Lecture 2 - Genes, Chromosomes, and Genomes Flashcards
When are chromosomes in the pair linked condensed sister chromatid form?
After replication at metaphase during mitosis
What are the 6 eras of DNA discoveries?
- DNA structure
- Nucleosomes
- Epigenome
- Genome topography
- Human genome project
- ENCODE project
What was the goal of the ENCODE project? What did it accomplish?
Identify all regions of transcription, transcription factor association, chromatin structure, and histone modification in the human genome => 80% of it now has at least 1 biochemical function associated with it
What is the classic definition of a gene?
Portion of chromosome that determines a phenotype
What is the definition of a gene for our purposes?
DNA that encodes the primary sequence of some final gene product + the DNA that regulates the expression of that product (transcription initiation region, exons, transcription termination signals)
Central dogma of molecular bio?
DNA is transcribed into
RNA, which is translated into protein
What is a pseudogene?
Gene that has a mutation and whose expression has been turned off
How many base pairs in our genome?
3 billion
How many genes in human genome? How does this number change overtime?
About 25,000
Decreases with time
Describe mtDNA.
Circular double stranded DNA
How many chromosomes in every normal human somatic cell?
46 chromosomes
Why do we inherit mtDNA from our mother?
Because mitochondrial endonuclease G mediates breakdown of paternal DNA upon fertilization
What does delayed removal of paternal mitochondria cause?
Increased embryonic lethality, demonstrating that PME (Paternal Mitochondrial Elimination) is important for normal animal development
What are exons?
DNA coding segments
What is a hypothesis that explains why eukaryotes conserved introns?
Functional domain hypothesis: if you look at any protein and separate out the functional domains (binding site, allosteric sites) they are segregated on individual exons and can be mixed and matched to create a new protein, therefore the introns are there to increase diversity
What are the 4 types of transposons and what % of our DNA do they comprise?
- Long interspersed elements (LINEs) - 21%
- Short interspersed elements (SINEs) - 13%
- Retroviruslike- 8%
- Transposon remnants that differ greatly in length - less than 3%
What % of our DNA do introns and noncoding segments comprise?
28.5%
What is an example of a retroviral DNA sequence with a specific and important biological function? When did this evolutionary adaptation occur and why?
Activation of salivary amylase in the human parotid gland is due to an LTR (long terminal repeat) enhancer that is part of a retroviral DNA sequence
The gene triplication of the amylase gene and its LTR enhancer to further enhance amylase secretion occurred after hominids split from chimpanzees. It may have provided selective advantage to the hominid lineage when they adopted a diet containing complex carbohydrates
What are the 2 types of miscellaneous DNA sequences?
- Simple-sequence repeats (SSR)
2. Large segmental duplications (SD): segments that appear more than once in different locations
What is an example of a retrovirus that has an important function in embryology? Explain when it’s expressed and what its function could be.
HERVK (human endogenous retrovirus type K) which is transcribed during normal human embryogenesis at the 8-cell stage and continuing through epiblast development preimplantation
Possible functions:
- Protect from other viruses by occupying receptors
- Express proteins to help implantation
- Act as chaperones inside cells
What class of proteins is most rapidly adapting to our environment?
VIPs = viral interacting protein
What class of proteins is most rapidly adapting to our environment?
VIPs = viral interacting protein
What happens to a DNA sequence if there is no evolutionary pressure to maintain the sequence?
It is mutated
What is the mean gene size?
27,000 base pairs
Size of largest gene?
2.4 x 10^6 base pairs
Mean exon size?
145 base pairs
Number of pseudogenes?
20,000
What is the JCV1 3.0 cell?
“Minimal” cell with the lowest number of genes possible (473) to survive
What is the human genome project write?
10 year extension of the Human Genome Project, to synthesize the human genome
What can shorten telomeres?
- Age
- Smoking
- Lack of exercise
- Overweight
What is the purpose of telomeres?
Repeating DNA sequences at the end of chromosomes to block presence of a blunt end of DNA that would be recognized as needing repair
Does the DNA supercoil only exist in chromosomes?
NOPE
What is topology?
The study of the properties of an object that do not change under continuous deformations
What does supercoiling affect? What is important to note?
Affects transcription and translation and is also affected by it (exacerbates the supercoil)
What can DNA supercoiling be used for? How come?
Supercoiling is an intrinsic property of DNA and can be used as a source of stored energy/strain as a means of doing work
What does supercoiling result from?
Results when DNA is subject to some form of structural strain (usually underwinding)
Other than through supercoiling, how else can underwinding be accommodated for by DNA?
Strand separation
How does a cell underwind its DNA? What does the resulting strain represent?
With enzymes: topoisomerases
The resulting strain represent a form of stored energy to either unwind or supercoil
What is the topological linking number used for?
To define the strain on individual DNA sequences based on the sign of the linking number difference:
+: adding turns = overwinding => positive supercoil = right-handed
-: removing turns = underwinding => negative supercoil = left-handed
Does a topological bond exist if there is a break in the DNA? What is the Lk?
NOPE
Lk is undefined
Does a topological bond exist if there is a break in the DNA?
NOPE
What are the 2 types of topoisomerases and each of their function?
- Type I: break 1 of the 2 DNA strands to change Lk in increments of 1
- Type II: break 2 of the 2 DNA strands to change Lk in increments of 2
How can one visualize topoisomers?
Because supercoiled DNA molecules are more compact than relaxed molecules, they migrate more rapidly during gel electrophoresis:
- Highly supercoiled DNA migrates in a single band, even though different topoisomers are probably present.
- Supercoiled DNA treated with topoisomerases: as the superhelical density of the DNA is reduced to the point where it corresponds to the range in which the gel can resolve individual topoisomers, distinct bands appear (the linking number decreases by 1 from one band down to the next)
On a gel electrophoresis how do I know which DNA is more relaxed and which is more coiled?
Relaxed is more towards the top, more coiled is towards the bottom
How are nucleosomes formed?
Binding of a histone core to form a nucleosome induces one negative supercoil (left-handed supercoil). In the absence of any strand breaks, a positive supercoil must form elsewhere in the DNA. Relaxation of this positive supercoil by a topoisomerase leaves one net negative supercoil (ΔLk = –1).
How many base pairs in a nucleosome?
~200
Describe the structure of Type II topoisomerase.
Multisubunit enzyme with gated cavities above and below the bound DNA are called the N-gate and the C-gate.
Describe the 5 steps of the catalysis conducted by Type II topoisomerase. What provides the energy of this reaction?
- Type II topoisomerase binds one DNA molecule
- A second segment of the same DNA molecule is bound at the N-gate, and is trapped.
- Both strands of the first DNA are cleaved
- The second DNA segment is passed through the break.
- The broken DNA is religated, and the second DNA segment is released through the C-gate.
2 ATPs are bound and hydrolyzed during this cycle
Describe the 7 levels of compaction of DNA in a eukaryotic chromosome.
- DNA
- Beads on a string chromatin
- 30 nm fiber
- One loop
- One rosette (6 loops)
- One coil (30 rosettes)
- Two chromatids (10 coils each)
What are 2 properties of regulatory regions of DNA?
- Extremely variable
2. Binding sites for DNA binding proteins
3 main components of DNA and their %?
- 30% genes
- 45% transposons
- 25% miscellaneous
What is the main difference between prokaryotic and eukaryotic chromosomes?
Eukaryotes have multiple origins of replication which facilitates more efficient replication
What is the centromere?
The center region of the chromosome where spindle attachment and sister chromatid separation occurs
What fold compaction do nucleosomes provide?
7 fold
