Terms Flashcards
How do nucleic acids grow?
By attachment of the 5’ phosphate group of the incoming nucleotide to the 3’ hydroxyl group of the last nucleotide
Double stranded DNA is
The most energetically favorable stage of DNA
Purines
The double-ring structure of Adenine and Guanine (A&G)
Pyrimidine
Single-ring structure of Thymine, Uracil, and Cytosine (T&U&C)
MRNA
Messenger RNA
Template for all protein synthesis
Encodes all information needed to produce proteins
Ribosomal RNA
Non-coding RNaa
Components of the ribosomes, the protein synthetic factories in the cell
Eukaryotes ribosomes contain 2 subunits (60 & 40 s)
Small nuclear RNa
Function in eukaryotic splicing
MicroRNA
Single-stranded RNA involved in transcriptional regular
Sanger sequencing
Chain termination method
Is 1st gen sequencing method
Mostly 16S ribosomal RNA, drug resistance, and genotyping
Next Gen Sequencing
Newer
Broadly used
Surveillance testing and some clinical diagnostic testing
Whole Genome Seq
Entire genome is sequenced instead of small region of interest
Pcr(Polymerase Chain Reqction)
Amplification of DNA(billions of copies)
Requires- specific primers, deoxyribose nucleotide triphosphates and heat stable DNA polymerase
Denatured Annealing Extension
Conventional PcR(end point)
Amplified products are detected at completion of thermal cycling
Typically through gel electrophoresis
Often as band and base pairs can be sized with a ladder
Quantitative Pcr
Measure quantity of target sequence( count of copy number, viral load)
Reverse Transcription Pcr
Starts with RNA that is transcribed to DNA(cDNA) and then amplified in PCR
Real time PCr
Combines amplification and detection in one step
Two types singplex- one gene target in one reaction
Multiplex- Multiple targets in single reaction
Can be single or multiple organisms targets
Requires fewer reagents
Less sensitive and more finicky the singleplex
Quality control
Testing known Sivan’s along with patient samples through analytical process to ensure results are accurate and precise
Quality assurance
Systematic approach to ensure products and services are high quality, defensible, and accurate
- monitoring supplies
-equipment validation/calibration
-personal training g
-proficiency testing
DNA ligase
Joins dna fragments formed by discontinuous synthesis dna replication or dna repair pathways
Nucleases
Digest nucleic acid by breaking phosphate bonds
- can be ss or ds dna/rna
Ex. Endonucleases digest acids from middle of molecule
Excesses digest acids at a free end either 3 or 5
Helicases
Use chemical energy to break nucleoside triphosphates
Ie Break hydrogen bonds between bases and unwind double helix into single strands (mostly ATP)
Topoisomerases
Enzymes with nuclease(digest) and ligase(join fragments) properties that change supercooling in dna
Polymerases
Join DNA or arms nucleotides together to form ss daugther using ss parent molecule as template
Ie makes new dna or rna
Typically proceeds in 5 to 3 direction
Reverse transcriptase
Mostly viral origin
Catalyzes dna synthesis from DNA or RNA template
What degrades DNA?
Exonucleases
Central Dogma
Replication>Transcription>Translation
Ex DNA>RNA>Ribosomes
Autonomies
22 pair per cell
Non sex linked genetic heredity info
Sex chromosome
1 pair per cell
Genetic traits linked to persons sex
GC box
Distinct patter. Of nucleotides found in promoter region ahead of TATA box ~110 bases in front of transcription initiation site
Tata box
Cis regulatory element found in promoter region- part of core promoter region
Caat box
Nucleotide consensus sequence occurs 75-80 bases in front of initial transcription site
Cis regulatory elements CREs
Non coding regions of dna that regulate the transcription of nearby genes
Trans acting element
DNA sequence that contains a gene coding for protein that is used in the regulation of another target gene (micro rna or similar molecule)
ATG
Transcription start site
Intro
Non coding sequence that is removed from mature mRNA prior to translation
Econ
Coding sequence of dna present in mature mRNA
3 statues of dna replication
- Initiation- repose(replication complex) form helicase unwinds dna, dna polymearase binds origin of replication and form replication form
- Elongation-two strands, leading strand continuously synthesized 5-3 by dna poly and the lagging strand which is formed 3-5 in short Okazaki fragments and joined together by liagse (more prone to errors)
- Termination- replication machinery dissociates
RNA transcription
Process of copying one strand of dna sequence info into mRNA
Poly a tail
Necessary for stablility and transportation to the cytoplasm
Is added to the 3 end
Translation
Process of converting mRNA to protein
Codon
3 nucleotide sequence that is specified to one amino acid
64 codons possibel
3 stop codons
Uaa, uag, uga
DNA repair types
Direct -single step reaction
Mismatch-checks for error in replication daughter strand is removed and replaced with correct match
Base excision-small non helix deforming adducts repairs
Nucleotide excision- removes bulky dna adducts( ex.thymine diners)
Double strand break repair- repairs cause by ionizing radiation and the like
What restores the correct sequence and integrity of the daughter strand during mismatch repair
DNA polymerase 3 and ligase
What type of mutation is sickle cell anemia
Point mutation
What type of mutation is Becker muscular dystrophy
An example of deletion/insertion
What type of mutation is duchenne muscular dystrophy
It is an example of deletion/insertion with a frame shift
What type of mutation is duchenne muscular dystrophy
It is an example of deletion/insertion with a frame shift
What mutation is Fragile X syndrome?
Amplification/trinucleotide repeat
What is chronic myelogenous leukemia and example of
Translocation
What are the three types of point mutation?
Silent-
Nonsense-
Missense-
What are the 3 types of reciprocal translocation
Balanced
Unbalanced
Robertsonian- movement of one entire chromosome to centromere of another chromosome
What are the two types of inversions
Paracentric-involves sequences within 1 arm of chromosome
Pericentric-includes centrome of inverted region
Autosomal Recessive
Specific phenotype can only be expressed when two mutated copies of the gene are present
25% of offspring from heterozygous parents
-examples include cystic fibrosis and hereditary hemochromatosis
X-Linked diseases
Mutant allele resides on X chromosome
Females are carriers but males are affected
No male to male transmission
-1/3 are novel mutations and mother isn’t affected mutation
Two types ie recessive or dominant
X-recessive-primarily males affected
All females obligate carriers
—ex red-green color blindness and quality-Aldrich syndrome
X linked dominant only one copy
All affected individuals have affected parent
Exs duchenne/becker muscular dystrophy, fragile X syndrome
Assay verification
Needs precision/reproducability
Accuracy and reference values
Assay validation
Is done on a in house test procedure
Needs precision/reporducability, accuracy, reference values, a reportable range, sensitivity and specificity
Needed if ANY modification is made to an FDA-approved assay
