Chapter 12: Chromosomes

Question 1

what are chromosomes?

Answer 1

structures made up of nucleic acids and proteins that store the genetic material within the nucleus

Question 2

what comprises all the genetic material that an organism posseses?

Answer 2

the genome

Question 3

what form are chromosomes found in bacteria?

Answer 3

bacteria contain a singular circular chromosome of double-stranded DNA compacted into a nucleoid, with a single nucleic acid and few if any associated proteins, usually only one chromosome per genome but with multiple copies, typical chromosome is a few million base pairs long

Question 4

what are the regions of the chromosome in bacteria?

Answer 4

protein-encoding genes make up the majority of the bacterial DNA with the non-transcribed DNA segments between genes being called intergenic regions, there must also be one origin of replication present and repetitive sequences may be present along the chromosome

Question 5

how is the chromosome compacted in bacterial cells?

Answer 5

circular chromosomal DNA is compacted into loops (microdomains) that resemble flower petals, the loops are then negatively supercoiled to compact them further

Question 6

what is responsible for the supercoiling of the chromosome within bacterial cells?

Answer 6

DNA gyrase (topoisomerase II) creates negative supercoils using energy from ATP but can also relax positive supercoils
DNA topoisomerase I relaxes negative supercoils and breaks one strand and rotates the DNA
these competing actions govern the overall supercoiling of bacterial DNA

Question 7

what enzyme is targeted to cure bacterial diseases?

Answer 7

gyrases ability to introduce negative supercoils into DNA is crucial for the survival of the bacteria so quinolones and coumarins can be used to inhibit gyrase but not eukaryotic enzymes, killing the bacteria

Question 8

what form are chromosomes found in eukaryotes?

Answer 8

contain one or more sets on chromosomes, each composed of several different linear chromosomes, the total amount of DNA in eukaryotes is greater than that of bacteria and chromosomes are located in the nucleus of eukaryotes

Question 9

what three types of DNA sequences are required from replication and segregation in the eukaryotic chromosomes?

Answer 9

origins of replication, centromeres, and telomeres

Question 10

what do centromeres do?

Answer 10

centromeres are a constricted region of the chromosome that ensure proper segregation during mitosis and meiosis

Question 11

what do kinetochore proteins do?

Answer 11

group of proteins that link centromere to the spindle apparatus

Question 12

what do telomeres do?

Answer 12

located at each end of the eukaryotic chromosomes to prevent translocations and maintain chromosome length

Question 13

how many genes does each chromosome have?

Answer 13

usually a few hundred to several thousand

Question 14

how is DNA compacted to fit within the nucleus?

Answer 14

an octomer is composed of two copies of of each of the four different core histones, DNA and proteins are then wound into small repeating units around the octomers called nucleosomes, these nucleosomes are further wound into 30nm-fiber and then into radial loop domains

Question 15

what are histone proteins?

Answer 15

proteins that contain many positively charged amino acids that bind to the negatively charged phosphates along the DNA backbone

Question 16

what are the five types of histones?

Answer 16

H2A, H2B, H3, and H4

Question 17

what does the linker histone (H1) do?

Answer 17

binds to linker DNA and nucleosomes

Question 18

how are 30-nm fibers formed?

Answer 18

nucelosomes are wound into a spiral through their linker regions, solenoid model proposes that the spiral contains 6 nucleosomes per turn while the zigzag model depicts the nucleosomes spread out in a zig zag with straight linker regions connecting them

Question 19

how are radial loop domains formed?

Answer 19

the internal nuclear matrix fills the interior of the nucleus and attaches to the nuclear lamina that lines the inner membranes, matrix-attachment regions (MARs)/ scaffold-attachment regions (SARs) anchor to the nuclear matrix in two sections to form a loop in between the attachment points which creates more surface area to store the DNA

Question 20

what are the steps of chromosome compaction from least to most compacted?

Answer 20

DNA helix
nucelosomes
30-nm fiber
radial loop domains
chromatin
chromosome

Question 21

heterochromatin vs euchromatin?

Answer 21

euchromatin is a less condensed region of the chromosome that is transcriptionally active (regions where 30-nm fiber forms radial loop domains)
heterochromatin is a tightly compacted region of the chromosome that is transcriptionally inactive (region where radial loop domains are compacted further at centromere and telomere)

Question 22

how is the chromatin structure regulated?

Answer 22

altering the specific histone proteins present in nucleosomes, modifications to histone tails (acetylation/methylation), or modifications to the DNA itself (methylation)
these factors contribute to “epigenetic” gene regulation (changing the DNA functions without changing its sequence)

Question 23

what is the C-value paradox?

Answer 23

the idea that there is a lack of correlation between genome size and organism complexity since larger genomes have more repeat sequences and not extra genes

Question 24

what is transposition?

Answer 24

the movement of a defined DNA segment (called a transposon or transposable element) from one genomic site to another

Question 25

what is simple transposition?

Answer 25

when the transposable element (called transposons) is removed from the original site and transferred to a new site by a “cut and paste” mechanism

Question 26

what is retrotransposition?

Answer 26

when the transposable element (called retroelements/retrotransposons) is transcribed into RNA, then reverse transcriptase makes a second copy of it in the DNA and integrase inserts that DNA back into the genome

Question 27

what are the three types of simple transposons (IS elements)?

Answer 27

flanking direct repeats: sequences that are repeated on both ends of a sequence
inverted repeats: sequence followed downstream by its reverse complement, potentially with a gap in the center
transposase gene: transposon capable of moving down the genome

Question 28

what are Tn elements?

Answer 28

a type of transposable element that can introduce multi-drug resistance onto bacterial plasmids by jumping from plasmid to bacterial chromosomes, spreading drug resistance between bacterial strains

Question 29

what are LTR retrotransposons?

Answer 29

type of retrotransposons that contain long terminal repeats at both ends that encode reverse transcriptase and integrase

Question 30

what makes a transposable element autonomous or nonautonomous?

Answer 30

transposable elements are autonomous when they contain all the information needed for transposition to occur and nonautonomous when they lack a gene that is needed for transposition to occur

Question 31

what does transposase do?

Answer 31

catalyzes the removal of a transposable element and its reinsertion at another location, can recognize inverted repeats at the ends of the transposable element and brings them closer together

Question 32

what does the target-site primed reverse transcription (TPRT) model of non-LTR retrotransposons describe?

Answer 32

retrotransposons are transcribed into RNA with a poly-A tail while target DNA sequence is cut open by endonuclease, RNA then binds to the exposed bases, reverse transcriptase then makes a DNA copy of the unbound section of RNA, endonuclease then makes a second cut nearby and the retrotransposon DNA is ligated into the target site and gaps are filled in by DNA polymerase and ligase