PID quiz 6

what is genetic material made of?

nucleic acids

what is building block of nucleic acids?

nucleotide

what is nucleotide composed of?

-nitrogenous base

-5 carbon sugar

-up to 3 phosphate groups

where see deoxyribose? where ribose?

deoxyribose in DNA

ribose in RNA

how label purines structure?

1 to 9

how label pyrimidines structure?

1 to 6

how label sugar carbons?

1 to 5 including a prime

what tells you that you are talking about a carbon from a sugar?

it will have a prime next to the number

what carbon of the sugar will the purine or pyrimidine be attached to in nucleotide?

C1’ of sugar

what carbon is phosphate attached to in nucleotide?

5’

what number placement makes connection with C1’ of sugar in nucleotide if have a purine?

N9 (nitrogen at position 9)

what number placement makes connection with C1’ of sugar in nucleotide if have a pyrimidines?

N1

what experiment showed that DNA is the transforming principal not protein?

-mice survived when injected with only killed virulent strain (s) and also survived when injected with only live avirulent strain (R)

-when live avirulent strain and killed virulent strain mixed together and injected in mouse the mouse died and live virulent strain was recovered as it underwent transformation

what bond type links nitrogenous base to position 1’ of sugar?

glycosidic bond

what is the structure of dna?

a right handed double helix with backbones made out of carbon sugar chains and horizontal rods of paired nucleotide bases

what does A always match with? how many hydrogen bonds do they form?

T

2 hydrogen bonds

what does G always match with? how many hydrogen bonds do they form?

C

3 hydrogen bonds

what is the central dogma of genetics?

DNA ←> RNA → proteins

what call the strand of DNA that bears the same sequence as mRNA?

coding or sense strand

what call the strand of DNA that directs synthesis of mRNA via complementary base pairing?

template or antisense strand

how is DNA sequence always read?

read sense strand from 5’ to 3’

what doe sit mean that DNA replication is semiconservitive?

a new DNA molecule is composed of one parental strand and one new strand

how is lagging strand formed in DNA replication?

using Okazaki fragments that get joined together

is the leading strand synthesized continuously?

yes

is the lagging strand synthesized continuously?

no

what is a 5 step summary of DNA replication?

1. helicase unwinds parental DNA

2. single stranded binding proteins stabilize unwound DNA

3. leading stand synthesized continuously from 5’ to 3’ by DNA polymerase

4. lagging strand synthesize discontinuously using RNA primer which is extended by DNA polymerase to form okazaki fragment

5. RNA primer replaced by DNA and DNA ligase joins okazaki fragments together

what are the 6 main differences between DNA and RNA?

DNA double stranded and RNA single stranded

DNA use deoxyribose and RNA use ribose

DNA use tymidynic acid and RNA use uridynic acid

DNA do A-T pair where RNA do A-U pair

DNA in nucleus where RNA in cytoplasm

DNA much more stable as double stranded where RNA degrade easy

what is transcription?

DNA to mRNA

how does transcription compare between prokaryotic and eukaryotic cells in 5 ways?

Pro uses single RNA polymerase where Eu uses RNA polymerase I,II and III

Pro uses no introns and EU splices introns out

Pro is polycistronic where Eu is monocistronic

Pro does no polyadenylation but Eu does poly a tail at 3’

Pro has to 5’ cpa but Eu uses 5’cap

what is polycistronic?

do transcrition and translation at same time since all occur in nuecleus

why can eukaryotes be polycistronic?

Seperation between nucleus and cytoplasm

how many nucleotides in a codon?

3

what was proof that codon is a triplet?

if add one or two nucleotides get mutations but if add 3 nucleotides the protein ends up normal

what is the start codon?

AUG (methionine)

what is the stop codons?

UAA

UAG

UGG

do transcription and translation occur simultaneously in bacteria?

yes

-called polyribosome

what is a mutation?

change the sequence of DNA

can any base pair of DNA be mutated?

yes

what induces mutations?

mutagens

what does mutagen do?

act directly by modifying a particular base or being incorporated into the nucleic acid

what are the 4 types of mutations? describe each

silent- mutation with no apparent effect as change in DNA does not change amino acid coded for or an amino acid is changed but doesnt change the proteins function

missense- a codon is changed resulting in a different amino acid which changes protein function

nonsense- a change in codon results in an early stop codon so translation stoped prematurely

frameshift- base pairs are inserted or deleted not in a multiple of 3

what is transformation?

Bacteria takes up DNA from its environment and incorporates it into its own DNA

what are the components of a nucleotide, the building block of genetic materials nucleic acids?

nitrogenous base

five carbon sugar

phosphate group(s)

what are 4 categories of diagnostic technique?

direct examination

culture

immunologic methods

molecular analysis

what is molecular diagnosis?

use of DNA, RNA or proteins to help identify the pathogenic agents

what is sensitivity in molecular diagnosis?

true positive rate

what is specificity in molecular diagnosis?

true negative rate

does molecular diagnosis reduce dependency on culture?

yes

what are 5 ways of molecular diagnosis?

electrophoresis

restriction fragment length polymorphism

hybridization

nuclear acid amplification

protein detection

what is electrophoresis?

Separate genetic material by size and charge in an electrophoretic field

how do small vs large move in electrophoresis?

small move fast and further

large move slower and dont go as far

what are 3 different shapes the genetic material can separated into using electrophoresis? Which moves fastest, which slowest?

supercoiled-fastest

linear

nicked circles-slowest

what direction move in electrophoresis?

negatively charged pieces move towards positive end

what is SDS-PAGE?

sodium dodecyl sulfate-polyacrylamide gel

what is restriction fragment length polymorphism (RFLP)?

analyze differences among homologous DNA sequences by restriction enzymes so DNA cut into smaller chunks and can analyze the chunks against each other to determine sequence

what do restriction enzymes do?

cut DNA at the specific recognition nucleotide sequences

are restriction enzymes sequence specific?

yes

What do bacteria use restriction enzymes for?

To protect themselves from viruses

how many restriction enzymes have been studied in detail?

over 6000

what is EcoRI in restriction enzymes?

Produces sticky end

Cuts GAATTC

what is Smal in restriction enzymes?

Form blunt end

Cut CCCGGG

can RFLP be used in forensic analysis?

yes

can RFLP be used for parenthood identification?

yes

what is hybridization diagnostic testing?

da enatured single stranded DNA probe will bind to a complementary single strand sequence

what are 5 different hybridization techniques used in diagnostic testing?

Dot

in situ

Southern

Northern

Microarray

what are 5 characteristics of probe used in hybridization?

-is a fragment of nucleic acids

-labeled using radioisotopes, enzyme or chemiluminescence

-detects complementary sequences in samples

-high degree of specificity

-various in size

what are 3 types of nucleic acid amplification?

target amplification

polymerase chain reaction

isothermal amplification (LAMP)

what is target amplification?

enzyme mediated process to synthesize copies of targeted nucleic acid

What is PCR?

Add nucleotides to 3’ end of fragments one at a time

is PCR and isothermal amplification highly sensitve? Which one more likely to give false positive?

yes

PCR more likely to give false positive

what is PCR fragment?

a ssDNA fragment that is complementary to sequences flanking the region to be amplified

the distance between PCR primer binding sites determines what?

the size of the PCR process

does the PCR primer determine the specificity?

yes

what are 2 types of PCR primers?

random

specific

what 3 things can PCR primers determine?

-product size

-specificity

-annealing temperature

does the PCR primer determine the nucleotide composition of the PCR?

yes

what are 4 PCR variations?

reverse transcriptase PCR

nested PCR

multiplex PCR

quantitative/real time PCR

what is real time/quantitative PCR (qPCR)?

use a probe or dye to generate a fluorescent signal from the product when that sequence is observed and the signal can be made into an exponential curve

what is the signal in real time/quantitiative PCR?

An exponential curve with a lag phase, log phase and stationary phase

what is log phase in real time/quantitative PCR inversely proportional to?

inversely proportional to the amount of starting material

what are 4 pros of LAMP?

no thermal cycler needed

Quick-1 hour

sensitivity is higher than PCR

visible results

what is a con of LAMP?

its complicated to design primer sets

what does western blot often detect?

specific antibodies

for PCR how calculate how many molecules/products get/have?

2ⁿ

n is number of cycles

what is LAMP?

What does southern blot detect?

Protein

What call PCR primer?

PCR amplicon

What does northern blot detect?

RNA