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BIO130H1 Lecture 5: The human genome, histones and packaging of DNA

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Biology
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BIO130H1
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Melody Neumann, Kenneth Yip

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BIO130H1 Lecture Notes - Lecture 4: Alpha Helix, Coiled Coil, Opioid Peptide

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BIO130H1 Lecture 5: The human genome, histones and packaging of DNA

6

BIO130H1 Lecture 6: Packaging of Nucleosomes & DNA Replication

BIO130H, Lecture 5: The human genome, histones and packaging of DNA
The human genome
● Only 1.5 per cent of our genes encode proteins
● Intronic sequences make up a big chunk of genes
● We also have promoter sequences, different types of regulatory sequences and some
other kinds of genes
● The rest of the non-repetitive DNA sequences are unknown in terms of what they are
and what they do
● We have repeated sequences which sometimes called “junk” DNA. This includes things
like minisatellites and microsatellites. They are highly repetitive.
● Then, there are transposons (DNA from viruses that went into the human genome).
Transposons came into our genome over evolutionary time. There are retroviral-like
elements. There are retrotransposons and a whole bunch of these viral type elements
that have evolved to become part of the human genome. There are different ways of
classifying this DNA. Some researchers think it provides some structure for the
chromosome and other people think it is the raw material for natural selection as it is
useful.
Packaging in the DNA cell
● Eukaryotes have a lot of DNA and they need to be packed tightly sometimes
● In a non packaged state, small prokaryotic genomes would occupy a large volume of the
cell volume. This is an even bigger problem in the eukaryotic cell. The eukaryotic cell is
much larger.
● The prokaryotic nucleoid is formed via twisting and folding the DNA about 1000 times
with proteins. The DNA is condensed.
● Important components o this packaging are:
○ Positively charged polyamines
○ Numerous nucleoid-associated proteins (NAPs) such as H-NS (histone-like
nucleo-structuring protein), the histone-like protein, IHF, FIS and HU
○ Topoisomerase which catalyzes the supercoiling of DNA. To imagine
supercoiling, think of having a rubber band and twisting it continuously, shrinking
its size down. There are different types of supercoiling but we do not need to
know the details of them.
Organization of the prokaryotic nucleoid
● Exponential phase of growth included a lot of growing
● Even when transcription occurs, we have the compaction of DNA
● Purplish black lines are the supercoiled helix
Getting Eukaryotic genome packed into cells: a big problem
● 6 billion base pairs per cell
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Document Summary

Bio130h, lecture 5: the human genome, histones and packaging of dna. Only 1. 5 per cent of our genes encode proteins. Intronic sequences make up a big chunk of genes. We also have promoter sequences, different types of regulatory sequences and some other kinds of genes. The rest of the non-repetitive dna sequences are unknown in terms of what they are and what they do. We have repeated sequences which sometimes called junk dna. Then, there are transposons (dna from viruses that went into the human genome). Transposons came into our genome over evolutionary time. There are retrotransposons and a whole bunch of these viral type elements that have evolved to become part of the human genome. There are different ways of classifying this dna. Some researchers think it provides some structure for the chromosome and other people think it is the raw material for natural selection as it is useful.

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Related Questions

Needs help asap

_______________ are transposable elements that move within the genome by being copied and reinserted as DNA sequences, avoiding the need for reverse transcription"

A.

Retrotransposons
B

Retrovirus-like elements
C

DNA transposons
D

Satellite DNAs
E

Long interspersed elements (LINEs)

F.Short interspersed elements (SINEs)

The large differences observed in genomic size among eukaryotes correspond primarily to differences in

A

the amount of protein-coding genes
B

the amount of noncoding DNA
C

the biological complexity of the organisms at hand
D

the length of the telomeres

E the size of the centromere

The study of lncRNAs has revealed

A

that protein-coding genes are distributed homogeneously throughout the genome
B

that splicing regulates more genes than initially expected
C

that miRNAs are mostly limited to intronic sequences
D

that only a relatively small fraction of the human genome is ever transcribed
E

the existence of genomic regions coding exclusively for rRNA and tRNA
F

that extensive regions of our genome are in fact actively transcribed even though they do not contain protein-coding genes

2.)

a.) Are viruses that infect Archaea different from other bacterial viruses?

Yes, they do not have protein coats because of the extreme conditions where they live.
No, they consist of nucleic acid and protein just like other bacterial viruses.
Yes, the structure of archaeal viruses is always completely different from other bacterial viruses.

Yes, they have only DNA genomes.

b.) Of the following examples, which is not a common part of many viral life cycles?

The pox virus genome is replicated by DNA polymerase.
Adenoviruses attach to the cell and the nucleocapsid is taken up by the cell.
Pox viruses replicate in the cytoplasm of the cell.

Once an adenovirus virion is inside a cell, host RNA polymerases transcribe early genes

c.) Some viruses are associated with cancer. There are a variety of ways in which viruses may affect a cell in a way that may lead to cancer. Based on your knowledge of the life cycles of viruses and of molecular genetics, what is one way that this might happen?

Viral genetic material inserts into a host genome close to the termination sequence, far downstream of the promoter, and causes a silent mutation.
Viral genetic material inserts into a host genome in a repetitive noncoding region.
Viral genetic material inserts into a host genome, placing a promoter in a new location and turning on a gene that had previously been turned off.
Viral genetic material inserts into a host genome and causes a mutation in a promoter, turning off a gene that had previously been turned on.

d.) Which statement describes the difference between the normal neuron protein PrPC and the pathogenic version PrPSc?

PrPC is just a protein and the PrPSc is a protein with nucleic acid inside.
The PrPC protein contains more beta sheets while the PrPSc protein contains more alpha helices.
The three-dimensional conformation is identical, but the amino acid sequence is different.
The amino acid sequence is identical, but the three-dimensional conformation is different.

For years we have been able to analyze the fossils of extincthumans like those of Neanderthals. Their bones gave us clues to howthey looked, how they lived, and how they might be related to us.In the last few years, we have been able to get a better view intothese extinct species and their relationship to our species. Thanksto next generation genomic sequencing technologies, we have beenable to obtain genetic data on Neanderthals, Denisovans and othersthat have allowed us to make direct comparisons between our speciesand theirs. In addition, we have been able to observe the presenceof DNA from these extinct species within our own genomes which tellus that we had kids with these now extinct humans.

If we take Neanderthal DNA as an example, we find that we share99.5 percent of our DNA with them. Which means that we andNeanderthals were separated from each other for more than 500,000years. This also means that we were genetically similar enough tobe able to have offspring with each other. We see evidence of thisgenetic introgression between us and Neanderthals when we look atour DNA. Interestingly, if we obtain one thousand DNA samples fromGrossmont College students, we estimate that we would be able toextract at least 20% of the Neanderthal genome from them. Thismeans that 20% of our collective nucleotide sequences are sharedwith Neanderthals but this doesn’t mean that 20% of our genes areNeanderthal specific genes. Of the twenty-one thousand genes thatNeanderthals had, only a few dozen of their genes survive withinour genome. The same holds true for Denisovans. What is moreinteresting is that older versions of ourselves have a tendency tohave higher levels of DNA from extinct humans compared toourselves. In other words, over the course of thousands of years wehave been slowly weeding out the DNA of the other humans from ourgenome in favor of our genes.

One basic question that we might like to ask is why have we beenlosing Neanderthal and Denisovan genes over time? Also, why do westill have a significant amount of DNA segments that don’t seem tobe going anywhere? The answer to this has to do with selection.

The answer to the first part of the question has to do with thefact that we were not fully genetically compatible with the otherhuman species to begin with. Basically, to have had Neanderthal orDenisovan genes in the past meant that an individual's level offitness was reduced. To get rid of their genes in favor of our ownwould mean that the relative fitness of individuals would increaseovertime.

The answer to the second question has to do with the fact thatDNA segments from Neanderthals and Denisovans that did not code forproteins remained because there was little selective pressureagainst them. As far as genes are concerned, the only Neanderthaland Denisovan genes that remain only exist because they had aselective advantage or at least have been neutral to ourspecies.

DNA segments that that were neutral or that had a selectiveadvantage, whether genes or not, simply remained because they wereadvantages or there was little selective pressure against them.

Your task for this week is to look for information about oneNeanderthal or Denisovan gene that survive within our species andto tell me what function that gene has and how that gene mayincrease the fitness of modern human populations.

  • In your post, discussONE Neanderthal orDenisovan gene that is currently found within our species.
    • Tell us about the gene and its function. Explain what it doesfor us. (Make sure you give a citation.)
    • Explain in your own words any possible advantages that yourNeanderthal or Denisovan gene might have. Make sure you give ininformed opinion that is grounded in your research.