Mass Review 2

Dark field microscopy

Dark field microscopy is another optical microscopy technique that allows researchers to view unstained samples of live cells. This is achieved by increasing the contrast between the sample and the field around the sample. Light enters from the bottom of the microscope. The dark field patch stop blocks light from the center from entering the object, which creates an outer ring of light. The condenser lens refocuses this light back onto the sample. Contrast is created by allowing only the light that passes through the sample and scatters to contact the light detector - all other light is blocked (including light that is directly transmitted through the sample). Only scattered light from the sample is transmitted. This means that the sample image will appear on a completely black background. As a result of this, the light intensity can be low.

divergent evolution vs convergent evolution

Divergent evolution: - Divergent evolution is the process by which related species become less similar in order to survive and adapt in different environmental conditions. Here, the same structure evolves in different directions in different organisms. Example: Forelimbs of whales, bats, cheetah, and humans perform different functions. Convergent Evolution: Convergent evolution is the process by which unrelated species become more similar in order to survive and adapt in similar environmental conditions. Here different structures evolve in the same direction in different organisms. examples: Wings of a butterfly, and of birds. Potato and sweet potato.

Electron Tomography

Electron Tomography creates a 3D image of a sample's internal structures. This is achieved by sandwiching a bunch of TEM images together. For this reason, it is not considered a type of microscopy. IT can help look at objects and their relative positions in 3D.

Epigenetics: 1. DNA methylation - reduce gene expression 2. Histone methylation - can reduce or increase gene expression 3. Histone acetylation - addition of acetyl groups that promote gene expression. 4. Histone deacetylation - removal of acetyl groups that reduces gene expression

Epigenetics involves heritable phenotypes that result from changes to the genome without modifying the nucleotide sequence. These changes include the following: 1. DNA methylation : addition of methyl groups that silence genes, leading to lower expression. 2. Histone methylation: addition of methyl groups that may increase or decrease expression depending on methylation site and quantity. 3. Histone acetylation: addition of acetyl groups that promote gene expression. 4. Histone deacetylation: removal of acetyl groups that reduces gene expression Epigenetics is the study of environmental influences on gene expression that occur without a DNA change Epigenetics is the study of how your behaviors and environment can cause changes that affect the way your genes work. Unlike genetic changes, epigenetic changes are reversible and do not change your DNA sequence, but they can change how your body reads a DNA sequence. Epigenetics literally means "above" or "on top of" genetics. It refers to external modifications to DNA that turn genes "on" or "off." These modifications do not change the DNA sequence, but instead, they affect how cells "read" genes. Examples of epigenetics Epigenetic changes alter the physical structure of DNA. One example of an epigenetic change is DNA methylation — the addition of a methyl group, or a "chemical cap," to part of the DNA molecule, which prevents certain genes from being expressed. Another example is histone modification. Histones are proteins that DNA wraps around. (Without histones, DNA would be too long to fit inside cells.) If histones squeeze DNA tightly, the DNA cannot be "read" by the cell. Modifications that relax the histones can make the DNA accessible to proteins that "read" genes. Epigenetics is the reason why a skin cell looks different from a brain cell or a muscle cell. All three cells contain the same DNA, but their genes are expressed differently (turned "on" or "off"), which creates the different cell types.

Eukaryotic flagella vs Prokaryotic flagella

Eukaryotic flagella Have microtubules made out of tubulin dimers Contains basal body. In eukaryotes, basal body serves as a nucleation site for the growth of microtubules. Eukaryotic flagella run in a bending movement using complex sliding filament system Eukaryotic flagella are ATP-driven Eukaryotic are larger and more complex than prokaryotic flagella Prokaryotic flagella prokaryotic flagella are made out of protein building blocks flagellin Prokaryotic flagella contains a basal body witch function as a rotary motor. Prokaryotic flagella run in a rotary movement using a rotary motor Prokaryotic flagella can be ATP driven (archaea) or proton driven (bacteria) by the flow of protons across a concentration gradient. Prokaryotic flagella are smaller and more simpler than eukaryotic.

Would a mutation in an intron that changes one DNA nucleotide for another lead to any issues or be silent (i.e., not seen)?

Even though introns are noncoding DNA, a mutation in an intron could lead to an effect in the protein if the mutation was apart of the DNA that signals that the intron needs to be spliced out (i.e., the 'splice signal'). If there was a mutation here, the spliceosome might not recognize the 'splice site' and the intron may not be removed.

Evolution

Evolution refers to the heritable changes in populations of species over generations. More specifically, evolution refers to the changes in allele frequencies in populations over time. For example, the allele that codes for white fur coat will become more common as a population of foxes begins to live in the arctic. Natural selection is the gradual, non-random process where alleles become more or less common as a result of the individual's interactions with the environment (as we'll discuss coming up - the genetic variations that lead to different traits in organisms are random, but natural selection itself is a non-random process). Those organisms better adapted to survive and reproduce are more successful in passing on their genes, resulting in the evolution of populations over time. Individuals do not evolve, populations evolve over generations.

cell fractionation

First Centrifugation: Nuclear Fragments Second Centrifugation: Mitochondria, Lysosomes, and Peroxisomes Sediment Third Centrifugation: Endoplasmic Reticulum Fragments, Microsomes, and other small vesicle sediments Microsomes are: vesicles derived from the endoplasmic reticulum (ER) when cells are broken down in the lab. Fourth Centrifugation: Ribosomes, Viruses, and macromolecules (carbohydrates, lipids, proteins, and nucleic acids)

Fixation

Fixation is the process of getting cells to 'stick' on a microscope slide, such that the cell is preserved in its most life-like state. Another benefit of cell fixation is that it makes it easier for cells to hold onto any stain that is applied. HEAT FIXATION First, freshly harvested cells will be placed on one side of a microscope slide. Then, the underside of that same slide will be passed over a Bunsen burner flame. This causes the slide to heat up, which 'glues' the cells on the slide. Heat fixation also preserves cells because the heat causes cell processes to stop - i.e. it kills them.

Frequency-Dependent Selection:

Frequency-Dependent Selection: here we see the survival and reproduction morph decline if that phenotype becomes too common in a population. If for example, a butterfly with a certain color pattern is being killed off by birds, the frequency of other color patterns would increase.

Freshwater fish vs Saltwater fish (marine) osmoregulation

Freshwater fish live in hypo-osmotic environment. Freshwater fish tend to take in a great deal of water through their gills and tend to lose much salt. They compensate by rarely drinking water, and actively absorbing salts through cells located in their gills. The freshwater fish excrete a great deal of dilute urine. Saltwater fish (marine) live in a hyperosmotic environment that causes water loss , thus they try to compensate by constantly drinking and actively excreting salt across their gills. They rarely urinate and have isotonic urine.

Smallest to largest particles:

Frog Egg > Pollen grain/human egg > animal/plant cell > Erythrocyte > mitochondria/bacteria >virus. As you can see, viruses are small and bad news. Some filtration systems developed can filter these agents from drinking water.

Geographic Variation-Ecocline:

Geographic Variation-Ecocline: For example 2 different variants of mice exist in two different areas of the United States separated by mountainous terrain. This is where we see an ecocline or just cline for short. Clines consist of forms of species that show gradual phenotypic and/or genetic differences over a geographical area. Rabbits in the North might have white fur, while rabbits in the South have brown fur...such a gradual difference in appearance is a good example of a directional cline. (Plant size decreases as you climb up mountains is an example of a cline too).

Homologous structures: Formed by Divergent Evolution-Common Ancestor

Homologous structures: Formed by Divergent Evolution-Common Ancestor These are structures that may or may not perform the same function, but are derived from a common ancestor Some signature examples that you may want to remember: Forearm of a bird and the forearm of a human Forearms within wings and human arms have different functions, but both have the same ancestral origin. Homologous structures: these structures or organs that are similar in morphology (shape), anatomy, genetics, and embryology, but have different functions. They may even look different! They have a common ancestor. The relationship between homologous structures is termed homology. Homologous structures include: Flipper of a whale Wing of a bat Leg of a cat Arm of a human When these are compared to each other, you are dealing with homologous structures. Homologous stuctures are formed due to divergent evolution. In divergent evolution we see an ancestral species form into a number of different species with both similar and different traits. Darwin's finch birds on the Galapagos Archipelago are a great example.

Homoplasy

Homoplasy: Homoplasy is where analogous structures develop in species that arise from different ancestors (convergent evolution). As a result, homoplasy refers to multiple ancestors, not a common ancestor.

Immunofluorescence microscopy

Immunofluorescence microscopy is a technique used to identify the localization of proteins of interest. This technique uses fluorescent tags (fluorophores) attached to antibodies that target the protein of interest (the antigen), which allows researchers to visualize the distribution of target proteins.

test cross

In a test cross, the organism with the dominant phenotype is crossed with an organism that is homozygous recessive (e.g., green-seeded):

What is a poly A signal VS the poly A tail?

In eukaryotes, the terminator sequence for protein-coding genes involves a poly-A signal. This signal tells certain enzymes to cut the transcript away from RNA polymerases, so transcription can be terminated. A detachment of the RNA polymerase occurs and our RNA transcript is released. m-RNA is now able to diffuse away from the DNA template. Poly-A signals are found just downstream of coding DNA, they signal to end termination of transcription. These signals are just a natural part of the DNA. It is important to realize that a poly a tail and a poly a signal are different things. Note -- we are speaking of a poly-A SIGNAL here, not the poly-A tail. The poly-A SIGNAL is an upstream code that aids in the termination of transcription AND is important for the later addition of the poly-A tail to the mRNA.

fluorescence microscopy

In fluorescence microscopy, fluorophores (a fluorescent chemical that will re-emit light upon being excited by another light source) are attached to parts of a specimen. Using different types of fluorophores allows researchers to view different parts of the cell. When a fluorophore absorbs light, electrons are excited to a higher energy level. When the electrons fall back down to their normal energy level, they release energy in the form of light. A light source is directed against a dichroic filter. This filter reflects certain wavelengths, and allows others to pass through. Some light is reflected onto the object, the fluorophores are then illuminated with ultraviolet light to produce colorful images of live cells. The fluorophores absorb and emit a different wavelength of light, and this new wavelength is read by the sensor.

Adaptive Radiation - Divergent evolution - a type of allopatric speciation

In this case, many new species arise from a single ancestor as they adapt to their respective environments differently. Adaptive radiation is a "burst of speciation" in which numerous species are produced from a common ancestory.

Microevolution Opposite of 'Large Random M&M' for the conditions for Hardy-Weinberg equilibrium will cause microevolution.

In this section, we will take on evolution from a micro perspective, which will revolve around the concept of allele frequencies. Allele frequency = gene frequency (could be used interchangeably). refers to the process when gene frequencies change within a population from generation to generation. Genes that translate into traits that best suit the environment will proliferate — they increase in frequency; whereas genes which become traits that suit the environment less optimally will die out — these unfavorable alleles decrease in frequency. Microevolution is the process when gene frequencies change within a population over generations (favorable genes increase, unfavorable decrease). Microevolution happens on a small scale within a single population. The changes would not result in the new organism being considered as different species. Example: A species has a color or size change. Thus, genes in a gene pool of populations = microevolution. The smallest scale that we can define evolution is termed microevolution. Microevolution is change in allele frequencies of a population over generations. 1. Genetic drift is a change in allele frequencies in a gene pool by chance. The fact that luck is involved differentiates genetic drift from natural selection, where allele frequencies are selected by the environment to increase or decrease. This is why genetic drift has a much bigger impact on small populations than big populations. Genetic Drift are random fluctuations in the relative allele frequencies of a small breeding population. In a large population, chance events do not do very much with regard to the gene pool, but can do much if the population is small. There are two signature extreme cases that result in genetic drift: Bottleneck Effect and Founder Effect Founder effects and population bottlenecks have similar effects: genetic diversity is reduced. Some genes are thrown out, some genes that were once rare, now become common. They are both random. In natural selection, the genes with the best chance of survival are the ones that are passed down to the next generation. In the founder effect or population bottleneck, this might not be the case. The genes that passed down are not necessarily the "good ones". Bottleneck effect - loss of alleles due to a disaster - smaller gene pool, some alleles may be lost easily through natural disasters. So in a bottleneck effect, something bad occurs such as a flood, tsunami, starvation, earthquake, or fire, that reduces the population size. By chance alone, some alleles may be underrepresented, others may be overrepresented, or lost all together. A loss of genetic variation occurs giving rise to a new population that is not representative of the original. Founder Effect: When there are a couple of individuals that migrated to and settled in a new location, these individuals would have a much smaller gene pool than their original population. The successive generations will descend from the founders, and their unique genetic makeup. So in the founder effect, a few members of a parent population may migrate to a new area. Once in the new area, this small population can establish a small, interbreeding population. Consider a newly formed volcanic island. Seabirds can bring seeds from the mainland. These seeds can now dictate the phenotypic range. When a small population distances itself from a larger one and colonizes the area, it is likely not representative of the original larger population. 2. Non-random mating- sexual selection, outbreeding, inbreeding This is when individuals choose who they want to mate with. This is a consequence of sexual selection, which we've covered beforehand. When certain traits are favored over others, they get passed onto offsprings and become more represented within the allele frequencies of future generations. 3. Mutations (a heritable change in DNA) happen with varying damage, to all organisms. Some mutations can happen and go into a 'dormant' phase until there is sudden environmental changes and the mutated traits suddenly become favorable and flourish. 4. Natural Selection Natural selection is the increase or decrease in allele frequency due to adaptations to the environment. No luck is involved, traits are selected for based on how they confer fitness within an ecosystem 5. Gene Flow Though the name sounds pretty similar, gene flow is actually portraying a different concept than genetic drift. Genetic drift is the result of a random change in allele frequency. Gene flow is the process of moving alleles between populations through individuals' migration. You can think of gene flow like how we are living in a global village nowadays — people emigrate and immigrate around the world and breed amongst different ethnicities. This causes alleles to mix and eventually make variations between populations smaller.

Macroevolution

Macroevolution is long-term and occurs at a level at or higher than species. In macroevolution species are reproductively isolated (via prezygotic and postzygotic isolating mechanisms) resulting in a lack of gene flow between species. In short, macroevolution looks at changes that occur at a level that is at or higher than species. Recall the 7 levels of taxonomy (Kingdom, Phylum, Class, Order, Family, Genus, Species). Since we are at least at the level of species, evolution will take time. We need to look from a long-term perspective to see evolutionary patterns. This is unlike microevolution, where genes can change within one generation. What is a species? Species are individuals that can interbreed. Therefore, two different species are reproductively separated, which means that their respective gene pool is also isolated, denying gene flow between species. A species represents a population of organisms that may display a range of genotypic and phenotypic variation, and members have the potential to interbreed and produce viable and fertile offspring. Species exist as a discrete unit in nature What is speciation? It is possible for two species of a population to evolve in different ways. As time goes on, they become more and more different until they can no longer interbreed. This is speciation. What is reproductive Isolation? The defining characteristic separating one species from another is that they are reproductively isolated. Reproductive Isolation is a major working criterion for species definition, but it is not perfect! For example, sometimes, occasional mating does occur between members of two different species. However, most of the offspring are sterile and have no evoutionary future. A male donkey (2N=62) and a female horse (2N=64), produce an offspring called a mule. Can you tell me the 2N chromosome number of a mule? Donkey gives 31, horse gives 32 (recall half of the chromosomes come from each parent). Thus, the mule has 2N=63. Nature secures reproductive isolation for each species through two ways: prezygotic and postzygotic isolating mechanisms.

ATMOSPHERE - CRUST NOA OSA

Main components of modern Earth's atmosphere: Nitrogen gas (78%) Most commoNNNNNNNN (N is for Nitrogen!) Oxygen gas (21%) Though this is what we rely on to survive, it is only the second most abundant. Argon gas (0.9%) Noble gas here The rest is small traces of carbon dioxide, methane, and ozone. Main components of modern Earth's crust (ranked by % by weight): Oxygen atom (47%) Careful here, in the Earth's crust oxygen is the most abundant atom. Whereas in the atmosphere, it is ranked second. Silicon atom (28%) Think of all the sand we can find on the beach, plenty of silicon! Aluminum (8%)

second inheritance law - law of independent assortment

Mendel's law of independent assortment states that the alleles of two (or more) different genes get sorted into gametes independently of one another. In other words, the allele a gamete receives for one gene does not influence the allele received for another gene. The law of segregation lets us predict how a single feature associated with a single gene is inherited. In some cases, though, we might want to predict the inheritance of two characteristics associated with two different genes. we need to know whether they "ignore" one another when they're sorted into gametes, or whether they "stick together" and get inherited as a unit. When Gregor Mendel asked this question, he found that different genes were inherited independently of one another, following what's called the law of independent assortment. This law is valid for those traits that are not related to each other such as seed color and seed shape. When an individual inherits two or more characteristics, those characteristics are assorted independently during the production of gamete. This gives the different traits an equivalent probability of occurring together. This indicates that the inheritance of one character will not influence the inheritance of the other.

the initiator amino acid for protein synthesis

Methionine is the initiator amino acid for protein synthesis for archaea and eukaryote N-Formyl methionine is the initiator amino acid for protein synthesis in bacteria and mitochondria of eukaryotic cells

How can peripheral proteins be removed?

Most frequently, peripheral proteins are removed by shifting the ionic strength or pH of the aqueous solution, thereby dissociating the ionic interactions of the peripheral protein with either phospholipid polar head groups or other membrane proteins. Hydrogen bonding and electrostatic interactions allow peripheral proteins to be associated with the membrane. Peripheral proteins are usually bound to the charged polar head group of the bilayer. Mild treatment with salts for example can remove them. peripheral membrane proteins are generally hydrophilic; held in place by H-bonding and electrostatic interaction. Disrupt/detach by changing salt cxn or pH to disrupt these interactions.

microRNA (miRNA)

non-coding RNA such as microRNA (miRNA) can bind to a complementary section of coding RNA, which can prevent translation (RNA to protein) by inducing cleavage, degradation or blocking translation in a process called RNA interference. These changes to gene activity can be passed on even if the original stimuli that triggered these changes is gone.

Mendel's Law of Dominance

the law of dominance states that recessive traits are always dominated or masked by dominant trait The recessive allele that is suppressed will remain "dormant". Nevertheless, it will be transferred to the next generation in the same way as the dominant allele is transferred. The suppressed trait shall be expressed only by the progenies having two copies of the allele. Also, these offspring can breed true when crossed by themselves.

Termination in replication vs termination in transcription

Termination in replication: Termination of DNA replication occurs when the replication fork can no longer progress forward. This may occur when 1. two replication forks meet or 2. there is a specific point in the DNA telling it to stop. For example, some sequences of DNA encourage protein binding, which physically stops the replication fork. Termination in transcription: Termination occurs when RNA polymerase transcribes a sequence that says the gene is finished. These sequences are called terminators. In eukaryotes, the terminator sequence for protein-coding genes involves a poly-A signal. This signal tells certain enzymes to cut the transcript away from RNA polymerases, so transcription can be terminated. So in termination, we now need to remove the RNA polymerase from the DNA, therefore RNA polymerase transcribes what is called a "terminator sequence" in the DNA. Although the mechanism for terminator does differ between prokaryotes and eukaryotes, the bottom line is this: A detachment of the RNA polymerase occurs and our RNA transcript is released. m-RNA is now able to diffuse away from the DNA template.

The cell theory

The cell theory has three fundamental statements: All lifeforms have one or more cells. The cell is the most simple unit of life. All cells come from other cells.

Electron microscopy

The cells are viewed indirectly via a computer after being bombarded with electrons which pass through magnetic fields in a vacuum. The vacuum prevents the electrons from deviating their path. Cells can be viewed at a much higher resolution than optical microscopy because the wavelength of an electron is smaller than that of light. Fixation is essential as it prevents proteins and structures from degrading. The metal coat may also be referred to as the stain, and it uses gold or palladium to coat the sample. In this way electron microscopy kills the cells

first law of inheritance - Law of Segregation

The law of segregation states that the alleles of a given locus segregate into separate gametes. The physical basis of Mendel's law of segregation is the first division of meiosis in which the homologous chromosomes with their different versions of each gene are segregated into daughter nuclei. The behavior of homologous chromosomes during meiosis can account for the segregation of the alleles at each genetic locus to different gametes. As chromosomes separate into different gametes during meiosis, the two different alleles for a particular gene also segregate so that each gamete acquires one of the two alleles. During the development of the gamete, each gene is segregated in such a way that the gamete consists of just one allele for that gene The copies of a gene are segregated when any individual produces gametes so that each gamete accepts only one copy. One allele is received by a gamete.

The modern cell theory

The modern cell theory tells us: All living things are composed of one or more cells Cells are the basic unit of structure, function, and organization in all organisms Cells carry hereditary information Energy flow, metabolism and biochemistry (energy flow) occur within cells, where all cells have the same chemical composition All cells have the same basic chemical composition All cells come from pre-existing, living cells through cell division hence each cell should have the same common ancestor. The common ancestor of all human cells is called the zygote. Through the process of exponential cell division, a zygote makes two cells, then four, then eight, then sixteen, etc. The modern cell theory does not apply to viruses because they are not living cells.

Nucleus

The nucleolus is inside of the nucleus and serves as the site of ribosome synthesis a. Ribosomes are synthesized using rRNA and ribosomal proteins which are imported from the cytoplasm. Once ribosomal subunits form, they are exported to the cytoplasm for final assembly into a complete ribosome. The nucleus is bound by double layer nuclear envelope with nuclear pores for transport (mRNA, ribosome subunits, dNTPs, proteins like RNA polymerase and histones). Note that there is no cytoplasm in the nucleus, instead there is nucleoplasm 2. Nuclear Lamina - a dense fibrillar network inside of the nucleus of eukaryotic cells (intermediate filaments + membrane associated proteins) that provides mechanical support; helps regulate DNA replication, cell division, and chromatin organization

paleontology

The study of fossils is also called paleontology. Fossils reveal a lot of information about prehistoric living organisms, including anatomy, lineage, behavior, habitat, etc. There are two types of fossils — one is fossils of the actual remains of the animal, another one is fossils of their traces (ichnofossils), which records down details like footprints and nests. You may also wonder, how do fleshy living organisms turn into solid rocks? This can be achieved through the process of petrification. As the body of the living organism becomes buried under layers of sediments, minerals slowly seep into its body and replaces organic materials, hardening the corpse.

How can integral proteins be removed?

They are hydrophobic so use detergent to destroy the membrane and expose the proteins. Use a mild one because harsh ones will denature it. It is more difficult to remove the integral proteins. Integral membrane proteins are held in the membrane by hydrophobic interactions with the lipids. Detergents, organic solvents, and ultrasonic vibrations are needed for their removal.

Timeline Facts:

Timeline Facts: The Big Bang gave rise to the Universe ~14 billion years ago. The Earth came ~4.5 billion years ago. The first prokaryotes came ~3.5 billion years ago. One billion years after Earth was born, we got the simplest life forms. The first eukaryotes came ~2 billion years ago.

Transmission electron microscopy (TEM)

Transmission electron microscopy (TEM) captures electrons that are transmitted through a thin slice of a sample. This allows researchers to view high resolution 2D images of a sample's internal structures Beam of electrons passed through a very thin section of a sample to product a 2D image of the thin slice. It helps to give a high resolution image and view internal structures.

DNA polymerase proofreads for errors during DNA replication, does RNA polymerase do the same in transcription?

Unlike DNA polymerase, RNA polymerase does not proofread for any errors...thus more errors occur during transcription than for replication. Several DNA polymerase enzymes have proofreading capabilities that allow them to 'double-check' their work and correct errors whenever they add a non-complementary base to the strand they are synthesizing. Luckily, an error during transcription gives a "bad" protein and not transmitted to the entire progeny if it occurred with DNA.

What are Mendel's three laws?

What are Mendel's three laws? Mendel stated three laws known as Mendel's laws of inheritance. These laws are: Law of Segregation Law of Dominance Law of Independent Assortment

Homoplasy - Seen in convergent evolution with analogous structures

When designing a phylogenetic tree, the tree with the least amount of assumptions is preferred because it minimizes homoplasy. Homoplasy, also known as convergent evolution, is a phenomenon that describes when two distinct clades develop strikingly similar characteristics (analogous structures) despite the fact that there is no common ancestor with the trait. Homoplasy: Homoplasy is where analogous structures develop in species that arise from different ancestors (convergent evolution). As a result, homoplasy refers to multiple ancestors, not a common ancestor.

siRNA (Small Interfering RNAs)

a class of small non-coding RNAs with a function analogous to microRNAs but act primarily by degrading the mRNA they bind to. RNAi (RNA interference) is the blocking expression via siRNA.

cell wall of archaea vs bacteria

cell wall of archaea: indiscriminate polysaccharide, pseudopeptidoglycan pseudomurein, a molecule that is analogous to peptidoglycan but with different peptide cross-bridges. Archaeal cell walls are also composed of sugars, proteins, and inorganic molecules

Ribosomes

-Found in both prokaryotes and eukaryoes -"The protein factories" made of rRNA and over 80 different proteins. This is the site of protein synthesis. Can be: a) attached to the endoplasmic reticulum b) attached to the nuclear envelope c) freely suspended in the cytosol -Cells making an enzyme will have a lot of ribosomes -They consist of two subunits which are made in the nucleolus of the cell. The subunits are made seperately in the nucleolus and exported to the cytoplasm for final assembly. The large and small subunit join together by binding an mRNA strand... Ribosomes function in protein translation (protein synthesis). Ribosomes are macromolecules that do not contain a membrane, and they are not organelles. Both eukaryotic cells and prokaryotes contain ribosomes; although, their structures are slightly different. Eukaryotic ribosomes have two subunits. One subunit is 60 S, while the other is 40 S (the unit "S" tells how heavy/dense a molecule is). These subunits come together to form a complete 80 S eukaryotic ribosome. Each of the subunits is produced in the nucleoplasm, coming together in the cytosol of the cell.

Role of smooth endoplasmic reticulum

-Involved the lipid biosynthesis such as phospholipids -Involved with holding and releasing calcium ions in a controlled manner, and released when needed. IT is specialized in skeletal muscle and called sarcoplasmic reticulum. -It is involved with steroid biosynthesis -It is involved with detoxification of drugs and poisons -Cells that are active in the synthesis of cholesterol, triglycerides, and steroids show an abundance of smooth ER. -In the liver, the smooth ER contains a large amount of cytochrome 450 and participates in detoxifying certain drugs. The cytochrome 450 catalyzes reactions to decrease drug toxicity. The hepatocyte (liver cell) is involved with drug detoxification, thus has a high % of smooth ER. The lipids and steroids produced by a smooth ER are essential molecules for energy storage, membrane structure (cholesterol), and hormone communication. The abundance of smooth ER in a cell depends on the functions of that cell. For example, a human liver is heavily involved with detoxification, so its cells tend to contain many smooth ER.

Role of Rough Endoplasmic Reticulum

-Part of it is continous with the nuclear envelope! -In an avergae liver cell, almost 15 million ribosomes are present. Ribosomes on the Rough ER are "membrane bound" and are involved in protein synthesis. -Cells that make enzymes such as pancreas and those of the GI tract have abundant Rough ER. -The Rough ER works with the ribosome and continues protein assembly. In most cases, proteins are moved to the Golgi complex for final modification and "finishing". They are either conveyed in vesicles or moved directly between the ER and Golgi complex before being delivered to their specific locations.

monocistronic mRNA (Eukaryotes) vs polycistronic mRNA (Prokaryotes)

-monocistronic: one mRNA strand codes for one polypeptide-- eukaryotes -polycistronic: one mRNA strand codes for more than one polypeptide-- prokaryotes The key difference between Monocistronic and Polycistronic mRNA is that monocistronic mRNA contains genetic information of a single protein while the polycistronic mRNA carries the genetic information of several genes which are translated into several proteins.

Compound Microscope

A compound microscope is a microscope that can be used to view simple, one-cell thick, live cells. They have more than one lens, and each lens magnifies the sample by a set amount. For example, a compound microscope could have an objective lens and an eyepiece lens that each magnify the sample 4x, so the total magnification would be 16x (4x * 4x). But the problem is without fixing and staining (which potentially kills the cell) provides us poor contrast and visibility.

The poly A signal in the mRNA stimulates polyadenylation of the transcript, what is this?

Additionally, the poly-A signal in the mRNA stimulates polyadenylation of the transcript, where 50-300 adenine nucleotides are added to the 3' end. These adenine nucleotides are added after termination. Polyadenylation is poly = many, adenylation = adenine nucleotides. What's the point of this? After termination in elongation, the newly synthesized mRNA is at risk of being degraded at it's 3' end and it's 5' end by exonucleases. To protect the mRNA from degrading, on the 3' end a method called polyadenylation occurs, allowing 50-300 adenine nucleotides to become added to the 3' end of the mRNA. To protect the 5' end of the mRNA, a 5' capping method occurs, in this method a 7-methylguanosine cap is adding to the 5' end of the mRNA during elongation. This cap functions to protect the 5' end of the pre-mRNA transcript from degradation. This 5' cap also helps ribosomes bind to processes mRNA during translations. These two methods are known as post-transcriptional modifications that happen after termination in elongation. These methods also tell the cell that this mRNA has passed checkpoints and should now move onto the next step in order to become translated into certain proteins. So the 5' cap and the poly-A tail are like the plastic aglet at the end of a shoestring, which protects the ends from fraying.

apoenzyme vs Holoenzyme

An apoenzyme is an inactive enzyme, activation of the enzyme occurs upon binding of an organic or inorganic cofactor. Holoenzyme-an apoenzyme together with its cofactor.

Polytomy/Multifurcation

An internal node of a phylogenetic tree can be described as a polytomy or multifurcation if it is linked to three or more branches. For example, only cladograms B and C below contain polytomies.

Confocal laser scanning microscopy

Confocal laser scanning microscopy can also be used to observe fluorescence in living cells, as long as they are mounted on thin slices. While this technique can be used without fluorescence tagging, it is more frequently used with fluorescence tagging to observe chromosomes during mitosis. visualizes fluorescent objects. Can be used without fluorescence tagging. Artifacts are reduced by focusing a beam of UV light onto the sample. This reduces intensity so samples must be illuminated longer.

Cryo-scanning electron microscopy (cryo-SEM)

Cryo-scanning electron microscopy (cryo-SEM) is a specific type of scanning electron microscopy where the sample is frozen in liquid nitrogen (cryogenic) instead of being dehydrated. This freezing process provides for a 3D image of the sample surface in its more natural form; however, it can sometimes create artifacts. Additionally, the fixation and staining processes kill the sample.

Cytoplasm

Cytoplasm - remember, this is an area, not a structure! Most of the cell's metabolic activity and transport occur here, and the area includes the cytosol and organelles. i. The streaming movement within the cytoplasm is known as cytoplasmic streaming 5. Cytosol/Cytoplasmic Matrix - the difference between the cytosol and cytoplasm is that the cytosol doesn't include the components suspended within the gel-like substance, it is JUST the gel-like substance. i. Think of this like a bowl of jello with candy embedded inside it — the cytoplasm is the jello + candy, and the cytosol is just the jello.

How many different types of RNA polymerases and DNA Polymerases exist in prokaryotes and eukaryotes.

DNA polymerase III adds free complimentary nucleotide triphosphates DNA polymerase I remove the RNA nucleotide of the primer and replaces them individually with DNA at the 3' end of the adjacent Okazaki fragment. RNA polymerase II is the one responsible for transcribing most eukaryotic genes.

What are the functional parts of a spliceosome and how does it work?

A spliceosome is a large and complex molecular machine found primarily within the nucleus of eukaryotic cells. ... The spliceosome removes introns from a transcribed pre-mRNA, a type of primary transcript. This process is generally referred to as splicing. What creates a spliceosome: 1) snRNA + protein = snRNP- small nuclear ribonucleicprotein particles knowns as snRNPs are described as complexes comprised of snRNAs and proteins which combine with various other proteins, ultimately forming the spliceosome. Splicing allows for increased genetic diversity without increasing the size of the genetic code through alternative splicing. Alternative splicing is where different mRNA molecules are produced from the same pre-mRNA primary transcript. The functional part of the spliceosome is made up of snRNA (small nuclear RNA) and proteins. Collectively, snRNA and proteins are referred to as snRNP's (small nuclear RiboNucleic Protein; pronounced 'snurps'). The spliceosome scans the pre-mRNA for 5' and 3' splice signals within the mRNA code; these sites signal the spliceosome to start and stop its splicing — precisely removing the intron. So to summarize, studies have shown that snRNPs and other proteins form a complex called a spliceosome..it is within this big spliceosome (yes it is big...almost the size of the ribosome!!) that the "cutting" occurs. Bottom line: After all this cutting..we have our mRNA molecule with exons!! The mRNA that now leaves the nucleus is much smaller than the original mRNA before this "cutting" occurred. Are you thinking what I am? This resembled a person making a video... and it was edited. This is exactly what has occurred.

Analogous structures: Formed by Convergent evolution-No common Ancestor

Analogous structures: Formed by Convergent evolution-No common Ancestor Analogous structures must perform the same function and must not have the same ancestry. These are structures that have the same functions but are not derived from a common ancestor. Both birds and bats evolved to have wings, but they originated from different lineages. Homoplasy: Homoplasy is where analogous structures develop in species that arise from different ancestors (convergent evolution). As a result, homoplasy refers to multiple ancestors, not a common ancestor. An example: A cat leg vs. a praying mantis leg Analogous: these are structures with the same function but evolved separately...they also have a similar appearance. There is no common ancestor. Analogous structures include: Wing of a bat and wing of a bird Wing of an insect and the wing of a bird Fish fins and whale flippers Jointed legs of insects and vertebrates used for locomotion The spine of a cactus and thorn of a rose Analogous structures evolve due to what is called convergent evolution. In convergent evolution, we see organisms that are not closely related independently evolve similar traits as a result of having to adapt to similar environments or ecological niches. The North American cactus and the African Euphorbia plant look alike. Both plants developed in harsh, arid desert climates, but both experienced convergent evolution since they have no common ancestor!

DNA splicing using a spliceosome

Arguably the most important stage of pre- mRNA processing associated with the primary transcript involves the removal of various portions of RNA molecules along with connecting the few portions that remain. How does this occur? What gets sliced, and what gets connected? First, a few things you need to be familiar with. This RNA splicing is seen in eukaryotic genes. Eukaryotic genes are composed of protein-coding sequences known as exons in addition to sequences called introns described as being non-coding DNA sequences that interrupts and/or intervenes in the sequence of a gene Pre-mRNA splicing: Small nuclear ribonucleoprotein particles (snRNPs) are complexes composed of snRNAs and proteins that combine with various other proteins to form a structure called the spliceosome. The newly formed spliceosome complex must be able to accurately locate the intron- exon junction to chop out the introns and stitch the exons back together. Accuracy is critical: intron splicing and exon rejoining is a result of a sequence-specific mechanism. Even an error of one wrongly spliced nucleotide will result in the entire reading frame shifting, not allowing exons to rejoin at the correct locations and leading to a dysfunctional protein. A brief overview will suffice: snRNA base pairs with introns, the spliceosome is formed, and the intron is looped out in a structure called a lariat which is excised. The exons are then rejoined back together and the spliceosome disassembles.

Genes vs Alleles

As humans, we have around 20,000 genes in our genome. And since we are diploid organisms, we will have about 40,000 alleles (two variations for each gene). Genes are sections of DNA that contribute to certain traits, characteristics or functions. Genes encode for proteins or parts of proteins that influence things like the immune system, skin pigmentation, hormone production, and eye color. Genes are transcribed into RNA molecules, which are then translated into proteins. Segments of DNA demarcated as genes consist of both coding and non-coding regions. Coding regions, also called exons, are the sections transcribed into eventual protein. Non-coding regions, or introns, are not transcribed, but are thought to fulfil numerous other functions such as regulation of transcription. Humans have approximately 20,000 protein-coding genes, which represent less than 2% of the total genome. Allele is the term used to describe these different versions of a gene. For example, at one particular loci, two alleles may exist, one that codes for a cytosine base and one that codes for a thymine base. Humans inherit two copies of their genome - one from each parent. As such, we are known as diploid organisms. The unique combination of these alleles across a genome is known as an individual's genotype. These gene variants still code for the same trait (i.e. eye color), but they differ in how the trait is expressed (an organism's phenotype). In most cases, there is not one single locus whose alleles determine how a trait is expressed. Let's consider eye color - blue, green, brown and hazel eyes are each encoded by unique set of alleles in particular genetic loci. A more in-depth look reveals that there are roughly 16 different genes responsible for eye color, although most of the influence comes from 2 of these 16 genes. The greater the number of potential alleles, the more diversity in a given heritable trait. This combination of genes and gene variants underlies human genetic diversity, and they are the reason why no two people are exactly alike.

autopolyploidy and allopolyploidy

Autopolyploidy appears when an individual has more than two sets of chromosomes, both of which from the same parental species. Allopolyploidy, on the other hand, occurs when the individual has more than two copies but these copies, come from different species. Autopolyploidy: organism has more than 2 sets of chromosomes all derived from a single species For example AAAA Additional chromosal set that is identical to parent species. For example, if Plant X has a 2N = 10, a new species Y, arises as an autodiploid from X has a 2N=20 Allopolyploidy: organism has more than 2 sets of chromosomes, derived from different species. For example AABB is the chromosomal composition I hope you can see this. The organism has another set of chromosomes from another species.

Hardy Weinberg Principle - Gene Equilibrium (No Evolution)

Before we talk about all the factors that cause changes, let's talk about a state of no change — gene equilibrium. In this state of equilibrium, there is no change in gene frequencies, hence there would be no evolution. According to the Hardy-Weinberg Principle, the genotypes and allele frequency in a given population will remain constant from one generation to the next, providing that only Mendelian segregation and recombination of alleles operate. Let us examine the five Hardy-Weinberg conditions: Large Population: gene frequency doesn't change as a result of chance alone Random Mating: inbreeding causes little mixing of genes No Mutations: a mutation modifies our gene pool No Natural Selection: survival differences can alter gene frequencies No Gene Flow: no immigration, no emigration, no pollen transfers (If a strong wind blows, pollen can move from Point A to Point B. We don't want this!! Another example of gene flow would be if a population has an influx of new members). Obviously, no natural population meets all of these criteria. Departure of any of these give conditions usually results in an evolutionary change. Any deviation from the five conditions listed can cause evolution. Factors like mutations, nonrandom mating, and non-inbreeding can all affect frequencies of homozygous and heterozygous genotypes, but usually has little effect on allele frequencies in the gene pool. Remember that alleles refer to different forms of a gene (yellow vs. green pea genes). Hence, allele frequencies basically means how often you can find a yellow allele vs. a green allele (gene variant) in a pea population.

Biochemical - Conserved DNA regions + Common Conserved Pathways

Biochemical - Conserved DNA regions + Common Conserved Pathways This is the newest type of evidence that supports the theory of evolution, as scientific analysis methods has gotten more and more advanced. When we compare DNA sequences in genomes, we see conserved DNA regions across species which are related. The higher the similarity, the stronger the relatedness. Chimpanzees have roughly 98% similarity with humans, showing a strong lineage connection. We also observe common conserved pathways in species that are related. For example, respiration (Kreb's cycle, ETC) can be seen in many eukaryotes like plants and animals, which provides evidence that both plant and animal eukaryotes evolved at one point from a common eukaryotic ancestor.

Bright Field Microscopes:

Bright field microscope are compound microscopes that have a bright light to illuminate the sample

Chordates

Notochord: A notochord is the length of cartilage extending along the body which will become part of the spinal discs. Chordata are animals that contain notochord. Notochords are cartilaginous rods that support the body of all chordates when they are in the embryonic stage. Most chordates will lose their notochord as they mature; however a select few will keep it into adulthood. In chordates, the notochord provides a flexible rod that functions as support and is eventually replaced by bone in most vertebrates. The notochord is derived from the mesoderm and defines the primitive axis of the embryo. Notochord in adults: Cephlachordata (Lancelets) Fish (Jawless) Dorsal Hallow Nerve Cord: in chordates it is the dorsal hallow nerve cord that eventually develops into the spinal cord (not the notochord). The dorsal hallow nerve cord goes into form the basis of the nervous system, including the brain. Pharyngeal Gill Slits: in chordates it is the pharyngeal Gill slits that go on to form the pharynx, gills and other feeding systems later in the animals development. The Pharyngeal Gill slits provide a channel across the pharynx to the outside body. They can go on to form other structures or disappear entirely during embryonic development. In mammals, the Gill pouch eventually forms the Eustachian tubes in the ears and various other head and neck structures. Post-Anal tail: in chordates: the muscular tail extending behind the anus (sometimes referred to as a muscular post-anal tail) does not describe the notochord. This tail is lost during the embryonic development of humans and many other chordates. Bilateral symmetry Triploblast and Eumetazoa Coelomate

Nucleolus

Nucleolus There is another subspace within the nucleus, called the nucleolus. The nucleolus is a dense region within the nucleus. This is where rRNA (ribosomal RNA) is produced, and is the site of ribosomal subunits production. -ribosomal production factory..makes ribosomes -non-membranous organelle -one of more may be found within the nucleus...rarely beyond three -In addition to rRNA synthesis, the assembly of large and small ribosomal subunits occurs here -Small amounts of DNA are present but does not stain with Feulgen stain -Interestingly, in cancer cells, the nucleolus is often hypertrophic meaning increased in size. But be careful, large nucleoli are not only encountered with rapidly growing malignant tumors, but are found in cells that are actively synthesizing proteins.

Optical microscopy

Optical microscopy: cells are viewed directly. Light shines on a sample and is magnified via lenses. Can observe living cells.

Phase contrast microscopy

Phase contrast microscopy uses light phases and contrast to view thin samples with LIVE CELLS to produce sharply defined images in which fine structures including internal structures can be seen in living cells. The cells do not have to be stained, or tagged because phase contrast microscopes have tremendous contrast. Light passes through an annular ring (which forms a cone of light), hits the object, and refracts when it passes through materials in the object with different densities. This changes the speed of the light, causing it to bend (refract). The difference between the refracted light (through the object) and unrefracted light (not through the object) creates a phase shift in the light. A phase shift is a subtle difference in the positioning of light that is detected by the phase contrast microscope. This creates tremendous contrast, and the microscope can compute what it is looking at by recompiling the image. Sometimes, the area around the specimen is distorted by large phase shifts. This is known as the halo effect, and it can be reduced by using phase plates to reduce the phase shift. Another strategy to reduce the halo effect includes using thinner samples.

Polyploidy

Polyploidy - a condition where an organism carries extra sets of chromosomes (usually due to an error during meiosis where homologous chromosomes fail to separate) i. Usually lethal in animals, but is common in plants and can lead to extra sets of genes that accumulate useful mutations that lead to improved survival over time Many animals are diploids, meaning that they have two copies of each chromosome, and therefore two alleles for each gene. Diploidy is beneficial because the dominant allele can mask the effect of the recessive allele, which is very helpful in cases where the recessive allele is harmful, such as sickle cell anemia. Most eukaryotes are diploid and much genetic variation lies hidden in the recessive allele. The recessive allele, that is harmful, for example, can remain hidden in the heterozygote individuals. This heterozygote form actually "protects" the recessive alleles which could eventually bring new benefits if circumstances in the environment were to change. Imagine if we only had one gene for hemoglobin, people who happen to have one copy of the sickle cell allele would suffer from that disease. But since we are diploids, we would need two copies of the sickle cell gene to have the disease — greatly reducing the number of sickle cell patients! Some plants are polyploids, meaning that they actually have multiple alleles for a gene. This introduces more variety and preservation of different alleles in the genome. You never know, one day an allele may come in handy when the environment changes! Polyploidy can occur when a mistake during cell division results in an extra chromosomal set. Thus, a plant for example, has a 4N chromosome number, instead of 2N. These 4N cells cannot breed with 2N cells, but the 4N cells can produce fertile offspring by self-pollinating or mating with other 4N cells.

What is eukaryotic post-transcriptional modifications?

Post-transcriptional modifications is when eukaryotic pre-mRNA is modified into processed mRNA. Processed mRNA is able to exit the nucleus (through a nuclear pore) and enter the cytoplasm, which is where translation occurs. There are three main types of post-transcriptional modifications in eukaryotes. 1. 5' capping 2. Polyadenylation of the 3' end 3. Splicing out introns Poly-A signal in the mRNA stimulates polyadenylation of the transcript, where 50-300 adenine nucleotides are added to the 3' end. These adenine nucleotides are added after termination. Polyadenylation is poly = many, adenylation = adenine nucleotides. What's the point of this? After termination in elongation, the newly synthesized mRNA is at risk of being degraded at it's 3' end and it's 5' end by exonucleases. To protect the mRNA from degrading, on the 3' end a method called polyadenylation occurs, allowing 50-300 adenine nucleotides to become added to the 3' end of the mRNA. To protect the 5' end of the mRNA, a 5' capping method occurs, in this method a 7-methylguanosine cap is adding to the 5' end of the mRNA during elongation. This cap functions to protect the 5' end of the pre-mRNA transcript from degradation. This 5' cap also helps ribosomes bind to processes mRNA during translations. These two methods are known as post-transcriptional modifications that happen after termination in elongation. These methods also tell the cell that this mRNA has passed checkpoints and should now move onto the next step in order to become translated into certain proteins. So the 5' cap and the poly-A tail are like the plastic aglet at the end of a shoestring, which protects the ends from fraying. Eukaryotic DNA and mRNA contain interruptions within the coding sequence for a gene. These interruptions are known as introns. The expressed, protein coding sequences are known as exons. Mnemonic: Introns = Interruptions and Exons = Expressed. Only eukaryotic cells contain introns for removal, or 'splicing'. Introns are removed from the pre-mRNA during mRNA processing via the spliceosome. The spliceosome is a molecule found only in eukaryotic cells.

nucleoid

Pro-Tip: The nucleoid region is found only in prokaryotic cells, while the nucleus is found only in eukaryotic cells Nucleoid - the irregular shaped region within prokaryote cells that contains all or most of the cell's genetic material

Prokaryotes vs Eukaryotes Transcription

Prokaryotes do not have membrane-bound organelles, so transcription of their DNA into mRNA has to occur in the cytosol. Eukaryotes do have membrane-bound organelles, so transcription of eukaryotic DNA into mRNA occurs in the nucleus. Eukaryotic Transcription: Prokaryotes do not have membrane-bound organelles, so transcription of their DNA into mRNA has to occur in the cytosol. Eukaryotes do have membrane-bound organelles, so transcription of eukaryotic DNA into mRNA occurs in the nucleus. Eukaryotic promoter includes an area rich in adenine and thymine about 25 nucleotides upstream from the transcriptional start point called a TATA box. Prokaryotes on the other hand have a Pribnow box instead of a TATA box. Proteins called transcription factors recognize an area within the promoter site (TATA box) and binding occurs. These transcription factors are in eukaryotes. Transcription factors and RNA polymerase make up the "TIC" or transcription initiation complex. In eukaryotic cells, RNA polymerases cannot directly detect and bind to the promoter region. They require the binding of transcription factors. Prokaryotes do not need transcription factors. This is because the job of transcription factors is that they are regulatory proteins that bind to promoter DNA and affect the recruitment of RNA polymerases. In Eukaryotes, RNA polymerases CANNOT directly detect and bind to the promoter region of the template strand, it needs the binding of transcription factors to help them. So the transcription factors bind to the promoter region, which then recruits the necessary polymerase. On the other hand, prokaryotes CAN directly bind the RNA polymerase to the template strand, so they do not need transcription factors. But keep in mind, even though RNA polymerases can directly bind to the template strand in prokaryotes, it lacks the ability to target promoter sites. To work around this, prokaryotic core RNA polymerase combines with the sigma factor to form RNA polymerase holoenzyme. This sigma factor provides RNA polymerase holoenzyme the ability to target the promoter region of bacterial DNA.

where do prokaryotes keep their DNA?

Prokaryotic cells do not contain membrane-bound nuclei. So where do prokaryotes keep their DNA? Prokaryotes house most of their genetic material in a dense and irregularly shaped region known as the nucleoid.

Protein Classification

Protein Classification - there are several different categories of protein classification based on composition, which are as follows: Simple - formed entirely of amino acids Albumins & Globulins - functional proteins that act as carriers or enzymes Scleroprotein - an insoluble (fibrous) structural protein such as keratin, collagen, or elastin. Conjugated - simple protein + non-protein Lipoprotein - protein bound to lipid Mucoprotein - protein bound to carbohydrate Chromoprotein - protein bound to pigmented molecule Metalloprotein - protein complexed around metal ion Nucleoprotein - contains histone or protamine, bound to nucleic acid

Protein Denaturation

Protein Denaturation: When proteins are taken out of their ideal temperature, pH range, or solvent, denaturation can occur. Protein denaturation means the protein is reversed back to its primary structure. Denaturation is usually irreversible, but in some cases, it can be reversed with the removal of the denaturing agent. Protein denaturation also implies that all of the information needed for a protein to assume its native state (its folded, functional form) is encoded in its primary structure.

Function of: RNA Polymerase I RNA Polymerase II RNA Polymerase III

RNA polymerase I - Located in the nucleolus and functions to synthesize rRNAs. rRNAs are structural RNAs because they are not translated into protein, they instead perform cellular roles which is important to produce ribosomal proteins that catalyze the assembly of amino acids into protein chains RNA polymerase II is the one responsible for transcribing most eukaryotic genes. RNA polymerase III - Transcribes various structural RNA molecules such as small nuclear pre-RNAs and pre-tRNAs (pre-transfer RNAs.)

RNAi - RNA interference

RNAi is short for "RNA interference" and it refers to a phenomenon where small pieces of RNA can shut down protein translation by binding to the messenger RNAs that code for those proteins. RNA interference is a natural process with a role in the regulation of protein synthesis and in immunity.

Survivorship curves

Survivorship curves: how mortality of individuals in a species varies during their lifetimes. a. Type I: most individuals survive to middle age and dies quicker after this age (human). b. Type II: length of survivorship is random (invertebrates-hydra). c. Type III: most individuals die young, with few surviving to reproductive age and beyond (oysters). Typical of species that produce free-swimming larvae - the few that survive being eaten become adults. There are three types of survivorship curves. Type I curves depict individuals that have a high probability of surviving to adulthood. Type II curves depict individuals whose chance of survival is independent of age. Type III curves depict individuals that mostly die in the early stages of their life. Type I. Humans and most primates have a Type I survivorship curve. In a Type I curve, organisms tend not to die when they are young or middle-aged but, instead, die when they become elderly. Species with Type I curves usually have small numbers of offspring and provide lots of parental care to make sure those offspring survive. Type II. Many bird species have a Type II survivorship curve. In a Type II curve, organisms die more or less equally at each age interval. Organisms with this type of survivorship curve may also have relatively few offspring and provide significant parental care. In this case, the probability of survival remains relatively constant regardless of the organism's age. Some organisms that demonstrate this type of survivorship include the hydra (a genus of small, freshwater organisms), lizards, rodents, reptiles, some birds, and some small mammals (mice and squirrels, for example). Type III. Trees, marine invertebrates, and most fish have a Type III survivorship curve. In a Type III curve, very few organisms survive their younger years. However, the lucky ones that make it through youth are likely to have pretty long lives after that. Species with this type of curve usually have lots of offspring at once—such as a tree releasing thousands of seeds—but don't provide much care for the offspring.

There are two main types of termination in bacteria: 1. Rho-independent termination 2. Rho-dependent termination

Rho-independent termination relies on a terminator sequence of DNA that causes the RNA transcript to fold into a hairpin loop (aka stem and loop). Hairpin loops can cause RNA polymerase to pause after a certain amount of time. Before the hairpin loop causes RNA polymerase to pause, transcription of a sequence of adenine DNA nucleotides into uracil RNA nucleotides will often occur. The combination of the weak bonds between adenine and uracil, as well as the pause caused by the hairpin loop, causes just enough instability for the RNA polymerase to fall off the DNA template and for the RNA transcript to be released. Rho-dependent termination involves a protein called Rho, which binds to the Rho binding site of the RNA transcript. Note: the information for the Rho binding site is encoded by the DNA, which is why it is ultimately expressed by the RNA transcript. Once bound, Rho moves along the RNA transcript in the 5' → 3' direction, which is the same direction that RNA polymerase is extending the transcript. Eventually, Rho will catch up to RNA polymerase because a region of DNA, called the transcription stop point, forcing RNA polymerase to pause. When Rho catches up to RNA polymerase, it displaces the RNA transcript and transcription ends.

Svedberg unit

Ribosomes - organelles made of rRNA, function to make proteins i. Composed of two subunits: 60S + 40S = 80S in eukaryotes and 50S+ 30S = 70S in prokaryotes; the two subunits are produced inside of the nucleolus and moved into the cytoplasm where they are assembled into a single larger ribosome ii. A larger S value (Svedberg unit) indicates a heavier molecule

Scanning electron microscope (SEM)

Scanning electron microscopy (SEM) captures electrons that are scattered by atoms found on the surface of dehydrated samples. For that reason, it allows researchers to visualize high resolution 3D images of the dehydrated sample surface.

Schizocoeloms vs Enterocoeloms

Schizocoeloms (occurs in protostomes): The mechanism works when coelom are created by splitting solid mass of mesodermal embryonic tissue, hence separating mesodermal cells during the developmental process. Enterocoeloms (occurs in deuterostomes): The mechanism works when coelom initially develop as a pocket of the primitive gut into the mesodermal space.

Sigma factors

Sigma factors are subunits of all bacterial RNA polymerases. They are responsible for determining the specificity of promoter DNA binding and control how efficiently RNA synthesis (transciption) is initiated by making sure it binds to specific promoters. prokaryotes CAN directly bind the RNA polymerase to the template strand, so they do not need transcription factors. But keep in mind, even though RNA polymerases can directly bind to the template strand in prokaryotes, it lacks the ability to target promoter sites. To work around this, prokaryotic core RNA polymerase combines with the sigma factor to form RNA polymerase holoenzyme. This sigma factor provides RNA polymerase holoenzyme the ability to target the promoter region of bacterial DNA.

What are siRNAs (small interfering RNA) and miRNA's (microRNA)--which are both considered as RNAi molecules (RNA interface molecules)?

Some other forms of post-transcriptional gene regulation and mRNA processing in eukaryotes include siRNAs and miRNAs. siRNAs (small interfering RNA) and miRNA's (microRNA), which are considered RNAi molecules. RNAi molecules (RNA interference molecules) silence certain gene expression. They interfere with mRNA via complementary base pairing; therefore, they prevent translation. MicroRNA molecules (miRNA) and small interfering RNA molecules (siRNA) can bind to the mRNA. These two molecules can: 1) Degrade mRNA 2) Bind to mRNA and therefore block translation.

How does splicing increase genetic diversity?

Splicing allows for increased genetic diversity without increasing the size of the genetic code through alternative splicing. Alternative splicing is where different mRNA molecules are produced from the same pre-mRNA primary transcript. Alternative splicing is where different mRNA molecules are produced from the same pre-mRNA primary transcript. A protein isoform, or "protein variant", is a member of a set of highly similar proteins that originate from a single gene or gene family and are the result of genetic differences. ... Many human genes possess confirmed alternative splicing isoforms.

Staining

Staining is the process of adding color to cells, such that researchers will have an easier time in seeing cell structures. However, staining is usually associated with cells that have been killed, either through the preceding fixation or the staining process itself. Many types of staining protocols will kill any living cells because alcohol is often used as a 'wash' for removing excess stain.

Stereo microscopes / Dissection Microscope

Stereo microscopes / Dissection Microscope : Uses visible light with low magnification to observe the surface of live specimens.