Chapter 7: Eukaryotic Nuclear Genomes

Question 1

Module 7

chromatin

Answer 1

• chromosome in dispersed state
• the entire complex of DNA and proteins that is the building material of chromosomes

Question 2

Module 7

heterochromatin

Answer 2

• highly condensed state thru cell cycle
• found @ centromeres, telomeres & other specific places, Y chromosome
• can be constitutive or facultative
• has repeated sequences & few genes

Question 3

Module 7

constitutive heterochromatin

Answer 3

• permanent heterochromatin

Question 4

Module 7

facultative heterochromatin

Answer 4

• condensed at certain times
• i.e. inactivated X chromosome

Question 5

Module 7

euchromatin

Answer 5

• condenses & decondenses thru cell cycle
• majority of chromosomal material
• where most transcription/crossing over happens
• On chromosome arms
• has unique sequences & many genes

Question 6

Module 7

nucleosome

Answer 6

• DNA wrapped about two times around an octamer of eight histone proteins
• two copies each of H2A, H2B, H3, and H4
• these eight proteins form a barrel-shaped: core octamer
• Between 140 bp and 150 bp of DNA (depending on the species) are associated with the nucleosome particle
• each nucleosome is separated by 50–70 bp of linker DNA
• thus, the repeat length of 190–220 bp shown by the nuclease protection experiments

Question 7

Module 7

linker DNA

Answer 7

• The DNA string between nucleosomes
• 50–70 bp in length
• made of H1 histone

Question 8

Module 7

linker histones, chromatosome

Answer 8

• in vertebrates these include histones H1a–e, H1⁰, H1t, and H5
• A single linker histone attached to each nucleosome
• precise position of the linker histone relative to the nucleosome is not known
• may act as a clamp, preventing the DNA from detaching from the outside of the nucleosome others suggest it is is inserted between the core octamer and the DNA

Question 9

Module 7

histones

Answer 9

• most abundant proteins in chromatin
• small, + charged proteins attract negative charges on phosphates of DNA
• 5 major types: H1, H2A, H2B, H3, and H4
• High percentage of arginine and lysine
• helps to package Chromosomal DNA is inside nuclei

Question 10

Each histone proteins in a nucleosome has a flexible “tail,” extending out. _____ charged amino acids in tails interact w/negative charge of _____ on DNA, keeping DNA & histones tightly associated & interact w/other nucleosomes for further ______

Answer 10

• Positively
• phosphates
• compaction

Question 11

Module 7

Nuclease protection analysis of chromatin from human nuclei.

• Chromatin is gently purified from nuclei and treated with a _____ _____
• Nuclease treatment: limiting conditions
  
  • DNA is cut, on average, just once in each of the linker regions between the _____ _____
  • After removal of the protein, the DNA fragments are analyzed by agarose gel electrophoresis and found to be _____ in length, or multiples thereof.
• Nuclease treatment: non limiting conditions
  
  • nuclease treatment proceeds to completion so all the DNA in the _____ ______ is digested
  • The remaining DNA fragments are all ______ in length
• Results show that in this form of chromatin, protein complexes are spaced along the DNA at ____ _____, one for each _____ bp, with _____ bp of DNA closely attached to each_____ _____

Answer 11

• nuclease enzyme
• Nuclease treatment: limiting conditions
  
  • bound proteins
  • 200 bp
• Nuclease treatment: non limiting conditions
  
  • linker regions
  • 146 bp
• regular intervals
• 200
• 146
• protein complex.

Question 12

Module 7

30 nm fiber

Answer 12

• more condensed version of the chromatin complex
• exact way in which nucleosomes associate to form the 30 nm fiber is not known
  
  • individual nucleosomes within the 30 nm fiber may be held together by interactions between the linker histones
  • or attachments may involve the core histones, whose protein “tails” extend outside the nucleosome
• this hypothesis is attractive because chemical modification of these tails results in the 30 nm fiber opening up, enabling genes contained within it to be activated
• There are 2 models of the 30 nm chromatin fiber. The solenoid model has bee in favor for several years but recent experimental evidence supports the helical ribbon

Question 13

The 30 nm fiber is probably the major type of chromatin in the nucleus during interphase, the period between _____ divisions. When the nucleus divides, the DNA adopts a more compact form of packaging resulting in the condensed ______ chromosomes.

Answer 13

• interphase
• nuclear
• metaphase

Question 14

Module 7

metaphase chromosome

Answer 14

• formed after DNA replication has taken place
• each one is, in effect, two chromosomes linked together at the centromere
• The arms are called the chromatids
• A telomere is the extreme end of a chromatid
• Individual chromosomes can be recognized because of the lengths of their chromatids and the location of the centromere relative to the telomeres

Question 15

Module 7

Chromatid

Answer 15

• prior to cell division, each chromosome replicates, making a copy of itself
• copy of newly copied chromosome
• is joined to the original chromosome by a single centromere
• each member of the pair is a Homolog

Question 16

Module 7

telomeres

Answer 16

• specific DNA sequences and proteins located at tips of chromosomes
• enables the cell to distinguish a real end from an unnatural end caused by chromosome breakage, essential because the cell must repair any breakage
• in humans
  
  • consists of hundreds of copies of a repeated motif, 5’–TTAGGG–3’ w/a short extension at the 3’
  • length of the 3’ extension is different in each telomere
  • Two proteins bind to the repeat sequences
    
    • TRF1: helps to regulate the length of the telomere
    • TRF2:
      
      • maintains the single-strand extension.
      • If inactivated then this extension is lost and the two polynucleotides fuse together in a covalent linkage
• protect & stabilize chromosome ends
• participate in limiting cell division, aging and cancer

Question 17

Module 7

kinetochore

Answer 17

• multiprotein complex that assembles on the centromere before cell division
• later spindle microtubules attach to the kinetochore
• During the anaphase period of nuclear division, individual chromosomes are drawn apart by the contraction of microtubules attached to the kinetochores

Question 18

Module 7

centromere

Answer 18

• constricted region of a chromosome where spindle microtubules attach, via the kinetochore, during cell division
• stains less strongly than the rest of the chromosome

Question 19

karyogram

Answer 19

• way used to depict chromosomes
• the way chromosomes are organised in the image makes them easy to visualize
• They are arranged into homologous pairs each of which is arranged into size order- from largest to smallest.

Question 20

Module 7

The DNA contained within centromeres and telomeres, and the proteins attached to this DNA, have

Answer 20

special features related to the particular functions of these structures

Question 21

Module 7

centromeric DNA

Arabidopsis thaliana plant

Answer 21

• nucleotide sequence of centromeric DNA in higher eukaryotes is best understood in this plant
• highly repetitive structures that characterize these regions
• the plants centromeres span 0.9–1.2 Mb of DNA, each one is made up largely of 180 bp repeat sequences, repeated 50,000 to 230,000 times (the sequence varies widely among different plant species)
• In humans the equivalent sequences are 171 bp in length and are called alphoid DNA, with 1500–30,000 copies per centromere
• contain multiple copies of genome-wide repeats, along with a few genes at a density of 7–9 per 100 kb compared with 25 genes per 100 kb for the noncentromeric regions
• The discovery that centromeric DNA contains genes was a big surprise because it was thought that these regions were genetically inactive

Question 22

Module 7

centromeric DNA

Saccharomyces cerevisiae yeast structure

Answer 22

• centromere is defined by a single sequence, 125 bp in length
• made up of two short elements, called CDEI (9 bp) and CDEIII (11 bp), which flank a longer element called CDEII (80 - 90 bp)
• CDEI & CDEIII
  
  • highly conserved
  • sequences are very similar in all 16 yeast chromosomes
  • a mutation in CDEI or CDEIII usually prevents the centromere from forming
• CDEII
  
  • sequence is variable
  • very rich in A and T nucleotides
  • Mutations rarely affect the function of the centromere

Question 23

Module 7

centromeric DNA

Saccharomyces cerevisiae yeast protein interaction

Answer 23

• The short, nonrepetitive nature of the yeast centromeric DNA has furthered our knownledge on how DNA interacts with proteins to form a functional centromere
• Cse4 chromosomal protein (similar in structure to histone H3) along with a second protein, Mif2 wraps around the CDEII sequence
• DNA appears to be held in place by two further proteins:
  
  • Cbf1: attaches to the CDEI sequence
  • Cbf3: attaches to the CDEIII sequence
  • Cbf1 and Cbf3 also bind to at least some of the 20 or so additional proteins that form the kinetochore
• To what extent this model of the yeast centromere also applies to other eukaryotes is not yet clear

Question 24

Module 7

centromeric DNA

Mammalian centromeres

Answer 24

• centromeres of higher eukaryotes contain nucleosomes
• some of them contain the protein CENP-A instead of histone H3
• CENP-A-containing nucleosomes are more compact and structurally rigid than those containing H3
• Mammalian centromeres contain both CENP-A- and H3-nucleosome. It has been suggested that
  
  • the H3-nucleosomes are located mainly in the central core of the centromere
  • and the CENP-A versions form an outer shell onto which the kinetochore is constructed.

Question 25

Module 7

• for human chromosomes, the density ranges from ___ to ___ genes per 100 kb
• there are two lines of evidence for this:

Answer 25

• 0 to 64
• evidence 1:
  
  • banding patterns that are produced when chromosomes are stained
  • dyes used bind to DNA molecules with preferences for certain base pairs
  • Giemsa, has a greater affinity for DNA regions that are rich in A and T nucleotides
    
    • dark G-bands are therefore thought to be AT-rich
    • base composition of the genome is 59.7% A + T so the dark G-bands must have AT contents > 60%
    • thus these regions have fewer genes because genes generally have AT contents of 45%–50%
    • confirmed when the genome sequence was compared with the human karyogram
• evidence 2:
  
  • isochore model of genome organization
  • genomes of vertebrates, plants & other eukaryotes are mosaics of segments of DNA
  • each segment at least 300 kb in length and w/a uniform base composition differing from adjacent segments
  • supported when genomic DNA is broken into 100 kb, treated w/dyes that bind to AT- or GC-rich regions & then separated by density gradient centrifugation
  • five fractions are seen, each representing a different isochore type with a distinctive base composition:
    
    • L1 and L2: AT-rich isochores
    • H1, H2, and H3: GC-rich isochores
    • H3, is the least abundant making up only 3% of the total, but contains over 25% of the genes

Question 26

Module 7

In most organisms, genes appear to be distributed more at less at _____, with substantial variations in gene density at _____ _____ within a chromosome

Answer 26

• random
• different positions

Question 27

The genes make up only a _____ part of the human genome. all the exons in the human genome make up only _____ Mb, just _____% of the total. In contrast, _____% of the genome is taken up by genome-wide repeats

Answer 27

• small
• 48
• 1.5
• 44

Question 28

Module 7

types of genome-wide repeat

Answer 28

• LINEs: long interspersed nuclear elements
• SINEs: short interspersed nuclear elements
• LTR: long terminal repeat
• DNA transposons

Question 29

Module 7

C-value paradox can be due to

Answer 29

• more complex eukaryotes have less compact genomes
• space is saved in the genomes of less-complex organisms because the genes are more closely packed together
  
  • genes are more compact, having fewer introns
  • as a result a region may contain more genes
  • few genes are discontinuous
  • spaces between the genes are relatively short
  • fewer genome-wide repeats, which play a role in dictating the compactness of a genome

Question 30

Module 7

How many genes are there

Answer 30

• suggest that the human genome contains 30,000–40,000 genes
• uncertainty due to difficulty in recognizing which sequences are genes and which are not
• alternative splicing is more prevalent than was originally appreciated
  
  • makes this question have no real biological significance
  • the number of genes doesn’t indicate the number of proteins that can be synthesized so it’s not a measure of the biological complexity of a genome

Question 31

Although alternative splicing enables one gene to specify several proteins, those proteins will have at least some parts of their ____ _____ sequences in common and so will usually have similar or related functions. Categorizing genes according to their ______ can therefore give meaningful information on the range of _____ _____ specified by a genome

Answer 31

• amino acid
• functions
• biochemical activities

Question 32

Module 7

human gene catalog

Answer 32

• functions of over half of the 30,000–40,000 human genes are known or can be inferred with a reasonable degree of certainty
• vast majority code for proteins
• less than 2500 specify the various types of functional RNA
• The pie chart
  
  • shows a categorization of the identified human protein-coding genes
  • omits approximately 13,000 genes whose functions are not yet known
  • “various other activities” includes, among others, proteins involved in biochemical transport processes and protein folding, immunological proteins, and structural proteins.

Question 33

Module 7

gene classification by function

Answer 33

• advantages
  
  • fairly broad functional categories can be further subdivided to produce a hierarchy of increasingly specific descriptions for smaller and smaller sets of genes
• weakness
  
  • functions have not yet been assigned to many eukaryotic genes
  • leaves out a proportion of the total gene set

Question 34

Module 7

domains

Answer 34

• protein molecule is constructed from a series of domains
• each has a particular biochemical function
  
  • zinc finger: one of several domains that enable a protein to bind to a DNA molecule
  • death domain: present in many proteins involved in apoptosis
• has a characteristic amino acid sequence, not exactly the same, but close enough for it to be recognizable

Question 35

Module 7

gene classification by the structures of the proteins that they specify

Answer 35

• gene is classified by their domains
• The amino acid sequence of a protein is specified by the nucleotide sequence of its gene, so the domains present in a protein can be determined from the nucleotide sequence of the gene
• genes in a genome can therefore be categorized according to the protein domains that they specify
• emphasizes the similarities between genomes,
• advantage
  
  • can be applied to genes whose functions are not known and hence can encompass a larger proportion of the set of genes in a genome

Question 36

Module 7

Relationship between the human gene catalog and the catalogs of other groups of organisms

Answer 36

• This analysis can only be done in an approximate way at present because only a few genome sequences are available
• The pie chart categorizes the human gene catalog according to the distribution of individual genes in other organisms
  
  • 22% of the human gene catalog is made up of genes that are specific to vertebrates, and that another 24% comprises genes specific to vertebrates and other animals.

Question 37

Module 7

domain approach shows that the human genome specifies a number of protein domains that are _____ from the genomes of the other organisms. it helps us confer the distinctive features of vertebrates compared with other types of eukaryote.

Answer 37

absent

Question 38

Module 7

Classification schemes that use domains to infer gene function suggest that

Answer 38

all eukaryotes possess the same basic set of genes, but that more complex species have a greater number of genes in each category.

Question 39

Module 7

multigene families

Answer 39

• groups of genes of identical or similar sequence
• are common features of many genomes
• some are clustered others dispersed
• simple / classical multigene families
  
  • all the members have identical or nearly identical sequences
  • arisen by gene duplication
  • i.e. rRNA genes
• complex multigene families
  
  • although similar in sequence, are sufficiently different for the gene products to have distinctive properties
  • i.e. mammalian globin genes
    
    • different because genes are expressed at different stages in human development:

Question 40

Module 7

pseudogenes

Answer 40

• nonfunctional gene copies
• evolutionary relic
• an indication that genomes are continually undergoing change
• human globin gene clusters contain five genes that are no longer active

Question 41

Module 7

pseudogenes

two types

Answer 41

• conventional pseudogene
  
  • has been inactivated because its nucleotide sequence has changed by a mutation
  • Once a pseudogene has become nonfunctional it will degrade through accumulation of more mutations, and eventually will no longer be recognizable as a gene relic
• processed pseudogene
  
  • arises by integration of mRNA into the genome
  • a copy of mRNA is transcribed from a functional gene
  • mRNA is reverse transcribed into a cDNA copy
  • cDNA copy integrates into the same chromosome as its functional parent, or possibly into a different chromosome
  • Because a processed pseudogene is a copy of an mRNA molecule
    
    • lacks introns and nucleotide sequences immediately upstream the region used to switch on expression of the parent gene, inactivating it

Question 42

Module 7

truncated genes

Answer 42

lack a greater or lesser stretch from one end of the complete gene

Question 43

Module 7

gene fragments

Answer 43

short, isolated regions from within a gene

Question 44

intergenic regions, aka junk DNA

Answer 44

• 62% of the human genome
• parts of the genome that lie between genes and which have no known function
• bulk is made up of repeated sequences of one type or another.
• can be divided into two categories
  
  • genome-wide or interspersed repeats
    
    • individual repeat units are distributed around the genome in an apparently random fashion
  • tandemly repeated DNA
    
    • repeat units are placed next to each other in an array.