Week 3 Textbook Flashcards
T/F humans have less DNA than E.coli but humans have more than amoeba
false
humans have more than e coli
amoeba have more than humans
how is genome size measured
it is measured in nucleotide pairs of DNA per haploid genome - it is per single copy of the genome
T/F we share a lot of our proteins with bacteria
true
they fall into closely related family groups
what does it mean when genes and their protein products are homologous
it means that genes from different organisms have very similar nucleotide sequences
- ancestral gene
T/F the vast bulk of our DNA does not code for proteins or for functional RNA molecules
true
- the vast bulk codes for regulating gene activity and complexity of gene expression at certain times
T/F the differences in DNA sequences are responsible for our phenotypes
true
hair, nails, eye colour, height = variation
what are some ways that a gene or genome can be altered
mutation in a gene (duplicates, deletes)
mutation is a regulatory gene
Gene divergence (changes in the gene and it continues to divide and infect others)
gene duplication
exon shuffling
transposition (chunks of gene removed and added)
horizontal transfer between organisms
difference between horizontal and vertical transfer of genetic information
horizontal = organism to another organism
vertical = parent to offspring pass of information
how can we use DNA sequence to trace the most distant evolutionary relationships
as relationships become more distant = less similarities in the genes but there is still a few hundred important genes that are shared by all
what gene to biologists look at when constructing a phylogenetic tree of all of our ancestors
they look on one gene that is in all living species, the one that codes for ribosomal RNA = rRNA
bc the process of translation is fundamental to all living cells
- comparing the tree of life allowed us to understand the division between bacteria and archaea
- the more similar the rRNA sequences, the more recently the two species diverged from a common ancestor
T/F Most of life’s genetic diversity lies in the world of eukaryotes
false
it is in the microscopic organisms
T/F less than 1% of the human genome are coding exons
true
this means that 1% are genes that code for our identity - coding for proteins
T/F more than half of our DNA is made up of transposons
true
they have been colonizing our genomes over evolutionary time
-most of the genome = repetitive nucleotides and non-protein coding DNA like rRNA, tRNA, RNA involved in splicing and telomere maintenance = cell remains good
what is in situ hybridization
allows a specific nucleic acid sequence - DNA or RNA to be visualized in its normal location
- scientists do not know where they are located
- it uses single-stranded DNA labelled with dye to detect complementary nucleic acid sequences within a call or tissue
- helped to explore how transcription regulators guide the development of multicellular organisms - this gives clues about when and where these genes carry out their functions
what is gene expression
it is the process by which the nucleotide sequence of a gene is transcribed into the nucleotide sequence of an RNA molecule and then translated into the AA of a protein
what are chromosomes
very long, DNA strands are packaged into chromosomes so that they can fit inside the nucleus - this is done by specialized proteins that bind and fold the DNA by making loops and coils that = higher level of organization - this prevents tangles = accessible to all enzymes and porteins to replicate and repair and interact
what is chromatin
it is when the long strand of DNA = thin is packed in a compact structure (linear compact structure)
what are homologous chromosomes
they are the maternal and paternal versions of each chromosome that is inherited
- the only nonhomologous chromosomes are the sex chromosomes in males and females, as females do not have a Y chromosome + inherit one X from the mom
how to do they make DNA visible to interpret
a traditional way of distinguishing one chromosome are with dyes that bind with a certain DNA sequence
what is a karyotype
it is a display in order of all 46 chromosomes and 23 pairs, showing the sex chromosomes as well
- used to detect abnormalities that are involved in inherited disorders
what is a gene
a segment of DNA that contains the instructions for making a particular protein or RNA molecule
- it is the functional units of heredity
- most DNA are not coded for protein but = excess - some of the DNA is interspersed between genes - mostly called junk DNA
T/F the more complex the organism the larger its genome
tru
what is the cell cycle
carrying genes, replicating, making copies, separating into new 2 daughter cells via cell division = series of events = cell cycle
IPMAT
explain the processes of interphase
the chromosomes are long and thin = messy - at this stage, they are referred as interphase chromosomes
they are not all tangled tho, they are spatially organized in a particular region of the interphase nucleus
- some chromosomal units are physically attached to the particular site on the nuclear envelope
- DNA gets replicated and cell is prepared to divide during this stage
- the replication starts at the replication origin (many eukaryotes have many start points)
- telomers are used to cap the ends of each chromosome
- the nucleolus is the most observable chromosomal organization in interphase
what are telomeres
they are repeated nucleotide sequences that are required for the ends of chromosomes to be fully replicated and not forgotten or cut halfway = protective cap
what are centromeres
it is a specialized DNA sequence that allows duplicated chromosomes to be separated during the M phase
- DNA coils up = compact structure = mitotic chromosomes
- the centromere is where the 2 duplicated chromosomes attach to be soon split into the daughter cells
what is the nucleolus
it is a large structure within the nucleus where ribosomal RNA is transcribed and ribosomal subunits are assembled
- seen under the light in the interphase part
- the parts of different chromosomes carrying genes that code for rRNA come together in the nucleolus
- they are then synthesized and combined with the proteins to form ribosomes
T/F mitotic chromosomes are thinner than interphase chromosomes
false
interphase chromosomes are thin but organized by region in the nucleolus
mitotic chromosomes are thicker and packaged significantly by other proteins
why is the DNA loosely packaged in interphase
this is because it needs to be throughouly prepped and checked for errors in the sequence before it contuines to mess up the daughter cells
- it also needs to be flexible and open for on-demand access to different regions of the chromosome
- unpacking enough to allow protein complexes to have access for DNA replication, DNA repair or gene expression
what are histones
protein that binds to DNA to form chromosomes
- the mass of one histone is the same as the mass of DNA itself
- when histones or non histone chromosomal proteins interact with DNA it is then turned into chromatin
what is a nucleosome
histones package DNA and stack to form nucleosomes
- it is a beadlike structural units
- nucleosomes convert DNA in interphase into chromatin fibre
when looking through a microscope, the long string and bead - the bead id called a nucleosome core particle
how did investigators determine the structure of the nucleosome core particles
they unfolded the string of beads using enzymes = nucleases - this cuts the phosphodiester bond between nucleotides (sugar and phosphate) = nuclease digestion
- when digested, only the exposed DNA between the core particles = liner DNA will be cleaved - this allows the core to be isolated
what did the investigators find when they used the nuclease enzyme to nuclease digest a nucleosome
they found that an individual nucleosome particle consists of a complex of 9 histone proteins, 2 H2A, 2H2B, 2H3, 2H4 with a double-stranded DNA rapped around this histone octamer which is all 8 of them together
there is DNA that is not being coiled around a histone, but it joining the beads together
explain the structure of a histone octamer
4 histones are small proteins that are positively charged - this helps them attract to the backbone of DNA = electrostatic interactions
- each histone has an unstructured N-terminal amnio trail that extends out from the nucleosome core particle
- the histone tails = reversible chemical modifications that control many aspects of chromatin structure
how are nucleosomes further packaged?
they do not stay in their string and bead form, they are further packed on top of each other = chromatin fiber - this type of packing is aided by the H1 histone protein which is the 5th one = linker histone = changes the path of DNA to coil = pulls side by side nucleosomes together
what is the next packing structure after chromatin and how does it happen
the linear chromatin fiber turns into a serieis of chromatin loops that extend from the center of the chromosomes to make bunny ears - this allows the interphase chromosome to fold into an even more circular compact form
- these loops are made because of a family of proteins = SMC = structural maintenance of chromosomes protein forms the actual ring
- the SMC forms a SMC ring complex and uses the energy of ATP hydrolysis to motor the DNA and push out a loop of DNA
what is cohesin
it is the SMC ring complex that organizes the structure of interphase chromosomes
- a special subset of cohesion holds together the sister chromatids after DNA has been replicated
- multiple cohesion load onto each interphase chromosome where they produce an extended series of loops
- they are not done randomly, except they will travel along the DNA until they run up against a special sequence-specific clamp protein
- this specific sequence draws together the DNA at the base of each loop
what dictates the size and shape of each chromosomal loop
the distance and placement of the sequence-specific clamp protein
the interaction of the clamp proteins stop further looping
explain the significance of the cohesion localized to the centromere
it plays a large role in the organizing of interphase chromosomes
- they hold together 2 sister chromatids in a duplicated chromosome
- this attachment is maintained throughout most of mitosis to have a proper segregation into the daughter cells
what packing occurs after the SMC ring complex 1
during mitosis, we now understand that there is a second set of SMC ring proteins called condensins
- they are built around the ring-shaped SMC proteins, but they have different accessory proteins
- as cells prepare to divide, the condensins replace most of the cohensins that formed the loops during interphase and use ATP to form loops of their own (loops within loops) = final level of condensation
what are chromatin-remodelling complexes
family of enzymes that use ATP to alter the arrangement of nucleosomes in eukaryotic chromosomes - this changes the accessibility of the DNA to other proteins to interact
- they are also known as ATP-dependent chromatin-remodelling complexes
- in mitosis, most of these complexes are inactivated which helps them maintain their coils and then activated when needed
what are histone-modifying enzymes
histone-modifying enzymes catalyze reversible chemical modifications of histones
- the tails of all 4 histone proteins = covalent modifications which include the addition or removal of an acetyl, phosphate, or methyl group
- these modifications have important consequences for the packing of chromatin fibre
- different patterns of modification attract specific sets of non-histone chromosomal proteins to a particular stretch of chromatin
- specific combinations of tail modifications have different outcomes, sometimes they can access a piece of chromatin to be newly replicated or actively expressed or shut down, this is why histone-modifiying enzymes work with ATP-dependent chromatin remodeling complexes to condense and relax stretches of chromatin according to the needs of the cell
T/F in interphase, the chromatin has different regions where the genes that are being actively expressed are less packed and the genes that are more silent are more packaged
true
this helps them check for errors of exons vs introns
what is heterochromatin
it is the most highly condensed form of interphase chromatin
- heterochromatin is about 40% of the interphase chromosome
- most of them remain permentaly condensed like around the cap of telomers
- the remaining heterochromatin are no longer needed if they are repressed
what is the form of euchromatin
while 40% of interphase chromatin = heterochromatin
the 60% is in the form of euchromatin
it is the form in gene-rich areas = less compact structures so that proteins can be involved in transcription
what is DNA replication
it is so that DNA can accuratly copy into daughter cells to multiply or grow
- the occurs before the cell divides to produce 2 same daughter cells
- they want to do this in an accurate yet efficient way, but also monitor for errors and repair genetic material to avoid mutations
- DNA can be damaged by the environment, tradition, mutations, etc
what is an example of a good mutation
when mutation can make bacteria resistant to antibiotics that are used to kill them
- if the mutations are not dangerous to the point where they are deadly, the accumulate for hundreds of years and are the main reasons for variation
what is a DNA template
it is known as a mold or template that can serve as a pattern for the production of other molecules
- one strand of DNA directs the synthesis of the complementary strand
S and serve as a template to make S’ while S’ can be a template for S since they are complementary
T/F Since one S strand is the template of another, one DNA double helice ends up with one original and one new strand that has been formed
true
this is said to be semiconservative
what are initiator proteins
the process of DNA synthesis is begun by these proteins to bind to specific DNA sequences called replication origins (nucleotide sequence to begin)
- the initiator proteins prey the H-bonds between the helix, it preys a small area at a time which doesn’t require lots of energy - this can also be done at room temperatures
- once the DNA opens up the helix, it attracts proteins that continue the process of replication, forms a machine.
T/F A-T base pairs are easier to pull apart by initiator proteins than G -C
true
they have fewer hydrogen bonds to make them less strong
T/F the human genome has DNA replication sequences at many places
true
this shortens the time a cell needs to copy its entire genome
why is it important that DNA synthesis only occurs once
it should only be initiated once at every replication origin
if done too many times = diseases
what are replication forks
DNA molecules are split and form Y-shaped junctions called forks
- at each fork you have replication machines moving along the DNA opening up the helix and making a new daughter strand based on the template (unzipping and copying DNA as they go)
- the 2 forks move away from each other
the replication process on both forks is bidirectional
what is DNA polymerase
the movement at the replication fork is driven by the action of the replication machine = this enzyme called DNA polymerase
- catalyzes the addition of nucleotides starting from the 3’ and building from 5’ to 3’
- using the template strand, it will build complementary bases A, G, C, T
explain the polymerization reaction that takes place from DNA polymerase when replicating
it involves the formation of phosphodiester bonds between the 3’ end of the growing chain and the 5’ end of the incoming nucleotide which enters the reaction as a deoxyribonucleoside triphosphate
- the energy is provided by the incoming deoxyribonucleoside triphosphate itself - bc it hydrolysis the high energy phosphate bonds which drives the reaction that links it to the chain
- this releases a pyrophosphate
which undergo another 2 molecules of phosphate which make the DNA polymerase process irreversible
explain how the replication fork is assymetrical
DNA is antiparallel which makes them run in opposite directions
- bc of this, the replication fork, one new DNA is made on the TEMPLATE that runs in the 3’ to 5’ and the other DNA strand being synthesized is running on the TEMPLATE in the 5’ to 3’ direction this causes a lag in one of the strand as the direction of replication is in the opposite direction (side the 5’ to 3’ on the template makes a good new strand that runs 3’ to 5’ in the same direction as the fork, but the other strand lags behind”
what happens to the one strand on the DNA replication fork that is moving in the opposite direction of the fork
it creates discontinuous separate small pieces of new DNA as it keeps moving backwards to keep up with the newly revealed DNA
these are called lagging strands because the polymerase needs to backstitch which delays the synthesis
what are okazaki fragements
it is the result of the DNA polymerase working in the opposite direction as the replication fork
- creates small pieces on the template strand
they are glued back together by another enzyme simultaneously
explain leading and lagging strands
the lagging strand = okazaki fragements
the leading strand is the one that is continuous, not delayed and it moving in the same direction as the replication fork opens
