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BI236: Cells > DNA and Chromosomes (Week 2) > Flashcards

DNA and Chromosomes (Week 2) Flashcards

1
Q

What are genes?

How many genes for the expressed human genome?

A
  • genes are segments of DNA that encode proteins

- not many; only about 1.5% of the human genome

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2
Q

What is a chromosome?

A
  • long continuous piece of DNA containing many genes (contains many genes, regulatory elements and other intervening nucleotide sequences)
  • eukaryotes chromosomes are structurally complex and are wrapped around proteins (histones)
  • only eukaryotes have chromosomes
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3
Q

What is chromatin? How long is the short region of the DNA double helix?

A
  • chromatin is DNA wound around proteins

- DNA is about 2nm long

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4
Q

What is karyotyping? what is a karyogram?

A
  • karyotyping is a test to identify and evaluate the size, shape, and number of chromosomes in a sample of body cells
  • a karyogram is the picture that you see of all the homologous pairs of chromosomes lined up
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5
Q

What is the flow of information in cells (hint Central Dogma)?

A

Within cell: DNA is in the nucleus and mRNA is transcipted in the nucleus
-this mRNA is then moved to the cytoplasm where ribosomes will translate it to make a a protein
Between Generations: DNA replication occurs in the nucleus before mitosis. It must be perfect or there will be errors

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6
Q

What is the DNA structure? Who discovered it?

A
  • Waston and Crick in 1952
  • Double helix with sugar phosphate backbone and nitrogenous bases connected by H bonding
  • DNA is anti-parallel (starts at 5’ ends at 3’)
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7
Q

What are Chargaff’s rules?

A

A=T (form 2 bonds) and G=C (form 3 bonds)
-harder to pull appart GC bonds
the number of purines (A,G)= the number of pyrimidines (C,T,U)

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8
Q

What is important about DNA’s structure? Why?

A
  • it has two forms: relaxed and super-coiled
  • seen in circular DNA and also in linear DNA
  • this helps DNA become for compact
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9
Q

What are topoisomerases? What is used in bacteria

A

-super-coils can form when compacting DNA
-enzymes that regulate the over-winding or under-winding of DNA
2 types: on for single strand breaks; two for double strand breaks (bacteria uses DNA gyrase); this one requires energy to work

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10
Q

What can be noted about the Double helix structure?

A

-anti parallel strands starting at 5’ end at 3’ (left)
(right goes 3’ to 5’)
-lots of CG makes it harder to separate the strands
-each strand acts as a template strand for the other strand
-phosphodiester bonds join carbon 5 with carbon 3

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11
Q

What’s the different between a nucleoside and and nucleotide?

A
  • side: Base and Pentose

tide: Base and Pentose and Phosphate group

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12
Q

What does DNA consist of (what are nucleotides made of)?

A
  • nucleotide: one of the bases A,G,C,T or U(RNA)
  • pentose sugar molecule
  • phosphate group
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13
Q

What is the difference in the forms of DNA (B-DNA, Z-DNA, and A-DNA)?

A

B-DNA: normal form; right handed DNA
Z-DNA: Zig-zag left-handed helix; longer and thinner than B-DNA
A-DNA: Right-handed helix; shorter and thicker than B-DNA; can be artificiality by dehydrating B-DNA
-RNA if double helix
-wide minor groove and narrow major groove

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14
Q

What affect does super coiling have on the DNA molecule?

A
  • it affects the spatial organization and the energy state of the DNA (affects the ability of the DNA to interact with other molecules)
  • Tighter winding (positive supercoil) reduces the chances of interaction
  • Negative supercoiling (unwinding) increases access to proteins involved in replication or transcription
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15
Q

What is a genome?

A

genome is one complete copy of all the genetic information of an organism

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16
Q

How do genomes/ organization of genomes vary in Prokaryotes and Eukaryotes?

A

> Viruses & Prokarytoes have single or small number of linear/circular DNA/RNA molecules
Eukaryotes have nuclear genome and multiple DNA molecules (chromosomes). These include mitochondria & chloroplast genome whose DNA is a circular molecule

17
Q

What are two ways DNA can be repeated?

A

-can be tandemly repeated or interspersed
-Tandem repeatsoccur inDNAwhen a pattern of
two or more nucleotides is repeated and the
repetitions are directly adjacent to each other
-Interspersed, repeated are scattered around genome
transposable elements (transposons, ‘jumping genes’)

18
Q

What are the two types of interspersed Repeats?

A

LINE: Long Interspersed Nuclear Elements (6000-8000pb); these genes can move by themselves
SINE: Short Intersperse Nuclear Elements (<500bp) these genes rely on other elements like Alu sequences to move them

19
Q

What are the two types of tandems repeats?

A

Micro satellites: repeats of sequences less than
about 2-6bpin length
Mini satellites: involve repeating of longer blocks
(10-60 bp)
Tandem repeats usually have a pattern of 2 or more nucleotides adjacent to each other

20
Q

What is it called when the number of repeats in a tandem sequence is not known?

A

-called variable number tandem repeat or VNTR

21
Q

What are the most common types of DNA in the human genome?

A

almost 44% is Interspersed repeated DNA
15% is tandem
1.5% is exons or expressed genes

22
Q

What are the 3 possible was that DNA can be replicated? Which is observed?

A
  • DNA can be replicated conservatively(make whole new strand), semi-conservatively (use other strand as template), or dispersive (bits of new (conservative) and old)
  • semi-conservatively is seen, with each parent strand being the template for the new strand
23
Q

What is the Messelson-Stahl experiment? What did they try and prove?

A

Wanted to prove semi conservative replication
-used radioactive isotope to tell the difference between old and new DNA
What they saw:
-grew e.coli in N14 medium as control; saw one band
-grew in N15 medium: saw one band
-took N15 and allowed to reproduce in N14; saw one band
-in N14, allowed cells to reproduce for a 2nd gen and saw two bands (one N14 14, one N15 14)
This proved semi conservative replication (had one old, and one new strand)

24
Q

Who does circular DNA replication differ from other DNA rep? Who does this?

A
  • Has single ORI
  • has replication forks and proceeds bidirectionally with both strands being replicated
  • theta replication (looks like theta symbol)
  • Bacteria do this (replication is followed by binary fission)
25
Q

What is a replicon? What organism has multiple of these?

A

Eukaryotes

  • Replicons are multiple replication units; have length of 50-300 kb pairs; often several thousands per chromosome
  • Works by having multiple replication bubbles with eventually fuse
  • Origin of Replication has special DNA sequence in the center
26
Q

Which way does DNA replication occur? Who is the hero?

A
  • Goes from 5’ to 3’ direction elongating the 3’ end
  • requires a small amount of DNA as a template (RNA primer)
  • adds dATP, dTTP, dGTP, & dCTP and PPi released to provide energy
  • DNA polymerase 3 is the hero here :)
27
Q

Give a summary of DNA replication

A
  • initiator protein binds to DNA or OR and slightly unwinds the DNA
  • Helicase bind to unwound DNA and keeps unwinding the DNA; Topoisomerase reduces the supercoil in front of helicase
  • SSBs help keep strands seperate
  • Primase lays down RNA primers on leading strand
  • DNA poly 3 uses the primer then starts replication (5’ to 3’)
  • RNA primer is put on lagging strand; DNA poly 3 extends down lagging strand as well
  • Okazaki strands are used to help synthesis
  • primers are removed by exonuclease DNA poly 1
  • ligase glues strands together after DNA poly 1
  • Exonuclease also proof reads and breaks anything that is wrong on the strand
28
Q

What kinds of damage can be found in DNA?

A
  • mutations can arise; most are beneficial and corrected

- most are cut out as introns

29
Q

What is a spontaneous mutation?

A
  • spontaneous: Depurination (loss of a purine base) or Deamination (removal of a base’s amino (NH2) group)
  • C most susceptible to deamination causing it to switch to U; results in insertion of A not G
30
Q

What type of things can occur with chemical mutagens?

A
  • base analogs – resemble nitrogenous bases incorporate into the DNA
  • base-modifying agents – react chemically with DNA bases to alter the structure
  • intercalating agents – insert themselves between adjacent bases of the double helix, distorting DNA structure
31
Q

What can occur with radiation?

A
  • UV: sunlight alters DNA triggering pyrimidine dimer formation, i.e. formation of covalent bonds between adjacent pyrimidine bases
  • ionizing radiation – X-rays and other rays emitted from radioactive substances. It removes electrons from biological molecules,making highly reactive intermediates that cause DNA damage
32
Q

How is DNA repaired if mutations found?

A

-Repairing DNA during replication translation synthesis (excision, synthesis)
-Repair endonucleases are recruited to DNA by proteins that recognize damage
- cleave the backbone adjacent to the damage site; other enzymes remove the defective nucleotides
DNA polymerase (I in E. coli) replaces the missing nucleotides
-DNA ligase seals the remaining nick in the repaired strand

33
Q

What are other types of DNA repair?

A

-single stranded DNA damage: a ‘cut-and-patch’ pathway removes the damaged or incorrect nucleotides from one strand, and the resulting gap is filled using the intact strand as template
Double-strand Breaks:
nonhomologous end-joining – uses a set of proteins that bind to the end of the two broken fragments and join them together
homologous recombination – the other intact chromosome is used as a template to guide repair of broken chromosome
(picture on W2-2 slide 24)

BI236: Cells (5 decks)

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