Chapter 5 - DNA and Chromosomes

THE REGULATION OF CHROMOSOME STRUCTURE

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THE STRUCTURE OF DNA

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THE STRUCTURE OF EUKARYOTIC CHROMOSOMES

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Define the terms "gene" and "genome."

A gene is a segment of DNA that contains the instructions for making a particular protein or RNA. (Little Picture) A genome is the total genetic information carried by a complete set of the chromosomes. (Big Picture)

Explain why a cell might decondense a particular segment of DNA.

Cells decondense segments of DNA in order to do a few tasks. It can transcribe it so the cell can make a protein. It can use it for DNA replication, so the cell can divide. It can use it for DNA repair, whenever there is something needed to be fixed on the DNA strand.

Compare the roles played by centromeres, telomeres, and replication origins.

Centromeres allow for duplicated chromosomes to be separated during the M-phase of mitosis. The microtubules spindles latch on the to centromeres and pull back towards their daughter cells, dividing it into two. Telomeres act as caps at the end of a chromosome. They are made from repeated nucleotide sequences that allows for the ends of chromosomes to be replicated. The cap serves as a barrier so it doesn't look like the end of chromosomes need repair. Replication origins are where DNA replication begins.

Explain how chromatin-remodeling complexes and histone-modifying enzymes regulate the accessibility of DNA.

Chromatin-remodeling complexes move the tail of the histone proteins. It uses ATP hydrolysis to change the position of the DNA, exposing it. Histone-modifying enzymes can add or remove acetyl, phiosphate, or methyl groups to the tails of the histone proteins. Each modification has it's purpose. For example, acetylation of lysines can reduce the affinity of the tails for adjacent nucleosomes, loosening the overall structure. Another example is that some of these modifications can help regulatory proteins dock onto the tails.

Explain how histone proteins are able to bind tightly to DNA.

DNA has an overall negative charge, while histone proteins have an overall positive charge. The difference in charges allow them to bind tightly through electrostatic interactions.

Contrast the functions of the DNA and protein components of chromosomes.

DNA holds the genetic information that encodes for numerous amounts of proteins in our body. Proteins in chromosomes act as regulators and aid in the inhibition and stimulation of transcribing DNA.

Describe how human chromosomes can be distinguished from one another and how such information can be of value.

Each human has 23 pairs of chromosomes. Each of these chromosomes can be stained a different color to show under a fluorescent microscopy. These dyes distinguish between DNA that is rich in A-T nucleotide pairs and those rich in G-C pairs. The resulting patterns has allowed each chromosome to be identified and numbered.

Explain the organization and attachments that keep interphase chromosomes from becoming extensively entangled.

Each interphase chromosome is in its own territory. Some of the interphase chromosomes are attached to the nuclear envelope or to the underlying nuclear lamina.

Contrast euchromatin and heterochromatin in terms of structure, gene activity, and location along an interphase chromosome.

Euchromatin is the less condensed form of the interphase chromatin. Since it's less condense, genes located are expressed more often. It's located in between the telomeres and the centromeres, unless heterochromatin is there. Heterochromatin is more condensed form of interphase chromatin. Gene expression is lessened due to the condensed state. It's right beside the telomeres and centromeres.

Explain how heterochromatin participates in gene silencing and provide an example.

Heterochromatin is so compact that genes have a hard time to be expressed, due to the fact that RNA polymerase can't even get to the transcription initiation site. An example is in the female cells. Females carry two X chromosomes, which one gets inactivated as a Barr Body. It gets inactivated by becoming highly condensed and the inheritance patterns of the next cells in the line will follow with the inactive X chromosome.

Compare the roles played by non-histone proteins and histone proteins (including histone H1) in the packaging of chromatin.

Histone proteins include H2A, H2B, H3, and H4 that makes up the histone octamer that DNA wraps around. Histone protein H1 links histones by pulling adjacent nucleosomes together in a repeating array. Non-histone proteins aid in the folding proteins by clamping them into loops.

Describe a full complement of human chromosomes in a diploid somatic cell, including sex chromosomes.

Humans are diploid organisms, as we have two sex chromosomes. Even though we have 23 pairs (46 total) chromosomes, one pair (2 total) are sex chromosomes. We have a pair of everything because we get a set from our maternal and a set from our paternal side.

Explain how heterochromatin is established and spreads.

Methylation of lysine 9 in the tail of histone H3 forms heterochromatin. After heterochromatin is established, it spreads since the histone tail modification attracts heterochromatin-specific proteins, which adds more modifications to the tails. It continues to spread until it reaches a barrier DNA sequence, DNA that is exposed and not wrapped around a octamer.

Distinguish between a nucleosome and a nucleosome core particle.

Nucleosomes are DNA that is coiled around a core of histone proteins called the histone octamer. The nucleosome core particle is just the histone octamer.

Recall how many molecules of DNA are in each eukaryotic chromosome.

One or Two?

Contrast prokaryotic and eukaryotic chromosomes in terms of structure and specialized sequence elements.

Prokaryotic chromosomes are single, circular DNA molecule. Eukaryotic chromosomes are very long, double stranded DNA molecules packed with proteins. As there are more than one chromosomes in eukaryotes, there are more than one strand of DNA.

Describe the relationship among gene number, genome size, and organismal complexity.

Some correlation exists between the complexity of an organism and the number of genes in its genome. However, the size of our genome is largely skewed because we contain a lot of junk DNA, extra DNA that is currently not seen as useful. Usually, the more complex the organism is, the larger its genome; however, there are exceptions, like how human genomes can be 30 times smaller than some plants.

Explain how the structure of DNA suggests a mechanism by which genetic information can be copied.

The 4-nucleotide sequences of DNA can be transcribed into an RNA molecule, which then can be translated into 20 different amino acids of a protein.

Explain how the structure of DNA carries information for producing proteins.

The A, C, T, or G nucleotide spell out sequences that produce genes.

Describe complementary base-pairing and explain how this arrangement gives rise to the twisting, consistently proportioned, double helical structure of DNA.

The DNA is a double-helix, meaning the bases will pair with the bases on the antiparallel strand. A pairs with T, and G pairs with C. The purine-pyrimidine pair is held together by hydrogen bonds, where A-T will have 2 hydrogen bonds, while G-C will have 3. The twisting, helical structure comes from how the complementary base-pairing requires one strand to run antiparallel from the other. The antiparalle sugar-phosphate strands twist around each other to form a helical structure, which is the most energetically favorable conformation.

Contrast the extents of compression in interphase and mitotic chromosomes.

The DNA is very long without compression. Interphase chromosomes are 20 times less condensed than that of mitotic chromosomes. Mitotic chromosomes need to be more compact in order to fully separate by pulling on the centromeres. This is also why we can see mitotic chromosomes easier than interphase chromosomes.

Explain why much "junk DNA" is thought to serve a biological function.

The junk DNA is highly conserved in its DNA sequence among many different eukaryotic species.

Describe the structure and function of the nucleolus.

The nucleolus is seen to hold genes that encode ribosomal RNAs. Several hundred copies of these genes are distributed in 10 clusters, located neat the tips of 5 different chromosome pairs.

Distinguish between the bonds that link together the subunits in a single strand of DNA and those that hold together the two strands in a DNA double helix, and summarize how these bonds affect the behavior of the DNA molecule.

The nucleotides are linked together via phosphodiester bonds between their 5' and 3' pentose sugars. Since the phosphodiester bond linkages are different on either side, it creates polarity in the DNA. The 3' will have a hole with a hydroxyl group, and the 5' will have a knob of a phosphate group.

Describe the chemical differences that dictate the polarity of a DNA strand.

The two ends of the DNA are chemically different in which the 5' end is a phosphate knob (negatively charged) and the 3' end is a hydroxyl group. However, the overall polarity of a DNA strand is negative as the hydroxyl group is neutral.