Biol 200 Midterm

What can modification of bases do to DNA bases and DNA polymerase during DNA replication?

It can alter original base pairing and block DNA polymerase activity during DNA replication

What two activities help base repair when DNA polymerase adds the incorrect base?

1. Polymerase complex’s proofreading exonuclease activity

2. Mismatch repair

Which polymerase is the main repair polymerase?

Pol delta

(Note Pol epsilon is for replication —> and has the main goal of replicating DNA in DNA replication)

Pol delta helps to form lagging strand, but also is a big part of mismatch repair 

What does base-excision repair do?

It cuts out a single nucleotide base that is incorrect, and replaces it with the correct base in time before it can become a permanent mutation

Different from Mismatch repair which takes out a chunk (segment) of DNA with the wrong base - BER uses a specific DNA glycosylase enzyme to take out a certain base (different glycosylase for each base) 

What causes single/double strand breaks?

Mutagen = ionizing radiation anticancer drugs like bleomycin

2 ways for repair of single/double strand breaks

1. NHEJ —> Non-homologous end-joining 

2. HR —> Homologous recombination

Is Rad51 or RecA used in homologous recombination in eukaryotes?

Rad51

What is a holiday junction?

The crossover structure formed between two strands one from top chromatid, other from bottom

The process that this happens is called Branch Migration

What’s the distance between nucleotide residues 

34 nm

What do nucleosomes consist of

Histones + DNA (basic unit of chromatin) 

2 models for condensed form of chromatin

1. Solenoid model 

2. Two-start helix model 

What factor of chromatin is transcription dependent on?

Level of condensation

Difference between heterochromatin and euchromatin

Heterochromatin = condensed chromatin DNA that is transcriptionally inactive (lots of non-coding DNA)

Euchromatin = decondensed chromatin DNA that is transcriptionally active (lots of coding DNA)

What do polytene chromosome puffs show us

Regions where chromatin decondensatuon is transcriptionally active 

What is condensin and what does condensin do for mitotic chromosomes?

Condensin = a specialized SMC that helps to tightly compact chromatin loops into packed chromosomes to get ready for mitotic division

• Condensin II forms a scaffold backbone that allows the chromatin loops to loop around it

• Condensin I compacts loops even more

3 elements needed for replication and stable inheritance of chromosomes

1. Origin of replication

2. Centromere

3. 2 telomere ends

Telomerase is only active in what kind of cells 

Germ cells

Stem cells 

What are the characteristics that make up a gene (what is part of its sequence?)

1. Coding Regions (Exons)

2. Non-coding regions (Introns

3. Control regions (promoter + cis-regulatory factors)

What technique is used to determine nucleic acid and protein sequence similari

BLAST technique and other sequence alighnment techniques

What are the two types of intragenic noncoding DNA

1. Introns

2. UTRs (untranslated regions of noncoding DNA) 

What types of DNA structures is minisatellite DNA found in?

1. Centromere

2. Telomere

Is microsatellite or minisatellite DNA associated with neuromuscular diseases?

microsatellite DNA —> when they get abnormally long