Genome Diversity & DNA Organisation Flashcards
Lecture 2 (Complete) (Video notes included)
Define the genome
The sequence of nucleotides in DNA that comprises the genetic makeup of an organism
How is the genome size given?
Genome size is total DNA contained within one copy of a single genome - for diploid organisms the genome size refers to the haploid DNA content
True or False:
Viral genomes can be DNA or RNA
True
True or False:
Viral genomes are made of DNA
False:
Viral genomes can be DNA or RNA
True or False:
Viral genomes are made of RNA
False:
Viral genomes can be DNA or RNA
True or False:
Viral genomes may be single-stranded or double stranded
True
True or False:
Viral genomes are single-stranded
False:
Viral genomes may be single-stranded or double stranded
True or False:
Viral genomes are double stranded
False:
Viral genomes may be single-stranded or double stranded
True or False:
Viral genomes may be circular or linear
True
True or False:
Viral genomes are circular
False:
Viral genomes may be circular or linear
True or False:
Viral genomes are linear
False:
Viral genomes may be circular or linear
True or False:
Viral genes may overlap
True
True or False:
Viral genes never overlap
False:
Viral genes may overlap
True or False:
Single-celled eukaryotes generally have fewer genes than multicellular organisms
True
True or False:
Single-celled eukaryotes generally have a similar number of genes to multicellular organisms
False:
Single-celled eukaryotes generally have fewer genes than multicellular organisms
What is the correlation between genome size, gene number and organism complexity?
There is no simple correlation between genome size, gene number and organism complexity
What does it mean if a genome has transposable elements?
It has pieces of DNA that copy themselves to another area in a genome, which leads to increases in genome size
True or False:
Similar organisms can show a large range in genome size
True
True or False:
Similar organisms show a small range in genome size
False:
Similar organisms can show a large range in genome size
What is the C-value?
The C-value is the amount of DNA in the haploid genome of an organism
What is the C-value paradox?
Genome size does not consistently correlate with organism complexity
Define a gene
A region controlling a discrete hereditary characteristic, usually a specific product like a protein
What is considered as ‘junk DNA’?
Transposable elements (repeating DNA) and coding for RNA species that are not translated
Fill in the gaps:
If a DNA sequence is classified as ‘_______’, this means there are one to a few copies per genome.
If a DNA sequence is classified as ‘unique’, this means there are one to a few copies per genome.
Fill in the gaps:
If a DNA sequence is classified as ‘________ ________’, this means there are few to 10^__ copies per genome.
If a DNA sequence is classified as ‘moderately repetitive’, this means there are few to 10^5 copies per genome.
Fill in the gaps:
If a DNA sequence is classified as ‘_______ ________’, this means there are 10^__ to 10^__ copies per genome.
If a DNA sequence is classified as ‘highly repetitive’, this means there are 10^5 to 10^7 copies per genome.
What sequence classification do prokaryotes tend to have?
Prokaryotes have mostly unique sequence DNA (which is why they tend to have small genomes)
What sequence classification do eukaryotes tend to have?
Eukaryotes have a mix of unique and repetitive sequences
(e.g. Human genome approximately 50% unique sequence, 50% repeat)
How is DNA sequence in genomes classified?
DNA sequence in genomes is classified by abundance
Either ‘unique’ , ‘moderately repetitive’ or ‘highly repetitive’.
What are the circular or linear units DNA is packaged into called?
Chromosomes
Describe a typical bacterial genome
Usually a single, circular, double stranded DNA chromosome (same for archaea), localised to the nucleoid
e.g. E.coli 4.6 Mb circular ds DNA chromosome, approximately 1.5 mm long = 500 x the length of E.coli cell (3 um)
(Plasmids are IN ADDITION to the genome and are non-essential and extrachromosomal)
What are some exceptions to a typical bacterial genome?
Linear bacterial genomes do exist
e.g. Borrelia burgdorferi (Lyme disease), one large dsDNA linear chromosome (0.91 Mb), 12 linear, 9 circular extrachromosomal elements/plasmids totalling 0.61 Mb
Fill in the gaps: DNA compaction in bacteria:
Binding of small _______ charged _______ along the DNA - counteracts _______ charges on DNA backbone (same in eukaryotes).
________ ________ ________ _______ (NAPS) including __________ _____ ______ (IHF) ____ DNA to facilitate packaging and supercoiling.
DNA arranged into ~ ____ independent __________ supercoiled looped domains each of ~__ kb.
_____________ generate supercoils.
Binding of small positively charged proteins along the DNA - counteracts negative charges on DNA backbone (same in eukaryotes).
Bacterial Nucleoid Associated Proteins (NAPS) including Integration Host Factor (IHF) bend DNA to facilitate packaging and supercoiling.
DNA arranged into ~400 independent negatively supercoiled looped domains each of ~10 kb.
Topoisomerases generate supercoils.
Fill in the gaps: Organising genomes in eukaryotic organisms.
The genome is distributed across ______, linear chromosomes with ______ DNA content (differing gene ______).
Every organism has a _____ number of chromosomes per cell. Each chromosome consists of one ______, ______-stranded DNA molecule.
Most are diploid and produce _____ gametes. The exception to this are _________ due to ________.
DNA is _________ with proteins into ______ to compact and organise it so it fits into a cell.
The genome is distributed across multiple, linear chromosomes with varied DNA content (differing gene density).
Every organism has a fixed number of chromosomes per cell. Each chromosome consists of one linear, double stranded DNA molecule.
Most are diploid and produce haploid gametes. The exception to this are hepatocytes (liver cells) due to polyploidy.
DNA is complexed with proteins into chromatin to compact and organise it so it fits into a cell.
Human cell chromosome number?
46 chromosomes
Vary in size, chromosome 1 ~ 249 Mbp
chromosome 22 ~ 60 Mbp
Kingfisher chromosome number?
132 chromosomes
How much DNA is in one human cell, compared to the nucleus diameter?
2m of DNA , 10 um nucleus diameter
What are the basic binding proteins for packaging DNA in eukaryotes?
Histones
How many core histones are there in eukaryotes?
Four
True or False:
The four core histones in eukaryotes are very highly conserved across organisms
True
True or False:
The four core histones in eukaryotes are weakly conserved across organisms
False:
The four core histones in eukaryotes very highly conserved across organisms
Histones are rich in which two amino acids?
Why?
Lysine and arginine.
Their positive charges counteract the negative charges on phosphate groups on DNA, stabilising the DNA-histone interaction and allowing the DNA to wrap around the histone complex.
What is the histone complex at the center when DNA wraps around it called?
The histone octamer
Define the histone octamer
The histone complex at the center, when DNA wraps around it. It is made up of eight histones - two each of the four core histones.
Define a nucleosome
A nucleosome is formed when DNA wraps around a histone complex
What is formed when DNA wraps around a histone complex
A nucleosome
Does DNA wrap around the histone complex in a left handed or right handed manner?
Left handed
What are the names of the four core histones?
H2A, H2B, H3 and H4
How are nucleosomes assembled?
Two H3-H4 dimers associate with DNA, stacked on top of each other
Two H2A-H2B dimers then associate to complete the octamer (these are also stacked on top of each other)
What length of DNA wraps around the octamer to form the nucleosome?
About 146bp
Fill in the gaps:
DNA is wound ~ ____ times around the histone octamer in a ____-handed direction. This forms _________ supercoils when the histone is removed.
DNA is wound ~ 1.75 times around the histone octamer in a left-handed direction. This forms negative supercoils when the histone is removed.
Removing a histone octamer results in what?
Why is this helpful?
Negatively supercoiled DNA, which makes strand separation easier for replication and transcription.
Describe the tails present in the nucleosome core.
Each core histone has an unstructured N-terminal “tail” extending outwards between DNA coils
Tails have undefined structure and are up to 25 amino acids (varies depending on histone)
Tails interact with other nucleosomes to further compact DNA
Tails can be chemically modified, important for chromatin and function
What are variant histones?
At special or random chromatin locations, variant histones may replace one (or more) of the 4 core histones, being incorporated into nucleosomes instead to perform a specific function
Give an example of a histone variant and it’s importance
CENP-A (centromere protein-A) is a variant of histone H3 which is incorporated into nucleosomes at centromeres.
It is essential for centromere formation and function.
What is the least compact, visualised chromatin?
The 10 nm fiber, which has a “beads on a string” appearance
Fill in the gaps:
The ___ _ fibre can be folded further into the ___ _ fibre, a _______ arrangement that brings nucleosomes together. DNA is compacted ~___-fold in ___ _ fibre.
The 10 nm fibre can be folded further into the 30 nm fibre, a regular arrangement that brings nucleosomes together. DNA is compacted ~50-fold in 30 nm fibre.
Describe the formation of the 30 nm fibre
H1 is a linker histone that binds to the linker DNA between successive nucleosomes, helping compaction
The core histone tails are also involved but it is not fully understood how
Fill in the gaps:
During __________ the 30 nm chromatin fibre is folded into ______ ______ via anchoring to a central __________ protein chromosome scaffold.
During metaphase the 30 nm chromatin fibre is folded into looped domains via anchoring to a central nonhistone protein chromosome scaffold.
Fill in the gaps:
In metaphase, chromosome-level __________ is achieved through packaging of the ___ _ fibre without ___ _ fibre intermediate.
In metaphase, chromosome-level condensation is achieved through packaging of the 10 nm fibre without 30 nm fibre intermediate.
Describe chromatin structure in interphase
Chromosomes are relatively uncondensed and genes are being transcribed. Compaction varies along a chromosome.
In relatively decondensed regions chromatin stains lightly (euchromatin) actively transcribed genes.
Chromatin in more compacted regions stain more darkly (heterochromatin) and transcription is less active.
Define euchromatin
Chromosome material which does not stain strongly, except during cell division. It represents the major genes and is most involved in transcription.
What is the name for chromosome material which does not stain strongly except during cell division?
Euchromatin
Define heterochromatin
Chromosome material of different density from normal (usually greater), in which the activity of the genes is modified or suppressed.
What is the name for chromosome material where the activity of the genes is modified or suppressed.
Heterochromatin
What 4 main things does chromatin structure affect?
Transcription
DNA replication
Recombination
Chromosome transmission
Which three specific regions of chromosomes are particularly rich in heterochromatin?
Telomeres (special DNA at ends of chromosomes)
DNA at or near centromeres (middle connection)
Regions with highly repetitive DNA sequences
How does chromatin structure affect transcription?
Translocation of a gene from a euchromatic to heterochromatic region can actively prevent transcription
How does chromatin structure affect DNA replication?
Rearrangements that place an origin of replication into heterochromatin result in late replication
How does chromatin structure affect recombination?
When DNA is broken and joined to a different DNA molecule, recombination is decreased in heterochromatic regions, protecting genome from rearrangements
How does chromatin structure affect chromosome transmission?
Special histone CENP-A is required to form a functional centromere, needed for proper chromosome separation
Discuss how modification to histones affects chromatin structure and function
Amino acid side chains in protruding N-terminal histone tails can be modified
Side chains in globular regions of histones can be modified
Histone modifications are reversible, specialised enzymes add and remove chemical groups
Euchromatin is more acetylated than heterochromatin
Combination of specific modifications influences function of DNA
Combination of specific modifications influences function of DNA
Fill in the gaps:
_____ ____ side chains in protruding _-______ histone tails can be modified.
Side chains in ________ regions of histones can be modified.
Histone modifications are ________, specialised _______ ___ and _______ chemical groups.
Euchromatin is more __________ than heterochromatin.
Changes in chromatin are key to regulation of gene activity. Combination of specific modifications influences _______ of DNA.
Amino acid side chains in protruding N-terminal histone tails can be modified.
Side chains in globular regions of histones can be modified.
Histone modifications are reversible, specialised enzymes add and remove chemical groups.
Euchromatin is more acetylated than heterochromatin.
Changes in chromatin are key to regulation of gene activity. Combination of specific modifications influences function of DNA.
What enzymes add acetyl groups to lysine side chains?
Histone acetyltransferases (HATs)
What enzymes remove acetyl groups?
Histone deacetylases (HDACs)
Fill in the gaps:
Histone acetyltransferases _____ _____ groups ___ _____ side chains. Histone deacetylases ______ them.
Histone acetyltransferases add acetyl groups to lysine side chains. Histone deacetylases remove them.
What enzymes add methyl groups to lysine and arginine side chains?
Histone methyltransferases (HMTs)
What enzymes remove methyl groups? (Histone modification)
Histone demethylases
Fill in the gaps:
Histone methyltransferases ______ ______ groups to ______ and _______ side chains. Histone demethylases _______ them.
Histone methyltransferases add methyl groups to lysine and arginine side chains. Histone demethylases remove them.
What enzymes add phosphates as histone modifications?
Kinases
What enzymes remove phosphates from histone modifications?
Phosphatases
How do kinases modify histones?
They add phosphates
How is ubiquitin added as a histone modification?
By a chain of enzymatic reactions
How is ubiquitin removes as a histone modification?
Via a deubiquitinating enzyme
What do ‘ori’ (in italics) and ‘ter’ (in italics) specify?
Origin of replication , replication termination
True or False:
In eukaryotes, centromeres direct chromosome segregation
True
True or False:
In eukaryotes, centromeres solve the problem of replicating chromosome ends
False:
In eukaryotes, centromeres direct chromosome segregation
Fill in the gaps:
In _______, sequences near the ____ determine distribution of replicated chromosomes to the daughter cells.
In bacteria, sequences near the ori determine distribution of replicated chromosomes to the daughter cells.
Why are telomeres important?
They stabilise the ends of chromosomes and help solve the problem of replicating chromosome ends
Fill in the gaps:
Telomers _______ the ____ of chromosomes and help solve the problem of _________ chromosome _____.
Telomers stabilise the ends of chromosomes and help solve the problem of replicating chromosome ends
Fill in the gaps:
Centromeres are found in all _________ chromosomes. Most species have a _______ centromere per _________. It is in a ____________ region, and is inherited ___________, marked by the H3 variant histone _________.
Centromeres are found in all eukaryotic chromosomes. Most species have a single centromere per chromosome. It is in a heterochromatic region, and is inherited epigenetically, marked by the H3 variant histone CENP-A.
Fill in the gaps:
After DNA replication but before ___________ separate, two _______ ________ are present. The centromere appears as a __________. Centromeres bind specific proteins to form a structure called a __________.
After DNA replication but before chromosomes separate, two sister chromatids are present. The centromere appears as a constriction. Centromeres bind specific proteins to form a structure called a kinetochore.
What is the function of a kinetochore?
During mitosis, kinetochores attach to microtubules from opposite spindle poles, allowing the spindle to separate sister chromatids.
Describe a typical mitochondrial genome
Usually circular
Double stranded, supercoiled DNA molecules, 2-10 copies per mitochondria
Not packaged into chromatin, but anchored to mitochondrial inner membrane
True or False:
Mitochondrial genes follow rules of Mendelian inheritance in mammals
False:
Mitochondrial gene inheritance is non-Mendelian. Mitochondria are inherited from the mother, maternal inheritance.
True or False:
Mitochondrial gene inheritance is non-Mendelian
True
Mitochondria are inherited from the mother, which is maternal inheritance
Fill in the gaps:
Mitochondrial genomes code for some _________ proteins. Animal cell mtDNA is compact, usually codes for __ proteins, __ _____ and __ _____ used in mitochondria specifically.
Mitochondrial genomes code for some mitochondrial proteins. Animal cell mtDNA is compact, usually codes for 13 proteins, 2 rRNAs and 22 tRNAs used in mitochondria specifically.
True or False:
Chloroplasts have RNA genomes
False:
Chloroplasts have DNA genomes
True or False:
Chloroplasts have DNA genomes
True
Fill in the gaps:
Chloroplast genomes vary in size but are large enough to code for ___ - ___ proteins as well as the _____ and ____.
Chloroplast genomes vary in size but are large enough to code for 50 - 100 proteins as well as the rRNAs and tRNAs.
Fill in the gaps regarding nucleosomes:
Each core histone has an __-______ “tail” extending outwards between DNA coils.
Tails have ________ structure and are up to ___ amino acids (varies depending on histone). They interact with ______ ________ to _______ _______ DNA.
Tails can be ________ _______, which is important for chromatin and function.
Each core histone has an N-terminal “tail” extending outwards between DNA coils.
Tails have undefined structure and are up to 25 amino acids (varies depending on histone). They interact with other nucleosomes to further compact DNA.
Tails can be chemically modified, which is important for chromatin and function.
