Genome Diversity/Dynamics in Time - After Midterm

Question 1

Expression

Answer 1

• Expression is just the process of getting from the gene itself to the functional product
• This means expression involves transcription, translation, and protein folding
• Expression is dynamic, and changes over the lifetime of a cell
• Phenotype depends (in part) on what parts of the genome are expressed

Question 2

Very Brief overview of Transcription in Prokaryotes

Answer 2

• There are sequences upstream of the gene called the -35 box and the -10 box that make up the promoter
• A protein? called the sigma factor binds to the boxes and recruits RNA polymerase, which then carries out transcription

Question 3

Very Brief Overview of Transcription in Eukaryotes

Answer 3

• Eukaryotic promoters are very different, as they can be made-up of different recognition elements (but the TATA box is usually one of them)
• The recognition elements recruit transcription factors
• These transcription factors then help recruit additional transcription factors, which then recruit the RNA polymerase

Question 4

RNA Dynamics

Answer 4

• The expressed part of the genome is in constant flux, so RNA will keep being produced as long as the machinery is present
• RNA will also degrade at a particular rate
• If the rates of RNA transcription and RNA degradation are perfectly balanced, there will be a steady amount of RNA in the cell
• the strength of the promoter will affect RNA production rates — different promoters with different sequences can have different binding affinities, with promoters with higher binding affinities being able to produce RNA at a faster rate
• regulatory elements either upstream or downstream of the binding sites can recruit other proteins that either increase or decrease transcription rates

Question 5

Regulatory Elements

Answer 5

• “regulatory elements” refers to the full collection of transcription factors and their DNA binding sites
• proteins that increase transcription are called ‘activators,’ and proteins that decrease transcription are called “repressors”
• DNA sequences that promote transcription are called “enhancers,” and DNA sequences that decrease or prevent transcription are called “silencers”

Question 6

Degradation of mRNA

Answer 6

• miRNA can do targeted degradation of mRNA
• miRNA “silences” these genes by cutting up their mRNA
• There are a variety of other components (transcription factors, miRNA, etc) that act together to influence the level of mRNA in the cell

Question 7

Transcriptomics

Answer 7

• The study of RNA expression levels across the genome, making comparisons both within genome (between genes) and between samples (different phenotypes)
• Is a “holistic” approach, like all other -omics approaches

Question 8

Combinatorial control

Answer 8

• the integration of many inputs to give an output
• a combination of genes, transcription factors, etc go into transcription rates
• transcriptomics is a good technique to use to measure combinatorial control since it offers a whole-genome perspective

Question 9

Types of Plastic Responses to the Environment

Explain them and draw them out

Answer 9

Direct response: When the cell’s phenotype changes as a direct response to an environmental trigger
- An example is mechanosensitive channels in cells
Gene mediated response: cell phenotype changes after an environmental trigger turns (a) gene(s) off or on
Histone modification: a signal in the environment triggers histone modification to occur, which can change gene expression, and thus change protein levels
- a well known example is when acetylation of the lysine residue on the histones causes the DNA to be more loose (euchromatin)
Methylation: an environmental signal triggers the methylation of specific DNA residues to occur, which leads to a change in gene expression and thus a change in protein levels
- The methylation of cytosine promotes heterochromatin formation, and thus decreases DNA transcription

• Histone modification and methylation are considered to be epigenomic modifications

Question 10

Siamese Cat Example: What type of plastic response is at play?

Answer 10

• In Siamese cats, their extremities tend to be black/darkly colored, and their bellies/undersides tend to be lighter
• The molecule responsible for the darker color is called melanin
• The pathway to produce melanin involves tyrosinase taking various chemical precursors and assembling them into melanin
• In siamese cats, their tyrosinase has a mutation in which the tyrosinase is temperature sensitive and can’t work at higher temperatures, and therefore can’t produce melanin in the warmer parts of the cat
  This phenotype is due to a direct response, because tyrosinase responsible for the phenotype (melanin or no melanin) is responding directly to the temperature

Question 11

Seasonal Coat Color Example: What type of plastic response is at play?

Answer 11

• Seasonal coat color change is due to a gene mediated response
• We can look at how different genes’ expression patterns differ when the fur is one color vs when the fur is another color to try and see which genes are responsible for this change, and what environmental cues they may be responding to
• One way we can measure gene expression levels is by doing RNA-seq

Question 12

Seasonal Coat Color: RNA-seq

Answer 12

• RNA-seq has a few basic steps. First, we synthesize cDNA from RNA so we can sequence it later on. We then fragment the cDNA, attach illumina adapters to the fragments and sequence them, then align (match up) the fragments to the genome and look at how much RNA is present (after normalizing, of course).
• RPK and RPKM by themselves for a gene don’t tell us much, because we have to have something to compare to
• One comparison that can be done is to compare to a housekeeping gene
• A housekeeping gene is one that is responsible for cell maintenance and won’t change much if at all between different organisms(might have to be in same species though) or different time-points in a single organism’s life
• A more popular way to compare genes is to do a direct comparison
• A direct comparison involves using mean-centered expression levels
• mean-centered expression levels involve taking the average for that same gene at different time points in the same organism (or maybe for the same gene in different organisms?), calculating the mean, and the calculating the fold above or below for each sample (see 11/8 lecture for examples)
• This type of gene expression profiling is useful for comparing samples with identical genomes and with mutated genomes!

Question 13

RPK

Answer 13

• Reads per kilobase
• RPK is how we normalize for gene length when looking at how much RNA is present in RNA-seq
• to calculate RPK, we use the following equation: # reads gene A/(length gene A/1000), which is the same as (# reads gene A / length gene A) x 1000

Question 14

Things I should do practice problems on:

• Calculating RPK (11/6 - 11/8)
• Calculating RPKM (11/8)
• Heat map examples (11/8)
• Mean-Centered expression levels (11/8)

Answer 14

Done

Question 15

RPKM

Answer 15

• Reads per kilobase per million reads sequenced
• RPKM is how we normalize for RNA sample size when doing RNA-seq
• The calculation is: RPK/total reads x 1,000,000

Question 16

GO

Answer 16

• Gene Ontology

- It is a formal naming scheme that assigns functions to genes and clusters them together

Question 17

Combinatorial Control vs Simple Control

Answer 17

• Simple control is when only one gene is responsible for a phenotype (I think?), and combinatorial control is when multiple things are working together/happening at once to give a particular phenotype

Question 18

Coregulation

Answer 18

• When gene expression of different genes go up or down together
• Co-regulation is a hallmark of genes that are turned on (or off) by the same transcription factor

Question 19

ChIP-seq

Answer 19

• Chromatin Immune Precipitation Sequencing
• Is used to tell where in the genome a protein of interest binds
• Is particularly useful for seeing where certain transcription factors bind, since the location of their binding can give insight into what genes they are regulating
  ChIP-seq works in the following way:
• You take your genome and cross-link the proteins to the DNA so they are covalently bound
• The genome is fragmented
• The fragments are then purified, usually be running over a column of some sort that has antibodies specifically for your protein of interest, so the DNA-protein complex of your protein of interest will stick to the beads while you wash everything out, and then you’ll elute your DNA-protein complex off
• The cross-linkages between the DNA and protein is then broken, and the remaining fragments can be sequenced and mapped to the genome
• Straight-up ChIP-seq data can’t really tell you if a gene is unregulated or not, because 1) it doesn’t tell you if the transcription factor is an activator or repressor, and 2) transcription factors don’t always bind directly in front of the gene they are acting on
• To overcome the first problem, we usually use ChIP-seq data with RNA-seq data to determine if up regulation or down-regulation is occurring

Question 20

Post-It Note: Why are some potential reasons individuals/species evolved to even bother with gene mediated responses in the first place?

Answer 20

• To set a threshold for response
• To be able to conserve resources
• To be able to adjust the level of response
• To be able to integrate multiple signals and affect multiple genes (combinatorial response)
• To control timing

Question 21

Histone Modification

Answer 21

• An epigenetic plastic response
• Typically has a longer-lasting affect than gene-mediated responses
• There are 8 histones that form a nucleosome, and each histone has a “tail;” these tails control how tightly the histones bind to the DNA
• When the tails are unmodified, they are positively charged and thus wrap tightly around the DNA, putting us in the heterochromatin state
• When the tails are acetylated, however, they become uncharged and they “let go”
• It should be noted that acetylation isn’t the only modification that can lead to this chromatin change, and that the acetylation that is being discussed isn’t the only acetylation that can cause this change
• In this example, it is the lysine residues in the tails that get acetylated, causing them to lose their positive charge
• Acetylation occurs by histone acetyltransferases (HATs)
• De-acetylation occurs by histone deacetylaces (HDACs_
• Since it is acetylation that leads to the DNA being more accessible, HAT promotes transcription and gene expression
• We can use ChIP-seq to target different histones to see which parts of the genome have histone modifications; we can even target specifically modified histones and not include un-modified histones

Question 22

Types of chromatin

Answer 22

• Euchromatin: open DNA in which the DNA isn’t tightly bound to the histones and is available for transcription
• Heterochromatin: “closed” DNA in which the DNA is wound tightly around the histones and is not accessible for transcription
• Heterochromatin can be converted into euchromatin via histone acetyltransferases (HATs). The HATs acetylate the lysine residues on the tails of the histones, which causes them to become neutral and not have a tight of a hold on the DNA
• Euchromatin can be converted back to heterochromatin via histone deacetylases (HDACs). The HDACs remove the acetyl groups from the lysines on the histone tails, causing them to bind more tightly to the DNA since they have regained their positive charge

Question 23

Methylation

Answer 23

• An epigenetic plastic response
• Methylation is longer-lasting than gene-mediated responses (and histone-modification?)
• Methylation is normally stable (unchanging) throughout and organism’s lifetime
• The methylation of C’s in the CpG islands that are adjacently upstream of 70% of genes represses the expression of those genes (these CpG islands are located in the promoters)
• ## The methylated cytosines in the CpG islands recruit HDACs, which promote heterochromatin formation and repress gene transcription

Question 24

Bisulfite sequencing

Answer 24

• A technique used to locate the methylated cytosines in a genome
• Bisulfite sequencing takes advantage of bisulfite conversion: un-methylated (normal) cytosine can be converted into uracil via bisulfite conversion
• If a cytosine is methylated, however, this conversion doesn’t happen
• Bisulfite sequencing has the following steps:
• First, the DNA from the cell type of interest is subjected to bisulfite conversion
• Next, Illumina sequencing is done on the DNA
• Lastly, we compare our generated sequence to a reference, and look for locations in our sequenced genome that are C’s in the same locations that they are C’s in the reference genome. These spots are where the methylated cytosines are
• Un-methylated cytosines will show up as T’s in our Illumina sequencing, because they will have been converted into U’s via bisulfite conversion

Question 25

development

Answer 25

• Changes in phenotype and the mechanism that carry them during the reproduction and growth of an organism
• these mechanisms often include change in gene expression that can be measured overtime and in space

Question 26

division of labor

Answer 26

• labor is divided in two different ways in a developing organism, in the following order:
  1) regional specification: setting up unique areas within the embryo that will eventually become different body parts
  2) differentiation: the process of cells within particular regions becoming more specialized

Question 27

The “-derms”

Answer 27

• ectoderm, endoderm, and mesoderm
• These are the “seed” cell types from which all specialized cell types arise
• ectoderm cells become things like skin cells, nerves, and pigment cells
• endoderm cells become things like lung cells, pancreas cells, and GI tract cells
• mesoderm cells become things like heart muscle cells and blood cells
• They are pluripotent stem cells

Question 28

stem cells

Answer 28

Def: cells from which multiple cell types could “stem”

• Stem cells have different levels of “potency”, meaning different levels of the ability of which they can turn into there cell types.
• The highest degree of potency is totipotent embryonic stem cells
• The second highest degree of potency is pluripotent embryonic stem cells
• The third level of potency are multipotent stem cells
• The last level, which are the most differentiated, are the differentiated cells
• Over an organism’s development, their cells go from originally being totipotent to fully differentiated
• de-differentiation is the process of going back up the scale to a more potent cell type to produce induced stem cells

Question 29

iPSCs

Answer 29

• induced pluripotent stem cells
• They are actually totipotent stem cells, meaning they can become any cell type (pluripotent stem cells are one of the three “-derm” cell types and are thus more limited in what they can be differentiated into)
• Scientists have been able to make iPSCs by taking a person’s skin cells and using either a chemical cocktail or specific gene transcription factors that can turn the cells back into totipotent embryonic stem cells
  
  • The chemical cocktails target known regulators of differentiation
• Creating iPSCs is basically reprogramming your cells by “tricking” them into thinking they’re young again
• The obvious potential therapeutic usage of iPSCs is that they can be differentiated into different cell types, maybe even regenerate an entire new organ to be able to do an organ transplant
• To make sure the reprogramming worked to turn the cells into iPSCs, we can compare the epigenome of normal vs our artificial stem cells
• There are two reprogramming “failure types” that we can get:
  1) retained “memory” of the differentiated cell, in which the expression pattern of our attempted iPSCs is similar to that of the somatic cells, or at least in some regions
  2) induction specific aberrations (problems)
• researchers want to ensure that the epigenome is normal before using the iPSCs for therapeutic use, since they could potentially be cancerous or cause other problems if not checked out first

Question 30

Environment in Developmental Biology: Drosophila example

Answer 30

• spacial variation in environmental determinants are responsible for initiating regional specification
• In drosophila embryos, there are spatial factors (bicoid mRNA) from the mom that get injected into the anterior part of the embryo
• The bicoid proteins get synthesized in this anterior region, and the proteins are then able to diffuse throughout the embryo, forming a gradient in which the level of the protein is highest the anterior region and lowest in the posterior region
• This gradient sets the stage for threshold induction of gene expression, in which genes get expressed in the locations that have protein levels above some threshold and don’t get expressed in locations that don’t have protein levels above the threshold
• If we then suppose there is some other gene that is inhibited by bicoid, then this gene’s products will exist in a gradient opposite that of the gene product of the gene that was turned on by bicoid.
• With combinatorial control, there may be even more genes and proteins in play here (in fact there definitely are)
• By looking at the transcriptome and epigenome in different regions overtime, we can start to understand how the expression of genes in different locations is coordinated

Question 31

Case Study for Regeneration: Sea Anemone

Answer 31

• sea anemones are able to regenerate
• To be able to understand their regenerative properties, we want to know what is being expressed in the cells at different time points in the regeneration process
• What scientists did was they cut a sea anemone into four sections and did RNA-seq on the sections at different time points, then generated a heat map of different expression of particular genes at the four different time points

Question 32

Regeneration in Humans

Answer 32

• When fully differentiated human cells are damaged they can’t be repaired
• Doctors would like to be able to fix this
• There are two main ways in which we study regeneration
• The first way is to look at other animals that are capable of regeneration (like sea anemones), figure out how they do it and then see if humans have any gene homologs or are capable of any of these mechanisms
• The second approach to studying regeneration is to make de-differentiated versions of our own cells by making iPSCs and then trying to differentiate them into the cells we would like them to be
• As adults, we don’t have any totipotent or pluripotent stem cells, but we do have some multipotent stem cells: bone marrow and umbilical cord/placental blood (if it was saved from our birth)
• When trying to solve some problem in an individual that requires making iPSCs, we would generally like to use that individual’s cells (cord blood)
• However, in cases in which the problem we’re trying to fix is an early childhood disease, like early childhood leukemia, the child’s own cells won’t likely be useful, because the disease is most likely genetic, so any cells from that individual will have the problem too

Question 33

Heat map organization

Answer 33

• Heat maps order things in a programmatic way, so it doesn’t just put all the samples at time 1 together and then all the samples at time 2 together and so on
• If samples at T1, T2 etc are grouped together, that can be reassuring because it tells you that there is an actual pattern going on, and that the differences aren’t just due to differences between the different samples

Question 34

Stem Cell Therapies

Answer 34

• allogenic stem cell therapy: uses multipotent stem cells harvested from a relative
• autologous stem cell therapy: uses your own multipotent stem cells- sometimes with genetic modification

Question 35

Cloning

Answer 35

• Cloning is the process of taking an adult cell and making a new organism from it
• We have only really been able to do this in mice so far (as far as animals go)
• Conservation scientists would like to be able to do this with endangered species
• The process would involve taking some of the animal’s cells and making frozen repositories of the somatic cells, making iPSCs from them, and then differentiating them

Question 36

Northern White Rhino Case Study

Answer 36

• The northern white rhinos are nearly endangered, with the only two left in the world being female
• The goal is to do cloning to help save the northern white rhino by making more of them
• The current “game-plan” for carrying this out is as follow:
  1) make iPSCs from rhino samples
  2) turn these iPSCs into gametes (sperm and oocytes)
  3) use in vitro fertilization to combine the gametes
  4) transfer the embryos into a southern white rhino surrogate mom

Question 37

Proteome

Answer 37

• The proteome is the collection of protein molecules present in the cell
• The questions we want to answer regarding a proteome are
  1) what proteins are present?
  2) how much of each protein is present?
  3) what modifications do the proteins have?

Question 38

Prokaryotic Translation Control

Answer 38

• prokaryotic mRNA contains sequences called Shine-Dalgarno sequences that act as binding sites for the ribosome
• different ribosome binding sites will have different rates of translation initiation

Question 39

Eukaryotic Translational Control

Answer 39

• Eukaryotic mRNA don’t have sequences that can affect the rate of translation like they do for transcription, but their secondary structures can affect the rate of translation
• Specifically, the secondary structure in the 5’ untranslated region can slow the rate of translation
• Codon usage can also control translation efficiency
  
  • Cells use codon sequences that correlate to the tRNAs that are more present in the cell when they want faster translation

Question 40

Protein Degradation

Answer 40

• Proteins get degraded by a molecule called the proteasome that basically acts as a paper shredder for proteins
• There are other enzymes in the cell that recognize the proteins that need to be degraded, and they will tag these proteins via ubiquitination
• The proteasome will recognize the ubiquitin tag on the protein and will cut the protein up

Question 41

“Sequencing” Proteins

Answer 41

• We can’t sequence proteins like we can sequence DNA, because
  a) there is no “protein polymerase”
  b) the ribosome is too complex to function well in a flow cell
  c) we don’t have reversible terminators for amino acids
  d) The proteome is made of discrete molecules, not a single genome with overlaps
• What we do instead is mass spectroscopy
• Mass spectroscopy involves breaking apart the proteins, measuring the mass and charge of the fragments, determine potential amino acids present and match each fragment to the database
• Mass spectroscopy gives us a snapshot of the active part of the genome
• Mass spec is limited in the number of proteins it can study at once, however
• Mass spec can help us…
  1) understand interactions, such as how proteins influence each other
  2) understand protein mechanisms, such as how a disease or a biological process works
  3) look for biomarkers, which are molecules in the blood stream that can be indicative of a disease

Question 42

Brief Overview of Natural Selection

Answer 42

• Natural selection is a mechanism of evolution; it is a way the evolution happens
• There are 3 main processes that occur in natural selection: mutation, selection, and replication
• Mutations first come about somewhat randomly. One or multiple mutations can allow some individuals to have better survival rates than others, which acts as a selective force, such as a mutation that allows an organism to “smell” when a predator is near. The organisms with these advantageous mutations are more likely to survive and pass on their advantageous mutation to their offspring
• Any time you have these three processes, you have natural selection
• Genomes enable heritable phenotypic variation; environments provide selective pressure
• In other words “ Natural selection explains the survival of the fittest, but not the arrival of the fittest”

Question 43

How variation is generated

Answer 43

• This mainly goes back to what we talked about earlier in types of mutations
• Variation can occur due to
  a) point mutations
  b) structural variation
  i) copy # variation: part of the gene varies in how many times it is represented
  ii) inversions/re-arrangments: portion of the genome flips direction
  iii) translocation: portion of the genome relocates
• copy number variation can occur at every scale in the genome; it can occur with single genes, chunks of genes, parts of gens, chromosomes, and even whole genomes
• point mutations and structural variation can be caused by DNA damage, mistakes in replication, mistakes in recombination, etc
• inversions and duplications can occur via recombination

Question 44

Fitness

Answer 44

• Fitness is basically just reproductive success of an individual
• fitness measures how good a genotype is at leaving offspring relative to other genotypes in a particular environment
• We can think about mutations in terms of how they will affect an organism’s fitness; there are three types of mutations in relation to fitness:
  1) beneficial: variant has a positive effect on fitness
  2) deleterious: variant has a negative effect on fitness
  3) neutral: variant doesn’t effect fitness

Question 45

adaptation

Answer 45

• a change or the process of change by which an organism becomes better suited to its environment

Question 46

Are mutations random?

Answer 46

• Individual mutations are random, but the frequency at which the mutations occur varies depending on the type of organism
• There exists a trend that the larger an organism’s genome size, the lower its mutation rate; meaning bacteria will have a higher mutation rate than humans
• Mutations typically happen anywhere in the genome at random

Question 47

Are mutations typically beneficial, deleterious, or neutral?

Answer 47

• Mutations tend to be deleterious because most proteins are sensitive to change, so changing just one amino acid can mess things up
• natural selection will purge these deleterious mutations, however, allowing for beneficial mutations to spread
• Neutral mutations may or may not stick around since they don’t have an affect on reproductiveness

Question 48

Sea Snail Adaptation Example

Answer 48

• There are two species of limpets along the west coast, which I’ll refer to as “northern” and “southern”
• There is an enzyme in the limpets called cytosolic malate dehydrogenase which is a key metabolic enzyme
• The enzyme’s activity decreases as the temperature increases, and it decreases at a faster rate in the northern species, hence why they live in the north
• The northern species of limpets has a point mutation in the gene for this enzyme, which causes it to have less hydrophobic interactions than the enzyme in the southern species does, making the northern species’ enzyme more sensitive to heat

Question 49

Re-sequencing

Answer 49

• Re-sequencing is a technique that involves sequencing the genome of an organism/cell for which you already have a reference genome for, and the comparing your newly sequenced genome to the reference to look for any mutations that may be contributing to the phenotype you see in your sequenced individual
• Is used by doctors and researchers to find the cause of antibiotic resistance in bacteria, and to find what mutations are present in cancer cells
• In the case of bacteria, they take the resistant strain, put it through next-generation sequencing, and find overlaps and map to the reference genome of a bacteria of that species that doesn’t have the antibiotic resistance mutation

Question 50

Antibiotic resistance in Bacteria

Answer 50

• Antibiotics typically work by binding to the active site on the bacteria for an important molecule the bacteria needs
• One type of mutation that leads to antibiotic resistance in bacteria is target modification, in which the target of the antibiotic changes so it can’t bind there anymore
• A mutation responsible for multi-drug resistance is a mutation in the efflux pump, which pumps out all of the things that are bad for the bacteria at a faster rate?

Question 51

Neutral Drift

Answer 51

• Neutral drift is just genetic drift of a neutral mutation
• Ex: say there are some birds that are usually blue, but one has a mutation that makes it red, and this mutation doesn’t effect its survival or reproduction in any way
• suppose the birds get caught up in a hurricane and get scattered across various islands, with only red birds ending up on one island
• All birds on that island will now be red as they red birds reproduce and pass on their mutation (assuming another mutation doesn’t occur), giving us two distinct populations; blue birds on one island and red birds on another
• This is an example of how a neutral mutation can spread
• Sometimes evolution is purely the result of chance

Question 52

Role of DNA Polymerase in Evolution

Answer 52

• Many mutations arise from DNA polymerase making mistakes
• DNA polymerase can make single nucleotide mistakes, in which is inserts an extra nucleotide, inserts the wrong nucleotide, etc; more dramatically, it can sometimes completely copy a gene, taking that cell from one copy of the gene to two (this is called gene duplication)
• Since these mutations can lead to evolution, we can say DNA polymerase is partially responsible for evolution

Question 53

Gene duplication

Answer 53

• When DNA polymerase copies a gene, taking us from one copy to two
• Gene duplication is kind of a way to “test out” mutations and experiment with the gene product, because as long as one gene is still intact, it can still carry out its function
• Mutations are random, however; its not like the cell realizes it has two copies, and therefore plays around with one and gives that one more mutations while keeping the other one completely the same
• Having multiple copies of a gene just means that, should a mutation occur in one copy, there is a higher likelihood that that mutation can get passed on and that copy can maybe acquire more mutations that lead to a completely different function, since the cell never loses its original functionality because the other copy is still there (assuming that copy doesn’t get any dramatic mutations as well)
• This process of copies of the same gene diverging from one another is responsible for making paralogs
• We can find gene duplication by doing a single genome scan, which takes each gene that is identified in the genome and searches the rest of the genome to see if it aligns somewhere else
• We can also get clues as to if gene duplication has occurred from next-generation sequencing; these genes with gene duplication will have unusually high coverage and the reads will map well to multiple places in the genome

Question 54

Abiogenesis

Answer 54

• Abiogenesis is the generation life from non-life
• The hypothesis for how life came about is that the laws of physics and the chemistry of the early earth led to the spontaneous emergence of life

Question 55

LUCA

Answer 55

• Last universal common ancestor

- There was life before LUCA!; life probably arose multiple times

Question 56

RNA World Hypothesis

Answer 56

• The hypothesis is that before LUCA, self-replication was carried out by ribozymes, with RNA also acting as the genetic material in an RNA world
• This hypothesis came about partially from the fact that RNA can form ribozymes, so it wouldn’t be too crazy to think that these ribozymes might have been able to carry our replication
• At some point along the way, amino acids came into the picture, and overtime they began to dominate the enzymes of the cell (if we can call them cells) because they had more functionality and variety, and could thus do more things
• This idea about proteins slowly coming into the picture and dominating arises from the study of the current-day ribosome, which is a mix of RNA and protein, with only RNA present in the active sites

Question 57

Endosymbiont Theory

Answer 57

• Mitochondria and chloroplasts used to be cells on their own that got engulfed by larger cells and developed a symbiotic relationship with them, leading to eukaryotic cells
• It’s believed that the first “blending” was of an archaebacteria engulfing a proteobacterium (giving us the basis for animal cells), and then this archaebacteria/proteobacterium system engulfed a cyanobacterium, giving us the basis for plant cells
• Comparative genomics has shown that the DNA in mitochondria and chloroplasts has shared homology with prokaryotes
• Varying amounts of mitochondrial and chloroplast DNA was transferred to the nucleus overtime as they continued their symbiotic relationship, most likely to help with coordination

Question 58

Post-It Essay: Does the total complexity of all genomes in a biosphere inevitably increase as the environment changes and organisms compete with one another? Why or why not?

Answer 58

• The majority of scientists argue yes, increasing complexity is inevitable, but just because it is inevitable doesn’t mean it’s directional
• Stephen Jay Gould, for example, believes there is a passive trend and that there is a wall of complexity, where if an organism isn’t complex enough to overcome that wall, they won’t be able to survive
• The wall is constantly, slowly increasing over time as organisms compete with one another

Question 59

Part of RNA World Post-It Essay: What is required for the RNA world Hypothesis to work/Questions necessary to answer for RNA hypothesis to work?

Answer 59

• A monomer source is required; nucleotides have to come from somewhere
  
  • The first line of evidence of nucleotides being present on early earth is from the Miller-Urey experiment, in which they tried to recreate primitive earth by using a primitive atmosphere + artificial lightning, and they were able to produce amino acids, sugars, and organic compounds
  • The second line of evidence that nucleotides were around back then comes from studying meteorites; people have found organic compounds in these meteorites, including nucleo- and ribonucleobases
• How was a chain of RNA produced?
  
  • It has been demonstrated in the laboratory that if you put certain active molecules with nucleotides, the nucleotides will form come together to form small strands
  • Another theory people have is that clay minerals may have acted as a scaffold or catalyst for forming bonds
• How can RNA be used as a template if it’s constantly being used as a ribozyme?
  
  • The answer to this question comes down to the unwinding process; people think that in hot spring water sources, natural thermocyclers formed
  • The RNA would have been bound tightly in the cool areas, and bound less tightly in the warm area (so that means it would have been being transcribed in the warm area and doing the transcription in the cool area? that doesn’t make sense, because it is doing both processes at the same time, and needs both unwound and wound at the same time to be able to do the processes)
• How RNA was able to be the genetic material if it’s not very stable
  
  • The most contributive “method” for getting over this fact is to have really active ribozymes to ensure that enough RNA is around

Question 60

Part of RNA World Post-It Essay: What is required to move out of the RNA world into the modern world?

Answer 60

• How the mechanism of passing on genetic material to offspring arose
  
  • Compartmentalization could help solve this problem; if we combine the ribozyme and the RNA it needs to copy (that makes the ribozyme) in the same compartment, that will help ensure that the right things are being replicated
  • Pores in rocks and minerals could have provided these compartments
  • Later on in evolutionary history, primitive proto-cells emerged from fatty acids; fatty acids will spontaneously form mycels, bilayers, and spheres, and some RNA and ribozymes may have gotten stuck in one of these structures
• How DNA arose from RNA without a transcriptase
  
  • In current cells, RNA is made first, and then an enzyme comes along and takes off the -OH group to make DNA
  • The emergence of DNA was probably just the removal of that -OH
• Why DNA is the dominant form of genetic material today
  
  • The mutations/mechanisms that led to DNA allowed DNA to be “tested out” as the genetic material, and over time DNA probably became more favored because it’s more stable
• When and why proteins emerged
  
  • Proteins/amino acids formed and emerged just like the nucleotides and other organic molecules (probably just like all molecules did)
  • Since they have many different chemical side chains, they have more functionality than RNA as enzymes, and this big selective pressure led cells to move towards using proteins as their enzymes instead

Question 61

Modern Day Ribosome

Answer 61

• The modern day ribosome contains both amino acids and ribonucleotides
• It is mainly protein, but the active sites are solely RNA, possibly indicating that the ribosome was originally all RNA

Question 62

Origin of Multicellular Life

Answer 62

• The first transition from unicellular life to multicellular life happened only 0.6 billion years ago, and it has happened more than once!
• To study how this transition first occurred, we can look at modern day species that are currently in the midst of making this transition, like Volvox
• Volvox is a type of algae in the process of evolving from being colonial to being multicellular
• To move into the multicellular realm, Volvox have done something which is key to multicellularity, which is undergo division of labor
• The first division (or at leas the first in the Volvox) was to separate into germ-line cells (germ) and somatic cells (soma)
• The germ-line cells are the cells used in reproduction, and the soma cells are the cells that carry out functions necessary for the survival of the organism, like in the case of the Volvox, swimming to be able to get sunlight
• Volvox form kind of a bubble, with their soma cells on the outside of the bubble and their germ cells on the inside
• One of the key differences between colonial and multicellularity is the division of labor
  
  • Researcher have looked at how this division of labor gets split up in the early stages of the transition to multicellularity (what Volvox are currently in) by dong RNA-seq on soma cells and reproductive cells of Volvox and looking at changes in gene expression between the two

Question 63

Key Differences between Colonial and Multicellular Organisms

Answer 63

1) There is division of labor in multicellular organisms - different cell types have different jobs
2) Individual cells in multicellular organisms can’t survive on their own
3) Natural selection starts acting on the organism as a whole in multicellular organisms instead of acting on single cells as it does in colonial cases

Question 64

Evo-Devo

Answer 64

• The study of evolutionary developmental biology (how development has evolved)
• It involves comparing development in different organism to understand how new forms have evolved
• The field was inspired by the observation that a lot of species that look vastly different start out with very similar looking embryos

Question 65

Hox genes

Answer 65

• Genes that code for transcription factors that are expressed at the end of the segmentation stage of differentiation in development (which is involved in early embryonic development)
• The hox-gene transcription factors’ targets are organ-specific genes
• There are many different hox genes that turn on a variety of genes, and they turn on the genes that are supposed to be on in a particular region
• The fact that hox genes are conserved among all metazoans has led scientists to believe that small changes in hox gene targets can change features without completely changing the organism;
• Hox genes thus allow for the the ability to have similar body plans without having to re-invent the wheel every time for a new organism
• Hox genes themselves don’t determine what an organism will look like, they only determine what genes get turned on it what parts of the organism
• In short: Hox genes result in an organism with different genes expressed in different cell types

Question 66

Evolution of Hox Genes

Answer 66

• The most likely explanation for how vertebrates ended up with the many differing Hox genes that they have today is that the original Hox gene in the common ancestor of all metazoans underwent two series of duplications; first to give two copies of the Hox gene, and then to give four copies since the two copies each duplicated
• The hox genes acquired different mutations over time, causing them to differ from one another more and more, and they underwent many more duplications as new species emerged, sometimes even with hox variations being lost, to lead to all the various hox genes we have today

Question 67

Multicellularity contract

Answer 67

• The “contract” cells in a multicellular organism have with one another, which states that they will only duplicate when necessary
• When a cell breaks this contract, and starts duplicating as it pleases, this can lead to cancer

Question 68

Down-side of evolution: Cancer

Answer 68

• Carcinogenesis is the transformation of normal cells into cancer cells
• Since our cells gain a mutation about every 3 replications, most of the cells in our bodies have accumulated a few mutations through growth, development, and replenishment but they typically aren’t too harmful or don’t have any (noticeable) effect
• Once we have multiple mutations that are related to phenotypes that cancer cells have, however, is when we can start to get cancer
• It should also be noted that DNA damage (not mutations) is the root cause of carcinogenesis
• Cancer cells act somewhat like unicellular organisms in terms of their goal; evolution goes back to occurring at the level of the cell, and NOT the level of the organism as the cancer cells “evolve” to spread and divide more

Question 69

Mutations that can lead to cancer include mutations that can…

Answer 69

• result in unrestrained cell division
• result in the loss of apoptosis
• allow the cell to do angiogenesis
• allow the cell to gain the ability to metastasize
• lead to increased mutation rate

Question 70

Re-sequencing in Antibiotic Resistant Bacteria

Answer 70

• Is used by doctors and researchers to find the cause of antibiotic resistance in bacteria
• Researchers take the resistant strain, put it through next-generation sequencing, and find overlaps and map to the reference genome of a bacteria of that species that doesn’t have the antibiotic resistance mutation

Question 71

Re-sequencing in Cancer Cells

Answer 71

• Re-sequencing can be used to find potential cancer-causing mutations in cancer cells
• If we were to do re-sequecing on our normal, non-cancerous cells, we would find a few mutations here and there, but probably not very many mutations in the same location in different overlapping fragments, so if we took the “average” of all the fragments, we would see no mutations
• When we do re-sequencing on cancer cells, however, we typically see more mutations, and not only that, but most of the cells tend to have at least one of the same mutations, so if we were to take the average of all the fragments, those prevalent mutations would show up
• This technique described above of finding the “average” is involved in a type? of re-sequencing known as deep-sequencing, which combines population level sequencing (how many times a given sequence is represented) with reference sequence comparisons
• We use deep sequencing to determine the abundance of mutations in a population of cells
• We can find the mutation frequency by dividing the # of reads in our alignment at that particular location that contains the mutation by the total # of reads at that particular location
• In deep sequencing, the more genomes you sequence, the rarer of a variant you can detect

Question 72

What can knowing the mutation in a cancer help doctor with?

Answer 72

• It can help them learn about what stage the cancer is in to be able to give the patient a prognosis
• It can help them select the best-suited combination of drugs
• It can help them understand the general process of tumor evolution, and possibly find ways to prevent it by combining the data with RNA-seq data as well

Question 73

Comparative Genomics in Cancer

Answer 73

• An example of comparative genomics in cancer is seen in Peto’s Paradox
• Peto’s Paradox states that larger animals (specifically, whales and elephants) have to undergo more cell divisions than humans to be able to reach their size, yet they tend to have lower cancer rates than in humans
• Scientists have been studying this paradox to see if there is something special about these larger animals that we can maybe apply to humans to help us out
• Nothing has been found for whales so far, but in elephants, researchers have found that they have 20 copies of the gene p53 that codes for a tumor suppressor, whereas humans only have one copy
• Another example of an organism that has a mechanism that helps prevent it get cancer that has lower cancer rates than humans is the naked mole rat
  
  • Naked mole rats cells secrete an extracellular compound called hyaluronan, which is secreted into the area between their cells (extracellular) and prevents the cells from becoming too dense and crowding one another