DNA, Chromosomes, and Genomes 1 Flashcards
DNA, Chromosomes, and Genomes 1 (82 cards)
1
Q
Building blocks of DNA…
A
nucleic acids
2
Q
What are the 5’ and 3’ ends of DNA?
A
5’: phosphoryl end 3’: hydroxyl end
3
Q
What are the linkages between nucleotides?
A
phophodiester linkages.
4
Q
Nucleotides are joined together by phosphodiester linkages to form…
A
nucleic acids
5
Q
A nucleotide is made up of…
A
5 carbon sugar, nitrogenous base, phosphate group
6
Q
DNA has 1 turn every ___ base pairs
A
10
7
Q
Purines are Pyrimidines are
A
Purines: adenine, guanine (Pure As Gold) Pyrimidines: cytosine, thymine (C U T . . . from purines)
8
Q
Adenine pairs with thymine and has how many hydrogen bonds?
A
2 hydrogen bonds
9
Q
Guanine pairs with cytosine and has how many hydrogen bonds?
A
3 hydrogen bonds
10
Q
A genome is . . .
A
a complete set of information in an organism’s DNA
11
Q
The human genome is distributed over ___ different chromosomes
A
24
12
Q
Chromatin =
A
DNA + protein
** chromatin consists of DNA bound to both histone and non-histone proteins. The mass of histone protein present is about equal to the total mass of non-histone protein. . . In total a chromosome is about 1/3 DNA and 2/3 protein by mass.
13
Q
Giemsa stain
A
- Under a light microscope this stain shows banding patterns which allows chromosomes to be identified and numbered.
- It’s still used in cytogenetics laboratories for karyotype analysis.
14
Q
Chromosome painting
A
Determines different chromosomes. Uses a flourescent tag which serves as a probe that picks out its complementary DNA seq. Lighting up the target chromosome anywhere it binds.
15
Q
Karyotype
A
the display of the 46 human chromosomes at mitosis
16
Q
Cytogeneticists use karyotyping to . . .
A
- detect inherited chromosome abnormalities
- to reveal the chromosome rearrangements in cancer cells
17
Q
Chromosome translocation
- When do they occur?
- What are balanced translocations?
- Where do they occur often?
A
- Can occur during an abnormal recombination event.
- Balanced translocations maintain the correct amount of genetic material.
- Translocations often occur in cancer cells.
18
Q
What information is found on chromosomes?
A
- Genes
- encoding proteins
- encoding RNA molecules
- Interspersed DNA that does not contain genes
- regulatory information
- “junk” DNA
19
Q
What happens to chromosomes during interphase?
A
chromosomes are replicated and decondensed to where they can’t be easily distinguished.
20
Q
What happens to chromosomes during mitosis?
A
chromosomes are highly condensed and separated into two daughter nuclei.
21
Q
What are the chromosome requirements?
A
to pass a copy to each daughter cell, the chromosome requires replication, separation of copies and partitioning to daughter cells.
- DNA replication origin: where DNA replication beings.
-
Centromere: allows one copy of each chromosome to be pulled into each daughter cell where the cell divides. The
- kinetochore protein complex attaches to the centromere.
- Telomeres: at the ends of a chromosome, contain repetitive sequence that enable the ends to be efficiently replicated.
22
Q
How do the chromosomes fit?
A
- Mitotic chromosomes are condensed 500 times compared to interphase DNA.
- Dynamic situation: must allow rapid localized access to DNA for gene expression.
- DNA binding proteins involved in forming chromosomes include histone and non-histone chromosomal proteins.
23
Q
A nucleosome is . . .
A
the most basic unit of chromosome packing.
24
Q
A nucleosome consists of . . .
A
a nucleosome core particle (DNA wrapped around a histone) plus an adjacent DNA particle. If partially unfolded it forms “beads on a string”.
25
How do nucleosomes breakdown?
Nuclease breakdown linker DNA between nucleosomes releasing a nucleosome core particle.
26
Each nucleosome core particle consists of . . .
8 histone proteins 2 molecules each of H2A, H2B, H3, H4 and double stranded DNA 147 nucleotide pairs long.
27
Linker DNA can be ____ long
few to 80nt
28
Nucleosomes repeat every . . .
200 nucleotide pairs or so
29
What is the structure of nucleosome core particle?
* N-terminal amino acid tail that extends out from the core which is subject to covalent modifications.
* important for chromatin regulation.
* Histone fold regions
* formed by all four of the core histones
30
Nucleosome core particle is ____ shaped with DNA wrapped _____ turns
Nucleosome core particle is disc shaped with DNA wrapped 1.7 turns
31
What are the interactions between DNA and histone?
* 142 hydrogen bonds are formed between DNA and the histone core in each nucleosome.
* Hydrophobic interactions
* Salt linkages
* Lysine and arginine (+ charges) comprise more than 1/5 of histone residues; effectively neutralize negatively charged DNA backbone.
32
Variation among histones
* Highly conserved; most changes would be lethal,
* only two differences between pea and cow H4
* Specialized variant histone proteins add to various possible chromatin structures.
33
How does Chromatin Remodeling work?
* Nucleosomes are in a constant state of flux.
* DNA is unrapped in the nucleosome 4 times per second, and remains unwrapped for 10-50 milliseconds before tightening up again.
* Chromatin remodeling complexes allow further loosening of DNA/histone contact.
* Proteins are related to helicases and are ATP dependent; bind to both protein core and DNA.
* Changes structure of nucleosome temporarily, making DNA less tightly bound.
* Repeated cycles catalyzes nucleosome sliding, making DNA available to other proteins in the cell.
34
What causes nucleosomes to stack so tightly on each other?
* Nucleosome packing forms a dense fibrous structure with a diameter of 30 nm called the **zig-zag model**.
* Stacking may be facilitated by histone tails (esp **H4**).
* Histone **H1**"linker histone" is present in 1:1 ratio with nucleosome cores.
35
How do histone tails help condense chromatin?
* Histone tails are unstructured, suggesting that they are highly flexible.
* Tails can form interactions with adjacent nucleosomes.
36
Histone H1
* Linker histone
* Larger than other histone proteins
* also less well conserved.
* Contacts both DNA and protein
* Changes the path of the DNA as it exits the nucleosome.
37
Zig-Zag Model
* A dense fibrous structure made from nucleosomes
* 30 nm in diameter
38
Epigenetics
* "A form of inheritance that is superimposed on the genetic inheritance based on DNA."
* Affects how genes are read by cells and not the geneic code itself.
39
Examples of Epigenetics
* DNA methylation
* Chromatin structure
* Histone modifications
40
Are histones more than just structural proteins?
* Historically, histones were thought to be only involved in packaging of DNA
* Challenges to this view:
* Mammalian chromatin contains equal mass of histone and non histone protein.
* Other proteins binding to histones suggest function other than structural
* Histones are highly conserved.
* One form of chromatin (heterochromatin) silences the genes it packages without regard to sequence and is direclty inherited by daughter cells.
41
Heterochromatin
* Characteristics?
* Where are they located?
* dark, dense and transcriptionally silent
* very condensed chromatin
* stains darkly
* late replicating and genetically inactive
* highly concentrated at centromeres and telomeres
* contains very few genes; those that are present are resistant to gene expression
* silances genes positioned next to it
42
Euchromatin
* less condensed, light and transciptionally active.
43
Position effect
* activity of a gene depends on position on chromosome.
44
Position effect variegation
* breakage events that bring heterochromatin near active genes tends to silance them.
* Zone of inactivation speads a different distance in diffferent cells.
45
Histone modification
* Amino acid side chains of histones are subject to a variety of covalent modifications
* occurs on the core of the histone as well as the tail.
* **Acetylation** of lysines (loosens chromatin structure)
* added by histone acetyl transferases (HATs)
* removed by histone deacetylase complexes (HDACs)
* Mono, di and tri-**methylation** of lysines
* added by methyl transferase
* removed by histone demethlyases
* **Phosphorylation** of serines
* Recruitment of these enzymes depends on gene regulatory proteins
* All are reversible but can persist long after regulatory proteins have disappeared
* Important consequences for the types of proteins the modified DNA attracts: this determines how/when/if gene expression takes place.
46
Variant histone proteins
* most are synthesized when?
* Inherited where and what do they require?
* Variants exist for each core histones expect for H4
* present in smaller amounts than core histones
* less well-conserved
* most are synthesized during interphase and inserted into already-formed chromatin. Requires histone exchange process catalyzed by chromatin remodeling complex.
47
Major histones are . . .
* synthesized during S-phase and assemmbled into nucleosomes on daughter DNA helices just behind replication fork.
48
What contributes to the diversity of histones
* thousands of combinations of **modifications** (methylation, acetylation, etc.) may exists; further diversity is created by **variant histones**.
49
Histone Code
* Code has specific meaning for cell, determining how/when DNA is packaged in nucleosome.
* Read by the **code reader complex**; involves joint recognition of histone tail and covalent modifications.
* Code can change as the cells need change.
50
Example of histone modification
* modification on the **histone H3 N-terminal tail**.
* a **small number of meanings are known**
* reading histone codes involves **joint recognition** of mark at other sites on the nucleosome along with tail recognition.
51
How can modified chromatin spread?
* The reader protein recognizes the mark and binds tightly to the newly modified nucleosome. It activates and attaches a writer enzyme and positions it near an adjacent nucleosome.
* Hand-over-hand mechanism along the chromosome.
* \*chain reaction can ensue.
* Code reader-writer enzymes spread the mark over chromosome.
52
How does the reader-writer complex remodel chromatin?
* Many reader-writer complexes contain an ATP-dependent chromatin remodeling protein.
* the reader, writer and remodeling proteins can all work together to condense or decondense long stretches of chromatin as the reader moves along the nuceosome-packaged DNA.
53
How do you contain remodeling to one area of the chromosome?
* Barrier sequences halt the spread of chromatin modifications.
* Several mechanisms
* Physical barrers
* Enzymatic barriers
* A combination of several of them may function at any one site.
54
HS4 region
* What does it do?
* What does it consist of?
* often added to both ends of a gene that is to be inserted into a mammalian genome, in order to protect that gene from the silancing caused by speading heterochromatin.
* In cells that are destined to give rise to red blood cells. HS4 separates the ß globin locus from region of silance
* **\*\* protects ß globin locus from silencing**
* **\*\* Contains a cluster of binding sites for histone acetlyase.**
55
Centromeric Chromatin
* Each centromere is embedded in a stretch of special centromeric chromatin.
* contains a centromere-specific H3 histone also known as CENP-A and other proteins that pack the nucleosomes into dense arrangements to form the kinetochore.
* Centromere sequences in humans consist of short repetitive DNA sequences called alpha satellite DNA .
* also found at non-centromeric positions
56
Kinetochore
* a structure required for attachment of the mitotic spindle
57
What are Neocentromere? How are they formed? What do they lack?
* New centromeres (neocentromeres) can form spontaneously on fragmented chromosomes.
* Some of which lack alpha satelite DNA.
58
Inheritance of chromatin structures
* *de novo* centromere formation requires a "seeding" event on alpha satellite DNA.
* H3-H4 tetramers are directly inhertited by the daughter strands at the replication fork.
59
Lampbrush Chromosomes
* Where are they from?
* What are they?
* from amphibian oocytes
* largest chromosomes known
* can be visualized by light microscopy
* series of large chromatin loops emanating from a linear chromosome axis
60
Chromatin organization in the nucleus
* Each chromosome occupies its own area in the nucleus
* Heterochromatin (red) preferentially associates with the nucleo lamina (notecard)
* Gene-rich regions (green) dispersed throughout.
61
How does chromatin structure change during gene expression?
* Decondensation of chromatin during gene transcription:
* "chromosome puffs"
* Actively transcribed genes extend outof it's chromosome territory, like an extended loop
* "chromosome loop"
62
How are different activities localized in the nucleus?
* Interior of nucleus is very heterogeneous
* Different "neighborhoods" have effects on gene expression
* Distinct biochemical environments have high local concentrations of enzymes and molecules for specific processes
* DNA repair "foci"
* RNA synthesis
63
Mitotic chromosomes
* How condensed are they?
* What level in chromosome packing?
* What does it consist of?
* What holds them together?
* Highly condensed
* final level in chromosome packaging
* Two daughter DNA molecules replicated in interphase are separately folded to produce two **sister chromatids**
* Chromatids are held together at their centromeres.
64
whats the purpose of condensation during mitosis
* Disentanglement of sister chromatids to allow separation for cell division
* Protection of fragile DNA molecules as separation occurs
65
Condensins
How do they use their energy?
* Compaction of chromatin aided by condensins
* Use ATP hydrolysis to coil the DNA molecules into chromatids
* Major structural component of the core of every metaphase chromsome.
* Exact mechanism unknown
* cells depleted of condensins have abnormal condensation.
66
Homologous
* Genes that are similiar in both sequence and function due to common ancestry.
* Human homologues exist in yeast, worms, fruit flies and bacteria.
67
What is a major clue for determining gene and protein function?
* Recognition of sequence similarity
68
Which is more tightly conserved, gene seqeunces or genome structure?
* Gene sequences
* size of genome, number of genes size of introns, abundance of repetitive seqeunces can be quite different
69
Does the number of genes correlate with phenotypic complexity of an organism? Why?
How does complexity arise?
* The number of genes only rougly correlate with phenotypic complexity of an organism.
* Complexity arises from duplication and expansion of related gene families.
70
How do genomic changes occur?
* Occur as mistakes in DNA replication and repair
* Rare occurrence: 1/1000 nucleotide pairs is randomly changed in the germ line every million years
* Movement of transposable elements also play a role
* Range of changes can occur
* Base pair substitution
* Large scale rearrangements
* Duplications
* Deletions
* Inversions
* Translocations
71
How do you compare genomics?
* Reconstruct genome evolution by comparing genomes of contemporary organisms
72
What are the reasons for sequence conservation?
* Not having much time for mutations to occur since lineages separated
* **purifying selection**
* Elimination of mutations that interfere with important genetic functions.
* e.g. sequence conservation with humans and chickens
73
Why does genome size vary considerable? e.g. puffer fish genome is 0.4 billion base pairs compared to 1 billion in other fish.
* Small size due to small introns
* Lacks repetitive DNA
* Intron position of huntingtin gene conserved compared to human gene.
74
Purpose of multispecies sequence comparision?
* Sequence comparision can provide insight into purpose or function
75
\_\_% of the human genome is conserved, but only \_\_% codes for proteins. Why is it highly conserved?
* 5% of the human genome is conserved, but only 1.5% codes for proteins.
* Must have an important function since it is highly conserved.
* RNA molecules
* Regulatory regions
* Much is unknown
76
Pseudogenes
* a duplicated gene that has become irreversibly inactivated by multiple mutations
77
Explain the process of "duplication and divergence"
* Another fate for gene duplications is for both copies to remain functional, while diverging in their sequence and pattern of expression, thus taking on different roles.
* Globin gene family derives from common ancestral gene.
* This process explains the presence of large families of genes with related functions in biologically complex organisms.
* It also plays a critical role in the evolution of increased biological complexity.
78
Evolution of globin gene family
* Duplication and mutation gave rise to β and α genes
* Translocation moved α to separate chromsome
* Further duplication and mutation resulted in more specialized β molecules
79
Analysis of Human Variation
* Human sequences vary 0.1% from one to another
* Human and chimps differ 1%
* Majority of mutations are neither harmful or beneficial
* Neutral mutations can become fixed in a population
* SNPs
* CNVs
80
SNPs
* Single-nucleotide polymorphisms
* Points in the genome where one group has one nucleotide and another group as another.
* Variation occurs at a high rate (1% or more)
81
CNVs
* copy number varients
* Presence of many duplications and deletions of large blocks of DNA
* Some blocks are common and others are rare; significance of most is unknown.
82
Heterochromatin preferentially associates with the . . .
Heterochromatin (red) preferentially associates with the nucleo lamina
