Exam 2 Flashcards by Mishell Lopez

Pathogenic

producing a toxin that causes disease in the host
organism; eg.
C. difficile, H. influenza, S. pneumoniae

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Non-pathogenic

**Most species of bacteria; soil bacteria

gut bacteria, lab strains for molecular cloning

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Why do bacteria seem to evolve so fast?

Natural Transformation
- Artificial Transformation
Conjugation
- Plasmids
- Genomic
Transduction (Phage)

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What are the two types of DNA transfer that can take place in conjugation?

Plasmid transfer and chromosome transfer

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Plasmids

1. Circular 
– like bacterial genome
2. Double Stranded (also like bacterial genome)
3. Much smaller than genome
4. Can occur in one or many copies in a cell
5. Carry protein coding genes
contributes to overall genotype
6.Has own origin of replication

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Exconjugant

any recipient cell that has stably

incorporated a portion of the donor genome

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Chromatin

complex of DNA, RNA and proteins that make up

chromosomes. Primarily DNA and histone proteins.

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In DNA replication, what does Toposiomerase do?

Unwinds supercoiled DNA

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In DNA replication, what does Helicase do?

Unwinds double strands and

separates them

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In DNA replication, what does Primase do?

Synthesizes short oligos (RNAs)

as DNA copies

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In DNA replication, what does DNA Polymerase do?

adds bases to the 3’ end

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tautomers

isomers

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What are the components of a PCR reaction?

Requires:
• DNA template (ds)
• Primers (ss)
• DNA polymerase (Taq
DNA Polymerase)
• Four deoxyribonucleotide
triphosphates

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SNP

Single Nucleotide Polymorphisms
Two ways to detect SNP:
1. Sequence a segment of DNA in homologous chromosomes and compare the homologous segments to spot the differences
2. RFLPs (Restriction fragment length polymorphisms)
-Two RFLPs used….one of which has the restriction enzyme target and the other which does not. The restriction enzyme will cut the DNA at the SNP containing the target and ignore the other SNP. The SNPs are then detected as different bands on an electrophoretic gel. RFLP sities can be between or within genes.

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SSLPs (Simple Sequence Length Polymorphisms) AKA VNTRs (variable number tandem repeats)

SSLPS commonly have multiple alleles, repetitive DNA in different individuals there are often different numbers of copies.
Two types of SSLPs are useful in mapping and other genome analysis
1. Minisatellite markers
2. Microsatelite markers

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Minisatellite Markers

based on variation in the number of tandem repeats of a repeating unit from 15 to 100 nucleotides long. in human the total length is from 1 to 5 kb. Minisatellite loci having the same repeating unit but different numbers of repeats are dispersed throughout the genome.

Microsatellite Markers

based on variable numbers of tandem repeats of a even simpler sequence, generally a small number of nucleotides such as dinucleotide. The most common type is a repeat of CA and its compliment GT

PCR Analysis

procedure to detect differences in simple sequence length polymorphisms by by taking advantage of the fact that homologous regions bearing different numbers of tandem repeats will be of different lengths. The different lengths of the amplified PCR products can be deteced by different mobilities of the sequences on an electrophoretic gel. In the case of minisatellites the pattern produced on the gel are sometimes called DNA fingerprints (highly individualistic)

How much match must there be in Nucleic Acid Hybridization

No firm answer. Usually around 85% if match is long enough. The longer the sequence the more mismatch is tolerated. If shorter sequence, less mismatch is tolerated due to other strong hydrogen bonds.
A few mismatches are inconsequential.

AKA Southern Blot…(DNA gel blot)
Genomic DNA run on a gel
– smear

What is the goal of the Southern Blot?

reveal where are the bands of the gene/genes

interested in

Probe

Highlights region of DNA interested in.

Restriction Fragment Length Polymorphism

•Restriction Fragment Length Polymorphism
genetic variants that differ in the length of a “restriction
fragment”
•Very often special subset of SNPs
- Single Nucleotide
Polymorphisms
SNP
– ANY variation that effects a single base change.
eg.
TTAACC

TAAACC
If this SNP happens to change the sequence of a restriction site, it is
ALSO a RFLP.

Insertion/Deletion
NOT a SNP
TTAACC 
TAACC
deletion, and NOT a SNP 
RFLPs 
– cheap/easy to detect
SNPs are used because they are numerous 
(1/1000 nucleotides) 
cost money to detect 
– requires sequencing to detect.

VNTRS

© 2014 Pearson Education, Inc.
VNTRs
•Animal 
– VNTRs 
- Variable Number Tandem Repeats
•Plants 
– SSR Single Sequence Repeats
several repeats of a sequence that is either 1, 2 or 3 
nucleotides long
TATATATATATATA
CGCCGCCGCCGCCGCCGC
•Not uncommon; usually occur in introns
number of repeats changes frequently across evolutionary 
time (100s
-1000s of generations)
not in a single generation 
*but, within a population of individuals that are not related, 
there will be variability
One allele will have 7, 20 5 repeats

What are the components of a PCR reaction?

Requires:
DNA template (ds)
Primers (ss)
DNA polymerase (Taq DNA Polymerase)
Four deoxyribonucleotide triphosphates

What are Primers in PCR and how do we use them?

• Use 2 primers – located at specific positions along our DNA template – usually flanking a region of interest. • Primers – like a probe, just NOT radioactively labeled. • They are specific to our gene of interest, they are single stranded, and after denaturing, will hybridize to our target DNA. • HAVE Directionality.

What is Taq Polymerase and what is its function in PCR?

The key to PCR is an unusual, heat-stable DNA polymerase called Taq polymerase. • Isolated from Thermus aquaticus • Lives in hot vents (first isolated from Yellowstone NP) – Kerry Mullis figured out that this was needed – Previously – kept adding enzyme every so often

Polymerase Chain Reaction (PCR)

• The polymerase chain reaction, PCR, can produce many copies of a specific target segment of DNA • A three-step cycle—heating, cooling (annealing), and replication (extension)—brings about a chain reaction that produces an exponentially growing population of identical DNA molecules • Primers become incorporated as part of your “amplification” sequence.

Describe Bacteria and why is it a model organism?

``` Prokaryotic Cells -no membrane bound nucleus -no organelles -can reproduce asexually or sexually Model Organism! -fast reproduction cycle -highly variable in size/shape/metabolism ```

Describe the Bacterial Genome

``` Single Chromosome - usually “bacterial genome” •90% of the DNA – protein coding •Compared to just ~5% of human genome is protein coding •Bacterial genome has NO INTRONS ```

What is the ploidy of Bacteria and why is this important?

•Haploid genome allows us to directly see the effects of mutations

Why do bacteria seem to evolve so fast?

Horizontal gene transfer (not necessarily via inheritance from cell division)

How do bacteria conjugate?

They use Pili Conjugating parents act “unequally”only one parent transferred DNA ie, they did not reciprocally transfer DNA to each other. Donor, Recipient Strains Donor can lose the ability to transfer DNA, but regain it after receiving donors.

Describe Eukaryotic Nucleosomes

The nucleosome consists of DNA wrapped around a histone core (histone octamer). - Core of eight histones (H2A, H2B, H3, H4) - Central DNA wrapped around the eight core histones - H1 histone on the side attached There are approximately 147 base pairs of DNA wrapped around a histone octamer

DNA in a chromosome is packaged in what two formats and where is there location relative to the centromere?

- heterochromatin is densely packaged (DNA around the centromere is usually packaged as heterochromatin) - euchromatin is less densely packaged

Tertiary Structure of DNA:

high- order folding that allows DNA to be packed into the cells

Epigenetics

Any potentially stable and heritable change in gene expression that occurs without a change in DNA sequence **Beyond Central Dogma

Acetlyation

DNA methylation is densest at the repetitive elements around the centromere. -Acetylation of histone tails results in altered chromatin. Heterochromatin DNA is highly methylated -DNA can be covalently modified by cytosine methylation. DNA methylation is reversible! -De-methylation returns the potential for gene expression -DNA Methylation turns OFF expression of a particular gene -CG methylation can be propagated during DNA replication (Met 1)