Week 3 Readings Flashcards
homologous genes
when genes from different organisms have very similar nucleotide sequences, it is highly probable that they descended from a common ancestral gene
the vast majority of our DNA does not code for proteins or functional RNA molecules; instead, it includes
a mixture of sequences that help regulate gene activity, plus sequences that seem to be dispensable
how is genome size measured?
in nucleotide pairs of DNA per haploid genome
list the 6 basic types of genetic change that are crucial in evolution
- mutation within a gene
- mutation within regulatory DNA sequences
- gene duplication and divergence
- exon shuffling
- transposition of mobile genetic elements
- Horizontal gene transfer
mutation within a gene
- may change, delete, or duplicate one or more nucleotides
- thus alter the splicing of a gene’s RNA transcript or change the stability, activity, location or interactions of its encoded protein
mutation within regulatory DNA sequences
gene expression may be affected by a mutation in the DNA sequence that controls transcription of the gene
gene duplication and divergence
- a cell can make an extra copy of a gene/genome
- as the cell continues to divide, the original DNA sequence and duplicate sequence can acquire different mutations and assume new functions and patterns of expression
exon shuffling
two or more existing genes can be broken and rejoined to make a hybrid gene containing DNA segments that originally belonged to separate genes
transposition of mobile genetic elements
can move from one chromosomal location to another, thus altering activity or regulation of a gene
horizontal gene transfer
a piece of DNA can be passed from the genome of one cell to that of another, even to that of another species
how have biologists constructed a phylogenetic tree that goes all the way back to the origins of life?
- focused on the gene that codes for the ribosomal RNA (rRNA) of the small ribosomal subunit
- because the process of translation is fundamental to all living cells, this component of the ribosome has been highly conserved in all living species
human genome sequence
the complete list of nucleotides contained in our 23 chromosomes
other than its primary aim, how has the Human Genome project helped us?
- improvements in sequencing technologies
- new tools for handling large amounts of data
- cost of DNA sequencing has dropped
significance of transposons in our DNA
almost half of our DNA is made up of transposons that have colonised our genome over evolutionary time. most can no longer move
the number of protein-coding genes in the human genome may be unexpectedly small, but their relative size is unusually large. what does this mean?
- only about 1300 nucleotide pairs are needed to encode an average-sized human protein of about 430 amino acids; yet the average length of a human gene is 26,000 nucleotide pairs.
- most of this DNA is non-coding introns or regulatory DNA sequences
what does in-situ hybridisation allow us to do?
allows a specific nucleic acid sequence - either DNA or RNA - to be visualised in its normal location
how does in-situ hybridisation work?
makes use of single-strand DNA or RNA probes labeled with either fluorescent dyes or radioactive isotopes to detect complementary nucleic acid sequences within a cell, tissue, or organism
state 2 main applications of in-situ hybridisation
- explore how transcription regulators guide the development of multicellular organisms, providing important info ab when and where these genes carry out their function
- detect particular DNA sequences in an individual chromosomes (eg diagnose genetic abnormalities)
why do females and males have different numbers of types of chromosomes?
males, with their Y chromosomes, have an extra type of chromosome
homologous chromosomes
maternal and paternal versions of each chromosome
karyotype
an ordered display of the full set of an organism’s chromosomes
define a gene
a segment of DNA that contains the instructions for making a protein or RNA molecule
different possible functions of an RNA molecule
- used to produce a protein or may be final product
- eg may have structural or catalytic roles
- may play a part in regulating gene expression
how do we know junk dna is important?
comparisons of the genome sequences from many different species reveal that small portions of junk DNA are highly conserved among relative species
give an example of how there is no simple relationship between gene number, chromosome number, and total genome size
- human genome is 30 times smaller than some plants and 10 times smaller than some species of amoeba
- humans have a total of 46 chromosome, but some species of deer have 7 and some carp have more than 100
interphase chromosomes
exist as long, thin threads of DNA in the nucleus and cannot be easily distinguished in the light microscope
replication origin
site where DNA replication begins
telomeres
mark the ends of each chromosomes and serve as a protective cap that keeps the chromosome tips from being mistaken by the cell as broken DNA in need of repair
centromere
allows duplicated chromosomes to be separated during M phase
how are interphase chromosomes specially organised?
- each tends to occupy a particular region of the nucleus to prevent entanglement
- some chromosomal regions are physically attached to sites on the nuclear envelope or lamina which help chromosomes remain within their distinct territories
proteins that bind to DNA to form eukaryotic chromosomes are traditionally divided into
histones and non-histone chromosomal proteins
function of histones
responsible for the first and most fundamental level of chromatin packing - the nucleosome
how did investigators determine the structure of the nucleosome core particle?
treated chromatin in its unfolded form with enzymes called nucleases, which cut the DNA by breaking phosphodiester bonds. when nuclease digestion is carried out for a short time, only the exposed DNA between the core particles (linker DNA) will be cleaved, allowing the core particles to be isolated
SMC
structural maintenance of chromosomes proteins
functions of SMCs
associate with additional proteins to form an SMC ring complex that uses the energy of ATP hydrolysis to motor along the DNA, pushing out a loop of DNA in its wake
cohesion
SMC ring complex that organises the structure of interphase chromosomes
- cohesion rings will travel along the DNA, extruding loops until they run up against a sequence-specific clamp protein
- these proteins stall the cohesions and bind to one another, which draws together the DNA at the base of each loop
- it is the spacing and location of the clamp proteins that dictates the size and contents of each chromosomal loop
condensins
SMC ring proteins containing difference SMCs and accessory proteins than cohesins
function of condensing
- as cells prepare to divide, condensing replace most of the cohesins that formed the loops in the interphase chromosome
- then use the energy of ATP hydrolysis to form loops of their own, which wind the chromatin into a tighter mass of coils
two ways to adjust local structure of chromatin
- ATP-dependent chromatin-remodelling complexes
- histone-modifying enzymes
ATP-dependent chromatin-remodelling complexes
large protein machines, present at about one copy for every 5 nucleosomes, which can use the energy of ATP hydrolysis to change the position of nucleosomes on the DNA. they can render DNA more or less accessible
histone-modifying enzymes
- generate reversible chemical modification of histones
- tails of all four of the core histones are particularly subject to these covalent modifications, which include the addition and removal of acetyl, phosphate, methyl groups
acetylation of lysines
can reduce the affinity of the tails for adjacent nucleosomes, thereby loosening chromatin structure and allowing access to particular nuclear proteins
how do modifications serve as docking sites on histone tails for a variety of regulatory proteins?
different patterns of modifications attract specific sets of non-histone chromosomal proteins to a particular stretch of chromatin. some of these proteins promote chromatin condensation whereas others promote chromatin expansion and facilitate DNA access
heterochromatin
- most highly condensed form of interphase chromatin
- makes up around 40% of typical interphase chromosome
- half remains permanently condensed (eg centromeres)
- the remaining contains genes whose activity has been silenced (ie embryogenesis genes)
euchromatin
- 60% of interphase chromatin
- a lightly packed form of chromatin (DNA, RNA, and protein) that is enriched in genes, and is often (but not always) under active transcription.
why is DNA replication called semiconservative?
each parent strand serves as the template for one new strand, so each of the daughter DNA double helices ends up with one of the original strands plus one completely new strand
what types of proteins begin DNA synthesis?
initiator proteins at replication origins
why is DNA rich in A-T base pairs typically found at replication origins
A-T base pair is held together by fewer hydrogen bonds than a G-C base pair. therefore, it is easier to pull apart
why is beginning DNA replication at many places at once helpful?
it greatly shortens the time a cell needs to copy its entire genome
why is it critical that DNA synthesis be initiated only once at every replication origin?
failure to regulate this process could cause genes to be copied too many times or even lost
