Genetics - Chapter 11

Which of the following is a characteristic of DNA sequences at the telomeres? A. One strand consists of guanine and adenine (or thymine) nucleotides B. They consist of repeated sequences C. One strand protrudes beyond the other, creating some ssDNA at the end D. All of the above

D. All of the above

What are some properties of unique-sequence DNA?

- Consists of a sequence that is present only once or a few times in the genome - Includes sequences that encode protein - Much DNA whose function is unknown - 25-50% of protein-encoding genes are unique-sequence

Why is mtDNA good for genetic study?

- High mutation rate - Small size of mtDNA - Abundant in cell - Rapid evolution (due to high mutation rate) - Maternal inheritance - track female lines of descent

What are the characteristics of euchromatin?

- Less condensed - Located on chromosome arms - Has unique type sequences - Frequently undergoes transcription - Crossing over is common - Found in prokaryotes nd eukaryotes

What are the characteristics of heterochromatin?

- More condensed - Located at centromeres, telomeres, and other specific places - Has repeated sequences - Infrequently undergoes transcription - Crossing over is uncommon - Found only in eukaryotes

What are some properties of moderately repetitive DNA?

- Repeated thousands of times - Some are multiple copies for the genes for rRNAs and tRNAs - Function is mostly unknown

What are some properties of highly repetitive DNA?

- Short sequences present in hundreds of thousands of copies repeated in tandem - Clustered in certain chromosomal regions (telomeres and centromeres) - AKA satellite DNA because it separates as satellite fraction in centrifugation because of differing proportions of base pairs - Rarely transcribed - Most has no known fucntion

Describe the mitochondrial genome.

- Single, double-stranded - Highly coiled - Circular DNA molecule(s) - Lacks histones - Smaller than nuclear genome

Describe the chloroplast genome?

- Single, double-stranded - Highly coiled - Lacks histone proteins

What is a centromere? Of what are they made? Why are they necessary?

Constricted region of chromosome that serves as the attachment site for kinetochore and spindle microtubules; made of heterochromatin; necessary for proper movement of chromosomes during mitosis and meiosis

How many copies of the H2B histone would be found in chromatin containing 50 nucleosomes?

100

What histone proteins make up the histone octamer core?

2H2As, 2H2Bs, 2H3s, 2H4s

What is a telomeric sequence?

A sequence found at the ends of a chromosome consisting of many copies of short, simple sequences (usually of A or T followed by several G) repeated one after another

In its organization, chloroplast DNA is most similar to... A. Bacteria B. Archea C. Nuclear DNA of plants D. Nuclear DNA of primitive eukaryotes

A. Bacteria

DNA is wrapped around histone proteins and coiled to form a dense fiber called chromatin. Which of the following statements describes the function of the chromatin conformation of DNA? A. DNA is wrapped around histone proteins to regulate gene expression B. ssDNA can be stored in the nucleus as chromatin C. Chromatin allows DNA to be degraded by histone proteins D. The condensed DNA in chromatin is transported out of the nucelus

A. DNA is wrapped around histone proteins to regulate gene expression

Most of the genes that encode proteins are found in... A. Unique-sequence DNA B. Moderately repetitive DNA C. Highly repetitive DNA D. All of the above

A. Unique-sequence DNA

What affect does acetylation have on chromatin structure?

Acetylation removes the positive charge on the histones, decreasing the interaction of the N termini of histones with the negatively charged phosphate groups of DNA - condensed chromatin becomes more relaxed = greater levels of gene transcription

What is the C-value paradox?

An organism's complexity is not determined by the amount of DNA per cell (it's C-value)

What group of plants have the largest and most complex mtDNA?

Angiosperms (flowering plants)

What is hybridization of DNA?

Annealing of two ssDNA molecules from different organisms - strands do not have to be complementary at all bases. just enough to hold strands together

Histone proteins... A. Interact with DNA during interphase to delay mitosis when conditions are unfavorable B. Associate with DNA and compact DNA within the nucleus C. Organize DNA into separate chromosomes at the beginning of mitosis D. Enable mitochondrial DNA to replicate with nuclear DNA before mitosis

B. Associate with DNA and compact DNA within the nucleus

Which of the following statements about euchromatin and heterochromatin are correct? Select all that apply. A. Heteroochromatin is less condensed that euchromatin B. Euchromatin undergoes condensation and decondensation throughout the cell cycle C. The majority of transcription takes place on euchromatin D. Most genes are present in heterochromatin E. Euchromatin largely consists of repeated sequences

B. Euchromatin undergoes condensation and decondensation throughout the cell cycle C. The majority of transcription takes place on euchromatin

Which of the following are true of endosymbiotic theory? A. Provides insight about why chloroplasts can survive outside of a eukaryotic cell B. Explains the origin of some eukaryotic organelles, such as mitochondria C. Explains the origin of all organelles found within a eukaryotic cell D. States that an ancestral eukaryotic cell engulfed an aerobic protobacteria E. Explains why chloroplasts contain their own genetic information

B. Explains the origin of some eukaryotic organelles, such as mitochondria D. States that an ancestral eukaryotic cell engulfed an aerobic protobacteria E. Explains why chloroplasts contain their own genetic information

Which statement about cellular DNA in incorrect? A. Supercoiling allows cellular DNA to be packed into a small space B. Most cellular DNA is positively supercoiled C. Supercoiling makes the separation of the two strands of DNA easier for replication and transcription D. Supercoiling of cellular DNA is controlled by topoisomerases E. DNA exists in the cell as very long, tightly packed molecules

B. Most cellular DNA is positively supercoiled.

A DNA molecule 300bp long has 20 complete rotations. This DNA molecule is A. Positively supercoiled B. Negatively supercoiled C. Relaxed

B. Negatively supercoiled

Select the examples of genetic material that are uniparentally inherited in sexually reproducing eukaryotes. A. Endoplasmic reticulum DNA B. Plastid DNA C. Nuclear DNA D. Mitochondrial DNA

B. Plastid DNA D. Mitochondrial DNA

Which of the following terms describes the tertiary structural organization of chromosomal DNA that allows the long strand to be packed and fit into the cytoplasm of the cell? A. Base pairing B. Supercoiling C. Telomere D. Centromere E. Double helix

B. Supercoiling

Neutralizing their positive charges would have which effect on the histone proteins? A. They would bind tighter B. They would bind less tightly to the DNA C. They would no longer be attracted to each other D. They would cause supercoiling of the DNA

B. They would bind less tightly to the DNA

What is a nucleoid?

Bacterial DNA confined to a definite region of the cytoplasm (DNA clump)

How does bacterial DNA differ from eukaryotic DNA?

Bacterial DNA is circular and not complexed with histone proteins

What are shelterin?

Bind to telomeres and protect the ends of DNA from being inadvertently repaired as a double-stranded break in the DNA

What does histone H1 do that is important to nucleosome structure?

Binds to DNA where DNA joins and leave the histone octamer and locks DNA into place onto the histone core

In a few organisms, traits encoded by mtDNA can be inherited from either parent. This observation indicated that in these organisms... A. Mitochondria do not exhibit replicative segregation B. Heteroplasmy is present C. Both sperm and egg contribute cytoplasm to the zygote D. There are multiple copies of mtDNA in each cell

C. Both sperm and egg contribute cytoplasm to the zygote

With what genetic discovery are Hermann Muller and Barbara McClintock credited? What organisms did each scientist study?

Chromosome breaks produce unstable ends that tend to stick together and allow the chromosome to become degraded and that telomeres prevent this; Muller studied fruit flies and McClintock studied corn

What is a chromatin?

Complex of DNA and proteins found in the eukaryotic nucleus

What is repetitive DNA?

DNA sequences that exit in multiple copies in a genome

What does DNase do? On what does its ability depend?

Digest DNA; ability depends on chromatin structure - DNA tightly bound to histone proteins is less sensitive to DNase and unbound DNA is more sensitive

In the endosymbiotic theory, chloroplasts arose from the _______ and evolution of ________ by an anaerobic eukaryotic cell.

Endocytosis; cyanobacterium

In the endosymbiotic theory, mitochondrion arose from the _______ and evolution of ________ by an anaerobic eukaryotic cell.

Endocytosis; proteobacterium

What are topoisomerases? How do they work?

Enzymes that add or remove rotations from a helix by temporarily breaking nucleotide strands, rotating the ends around each other, and rejoining the broken ends

What is promiscuous DNA?

Exchange of genetic material between nuclear, mitochondrial, and chloroplast genomes

What is a gene family?

Genes within unique-sequence DNA that are present in several similar, but not identical, copies

What types of cells have telomerases?

Germ-cells (gametes), stem cells (embryonic stem cells), cancer cells, white blood cells

What is a polytene chromosome? How does one arise?

Giant chromosome in the salivary glands of Drosophila melanogaster - each polytene consists of a number of DNA molecules laying side by side; arise when repeated rounds of DNA replication occur without cell division

What are the heavy and light strands of mtDNA and how are they organized?

Heavy strand has more guanine nucleotides and the light strand has more cytosine nucleotides; heavy strand is the outer one and light strand is the inner strand

What is facultative heterochromatin?

Heterochromatin a certain developmental stages (Ex: one entire X chromosome in female mammal when X becomes inactivated)

What do studies in telomere length show about the affect of childhood adversity?

High stress situations and abuse or chronic illness result in shorter telomores

What makes histones positively charged? Why is it important that histones are positively charged?

Histones have high percentages of arginine and lysine (positively charged amino acids); the positive charge attracts negative phosphates - holds DNA incontact with histones

What are variant histones? How do they alter chromatin structure and influence its function?

Histones with somewhat different amino acid sequences; can make DNA more or less condensed and thus less or more transcriptionally reactive

How are the 30nm fibers organized?

In a series of loops anchored at the base by proteins (300nm in length, 250nm wide)

Why must DNA be so tightly packed?

In order to fit in the nucleus of the cell

What happens to a chromosome that loses its centromere?

It will not segregate into the nucleus in mitosis and is usually lost

What would happen to a chromosome at each replication that does not have telomeres?

It would shorten progressively with each cell division

What is a chromosome puff?

Localized swellings of chromosome where chromatin are relaxed and transcription is actively taking place

What are some pieces of evidence that support the endosymbiotic theory?

Major: - Sequences in mtDNA and cpDNA are most closely related to sequences in the genes o bacterial than they are to those in eukaryotic nucleus - Mitochondria and chloroplast ribosomes are similar in size and structure to bacterial ribosomes - Many modern single-celled eukaryotes (protists) are host to endosymbotic bacteria Minor: - Mitochondria and chloroplasts are similar in size to present-day bacteria and posses their own DNA - DNA of mitochondria and chloroplasts share many characteristics with bacterial DNA - Antibiotics that inhibit protein synthesis in bacteria also inhibit protein synthesis in mitochondria and chloroplasts

What affect does methylation have on chromatin structure?

Methylation weakens chemical attractions between histone tails and DNA - condensed chromatin becomes more relaxed = greater levels of transcription

Is most DNA positively or negatively supercoiled? Why?

Negatively; in negatively supercoiled DNA strand separation is much easier during replication and transcription, so separation is more rapid and requires less energy and it packs into a smaller space than positively supercoiled DNA

What is homoplasmy?

Occurrance of one variety of DNA within the cytoplasm of a single cell (receive ONLY mutant or ONLY normal DNA sequences

What is heteroplasmy?

Occurrence of two distinct varieties of DNA within the cytoplasm of a single cell (receive normal AND mutant DNA sequence)

What is positive supercoiling?

Overrotation of a DNA molecule (rotated to the right)

What is constitutive heterochromatin?

Permanent heterochromatin - telomeres and centromeres

What affect does phosphorylation have on chromatin structure?

Phosphorylation promotes interactions between other histone modifications and provides a platform for effector proteins - condensed chromatin becomes more condensed = lower levels of transcription

What is renaturation?

Process by which two complementary ssDNA molecules pair (reannealing)

What is denaturation?

Process that separates the strands of dsDNA when DNA is heated (melting)

What are telomeres?

Protective structures found at ends of each chromosome (don't contain genes) - prevent chromosome degradation at ends

What are chromatin-remodeling proteins?

Proteins that bind to a DNA sequence and disrupt chromatin structure, causing DNA to become more accessible to RNA polymerases and other proteins

What is replicative segregation?

Random segregation of organelles into progeny cells in cell division - if two or more versions of an organelle are present in the parent cell, chance determines the proportion of each type that will segregate into each progeny cell

What is the d-loop in mtDNA?

Region that contains an origin of replication and promoters - transcription initiated here

What is linker DNA?

Separate nucleosomes at regular intervals

What are plasmids?

Small, circular DNA molecule found in bacteria cells that is capable of replicating independently from the bacterial chromosome

What are histones?

Small, positively charged proteins found in eukaryotes

What is formed when the G-rich strand folds over and pairs with a short stretch of DNA?

T-loop

What are tandem and interspersed repeats? Under what type of repetitive DNA do they fall?

Tandem repeats: occur one after another and are clustered at particular locations on a chromosome Interspersed repeats: occur scatter throughout the genome - consists of short and long interspersed elements (SINEs and LINEs) Both are moderately repetitive DNA

What is supercoiling?

Tertiary structure that forms when a DNA molecules is subject to strain by being overwound or underwound

What is the C-value?

The amount of DNA per cell

What is a nucleosome?

The basic repeating unit of chromatin, consisting of histone core with DNA wrapped around it

What happens when a chromosome's ends get too short?

The chromosome is so reduced that the cell stops dividing, becomes inactive, and dies

How is hybridization a useful tool in evolutionary research?

The extend to which two ssDNA hybridize can serve as a measure of similarity of nucleic acid sequences and to assess evolutionary relationships

What is the G-rich strand?

The guanine-rich 3' end of DNA that protrudes after DNA replication

What is the relaxed state of a DNA molecule?

The lowest-energy state - has the normal number of base pairs per helical turn (10bp) - changing the relaxed state by adding or removing coils requires energy

What did Boris Ephrussi discover while researching yeast colonies?

The petite mutation is a result of large deletions in mtDNA or the absense of mtDNA entirely, so the cells cannot produce the same amount of ATP

What is the endosymbiotic theory?

Theory stating that come membrane-bound organelles (mitochondria and chloroplasts) originated as free-living eubacterial cells that entered into a symbiotic relation with a eukaryotic host cell and evolved into he present-day organelles

Do topoisomerases induce or relieve supercoiling?

They can do both, but not all topoisomerases do

How do free ends of a DNA molecule behave when positive or negative supercoiling occurs?

They turn as extra rotations are added or removed and spontaneously revert back to the molecule's relaxed state

Of what does the "30nm fiber" consist?

Two interwoven stcks of ucleosomes criss-cossing back and forth in the interior of the fiber (its the condensed form of chromatin)

What is a pronuclei?

Two nuclei in a zygote

What is negative supercoiling?

Underrotation of a DNA molecule (rotated to the left)

When does supercoiling occur?

When over- or under-rotating cannot be compensated by turning ends of the double-helix or when the DNA is circular and there are no free ends

Is the tertiary structure of DNA static or dynamic? Why?

dynamic; the tertiary structure changes depending on the cell cycle

In eukaryotes, the inheritance of which type of DNA is uniparental?

mtDNA and cpDNA