/Inguinal

A

Descending colon
Sigmoid colon
SI
L ovary/uterine tube

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13
Q

Normal Liver span at midsternal line

A

4-8 cm in midsternal line

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14
Q

Normal Liver span at midclavicular line

A

6-12 cm in R midclavicular line

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15
Q

Visceral peritoneum:

A

Peritoneum surrounding visceral organs within the abdominal cavities

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16
Q

Parietal peritoneum:

A

Peritoneum lining the walls of the abdominal cavity

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17
Q

Uses for DNA Technology

A

1) Dx genetic conditions
2) Predict multifactoral diseases
3) Preventative med
4) Predict drug responses
5) Manufacture of biopharms
6) Cancer genomics - prognosis, treatments
7) Genomic editing/Gene therapy

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18
Q

Techniques to see DNA/RNA

A

Light Microscopy
Electrophoresis
Blotting
DNA sequencing

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19
Q

Ways to see DNA with “naked” eye

A

Compact DNA with dyes/proteins
Cut and dye DNA
Copy DNA with dye attached

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20
Q

DNA/RNA and Light Microscopy

A

Chromosomes locked in metaphase
Able to visualize histones
DNA partially denatured then labelled with probe

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21
Q

DNA/RNA and Sequencing

A

DNA extended with DNA polymerase
Terminated with 2’,3’ dideoxynucleotide

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22
Q

DNA/RNA and Electrophoresis

A

Separation of DNA/RNA by size

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23
Q

DNA/RNA and Blotting

A

Immobile DNA/RNA detected via specific sequence
Hybridizes with Probe that is tagged and can be visualized

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24
Q

Purpose of Light Microscopy and DNA?

A

Looks for LARGE abnormalities
Trisomy/Monosomy, Ring structures

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25
Describe non-denaturing gels:
Detects larger differences or secondary structure effects Ranges from 50,000 bp - 100 bp
26
Purpose of Electrophoresis and DNA?
27
Purpose of Blotting and DNA?
28
Purpose of Sequencing and DNA?
29
FISH is used to detect?
Chromosomal rearrangements Large insertions/deletions in chromosomes Trisomy/monosomy
30
Fluorescent In Situ Hybridization
FISH Multiple probes added to detect multiple sequences
31
Types of Gel for Electrophoresis
Denaturing Non-denaturing
32
Describe denaturing gels:
Detection of single nucleotide differences Ranges from 1-2000 nucleotides
33
Denaturing gels for electrophoresis are useful for?
Sequencing Copy number variation Other analysis for differentiation in length of NA
34
DNA size determined via
Electrophoresis
35
Huntingtons Disease caused by
CAG repeats within the htt gene
36
Techniques for proteins
Microscopy Blotting Sequencing
37
Purpose of Sequencing and Proteins?
Chemical removal of one AA at a time Determine AA Edman Degradation and Mass spec.
38
Purpose of Blotting and Proteins?
Western: separate proteins and probe with another protein ELISA: one protein in spot; attached to matrix; 2nd protein binds to first; probe binds to 2nd protein
39
Purpose of Microscopy and Proteins?
Look at stained proteins Gram stained or Hematoxylin and Eosin
40
DNA Blotting Technique
Cleaved by size Fragments transferred to matrix 2nd DNA sample labeled with dye/radioactivity Hybridize/bind probe to first DNA Analysis
41
Allele Specific Oligonucleotide Probes
- Synthesized chemically - Up to 100 bp - Hybridize to cDNA - Differentiates single base pair with probe
42
Allele Specific Oligonucleotides used for?
Primers ID alleles on blot
43
Types of Blotting Techniques:
Southern Northern Western Dot Microarray
44
Use of Southern Blot
Electrophoresis of DNA Separate by size Labelled with DNA/RNA
45
Use of Western Blot
Electrophoresis of protein Separate by size Labelled with antibody (Ab)
46
Use of Northern Blot
Electrophoresis of RNA Separate by size Labelled with DNA/RNA
47
Use of Dot blot
DNA/RNA used without size separation Probe added with labelled DNA/RNA
48
Use of microarray
Visualization of macromolecules (RNA, DNA, carbs, proteins, lipids, tissues, viruses) Multiple tiny dots at one time
49
Southern blotting used to detect?
Restriction Fragment Length Polymorphisms (RFLP)
50
Dot blots used for?
Tell relative amount of DNA/RNA with specific sequence Small as single nucleotide polymorphism
51
Northern blotting used for?
Detect lengths of RNA
52
Sanger DNA Sequencing Method
Single strand DNA of unknown sequence used as template Primers added with labelled deoxynuclotides as well Split sample into 4 tubes Add one of 4 dideoxynuclotides to each tube Allow synthesis to continue until it stops Read electrophoresis gel
53
Why do dideoxynucleotides stop DNA synthesis?
No 3' hydroxyl group to bind to to keep adding nucleotides to chain
54
Uses of Sequencing in terms of Discovery tool:
1) Single gene disorders 2) Polymorphisms 3) Protein prediction 4) Variants in polygenic disorders 5) Localize genes from linkage
55
Uses of Sequencing in terms of Diagnostic tool:
1) Genetic testing 2) Genotyping 3) IVF 4) ID Infectious pathogens
56
Uses of Sequencing in terms of Predictive tool:
1) Susceptibility 2) Drug sensitivity/insensitivity 3) Treatment response 4) Morbidity
57
Best ways to amplify DNA
PCR Recombinant DNA cloning cDNA ASO
58
Define: Recombinant DNA
DNA inserted into vector from another organism Is grown in organism that can replicate vector
59
Cloning vectors usually carry?
1) Selectable markers 2) Reporter Gene 3) Multi-cloning site 4) Origin of replication
60
Define: Selectable marker
Grow only in cells with plasmid is media is medicated Indication of plasmid in cell
61
Define: Reporter gene
Blue/white screening White positive for DNA inserted into gene Indication of DNA inserted/cloned into plasmid
62
Define: Multi-cloning site
Restriction enzyme sites that will disrupt reporter gene Allows for easy insertion of gene
63
Define: Origin of replication
Replicate DNA with high copy number
64
DNA of interest cut with? What does it leave on DNA?
Restriction enzymes Sticky ends on DNA
65
What enzyme repairs sticky ends on DNA strands?
DNA Ligase
66
How is cDNA made
Copying mRNA and reverse transcriptase it to cDNA
67
Uses for cDNA?
1) Exome sequencing 2) Cloning genes without introns in bacteria 3) Study gene expression (stability of mRNA; splice site variant; expression levels of mRNA) 4) Hybridization probe 5) Gene therapy
68
Steps in PCR:
1) Denature DNA 2) Cool down and add annealing primers 3) Extend primers with DNA polymerase II 4) Continue to repeat until enough copies of DNA present
69
Uses of PCR to amplify DNA:
Used when tiny amount of DNA available Just need on molecule to amplify
70
Uses of PCR to Genetic testing:
Pre-natal testing IVF Paternity Ancient DNA from fossils Genealogy
71
Uses of PCR to make probes:
Easily labelled Quick to produce
72
Uses of PCR to map out genetic changes:
Detection of single nucleotide polymorphism Detect restriction fragment length polymorphism ID pathogens
73
Types of probes used in DNA tech:
PCR cDNA Oligonucleotides
74
PCR as a probe type
Ranges from 50 bp to 2kb DNA amplified to millions of copies
75
cDNA as a probe type
Segments of 50 bp 10 kb DNA
76
Oligonucleotides as a probe type
Synthetic DNA from 2bp to 100 bp
77
Types of Labelling in DNA Tech
Radioactive probes Fluorescent probes Oligonucleotides
78
Radioactive probe labels
Radioactive phosphorus on 5' end All molecules will look the same with 5' radiolabelled
79
Fluorescent probe labels
Linked to chemicals that fluoresce Able to use several probes of different colors at the same time
80
Oligonucleotide labels
Label added during production or after production
81
Restriction endonucleases
AKA Restriction enzymes
82
Method of action for restriction enzymes
Cut sequence-specific DNA sequences
83
Primarily made of?
dsDNA
84
Restriction enzymes bind to
Palindromic sequences in DNA
85
If palindromic sequence in DNA mutated - what becomes of restriction enzymes?
They are unable to cut sequence DNA since palindromic sequence is mutated
86
Gain or loss of restriction sites can be exploited in what way?
Analysis of Restriction Fragment Length Polymorphism
87
Bacteria will protect their DNA how?
Methylation
88
Restriction enzyme TaqI
Formulated from Thermus aquaticus Recognizes T/CGA sequences to create sticky ends on fragments
89
Restriction enzyme HaeIII
Formulated from Haemophilus aegyptius bacteria Recognizes 5'-GG/CC-3' sequences to create blunt ends on fragments
90
Dot Blotting
DNA/RNA fixed to membrane then probe added to detect sequence ONLY complementary DNA/RNA sticks to blot
91
Dot blotting useful for?
Drug response on expression of genetic markers Classification of tumors in cancers Gene expression levels in different cells Show progression of disease Localization of tissue specific expression
92
Variable Number Tandem Repeats
Occur in clusters with number of repeats varying in people Makes use of microsatellites/repetative DNA
93
Restriction Fragment Length Polymorphism takes advantage of
Mutational changes
94
Mutations affect RFLP in what ways?
1) Longer/shorted fragments Insertions yield longer fragments Deletions yield shorter fragments Point mutation NOT SEEN unless form/delete restriction site
95
RFLP used to show?
Fragment has been cloned as expected DNA fingerprinting Genome mapping Disease detection
96
RFLP and Electrophoresis: Use of agrose gel? Use of Southern blotting?
Agarose gel only if DNA sample pure with few fragments Southern blotting AFTER gel if whole genome needed or too many fragements
97
Microarrays in diagnostic testing
Detected viral strains, bacterial strains, drug resistance, and forensic contact
98
Genomic Wide Association Studies are used for?
- Find predisposing genes in multivariant diseases *Find genes that are either upregulated that shouldn't be or down regulated that shouldn't be
99
Comparative Staging Expression Microarrays
More likely to be used for staging cancers via gene expression *Detect normal, early or late staging
100
Screening Microarrays
ID Pathogens Disease typing
101
Genotyping
Detect mutant/variant type DNA
102
Gene expression microarray
Amount of mRNA, timing of expression and splice variants in DNA
103
Single nucleutide polymorphisms
Detection on single point mutation in DNA
104
Describe interphase chromosomes
Not condensed Barr body is only consolidation of genetic material
105
Barr body
Inactivated X chromosome that condenses down
106
Found evidence of the Barr body
Dr. Lyons
107
Structure of a chromatid
Centromere p arm (shorted) q arm (longer) Telomeres at very end
108
Which phase of cell cycle to we arrest chromosomes to look at?
Metaphase
109
Karyotyping
Ordered display of all chromosomes from ONE cell
110
How are chromosomes ordered in karyotyping?
By size and/or position of centromere
111
Classification of this chromosome?
Metacentric
112
Classification of this chromosome?
Acrocentric
113
Classification of this chromosome?
Submetacentric
114
Chromosome numbers associated with acrocentric chromosomes?
13, 14, 15, 21, 22 & Y
115
Why are chromosomes 13, 14, 15, 21, 22, and Y so important?
Involved in Robertsonian translocation
116
Assignment of bands to chromosomes
Begin a centromere and work out First number is REGION of chromosome Second number is BAND ON chromosome in THAT region
117
Features of Dark G bands on chromosomes?
Later replication Fewer transcriptionally active genes More condensed Higher AT base pairs
118
Define: Polyploidy
Multiple copies of chromosomes (usually 3) Not viable with life Triploid
119
Define: Trisomy
Excess of one extra chromosome Only ones viable with life - 13, 18, 21 Written as (47, XX, +21)
120
Define: Monosomy
Lack of one chromosome Monosomy X compatible with life (45, X) / (45, XY, -16)
121
Trisomy and monosomy due to
Non-disjuction in meiosis I
122
Define: aneuploid
Wrong number of chromosomes
123
Define: euploid
Correct number of chromosomes
124
Maternal Age Effect:
Older a female gets, greater risk for non-disjuction events to occur Eggs have been stuck in Prophase I since birth - that's a long time to sit and stew.
125
Only trisomy with no affects from maternal age?
Trisomy 16
126
Describe sections of karyotype nomenclature
Number = number of chromosomes XX/XY = sex chromosomes present inv/del/dup/ins/r/t/rob/i Number of chromosome involved (Breakpoint in abnormality)
127
Balanced chromosomes
Nothing gained/lost
128
Unbalanced chromosomes
Too much gained or too much lost
129
Duplication (dup)
Describe events within one PAIR of chromosomes Having 2 copies of same chromosomal segment
130
Insertion (ins)
Section of chromosome is copied and inserted into different chromosome Recip chromosome mentioned first; donor chromosome mentioned second
131
Deletion/Insertion combo
Section excised from one place and inserted somewhere else
132
Isochromosome Formation (i)
Chromosome with 2 identical arms Due to misattachment of spindle apparatus - separated from top to bottom, not side to side
133
Ring (r)
Any chromosome that loses telomeres at BOTh ends will become a ring structure Causes instability of cell - DNA unable to replicate ring structure Seen more often in cancer cells
134
Define reciprocal translocation (t)
Exchange of 2 acentric fragments of chromosomes Breaks within arms that switch places with one another
135
Define Robertsonian translocation (rob)
Usually occurring in the acrocentric arms of chromosomes (13, 14, 15, 21, 22, Y) Satellites break off at ends of chromosomes and centromeres fuse together Common cause of losing a chromosome (46 -> 45)
136
Results of Reciprocal translocations:
Every case is phenotypically different Developmental defects ARE common Able to mimic known syndromes Leads to multiple affected tissues (heart)
137
Results of Robertsonian translocations
Genes in satellite are found in SEVERAL places No symptoms in balanced form
138
Philadelphia chromosome
Short chromosome containing centromere of 22 and tip of q-arm of 9 Product of reciprocal translocation Joins chromosomes 9 and 22 together