Genetics CH 11

Which of the following is not a form of chemical modification to DNA that we discussed in class? A. Acetylation B. Methylation C. Phosphorylation D. Pronation

D. Pronation

Most of the centromere and telomere structures consist of

heterochromatin

the inactive form of chromatin is

heterochromatin

The more darkly staining form of a chromatin is

heterochromatin b/c density of stain correlates w/ density of chromatin

A core composed of ____ proteins interacts with DNA through hydrogen bonding and ionic bonds.

histone

Origin of replication

initiates DNA replication

Features of both euchromatin and heterochromatin

is a state of DNA organization

If DNA is twisted in the __________ direction it becomes underwound

left-handed

The largest and most complex mitochondrial genomes come from

flowering plants

Prokaryotic DNA structure

-DNA is circular -condensed only by DNA supercoiling -occurs as a single looped structure -does not have a telomere region

Eukaryotic DNA structure

-DNA is linear -condensed around histone proteins -occurs as multiple chromosomes -has repeating telomere region

Features of euchromatin

-Is loosely packed -Has a high level of transcriptionIs -Found in prokaryotes -Is the major state of most genes

Features of heterochromatin

-Is tightly packed -Has a low level of transcription -Is the major state of the inactive X chromosome

Select all statements that accurately describe the structures or functions of mitochondria. -Mitochondria have a permeable inner membrane and an impermeable outer membrane. -Mitochondria regulate apoptosis. -Mitochondria are the sites of aerobic metabolism. -Mitochondrial DNA is packaged with histones. -Mitochondria are included in the endomembrane system. -The configuration of mitochondria does not change.

-Mitochondria regulate apoptosis. -Mitochondria are the sites of aerobic metabolism.

In 1979, bones found outside Ekaterinburg, Russia, were shown to be those of Tsar Nicholas and his family, who were executed in 1918 by a Bolshevik firing squad in the Russian Revolution. To prove that the skeletons were those of the royal family, mtDNA was extracted from the bone samples, amplified by PCR, and compared with mtDNA from living relatives of the tsar's family. Select options indicating why DNA from the mitochondria analyzed instead of nuclear DNA. -Mitcohondrial DNA is circular and is more stable over time. -Mitochondrial genomes are present in multiple copies in the cells. -Mitochondrial DNA does not undergo recombination. -Mitochondrial DNA is inherited from both parents.

-Mitochondrial genomes are present in multiple copies in the cells. -Mitochondrial DNA does not undergo recombination.

Could this disorder be caused by an autosomal dominant allele? Select the answer or answers that correctly explain why or why not. -Yes, the disorder can be caused by an autosomal dominant allele because it seems to affect both male and female offspring equally. -No, males with the disorder do not pass the condition to their offspring, and therefore, the pattern is not consistent with autosomal inheritance. -No, the pattern of females with the disorder passing the trait to their offspring at a relatively high frequency does not support autosomal inheritance. -No, the disorder cannot be caused by an autosomal dominant allele because not enough people are affected by the condition in six generations. -Yes, the pattern of parents with the disorder passing the trait to their offspring at a relatively high frequency supports autosomal inheritance.

-No, males with the disorder do not pass the condition to their offspring, and therefore, the pattern is not consistent with autosomal inheritance. -No, the pattern of females with the disorder passing the trait to their offspring at a relatively high frequency does not support autosomal inheritance.

Eukaryotic DNA consists of

-Unique sequences of DNA -Highly repetitive DNA sequences -Moderatley repetitive DNA sequences

Select the examples of genetic material that are uniparentally inherited in sexually reproducing eukaryotes. -nuclear DNA -chloroplast DNA -mitochondrial DNA -endoplasmic reticulum DNA

-chloroplast DNA -mitochondrial DNA

Identify at least 1 key feature of the COVID-19 virus

Contains positive ssRNA, which means the inserted RNA is ready to be translated

Which of the statements are true of endosymbiotic theory? -states that an ancestral eukaryotic cell engulfed a photosynthetic protobacteria -provides insight about why mitochondria can survive outside of a eukaryotic cell -explains the origin of all organelles found within a eukaryotic cell -explains the origin of some eukaryotic organelles, such as chloroplasts -explains why mitochondria contain a double membrane

-states that an ancestral eukaryotic cell engulfed a photosynthetic protobacteria -explains the origin of some eukaryotic organelles, such as chloroplasts -explains why mitochondria contain a double membrane

What are two reasons for supercoiling?

1. Compaction 2. Negative supercoiling creates tension that is released by the two strands separating transcription and replication

What are two reasons the formation of a radial loop domain is important?

1. It plays a role in gene regulation 2. It serves to organize the chromosomes within the nucleus

What are the two ways to compact a bacterial chromosome?

1. Loop domains 2. supercoiling

Nalidixic acid is an antibiotic that inhibits DNA synthesis by preventing the action of DNA gyrase. DNA gyrase introduces negative supercoils into DNA. Which statements explain why inhibiting negative supercoiling in bacteria inhibits overall bacterial growth? 1. Negative supercoiling aids in DNA synthesis by making separation of the DNA strands possible. 2. Negative supercoiling results in the complete unwinding of DNA, allowing synthesis to occur. 3. Negative supercoiling increases the size of the chromosome, making it easier to replicate. 4. Negative supercoiling aids in chromosome compaction, which ensures the transmission of chromosomes to daughter cells. 5. Negative supercoiling decreases chromosome compaction, which increases DNA synthesis in bacteria.

1. Negative supercoiling aids in DNA synthesis by making separation of the DNA strands possible. 2. molecule that is completely unwound would not be supercoiled 3. Size of chromosome does not increase b/c of negative supercoiling 4. Negative supercoiling aids in chromosome compaction, which ensures the transmission of chromosomes to daughter cells. 5. ^aids in chromosome compaction, if not properly compacted, bacteria can't transfer chromosomes to daughter cells

Name 2 pieces of evidence that support the endosymbiosis theory

1. Organelles have circular chromosomes (like bacteria) 2. Organelle genes are more similar to bacterial genes than to those found within the nucleus

Label the diagram

1. chromosome 2. chromatin 3. DNA molecule 4. protein

The diagram depicts the origin of chloroplasts and mitochondria in eukaryotic lineages through endosymbiosis. Assign the appropriate descriptions to the events in the diagram.

1. host cell ingested aerobic bacteria 2. host cel; ingested cyanobacteria 3. undigested bacteria evolved into chloroplasts 4. divergence of early eukaryotes occurred 5. undigested bacteria evolved into mitochondria

Label the diagram

1. p arm short arm 2. centromere 3. q arm long arm 4. telomere 5. G1 phase, anaphase 6. G2 phase, metaphase

Which represents the 300 nm fibers?

D

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

100

When nucleosomes join a _____ is formed. Combined with the 7 fold shortening that occurs by the formation of nucleosomes, the total shortening at this point is around _____ fold.

30 nm fiber; 50

intergenic regions

: the nontranscribed DNA between adjacent genes

What happens to a chromosome that loses its centromere?

A chromosome that loses its centromere will not segregate into the nucleus in mitosis and is usually lost

Describe the bacterial chromosome

A circular molecule that is typically a few million nucleotides in length

What is a virus?

A small infectious particle that contains nucleic acid surrounded by a protein capsid

Where are genes located in the chromosome? A. Between the centromere and telomere regions along the entire chromosome B. The entire chromosome C. Between the centromere and telomere in specific regions of the chromosome D. Between the telomeres E. Telomeres and the length of the chromosome but not the centromere

A. Between the centromere and telomere regions along the entire chromosome

Which of the following histone is not found in the octamer? A. H1 B. H2A C. H2B D. H3 E. H4

A. H1

A DNA molecule is 400 base pairs long and has 20 complete rotations. Which correctly describes the DNA? A. Negatively supercoiled B. Positively supercoiled C. No supercoiling D. Cannot be determined

A. Negatively supercoiled 400 bp / 20 complete rotations = 20 base pairs per rotation

Which type of amino acid is most likely to be found in a histone? A. Positively charged B. Negatively charged C. Polar D. Neutral

A. Positively charged

Structural genes and intergenic regions are: A. Unique or nonrepetitive B. Moderately repetitive C. Highly repetitive

A. Unique or nonrepetitive

What is an example of a covalent modification and where is it generally made?

Acetylation, usually made at the histone tails Phosphorylation, usually made at the histone tails Methylation can occur at histone tails or at cytosines CpG islands

Describe the role of H1 in the 30nm fiber

At moderate salt concentrations, H1 is removed, resulting in the classic beads on a string morphology At low salt concenterations, H1 is bound, beads associate together into a more compact morphology

Which represents a nucleosome?

B

Chromosomal replication and segregation requires all of the following DNA sequence types except: A. Centromeres B. Kinetochore C. Telomeres D. Origin of replication

B. Kinetochore

Genes for rRNA, tRNA, and histones as well as origins of replication are: A. Unique or nonrepetitive B. Moderately repetitive C. Highly repetitive

B. Moderately repetitive

How does bacterial DNA differ from eukaryotic DNA?

Bacterial DNA is not complexed with histone proteins and is circular

A 600 base pair DNA molecule is positively supercoiled. How many turns do you expect to see? A. 40 B. 60 C. 80 D. None of the above

C. 80 600 bp / 10 bp per turn = 60 turns if no supercoiling Greater than 60 turns

Satellite DNA are: A. Unique or nonrepetitive B. Moderately repetitive C. Highly repetitive

C. Highly repetitive

The endosymbiosis theory can be used to describe the origins of A. Mitochondria only B. Mitochondria and lysosomes C. Mitochondria and chloroplasts D. Chloroplasts and lysosomes

C. Mitochondria and chloroplasts

Describe the function of the centromere and kinetochore in mitosis and meiosis

Centromeres are required for proper segregation during mitosis and meiosis Kinetochore proteins link the chromosome to the spindle apparatus

How does chromosome compaction differ during metaphase and interphase in eukaryotes?

Chromosomes are more compacted in metaphase than in interphase.

Compare and contrast constitutive heterochromatin and facultative heterochromatin:

Constitutive heterochromatin: regions that are always heterochromatic, permanently inactive with regard to transcription, usually contain highly repetitive sequences Facultative heterochromatin: regions that can interconvert between euchromatin and heterochromatin, Ex. Barr body formation during development in female

Which two molecules of DNA has the lower melting temperature? Why?

DNA 1, because it has a lower percentage of G-C base pairs that stabilize DNA duplexes. C-G have 3 hydrogen bonds, in contrast A-T have 2 hydrogen bonds, requiring less energy (less heat)

In a cell, DNA gyrase has a loss of function mutation. What is the result on the cell? What if this loss of function mutation occurred in DNA topoisomerase 1?

DNA gyrase: add negative supercoils or remove positive supercoils A loss of function: no or less negative supercoiling DNA topoisomerase 1: add positive supercoils A loss of function: no or less positive supercoiling

What are the two enzymes responsible for supercoiling?

DNA gyrase: introduces negative supercoils, or relax positive supercoils Topoisomerase: relaxes negative supercoils

DNA is wrapped around histone proteins and coiled to form a dense fiber called chromatin. Which statement describes the function of the chromatin conformation of DNA? -The condensed DNA in chromatin is transported out of the nucleus. -Chromatin allows DNA to be degraded by histone proteins. -DNA is wrapped around histone proteins to condense and organize DNA. -Single‑stranded DNA can be stored in the nucleus as chromatin.

DNA is wrapped around histone proteins to condense and organize DNA.

If DNA structure is described as "beads-on-a-string," a "sting" is a

DNA molecule

Which statements about euchromatin and heterochromatin are correct? -Heterochromatin is less condensed than euchromatin. -Euchromatin undergoes condensation and decondensation throughout the cell cycle. -Most genes are present in heterochromatin. -Euchromatin largely consists of repeated sequences. -The majority of transcription takes place on euchromatin.

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

Compare and contrast euchromatin and heterochromatin:

Euchromatin: less condensed regions of chromosomes, transcriptionally active, regions where 30 nm fiber forms radial loop domain Heterochromatin: tightly compacted regions of chromosomes, transcriptionally inactive (in general), radial loop domains compacted even further

T/F: : the chromosomal DNA in bacteria is positively supercoiled

False

T/F: Eukaryotic species tend to have less DNA than bacterial species

False

T/F: The C value, which indicates the amount of DNA in a haploid genome, always correlates to the complexity of the organism.

False

T/F: The radial loop domains represents a level of compaction between the 30 nm fiber and the uncompacted DNA helix

False

T/F: There is no crosstalk between the various chemical modifications

False

T/F: eukaryotic chromosomes have a single origin of replication

False

T/F: gene transfer between organelles and the nucleus is entirely bidirectional

False It is mostly unidirectional from organelles to nucleus

T/F: Mitochondria and chloroplasts retained the majority of their genes after being engulfed by the larger eukaryote

False Most of their gene migrated to the nucleus of the larger eukaryotic cell, but they retain some genes as well las their own ribosomes

T/F: Eukaryotic genomes vary widely in size due to the complexity of the organism

False The variety in size is not due to the complexity of the organism

T/F: in eukaryotes, the genome is composed of one set of nuclear chromosomes, mitochondrial DNA, and (if applicable) chloroplast DNA

False Just nuclear DNA

T/F: chromosomes are structures that contain the genetic material and are therefore only made of DNA

False also contain proteins

The eukaryotic protein critical for organizing chromatin structure is histone. Which histone protein is not included in the histone "core" that is often described as the "beads"?

H1

What is the purpose of H1?

It is a linker that binds to linker DNA

What is one difference in the genes between a lower eukaryote and higher eukaryote?

Lower eukaryote: smaller genes with few short introns Higher eukaryotes: longer genes and many introns

What evidence suggests that a gene in the mtDNA is causing this disorder? -Males do not pass on the trait, but females pass it to offspring at a high frequency. -Males are more often affected but do not pass on the trait. The disorder is always present in the offspring of an affected parent. -Males and females are both affected and both likely to pass on the trait. -The disorder exhibits a high degree of penetrance from generation to generation.

Males do not pass on the trait, but females pass it to offspring at a high frequency.

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

Most cellular DNA is positively supercoiled.

What is uniparental inheritance

One parent transmits all genetic information to all offspring.

Describe the endosymbiosis theory

Organelles originated when bacteria were engulfed by a primordial eukaryotic cell. Chloroplasts originated as cyanobacteria and mitochondria as Gram-negative nonsulfur purple bacteria.

T/F: Histone proteins are basic and have positively charged lysine and arginine to bind to the negatively charged phosphates of DNA

True

T/F: Organelle DNA can encode some polypeptides, rRNA, and some tRNA

True

Compare and contrast Eukaryotic and prokaryotic chromosomes

Prokarotic chromosomes: one circular chromosome, one ORI, no histones Eukaryotic chromosomes: many linear chromosomes, many ORI per chromosome, histones

T/F: The degree of chromosome compaction is determined by proteins binding to the DNA

True

T/F: in bacteria, the genome typically consists of a single circular chromosome

True

Why is supercoiling important?

Supercoiling helps in the compaction of chromosomes and creates tension that is released by strand separation to enhance replication and transcription

What does a telomere do? Why is this important?

Telomeres prevent chromosome sticky ends which could lead to translocations and shortening

T/F: mtDNA and cpDNA contain rRNA and tRNA genes of their own for their organelle‑specific functions.

True

Why does the disappearance of the puff at position 3C roughly coincide with lack of the secretion of protein fraction 4? -The disappearance of the puff at region 3C indicates a lack of transcription from the region with the gene for protein fraction 4. -The disappearance of the puff at region 3C indicates decreased protein expression from the entire chromosome. -The disappearance of the puff at region 3C indicates fewer copies and limited expression of the genes encoding protein fraction 4. -The disappearance of the puff at region 3C indicates decreased expression of a repressor of the gene for protein fraction 4.

The disappearance of the puff at region 3C indicates a lack of transcription from the region with the gene for protein fraction 4.

You are trying to treat a patient with a bacterial disease. Your options for drugs are a drug that blocks the function of DNA gyrase or topoisomerases. Which would you choose and why?

The drug that blocks DNA gyrase because negative supercoils are needed for bacteria to survive

In 1979, bones found outside Ekaterinburg, Russia, were shown to be those of Tsar Nicholas and his family, who were executed in 1918 by a Bolshevik firing squad in the Russian Revolution. To prove that the skeletons were those of the royal family, mtDNA was extracted from the bone samples, amplified by PCR, and compared with mtDNA from living relatives of the tsar's family. From which living relatives would mitochondrial DNA provide useful information for verifying that the skeletons were those of the royal family? -The mtDNA from the tsar's living relatives of maternal descent should be analyzed. -The mtDNA from the tsar's living relatives of both paternal and maternal descent should be analyzed. -The mtDNA from the tsar's living relatives of paternal descent should be analyzed.

The mtDNA from the tsar's living relatives of maternal descent should be analyzed.

Describe the nucleosome

The repeating structural unit within eukaryotic chromatin, it is composed of double stranded DNA wrapped around an octamer of histone proteins and therefore resembles beads on a string

Neutralizing their positive charges would have which effect on the histone proteins?

They would bind less tightly to the DNA

T/F: : most bacterial species contain only a single type of chromosome, that may be present in multiple copies

True

T/F: Gene transfer can occur between organelles

True

nuclear lamina

fibers that line the inner nuclear envelope

What is the chromosome puff at position 3C? -a region of DNA replication -a region of active transcription -a region of positive supercoiling -a region of heterochromatin

a region of active transcription relaxed state. puffs are not associated w/ heterochromatin, +/- supercoiling, or DNA replication

Which of the following chemical modifications is associated specifically with increased gene activity? a. acetylation of histones b. methylation of DNA c. demethylation of histones d. phosporylation of DNA

a. acetylation of histones

histone proteins

attach to DNA and form compacted DNA-protein associations

In its organization, chloroplast DNA is most similar to

bacteria

Arrange the features of eukaryotic chromosome packaging in order from the smallest unit to the largest unit. -base pair -chromosome -30nm fiber -nucleosome -genome

base pair, nucleosome, 30nm fiber, chromosome, genome

In a few organisms, traits encoded by mtDNA can be inherited from either parent. This observation suggests that in these organisms,

both sperm and eggs contribute mitochondria to the zygote

internal matrix proteins

connected to nuclear lamina and fills interior of nucleus

When a solution containing double‑stranded DNA is heated, the hydrogen bonds that hold the two strands can be weakened and eventually broken, separating the strands completely. This process is called

denaturation

structural gene sequences

encode proteins

the less condensed form of chromatin is

euchromatin

Which organelle or organelles contain DNA of their own?

mitochondria and chloroplast

One effect of ______ supercoiling in bacterial chromosomes is to promote separation of the two strands of DNA in the double helix

negative

Underwinding results in ______________ supercoiling

negative

When a circular DNA gets underrotated by the action of cellular enzymes, the DNA is said to exhibit

negative supercoiling

A DNA molecule 300 bp long has 20 complete rotations. This DNA molecules is

negatively supercoiled

A distinct clump of prokaryotic DNA observed via electron microscopy is referred to as a

nucleoid

A _______ is a DNA-protein complex

nucleosome

If DNA structure is described as "beads-on-a-string," a "bead" is a

nucleosome

Chromosomes in eukaryotes are located in the _____. This is accomplished by the binding of many _______ (carbohydrates, lipids, proteins). This complex is called a ____.

nucleus; proteins; chromatin

Overwinding results in _____ supercoiling

positive

Assume that the disorder shown in the pedigree is a rare disease that results from a defect in mitochondrial DNA. If individual III‑8 has a daughter, determine the probability that the daughter will inherit the muscle disorder from her affected parent. Answer as a decimal.

probability= 0.0

If DNA is twisted in the _______ direction, it becomes overwound

right-handed

In a circular bacterial chromosome, the structure of DNA is a ______ double helix

right-handed

Which term describes the tertiary structural organization of chromosomal DNA that allows the long strand to be packed and fit into the cytoplasm of the cell?

supercoiling

The function of the centromere in the transmission of genetic information

the attachment point for sister chromatids they must stay joined together by centromere until it is time to be physically pulled into the two further daughter cells

Most of the genes that encode protein are found in

unique sequences DNA