1
Q
What is the difference between Eukaryotic DNA and Prokaryotic (specifically bacteria) DNA?
A
- ## Bacterial chromosomes contain circular molecules of DNA segregated into about 50 domains → supercoil
2
Q
What is the length of E. coli DNA?
A
- 1500 micrometers
3
Q
What is the diameter of the E. coli DNA
A
- Due to E. coli being a prokaryote, it’s DNA is in in the form of a circle and so its diameter is 1-2 micrometers
4
Q
How does a circular, unfolded chromosome become a folded chromosome?
A
- The two DNA strands in the circular chromosome bind to the structural RNA (which have formed a circle in the middle of the circular chromosome) and starts to make about 40 to 50 loops
5
Q
What happens to the Folded chromosome?
A
- Once a circular chromosome has folded into about 40 to 50 loops it becomes super coiled. This means that each loop, which is independently super coiled, will fold back on its self to form many smaller loops.
6
Q
What happens to a folded chromosome after it has been super coiled?
A
- After it has been super coiled, the chromosome can either become partially unfolded or partially uncoiled
7
Q
What does “Domain” mean in structural biology?
A
- A certain piece of a protein that can stand alone
8
Q
What does it mean when a Folded Chromosome becomes Partially Unfolded?
A
- This is when the super coiled, folded chromosome has partial RNase digestion and so the structural ring of RNA is cleaved, hence some of the 40-50 loops will start to unfold from the RNA
9
Q
What does it mean when a Folded Chromosome becomes Partially uncoiled?
A
- This is when the super coiled, folded chromosome has partial DNase digestion and so the DNA becomes Nicked (small cut or snap). Due to each loop being independently super coiled, this means that whichever loop has been nicked will return to a smooth loop in the folded chromosome.
10
Q
Draw and label a diagram of the Folded Chromosome Process.
A
https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing
11
Q
Why are Eukaryotic Genomes different to Prokaryotic Genomes?
A
- This is because Eukaryotic genomes contain levels of complexity that are not encountered in prokaryotes. This is mainly due to the fact that most Eukaryotes are multi cellular
12
Q
How much DNA is in a haploid and diploid chromosome?
A
1000 mm DNA/haploid chromosome:
- Subdivided among 23 chromosomes of varying size and shape
2000 mm/diploid cell
13
Q
What are Histones?
A
- Any of a group of basic proteins found in chromatin.
- Histones play major role in chromatin and are present in all eukaryotes at amounts equivalent to amounts of DNA
14
Q
What is chromatin?
A
- The material of which the chromosomes of organisms other than bacteria (i.e. eukaryotes) are composed, consisting of protein, RNA, and DNA
15
Q
What are Chromosomes made of?
A
Chromatin:
- DNA
- Histones
- Non-histone proteins
16
Q
What are the Five classes of Histones?
A
- H1 = High Lysine Content
- H2a & H2b = Moderate Lysine Content
- H3 and H4 = High Arginine Content
17
Q
What charge does DNA have?
A
- DNA is Negatively Charged
18
Q
What causes the Histones and DNA to form chromatin?
A
- Histone proteins are positively charged and DNA is negatively charged, hence they are attracted to each other.
19
Q
Draw and label the pie chart for the components of a chromosome.
A
https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing
20
Q
Can DNA exist without Histones?
A
- No, The DNA and Histones exist together in the chromatin in equal quantities
21
Q
What are the two most abundant Histone proteins and why?
A
- Arginine and Lysine are most abundant because they are positively charged and so they are attracted to DNA
22
Q
Why are Histones “Highly Conserved proteins”?
A
- This means that Histones have been conserved from ancient organisms all the way through to man. The sequence (of DNA bases) doesn’t change much because the residues (amino acids) are critical to our existence.
23
Q
What is the best way to describe what a chain of Nucleosomes looks like?
A
- Beads on a string
24
Q
How were Nucleosomes discovered?
A
- Isolated chromatin from interphase cells were examined by electron microscopy revealed beads-on-a-string structure
25
What is a Nucleosome?
- A structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones.
26
What links the Nucleosomes together?
- DNA strands hold them together, they are called DNA linkers and they are wound between the nucleosomes → condensed 11 nm fiber
27
What is a Nucleosome Core?
- 146 nucleotide pairs of DNA wrapped as 1 3/4 turns around an octamer of histones
28
How long are Linker DNA
- In mammals, the Linker DNA between the Nucleosomes vary in length from 8 to 114 nucleotide pairs
29
Draw and label a diagram of the Nucleosome bead chain
https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing
30
What is the diameter of double stranded DNA?
- 2nm
31
What is the diameter of Nucleosome Bead Chains?
- 11nm
32
What is a Histone Octamer?
- The eight protein complex found at the center of a nucleosome core particle
33
What is Nuclease?
- An enzyme that cleaves the chains of nucleotides in nucleic acids into smaller units
34
Why are Nucleosome cores important?
- It's a nuclease-resistant structure which is important because it prevents the DNA around the Nucleosome from being digested by the nuclease
35
What is a nucleosome core composed of?
- This structure consists of a 146-nucleotide-pair length of DNA and two molecules each of histones H2a, H2b, H3, and H4
- Physical studies of nucleosome-core showed that the DNA is wound as 1.65 turns of a superhelix around the outside of the histone octamer
36
Why are the Histones important in a Nucleosome?
- The histones protect the segment of DNA in the nucleosome core from cleavage by endonucleases
37
Draw and label a diagram of the Nucleosome core
https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing
38
What are the components of a complete Nucleosome?
- The nucleosome core, the linker DNA, and the associated nonhistone chromosomal proteins, all stabilized by the binding of one molecule of histone H1 to the outside of the structure
39
What is the difference between a complete nucleosome and a nuclosome core?
- Complete nucleosome contains two full turns of DNA superhelix (a 166 nucleotide-pair length of DNA) on the surface of the histone octamer, and the stabilization of this structure by the binding of one molecule of histone H1
40
Draw and label a diagram of a complete nucleosome.
https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing
41
What does the Histone H1 do?
- Once the nucleosome core is developed, it locks over the top of the DNA superhelix turns and the octamer of histones to keep it in place and stabilise it
42
What are Chromatin Fibres?
- Chromatin fibres are fibres that are found in the chromosomes however their exact composition is unknown
- These chromatin fibres have an average diameter of 30 nm
43
What does "In Vivo" mean?
- (of processes) performed or taking place in a living organism
44
What does "In Vitro" mean?
- (of a process) performed or taking place in a test tube, culture dish, or elsewhere outside a living organism.
45
What does the structure of a chromatin fibre depend on?
- The structure of the 30 nm chromatin fibres seems to be quite variable and depends on the procedures used to isolate and view them
46
What two structures of chromatin fibres have been found?
- Electron microscopy during earlier stages of meiosis found that 30-nm fibers are tightly packed or condensed
- Cryoelectron microscopy found that 30-nm fibres show less tightly packed “zigzag” structures
https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing
47
What two models have been formed for the 30nm Fibres and how are they estimated to be formed?
- Two most popular models are the solenoid (c) and zigzag models (d)
- In vivo, the nucleosomes interact with one another to condense the 11-nm nucleosomes into 30-nm chromatin fibres, however the exact structure is unknown (solenoid or zigzag or both)
48
What is certain about the 30nm Fibres?
- Chromatin can expand and contract in response to chemical modifications of H1 and the histone tails that protrude from the nucleosomes
49
Draw and label diagrams of the two different models for the 30nm Fibres.
https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing
50
What is the significance of a Metaphase chromosome?
- Metaphase chromosomes are the most condensed of normal eukaryotic chromosomes
- The basic structural unit of the metaphase chromosome is the 30-nm chromatin fiber
51
How was the DNA scaffolding discovered?
- Electron micrographs of isolated metaphase chromosomes from which the histones have been removed reveal a scaffold, or central core composed of nonhistone chromosomal proteins
52
What is DNA Scaffolding?
- The non-histone collection of proteins that act as the scaffold into which the 11nm chromatin fibres condense into a metaphase shape
- Usually composed of RNA and other non-histone molecules
53
How many levels of packaging is requires to create a Metaphase Chromosome?
- At least three levels of condensation are required to package the 103 to 105 µm of DNA in a eukaryotic chromosome into a metaphase structure a few microns long
54
What are the three levels of packaging DNA?
- 2nm DNA molecules
- 11nm nucleosomes
- 30nm chromatin fibres
- (these all then lead into the metaphase chromosome)
55
What happens during the first level of packaging DNA?
- Condensation involves packaging DNA as a negative supercoil into nucleosomes to produce the 11-nm-diameter interphase chromatin fiber.
- This involves an octamer of histone molecules, two each of histones H2a, H2b, H3, and H4.
56
What happens during the second level of packaging DNA?
- Condensation involves an additional folding or super coiling of the 11-nm nucleosome fibre to produce the 30-nm chromatin fiber.
- Histone H1 is involved in this super coiling of the 11-nm nucleosome fibre to produce the 30-nm chromatin fibre
57
What happens during the third level of packaging DNA?
- Non-histone chromosomal proteins form a scaffold that is involved in condensing the 30-nm chromatin fibre into the tightly packed metaphase chromosomes.
- This level of condensation appears to involve the separation of segments of the giant DNA molecules present in eukaryotic chromosomes into independently supercoiled domains or loops.
58
Draw and label a diagram of the three levels of DNA packaging.
https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing
59
What are three different kind of anaphase?
- During anaphase I and anaphase II of meiosis, and the single anaphase of mitosis, the sister chromatids of each chromosome move to opposite spindle poles and become daughter chromosomes
60
What do the anaphase movements depend on?
- The three types of anaphase movements depend on the attachment of spindle microtubules to specific regions of the chromosomes, the centromeres
61
What is one of the key steps in the transition from metaphase to anaphase
- The production of two functional centromeres is a key step in the transition from metaphase to anaphase
- The centromere of a metaphase chromosome can usually be recognized as a constricted region
62
Why is the production of two functional centromeres important?
- A functional centromere must be present on each daughter chromosome to avoid the deleterious effects of non-disjunction
63
What is different about the DNA of higher plants and animals?
- The centromeres of higher plants and animals contain large amounts of DNA sequences in long tandem arrays
- Other DNA sequences are often found embedded within these tandem arrays. Eg. Centromere of human chromosomes contain 5,000 to 15,000 copies of a 171 base pair-long sequence called the alpha (sometimes “alphoid”) satellite sequence
64
how many base pair segments are needed for centromere function?
- 450,000 base-pair segment of the centromere of the human X chromosome is sufficient for centromere function
- Consists mostly of alpha satellite sequences but contains interspersed centromere protein (CENP) binding sites called CENPB boxes
- Both components are essential for centromere function
65
What is a Telomere?
- A compound structure at the end of a chromosome
66
What are the functions of a Telomere?
Functions of telomeres (or ends of eukaryotic chromosomes)
- Protect the ends of linear DNA molecules from deoxyribonucleases
- Prevent fusion of chromosomes
- Facilitate complete replication of the ends of linear DNA molecules
67
What is the sequence of a Telomere?
- Most telomeres contain repetitive sequences and a distinct structure
- In vertebrates the sequence TTAGGG is highly conserved
- In normal human somatic cells telomeres contain 500 to 3000 TTAGGG repeats that shorten with age
- Telomeres of germ-line cells and cancer cells do not shorten with age
68
What is the structure for Telomeres in humans called?
t-loops
69
What are the 1st and 2nd steps in forming a t-loop?
- Single strand at the 3ʹ terminus invades an upstream telomeric repeat and pairs with the complementary strand
- The displaced strand is protected from degradation by being coated with a protein called POT-1 (Protection Of Telomeres-1)
- The t-loop structure nicely protects the free end of the DNA molecule
70
What are the 3rd and 4th steps in forming a t-loop?
- Two telomere-specific protein complexes—TRF-1 and TRF-2—are associated with these t-loops
- One of the proteins within these complexes is an enzyme that unwinds DNA and can disrupt the special H bonded structures formed by G-rich telomere sequences, allowing the 3ʹ terminus to invade an upstream telomere region and form a t-loop
71
Draw and label a diagram of a t-loop.
https://docs.google.com/document/d/1Nzo4FTzXCbwOZjpoc_J_4IF3gsOXPcoyC2BowELmx0U/edit?usp=sharing
Genetics & Evolutionary Biology
flashcards
Decks in class (16)
# Cards
-
Major Milestones of Genetics17
-
Review of the cell and cell cycle66
-
Mitosis26
-
Meiosis37
-
Mendelian Genetics31
-
Human Genetics32
-
Chromosome Inheritance45
-
X-linked57
-
M2 - Central Dogma29
-
DNA Structure29
-
Chromosome Structure71
-
DNA Replication72
-
Transcription and Translation87
-
Inheritance and Mutations39
-
Molecular Basis of Mutations25
-
DNA Repair Mechanisms32
