PCB 3063 Exam 3
Eukaryotic Chromosomes - ✔️✔️The multiple linear chromosomes in a eukaryotic
nucleus are highly condensed
Degree of coiling and packing changes throughout cell cycle
Interphase: relatively more relaxed = less condensed
Mitotic phase: relatively more compact = fully condensed for movement of individual
chromosomes during cell division
Genome size - ✔️✔️The genomes of different species contain different amounts of
DNA.
The complexity of an organism doesn't necessarily match the amount of DNA in its
genome
Humans have a 6 billion base pair genome
a single-celled protist, Polychaos dubium, has the largest genome of all organisms with
670 billion base pairs
Regardless of genome size, all organisms must contain their genetic information inside
the cell
Levels of DNA structure: Primary - ✔️✔️Nucleotide sequence
Levels of DNA structure: Secondary - ✔️✔️Double helix of antiparallel strands
Levels of DNA structure: Tertiary - ✔️✔️Folding and packing to fit in confined space of
cell
The 1˚ and 2˚ molecular structure of DNA - ✔️✔️Its function: to store, replicate, and
transmit genetic information
The 3˚ structure of DNA - ✔️✔️Determines its ability to express the encoded
information as a phenotype
Relaxed helical DNA - ✔️✔️Not supercoiled.
10 turns = 100 bp of DNA
The lowest energy state is B-DNA with 10 bases per turn
Supercoiling - ✔️✔️Stress on the helix that over-winds or under-winds it will cause the
helix to twist back on itself
Positive supercoiling - ✔️✔️Over-rotated
Negative supercoiling - ✔️✔️Under-rotated
,Topoisomerases - ✔️✔️Enzymes that can add or remove a turn in DNA by breaking
sugar-phosphate backbone, rotating, and then rejoining ends
Most DNA is negatively supercoiled - ✔️✔️Helps pack DNA into small space
Strand separation during replication and transcription is more rapid and requires less
energy
Most Bacterial genomes are contained in a single circular chromosome - ✔️✔️Bound
proteins help compact the DNA circle into supercoiled loops in the nucleoid region of the
cell
Many bacteria also have additional DNA in small circular, plasmids that replicate
independent of the chromosome
DNA's 3˚ structure must be flexible and dynamic - ✔️✔️A vast amount of genetic
information must be packed into a cell of limited size
This material must be tightly condensed for chromosomes to move as individual units
during cell division
But DNA must be de-condensed at other times to be accessible for replication and
transcription
Chromatin - ✔️✔️DNA complexed with proteins; 2 types
Euchromatin - ✔️✔️Will become more condensed and less condensed during different
stages of the cell cycle, making DNA more and less accessible for transcription
Heterochromatin - ✔️✔️Remains highly condensed throughout cell cycle, preventing
most transcription
Constitutive: Permanent; telomere and centromere regions
Facultative: Changeable condensation; X-inactivation
Most chromatin is composed of histone proteins - ✔️✔️5 types: H1, H2A, H2B, H3 &
H4
Histones contain a large proportion of positively-charged arginine and lysine amino
acids
DNA is composed of negatively-charged phosphates, so histones are attracted to and
bind tightly to DNA
Nucleosomes - ✔️✔️"Beads" made of DNA wrapped 2x around 8 histone proteins (2
each of H2A, H2B, H3 & H4)
Each histone has a positively charged "tail"
Chromatosomes - ✔️✔️Histone H1 (not in the octet), binds to wrapped DNA to clamp
nucleosome in place: nucleosome + H1
,Linker DNA - ✔️✔️Stretches of DNA between nucleosomes
Change in Chromatin Structure & Transcription - ✔️✔️For DNA to be transcribed,
chromatin structure must relax to allow access for the transcriptional enzymes
Chromosome puff - ✔️✔️Drosophila giant polytene chromosomes
A localized swelling of relaxed chromatin
Active transcription correlates with chromosomal regions of relaxed chromatin
How does chromatin structure change? - ✔️✔️1) If attraction between histones and
DNA decreases, then chromatin packing decreases = more relaxed, permitting
transcription factors to bind to DNA.
How to decrease attraction? = Make histones LESS positive
Acetyltransferases: Enzymes that attach acetyl groups to lysines of histone tails, make
histones less positive
Increase transcription
2) DNA methylation can also alter chromatin structure to inhibit binding of transcription
factors
Decrease transcription
3) Add variant histones to nucleosome
Epigenetics - ✔️✔️Some changes in chromatin structure may be passed on through
cell division or to future generations
ex: Different cell types differentiate during embryonic development
Some genes expressed only in particular cell types
Chromatin remodeling can help determine which genes are expressed where and when,
and which genes are not.
Epigenetic - "on top of the DNA sequence"
Epigenetic change - ✔️✔️Stable alteration of chromatin
DNA sequence is not changed, but its expression can change, leading to changes in
phenotype
Environment can affect epigenome - the overall pattern of chromatin modification
possessed by an individual
Centromeres - ✔️✔️Constricted region of chromosome where spindle microtubules
attach to kinetochore.
Mostly heterochromatin = no genes
Defined NOT by the DNA sequence
Defined by nucleosomes containing a variant histone called CenH3 that alters
chromatin structure to promote formation of kinetochore
, Telomeres - ✔️✔️Natural ends of linear chromosomes; heterochromatin
Serve as a cap that stabilizes chromosome end so it is not degraded (as a broken
chromosome would be)
Provide a means for replicating the end of a chromosome
Telomeric sequences - ✔️✔️Repeats of A or T followed by Gs
In humans, 5'-TTAGGG-3' repeated 100's-1000's X
G-rich strand extends beyond C-rich strand as a 3' overhang
Proteins bind to the overhang to help prevent degradation and prevent ends from
sticking together
In some cells, the G-rich 3' overhang can loop back to pair with a short stretch of DNA
(in a triplex) to form a T-loop to protect DNA end from degradation
Shelterin - ✔️✔️Prevents ends from being repaired as a double stranded DNA break
Models Proposed for DNA Replication: Conservative - ✔️✔️Original DNA strands
reform original double helix
Two new DNA strands form a new double helix
Models Proposed for DNA Replication: Dispersive - ✔️✔️Original DNA strands break
down into pieces
New DNA reassembled as a mixture of old and new pieces of DNA
Models Proposed for DNA Replication: Semi-conservative - ✔️✔️Original DNA strand
remains intact and combines with a new DNA strand
Meselson and Stahl - ✔️✔️Cells can incorporate either a light nitrogen isotope 14N, or
a heavy 15N isotope into their nitrogenous bases.
Separate molecules based on density.
Modes of Replication: Bacteria - ✔️✔️Circular chromosome
Single origin of replication (ori) - the DNA sequence where replication starts
Modes of Replication: Eukaryote - ✔️✔️Linear chromosomes
Multiple origins of replication
Ends of linear molecules require special replication
Bacteria: Theta Replication - ✔️✔️Initiator proteins bind and destabilize the double
helix at ori
1. Double stranded DNA unwinds at the replication origin
2. Producing single stranded templates for the synthesis of new DNA. A replication
bubble forms, usually having a replication fork at each end.
3. The forks proceed around the circle
Eukaryotic Chromosomes - ✔️✔️The multiple linear chromosomes in a eukaryotic
nucleus are highly condensed
Degree of coiling and packing changes throughout cell cycle
Interphase: relatively more relaxed = less condensed
Mitotic phase: relatively more compact = fully condensed for movement of individual
chromosomes during cell division
Genome size - ✔️✔️The genomes of different species contain different amounts of
DNA.
The complexity of an organism doesn't necessarily match the amount of DNA in its
genome
Humans have a 6 billion base pair genome
a single-celled protist, Polychaos dubium, has the largest genome of all organisms with
670 billion base pairs
Regardless of genome size, all organisms must contain their genetic information inside
the cell
Levels of DNA structure: Primary - ✔️✔️Nucleotide sequence
Levels of DNA structure: Secondary - ✔️✔️Double helix of antiparallel strands
Levels of DNA structure: Tertiary - ✔️✔️Folding and packing to fit in confined space of
cell
The 1˚ and 2˚ molecular structure of DNA - ✔️✔️Its function: to store, replicate, and
transmit genetic information
The 3˚ structure of DNA - ✔️✔️Determines its ability to express the encoded
information as a phenotype
Relaxed helical DNA - ✔️✔️Not supercoiled.
10 turns = 100 bp of DNA
The lowest energy state is B-DNA with 10 bases per turn
Supercoiling - ✔️✔️Stress on the helix that over-winds or under-winds it will cause the
helix to twist back on itself
Positive supercoiling - ✔️✔️Over-rotated
Negative supercoiling - ✔️✔️Under-rotated
,Topoisomerases - ✔️✔️Enzymes that can add or remove a turn in DNA by breaking
sugar-phosphate backbone, rotating, and then rejoining ends
Most DNA is negatively supercoiled - ✔️✔️Helps pack DNA into small space
Strand separation during replication and transcription is more rapid and requires less
energy
Most Bacterial genomes are contained in a single circular chromosome - ✔️✔️Bound
proteins help compact the DNA circle into supercoiled loops in the nucleoid region of the
cell
Many bacteria also have additional DNA in small circular, plasmids that replicate
independent of the chromosome
DNA's 3˚ structure must be flexible and dynamic - ✔️✔️A vast amount of genetic
information must be packed into a cell of limited size
This material must be tightly condensed for chromosomes to move as individual units
during cell division
But DNA must be de-condensed at other times to be accessible for replication and
transcription
Chromatin - ✔️✔️DNA complexed with proteins; 2 types
Euchromatin - ✔️✔️Will become more condensed and less condensed during different
stages of the cell cycle, making DNA more and less accessible for transcription
Heterochromatin - ✔️✔️Remains highly condensed throughout cell cycle, preventing
most transcription
Constitutive: Permanent; telomere and centromere regions
Facultative: Changeable condensation; X-inactivation
Most chromatin is composed of histone proteins - ✔️✔️5 types: H1, H2A, H2B, H3 &
H4
Histones contain a large proportion of positively-charged arginine and lysine amino
acids
DNA is composed of negatively-charged phosphates, so histones are attracted to and
bind tightly to DNA
Nucleosomes - ✔️✔️"Beads" made of DNA wrapped 2x around 8 histone proteins (2
each of H2A, H2B, H3 & H4)
Each histone has a positively charged "tail"
Chromatosomes - ✔️✔️Histone H1 (not in the octet), binds to wrapped DNA to clamp
nucleosome in place: nucleosome + H1
,Linker DNA - ✔️✔️Stretches of DNA between nucleosomes
Change in Chromatin Structure & Transcription - ✔️✔️For DNA to be transcribed,
chromatin structure must relax to allow access for the transcriptional enzymes
Chromosome puff - ✔️✔️Drosophila giant polytene chromosomes
A localized swelling of relaxed chromatin
Active transcription correlates with chromosomal regions of relaxed chromatin
How does chromatin structure change? - ✔️✔️1) If attraction between histones and
DNA decreases, then chromatin packing decreases = more relaxed, permitting
transcription factors to bind to DNA.
How to decrease attraction? = Make histones LESS positive
Acetyltransferases: Enzymes that attach acetyl groups to lysines of histone tails, make
histones less positive
Increase transcription
2) DNA methylation can also alter chromatin structure to inhibit binding of transcription
factors
Decrease transcription
3) Add variant histones to nucleosome
Epigenetics - ✔️✔️Some changes in chromatin structure may be passed on through
cell division or to future generations
ex: Different cell types differentiate during embryonic development
Some genes expressed only in particular cell types
Chromatin remodeling can help determine which genes are expressed where and when,
and which genes are not.
Epigenetic - "on top of the DNA sequence"
Epigenetic change - ✔️✔️Stable alteration of chromatin
DNA sequence is not changed, but its expression can change, leading to changes in
phenotype
Environment can affect epigenome - the overall pattern of chromatin modification
possessed by an individual
Centromeres - ✔️✔️Constricted region of chromosome where spindle microtubules
attach to kinetochore.
Mostly heterochromatin = no genes
Defined NOT by the DNA sequence
Defined by nucleosomes containing a variant histone called CenH3 that alters
chromatin structure to promote formation of kinetochore
, Telomeres - ✔️✔️Natural ends of linear chromosomes; heterochromatin
Serve as a cap that stabilizes chromosome end so it is not degraded (as a broken
chromosome would be)
Provide a means for replicating the end of a chromosome
Telomeric sequences - ✔️✔️Repeats of A or T followed by Gs
In humans, 5'-TTAGGG-3' repeated 100's-1000's X
G-rich strand extends beyond C-rich strand as a 3' overhang
Proteins bind to the overhang to help prevent degradation and prevent ends from
sticking together
In some cells, the G-rich 3' overhang can loop back to pair with a short stretch of DNA
(in a triplex) to form a T-loop to protect DNA end from degradation
Shelterin - ✔️✔️Prevents ends from being repaired as a double stranded DNA break
Models Proposed for DNA Replication: Conservative - ✔️✔️Original DNA strands
reform original double helix
Two new DNA strands form a new double helix
Models Proposed for DNA Replication: Dispersive - ✔️✔️Original DNA strands break
down into pieces
New DNA reassembled as a mixture of old and new pieces of DNA
Models Proposed for DNA Replication: Semi-conservative - ✔️✔️Original DNA strand
remains intact and combines with a new DNA strand
Meselson and Stahl - ✔️✔️Cells can incorporate either a light nitrogen isotope 14N, or
a heavy 15N isotope into their nitrogenous bases.
Separate molecules based on density.
Modes of Replication: Bacteria - ✔️✔️Circular chromosome
Single origin of replication (ori) - the DNA sequence where replication starts
Modes of Replication: Eukaryote - ✔️✔️Linear chromosomes
Multiple origins of replication
Ends of linear molecules require special replication
Bacteria: Theta Replication - ✔️✔️Initiator proteins bind and destabilize the double
helix at ori
1. Double stranded DNA unwinds at the replication origin
2. Producing single stranded templates for the synthesis of new DNA. A replication
bubble forms, usually having a replication fork at each end.
3. The forks proceed around the circle
