Review Cards - Molecular Diagnostics Flashcards
1
Q
DNA & ribonucleic acid (RNA)
A
Nucleus acid
2
Q
Nucleic acid that carries genetic information; in eukaryotes, located in chromosomes in nucleus & small amount in mitochondria; also present in bacteria & DNA viruses
A
DNA
3
Q
Double-stranded DNA
A
dsDNA
4
Q
Single-stranded DNA
A
ssDNA
5
Q
DNA in chromosomes
A
Genomic DNA
6
Q
Circular piece of DNA found in mitochondria of eukaryotes; codes for polypeptides involved in oxidative phosphorylation; transmitted by maternal inheritance (mitochondria in ova, not sperm); used in forensics, lineage & population studies
A
Mitochondrial DNA
7
Q
Piece of coiled DNA containing many genes; humans have 23 pairs of chromosomes; 1 set from mother, 1 from father; 22 pairs of autosomes, 1 pair sex chromosomes (X,Y)
A
Chromosome
8
Q
Specific sequence of nucleotides (1,000-4,000) at particular location on chromosome; starts at 5’ end with promoter region that initiates transcription & ends at 3’ end with terminator sequence that ends transcription
A
Gene
-humans have about 30,000 genes
-DNA sequence in genes is 99.9% the same in all people
9
Q
DNA sequences on chromosomes that code for amino acids/proteins
A
Exons
10
Q
Noncoding regions between exons
A
introns
11
Q
all hereditary information for an individual
A
genome
12
Q
relationship between sequence of bases in DNA or its RNA transcript & sequence of amino acids in proteins
A
genetic code
13
Q
nucleic acid that converts genetic information from DNA into specific proteins; some has regulatory and structural function; present in nucleus & in cytoplasm where it’s associated with ribosomes (free or attached to ER); source of genetic information in retroviruses
A
RNA
14
Q
pentose sugar with nitrogen base attached; dephosphorylated nucleotide; adenosine, guanosine, cytidine, thymidine
A
nucleoside
15
Q
building blocks of DNA & RNA; a pentose sugar with nitrogen base attached to 1’C & 1-3 phosphate groups attached to 5’C; nucleotide sequences always written in 5’ to 3’ direction, e.g., 5’ATCGAACAGTAC3’
A
nucleotide
16
Q
sugar with 5 carbons (C); carbons are numbered 1’-5’ starting with the carbon to the right of oxygen & going clockwise; superscript (prime) differentiates carbons in sugar from carbons in bases, which are numbered 1-9
A
pentose
17
Q
5-carbon sugar found in RNA
A
ribose
18
Q
5-carbon sugar found in DNA; similar to ribose, but with one less oxygen
A
deoxyribose
19
Q
carbon-nitrogen ring structures attached to 1’ carbon of sugar in DNA & RNA: adenine (A), guanine (G), cytosine (C), thymine (T), & uracil (U);
A
nitrogen bases
20
Q
Nitrogen bases in DNA
A
A, G, C, T
21
Q
Nitrogen bases in RNA
A
A, G, C, U
-U is similar to T in DNA, except it lacks a methyl group
22
Q
purine from 1 strand of nucleic acid& pyrimidine from another strand joined by hydrogen bonds; A forms 2 H bonds with T or U; G forms 3 H bones with C
A
base pairs
23
Q
opposite or partner base in base pair, e.g., A is complementary to T or U; G is complementary to C
A
complementary
24
Q
nitrogen bases with single C-N ring (C, T, U)
A
pyrimidine
25
nitrogen bases with 2 C-N rings (A, G)
purine
26
bonds that join nucleotides in nucleic acid; 5' phosphate group of 1 sugar attaches to 3' hydroxyl group of adjacent sugar; a molecule of H2O splits off
phosphodiester bonds
27
Comparison of DNA and RNA - DNA - function
carries genetic information, serves as template for synthesis of RNA
28
Comparison of DNA and RNA - DNA - location
nucleus (except mitochondrial DNA)
29
Comparison of DNA and RNA - DNA - composition
repeating nucleotides linked by phosphodiester bonds between 5' phosphate group of 1 sugar & 3' hydroxyl group of next
30
Comparison of DNA and RNA - DNA - sugar
deoxyribose
31
Comparison of DNA and RNA - DNA - pyrimidines
C, T
32
Comparison of DNA and RNA - DNA - purines
A, G
33
Comparison of DNA and RNA - RNA - function
-converts genetic information from DNA into proteins
-some has regulatory or structural function
-source of genetic information in RNA viruses
34
Comparison of DNA and RNA - RNA - location
nucleus & cytoplasm
35
Comparison of DNA and RNA - RNA - composition
repeating nucleotides linked by phosphodiester bonds between 5' phosphate group of 1 sugar & 3' hydroxyl group of next
36
Comparison of DNA and RNA - RNA - sugar
ribose
37
Comparison of DNA and RNA - RNA - pyrimidines
C, U
38
Comparison of DNA and RNA - RNA - purines
A, G
39
Comparison of DNA and RNA - DNA - usual structure
-double stranded
-each strand has 5' end (phosphate group attached to 5'C) & 3' end (OH group attached to 3'C)
-strands are antiparallel, i.e., one in 3' to 5' direction, other 5'-3'
-2 strands coil around each other to form double helix with alternating sugar & P groups on exterior & bases on interior
-strands held together by hydrogen bonds between complementary bases
40
Comparison of DNA and RNA - DNA - usual structure
-single stranded
-shorter than DNA
-irregular 3D structure
41
Nitrogen bases - Purines - DNA & RNA
A, G
42
Nitrogen bases - pyrimidines - DNA & RNA
C
43
Nitrogen bases - pyrimidines - DNA only
T
44
Nitrogen bases - pyrimidines - RNA only
U
45
Nitrogen bases - base pairing - DNA & RNA
G-C
46
Nitrogen bases - base pairing - DNA only
A-T
47
Nitrogen bases - base pairing - RNA only
A-U
48
Nitrogen bases - # of H bonds in base pair - DNA & RNA
3
49
Nitrogen bases - # of H bonds in base pair - DNA only
2
50
Nitrogen bases - # of H bonds in base pair - RNA only
2
51
Nucleotides - base - adenine:
-sugar:
-phosphates:
-nucleotide:
Sugar: ribose
Phosphates - Nucleotide:
1 - adenosine monophosphate (AMP)
2 - adenosine diphosphate (ADP)
3 - adenosine triphosphate (ATP
52
Nucleotides - base - guanine:
-sugar:
-phosphates:
-nucleotide:
Sugar: ribose
Phosphates - Nucleotide:
1 - guanosine monophosphate (GMP)
2 - guanosine diphosphate
(GDP)
3 - guanosine triphosphate (GTP)
53
Nucleotides - base - cytosine:
-sugar:
-phosphates:
-nucleotide:
Sugar: ribose
Phosphates - Nucleotide:
1 - cytidine monophosphate (CMP)
2 - cytidine diphosphate (CDP)
3 - cytidine triphosphate (CTP)
54
Nucleotides - base - uracil:
-sugar:
-phosphates:
-nucleotide:
Sugar: ribose
Phosphates - Nucleotide:
1 - uridine monophosphate (UMP)
2 - uridine diphosphate (UDP)
3 - uridine triphosphate (UTP)
55
Nucleotides - base - adenine (DNA):
-sugar:
-phosphates:
-nucleotide:
Sugar: doxyribose
Phosphates - Nucleotide:
1 - deoxyadenosine monophosphate (dAMP)
2 - deoxyadenosine diphosphate (dADP)
3 - deoxyadenosine triphosphate (dATP)
56
Nucleotides - base - guanine (DNA):
-sugar:
-phosphates:
-nucleotide:
Sugar: deoxyribose
Phosphates - Nucleotide:
1 - deoxyguanosine monophosphate (dGMP)
2 - deoxyguanosine diphosphate (dGDP)
3 - deoxyguanosine triphosphate (dGTP)
57
Nucleotides - base - cytosine (DNA):
-sugar:
-phosphates:
-nucleotide:
Sugar: deoxyribose
Phosphates - Nucleotide:
1 - deoxycytidine monophosphate (dCMP)
2 - deoxycytidine diphosphate (dCDP)
3 - deoxycytidine triphosphate (dCTP)
58
Nucleotides - base - thymine (DNA):
-sugar:
-phosphates:
-nucleotide:
Sugar: deoxyribose
Phosphates - Nucleotide:
1 - deoxythymidine monophosphate (dTMP)
2 - deoxythymidine diphosphate (dTDP)
3 - deoxythymidine triphosphate (dTTP)
59
reproduction of DNA during cell division
replication
60
newly synthesized strand of DNA consists of 1 strand of original DNA & new daughter strand; original DNA is conserved
semiconservative replication
61
newly synthesized strand of DNA consists of 1 strand of original DNA & new daughter strand; original DNA is conserved
semiconservative replication
62
enzyme that unwinds section of DNA by breaking bases' hydrogen bonds to form 2 single-stranded templates for replication
helicase
63
location where double stranded DNA (dsDNA) separates into single stranded DNA (ssDNA) & synthesis of DNA begins
replication fork
64
strand of DNA that serves as pattern for new strand of DNA or RNA
template
65
RNA polymerase that synthesizes RNA primers needed to initiate replication
primase
66
segment of RNA formed on DNA template to start replication; provides 3'OH needed for phosphodiester bond formation with incoming nucleotide
RNA primer
67
enzyme that synthesizes daughter DNA by reading code on DNA template; can only synthesize DNA from 5' end to 3' end because 3'OH needed to receive incoming nucleotides & form phosphodiester bonds; can only extend a nucleotide chain; can't start one; needs primer to start
DNA polymerase
68
synthesis of daughter strand of DNA from 3'-5' target strand; DNA polymerase proceeds in linear fashion, assembling series of joined nucleotides in leading strand
continuous synthesis
69
synthesis of daughter strand of DNA from 5'-3' target strand; DNA polymerase must read target in 3' to 5' direction, so must proceed in nonlinear fashion, reading a section, assembling appropriate nucleotides, then moving back upstream to read another section in 3' to 5' direction; new strand called lagging strand; consists of unconnected DNA fragments called Okazaki fragments separated by RNA primers
discontinuous synthesis
70
daughter strand synthesized continuously from 3'-5' template
leading strand
71
daughter strand synthesized discontinuously from 5'-3' template
lagging strand
72
short fragments of unconnected DNA formed during replication of 5'-3' template
Okazaki fragments
73
enzyme that removes RNA primers from daughter strands of DNA
RNase H
74
enzyme that joins DNA fragments together
ligase
75
DNA replication - helicase unwinds section of dsDNA to form replication forks; both original strands will serve as templates; replication will proceed simultaneously on both strands, in opposite directions
strand separation
76
DNA replication - primase reads section of code on DNA, attaches complementary nucleotides to form RNA primer that provides 3'OH end needed to grow nucleotide chain
synthesis of primers
77
DNA replication - DNA polymerase reads template, attaches complementary nucleotides starting at 3'OH of primer; code is read in 3'-5' direction; synthesis of 3'-5' template is continuous, forming leading strand; synthesis on 5'-3' template is discontinuous, forming lagging strand of disconnected Okazaki fragments
extension of primers
78
DNA replication - RNase H removes RNA primers
removal of primers
79
DNA replication - DNA polymerase places nucleotides where primers used to be
replacement of primers
80
DNA replication - DNA ligase joins DNA fragments together
joining of Okazaki fragments
81
Primer extension - template DNA: 3' AGCA 5'
-daughter strand:
-polymerase reads:
-phosphodiester bond:
-daughter strand: 5' TCGT 3'
-polymerase reads: template in 3' to 5' direction; new strand grows in 5' to 3' direction
-5'P of incoming nucleotide attaches to 3'OH of last nucleotide on strand, forming phosphodiester bond
82
Discontinuous synthesis of DNA on lagging strand - template DNA:
5' AGCTTGAC 3'
-daughter strand:
-first pass:
-second pass:
-daughter strand:
3' TCGAACTG 5'
-first pass: polymerase reads positions 4 to 1 on template - TCGA, assembles AGCT on daughter strand
-second pass: polymerase reads positions 8 to 5 on template - CAGT, assembles GTCA on daughter strand
83
synthesis of specific proteins based on DNA code
gene expression
84
RNA that transcribes DNA code in nucleus & carries it to cytoplasm where it's translated into protein; about 1-2% of total cellular RNA
messenger RNA (mRNA)
85
RNA associated with ribosomes, site of protein synthesis
ribosomal RNA (rRNA)
86
RNA that reads code in mRNA & transports amino acids to growing polypeptide chain
transfer RNA (tRNA)
87
tiny regulatory RNAs involved in control of gene expression
micro RNA (miRNA)
88
conversion of genetic information from DNA into complementary strand of mRNA; if DNA sequence is AGCT, mRNA sequence will be UCGA
transcription
89
strand of DNA that doesn't serve as template for synthesis of mRNA; its sequence is same as mRNA that is translated into protein (except it has T where RNA has U)
sense strand
90
strand of DNA that serves as template for synthesis of mRNA
antisense strand
91
region of DNA that binds RNA polymerase, initiating transcription
promoter
92
3 nucleotides that code for an amino acid, e.g., GCC codes for alanine
codon
93
How many codons code for 21 amino acids?
64
94
How many codons does each amino acid have?
2-6 for each, except methionine & tryptophan which only have 1
95
AUG, codes for methionine
start codon
96
UAA, UAG, UGA; not associated with any amino acid; signal to stop protein synthesis
termination codons
97
3-nucleotide sequence on tRNA that attaches to codon on mRNA, bringing with it specified amino acids
anticodon
98
organelles in cytoplasm & on surface of rough ER; made of tRNA & protein; site of protein synthesis
ribosomes
99
Protein synthesis:
1. RNA polymerase binds to promoter region of gene.
2. DNA separates into 2 single strands
3. RNA polymerase adds complementary nucleotides to produce strand of mRNA; if DNA sequence is 3' ATTCGA 5', mRNA will be 5' UAAGCU 3'
4. mRNA is released from DNA
5. DNA strands reanneal.
Transcription
100
Protein synthesis:
1. mRNA associates with ribosomes in cytoplasm
2. ribosome moves along mRNA, reading genetic code; always begins with codon AUG
3. tRNA with complementary 3-nucleotide sequence (anticodon) attaches to codon on mRNA, bringing with it amino acid specified by codon, e.g., anticodon UAC on tRNA attaches to codon AUG on mRNA, bringing with it amino acid methionine
4. as ribosome moves along mRNA, other tRNAs bring in other amino acids
5. peptide bonds form between amino acids
6. process continues until ribosome reaches stop codon
7. protein is released
translation
101
analysis of DNA & RNA; nucleic acid testing (NAT)
molecular diagnostics (MDx)
102
isolation of DNA/RNA from other cellular components
extraction
103
enzyme that degrades RNA; ubiquitous in environment
RNase
104
enzyme that degrades DNA
DNase
105
specific section of DNA under investigation
target
106
pairing of complementary strands of nucleic acid, 1 from sample & 1 a reagent; resulting hybrids can be DNA:DNA, DNA:RNA, or RNA:RNA
hybridization
107
product of hybridization
hybrid
108
stability of bonding during hybridization; based on degree of match & base composition; influenced by temperature, pH, & salt concentration; increased temperature, decreased salt ensure only most perfectly matched strands will remain paired
stringency
109
short strand of DNA or RNA with known base sequence
nucleic acid probe
110
Blood collection tubes for MDx - lavender:
-content:
-use:
content: EDTA
use: isolation of DNA & detection of viruses
111
Blood collection tubes for MDx - white:
-content:
-use:
content: K2EDTA & gel barrier
use: isolation of plasma; gel forms barrier between plasma & cells
112
Blood collection tubes for MDx - blue/black:
-content:
-use:
content: sodium citrate, gel, density gradient fluid
use: isolation of mononuclear cells; gel forms barrier between mononuclears in plasma & RBCs/granulocytes
113
Blood collection tubes for MDx - yellow:
-content:
-use:
content: acid citrate dextrose (ACD)
use: enhanced recovery of WBCs for several days after collection
114
Blood collection tubes for MDx - green:
-content:
-use:
content: heparin
use: generally not recommended; heparin inhibits polymerase; unacceptable for testing that involves PCR
