Chpt 4: DNA, Chromosomes, and Genomes Flashcards
what did Watson and Crick discover
the structure of DNA
what solved the problem of how info in DNA might be replicated
the double-helical structure
describe the first experimental demonstration that DNA is the genetic material
- 2 strains of s. pneumoniae were used
- one was smooth (S) and causes death, the other was rough (R) and is nonlethal
- R cells were grown in the presence of heat-killed S, and some of the R transformed into S
- molecules that can carry heritable info are present in S
- R strain was incubated w various types of molecules purified from the S
- RNA, protein, lipid, carbs all did not convert R. to S
- DNA did convert R to S
- DNA is the molecule that carries heritable info
what is gene expression
the process through which the info encoded in DNA is interpreted by the cell to guide the synthesis of proteins
what is the process through which the info encoded in DNA is interpreted by the cell to guide the synthesis of proteins
gene expression
what bonds hold the nucleotides together across diff strands
H bonds
what does DNA stand for
deoxyribonucleic acid
what is this
uracil
what is this
thymine
what is this
cytosine
what is this
adenine
what is this
guanine
what bonds hold the backbone together
covalent
where does the 3D structure of DNA arise from
the chem and structural features of its 2 polynucleotide chains
what enables the base pairs to be packed in the energetically most favourable arrangement in the interior of the double helix
complementary base pairing
there is one complete turn of the helix every _____ base pairs
10.4
a pre-existing strand of DNA works as a _______ for the synthesis of a new complementary strand
template
describe the structure of a cell nucleus
- surrounded by a nuclear envelope
- outer nuclear membrane is connected to endoplasmic reticulum
- nuclear envelope is supported internally by the nuclear lamina
describe the structure of a chromosome in a eukaryotic cell
a single DNA molecule along w proteins
the complex of DNA and tightly bound protein is called what
chromatin
describe DNA structure in bacteria
- carry their genes on a single DNA molecule (often circular)
- w proteins that package and condense it (but diff than ones in eukaryotes)
- this is cause they lack a special nuclear compartment
how many copies of each chromosome do we have
2 (except for gametes)
the maternal and paternal chromosomes of a pair are called what
homologous chromosomes (homologs)
what are the only nonhomologous chromosome pairs
sex chromosomes in males (Y from dad, X from mom)
what is an intron
Nucleotide sequence within a gene that is removed via RNA splicing during maturation of the final RNA product
what is an exon
Nucleotide sequence within a gene that becomes part of mature RNA molecule
how are all of the chromosomes typically displayed to produce an image
karyotype
what is a gene
a segment of DNA that contains the instructions for making a particular protein (this is a narrow def tho)
is there a correlation between the complexity of an organism and the number of genes in its genome
there can be (a lot of the differences is noncoding DNA tho)
what accounts for the astonishing variations in genome size that we see when we compare one species with another
differences in the amount of noncoding DNA
how much of the human genome codes for proteins
very little (about 1%)
what size is the average gene size
large (about 26k nucleotide pairs)
what ensures that genes are turned on or off at the proper time
regulatory DNA sequences
do all RNA molecules produce proteins
no
each DNA molecule that forms a linear chromosome must contain what
- centromere
- 2 telomeres
- replication origins
The highly condensed chromosomes in a dividing cell are known as what
mitotic chromosomes
what is the name of the nucleotide sequence at which duplication of DNA begins
replication origin
what is a centromere
- specialized DNA sequence
- allows one copy of each duplicated and condensed chromosome to be pulled into each daughter cell when a cell divides
what attaches the chromosome to the mitotic spindle
kinetochore (a protein complex)
what are some examples of specialized DNA sequences
- centromere
- telomere
what is a telomere
- specialized DNA sequence
- the end of chromosomes
- repeated nucleotide sequences that allow the ends of chromosomes to be efficiently replicated
- protect the ends of chromosomes from being mistaken for a broken DNA molecule in need or repair
the proteins that bind to DNA to form eukaryotic chromosomes are divided into which classes
- histones
- non-histone chromosomal proteins
the complex of both classes of proteins with nuclear DNA of eukaryotic cells is known as what
chromatin
what is chromatin
the complex of both classes of proteins with nuclear DNA of eukaryotic cells
what are responsible for the 1st level of chromosome packing: nucleosome
histone
describe the beads on a string visual
- string is DNA
- each bead is a nucleosome core particle (DNA wound around a histone)
what is a nucleosome
DNA wound around a histone
what is linker DNA
the DNA in between each nucleosome core particle
describe the histones in the nucelosome core particle
- histone octamer
- 2 of each: H2A, H2B, H3 and H4 proteins
describe the interface between DNA and histone
142 H bonds in each nucleosome
describe the overall structure of histones
- highly folded due to the basic AA
- has a largely unstructed N-terminal AA “tail”
what causes nucleosomes to stack on each other
- nucleosome to nucleosome attractions
- involve histone tails (often the H4 tail)
- histone H1 is ofren present in a 1:1 ratio w nucleosome cores (called a linker histone)
is chromatin structure static?
- highly dynamic
- must allow access to the DNA
- some spontaneous wrapping/ unwrapping occurs
- also through ATP-driven chromatin-remodling complexes
what are ATP-driven chromatin-remodeling complexes
- cells have a lot of these complexes
- they allow nucleosome cores to be repositioned, reconstituted w diff histones, or completely removed to expose the underlying DNA
are there multiple diff chromatin structures
- a variety are possible
- but in the chromosomes of eukaryotes, DNA is only in long strings of nucleosomes
why is a variety of diff chromatin structures allowed
based on a large set of reversible covalent modifications of the 4 histones in the nucleosome core
what modifications can be done on the 4 histones in the nucleosome core
- mono-, di- and trimethylation of many diff lysine side chains
- acetyl groups are added/ removed
- methyl groups can be added/removed
what facilitates the addition/removing of acetyl groups to histones
- Added to specific lysines by histone acetyl transferases
- Removed by histone deacetylase complexes
what facilitates the addition/removing of methyl groups to histones
- Added to lysine chains by histone methyl transferases
- Removed by histone demethylases
where is heterochromatin commonly found
around centromeres and telomeres (but can be elsewhere)
what is heterochromatin, where is it found, and what is its relationship to transcription
- Tightly packed form of DNA
- Usually localized to the periphery of the nucleus
- Was thought to be inaccessible to polymerases (not transcribed), but now we know that’s not true
What is euchromatin, and what is its relationship to transcription
- Lightly packed form of DNA
- Often (but not always) under active transcription
- “beads on a string”
the enzymes that add/ remove modifications to histones in nucleosomes are part of what
multisubunit complexes
after a modifying enzyme writes its mark on one or more neighbouring nucleosomes, what happens
- writer enzyme works with a reader protein located in a protein complex
- the reader contains a module that recognizes the mark and binds right to the newly modified nucleosome, activating an attached writer enzyme, and positioning it near an adjacent nucleosome
what is a histone code
(a hypothesis) DNA transcription is largely regulated by post-translational modifications to these histone proteins
describe how barrier action can occur for heterochromatin
- tethering of a region of chromatin to a large fixed site (like a nuclear pore), forms a barrier that stops the spread of heterochromatin
- tight binding of barrier proteins to a group of nucleosomes can make chromatin resistant to heterochromatin spreading
- highly active histone-modifying enzymes can erase the histone marks that are required for heterochromatin to spread
what is a key characteristic of heterochromatin
self propogating
explain the heterochromatin propogation mechanism
- a modifying enzyme writes its mark on one or more neighbouring nucleosomes
- the reader contains a module that recognizes the mark and binds right to the newly modified nucleosome, activating an attached writer enzyme, and positioning it near an adjacent nucleosome
- heterochromatin continues to spread until it reaches a barrier DNA sequence (then it stops)
- reader-eraser proteins will then bind and remove heterochromatin specific marks and will return it to before
done gene expression occur during mitosis
no (it shuts down completely)
how do interphase chromosomes condense to form mitotic chromosomes
- in early M phase, gene expression shuts down, and histones are modified (this helps reorganize chromatin)
- cohesion proteins organize interphase chromosomes, which allows condensin to come in and form a linear chromosome axis
