test 8 Flashcards
- What is the difference between prokaryotic and eukaryotic gene expression?
-Prokaryotic: Travel farther because you are doing everything in the nucleus. Using 3 types of enzymes.
-Eukaryotic: You have to travel from the nucleus all the way out and do everything in the ribosome. Using 1 type of enzyme.
- What is the key to the transcription process?
RNA polymerase
- What controls the RNA polymerase during the transcription process?
All different types of regulatory proteins (different types of enzymes and proteins created that modulate the ability that RNA polymerase is going to work) Can have positive or negative controls and control ability of RNA polymerase to bind or stop (regulatory proteins)
- Regarding prokaryotic and eukaryotic organisms, which gene expression process is faster? (and know why)
Prokaryotes; can do it faster than eukaryotes, don’t have as many polymerases, can do translation and transcription at the same time
- What is a difference between a prokaryotes and eukaryotes method of gene control?
If you are a bacterial cell, you can’t be multicellular. Control things by looking at immediate environment.
- Negative control is mediated by proteins called ______________ (which are proteins that bind to the regulatory site on DNA called operators to prevent or decrease the initiation of transcription). Fill in the blank.
repressors
- The repressors do not work alone. Each responds to specific _____________ molecules which can alter the conformation of the repressor to either enhance or abolish its binding to DNA (just like an allosteric protein and cofactor). Fill in the blank.
effector
- Positive control is mediated by ______________, which is another class of regulatory proteins. They can bind to DNA and stimulate the initiation of transcription. Fill in the blank.
activators
- Know this diagram (i.e. the basic parts and what process it is representing).
- Know this diagram (i.e. the basic parts and what process it is representing).
- Prokaryotic gene are often organized into ________________ (multiple genes that are part of a single transcription unit having a single promoter). Fill in the blank.
operons
- _____________ occurs when enzymes for a certain pathway are produced in response to a substrate. For example, if bacteria encounters lactose, it beings to make the enzyme necessary to utilize lactose (i.e. lactase). Fill in the blank.
induction
- _____________ occurs when bacteria are capable of making biosynthetic enzymes and they are not actively producing them (i.e. do not make it if you do not need it). Fill in the blank.
repression
- Know what the difference between these two diagrams is (i.e. know which one is activated and which one is not activated).
- The presence and absence of lactose is not the only factor which can affect gene expression of lactase. What else discussed in class can affect the gene expression of lactase?
There are so many substances and don’t know which one can take priority; glucose breaks down in aerobic respiration and its easy and gives us ATP molecules, much more than lactase. If glucose is present, lactase enzymes are usually not created.
- Some small RNAs were discovered within eukaryotic cells (which are not located within prokaryotic organisms). One type of regulatory RNA is now called a micro-RNA or mi-RNA. Which statement describes any information discussed in class regarding mi-RNA?
discovered in an animal called nematode, discovered a new RNA (mi-RNA), some polymerases can make these micro RNAs, affect how introns and exons are recognized and removed, ⅓ of human genome is decided by mi-RNA
- Some small RNAs were discovered within eukaryotic cells (which are not located within prokaryotic organisms). One type of regulatory RNA is now called small interfering RNAs or siRNAs. Which statement describes any information discussed in class regarding si-RNA?
small interfering; found in plants, doesn’t mean they can only be used in plants, if you put them in they can stop something from being encoded into the genome, have better control because they have control over what can be read, silence a certain part of your genome, don’t really know much about these yet, very specific
- The translation of processed mRNA transcript by ribosomes in the cytoplasm involves a complex of proteins called _______________ (gene expression is regulated by the modification of one or more of these factors). Fill in the blank.
translation factors
- _______________ shut down translation by binding to the beginning of the transcript so that it cannot attach to the ribosome. Fill in the blank.
Translation repressor proteins
- How can the initiation of translation be controlled? (know the information discussed on slide 9 Ch 16 PowerPoint)
factors let and help translation steps occur, repressors mean it stops translation from happening because the repressor will attach and shut down the steps. These two work together by working as an on and off switch.
- Know the different mechanisms for the control of gene expression. They are all located within this diagram.
- According to the video How Cells Become Specialized, what is special about stem cells inside a human blastocyst?
those cells will give rise to the placenta, they are like blank slates, they can become any type of body cell
- According to the video How Cells Become Specialized, how do transcription factors play a role in cell differentiation?
typically but not always- proteins and determine which areas of the DNA code will get transcribed into mRNA, then can make specific proteins that impact what a cell looks like and does
- According to the video How Cells Become Specialized, stem cells are not only found in embryos, which of these cells stated below can contain somatic stem cells as well?
muscle, skin, liver, or bone marrow
- According to the video How Cells Become Specialized, what does it mean if a cell is multipotent?
can become many types of body cells, but not as many as the embryonic stem cells
- According to the video How Cells Become Specialized, what are pluripotent stem cells?
person’s own stem cells potentially could be induced into a pluripotent state… potential that they could differentiate into tissues or organs that the person may need
- What does determination mean cellularly speaking?
cells choose a developmental pathway totipotent to specialized cells
- How many differentiated cells does a human body have?
300 different types of major cells
- This was the standard test for determination discussed in class. Know what is occurring in this diagram and be able to describe what is occurring during this experimental test.
- How do cells initiate developmental changes?
going to use all of your transcription factors
- Cells can become committed to follow a particular developmental path in one of two ways. Which statement explains one of these way?
Cytoplasmic determinants: when you go and have egg and sperm breed and the egg will have oogenesis. A lot of information will determine which cells will program in your body and how. Paternal inheritance
Cell-to-cell interactions: from environmental and secondary factors ie. temperature (will be produced in embryo), medications, pH, smoking, drinking
- The ability to isolate and manipulate DNA revolutionized biotechnology. The construction of _______________ (a single-DNA molecule made from different genetic sources) began in the 1970s. Fill in the blank.
recombinant DNA
- What were the contributions of either Paul Berg or Herbert Boyer and Stanley Cohen to biotechnology discoveries?
1972 Paul Berg: 1st one to ever create a recombinant DNA molecule, DNA was able to replicate and stayed within, proven you can take a spliced viral DNA and it will always be able to replicate
1973 Herbert Boyer and Stanley Cohen: took genes from a toad and put bacteria to see if it could be passed into multiple generations
- Early cloning experiments were some of the first to utilize new tools called restriction enzymes and endonucleases. Why are they important? (we discussed two reasons)
Can cut DNA into very specific fragments and their cutting abilities can be applied to genome mapping
- How do you create recombinant DNA?
In electrophoresis you take a fragment of DNA and make copies to create recombinant DNA. take a bunch of fragments and have to purify them (pieces of codon you actually want to make copies of)
- A common technique to separate different fragments of cut DNA so that they can be isolated is ____________. This technique takes advantage of the negative charge on DNA by using an electrical field to separate DNA molecules based on size. Fill in the blank.
electrophoresis
- Which statement does not describe the main steps of electrophoresis?
2 restriction enzymes - cutters depend on each enzymes recognition sequence
Load fragment into gel
Fragments move based on size
- What can occur after finishing electrophoresis? (i.e. what is the final product and what can you do with it)
You can take fragments and put them together to make recombinant DNA. put together sticky ends, DNA ligase is the enzyme that puts fragments together
- DNA libraries are collections of recombinant DNA molecules that can be stably maintained and replicated , via ______________, in a suitable host organism. Fill in the blank.
cloning vectors
- According to the video PCR, what is the main function of PCR (polymerase chain reaction)?
it provides a way to make more copies of a portion of DNA
- According to the video PCR, why do we complete PCR (i.e. how can it be utilized)?
-crime scene investigation
-diagnosis of a disease caused by a virus
- According to the video PCR, why do we have to use reverse transcriptase in order to complete PCR to diagnosis the disease COVID-19?
have to convert RNA into DNA
- ______________ mimics the process of DNA replication and an individual reaction is cycled through a series of steps in which each step is analogous to a step in DNA replication. Fill in the blank.
PCR
- During PCR, ______________ is when heat is used to separate strands of double-stranded DNA, _______________ is when primers provide the 3’ OH required for elongation by DNA polymerase, and _____________ is the last step and when the DNA polymerase makes new DNA. Fill in the blanks.
denaturation
annealing of primers
synthesis
- Who is using DNA fingerprinting?
Law enforcement organizations (used in crimes)
- What is DNA fingerprinting?
Trying to find inside’s someone’s DNA “short tandem repeats” of noncoding information you can tell one individual from the other
- Which statement does not describe one of the three things we can now do involving gene editing?
Change a gene’s sequence
Inactivate a gene
Interfere with the expression of the gene in the cell
- Which statement describes one of the main ways we can edit genes in vivo (we discussed two in class)?
Transcription activator-like effector (tale proteins)
CRISPR/Cas9
- According to the video CRISPR Gene-Editing Reality Check, how does CRISPR/cas9 work? (know the steps discussed in the video)
it’s a protein that acts like scissors, and could also cut the DNA exactly where it is needed. once DNA is cut it will try to repair itself and have ability to edit genes
- According to the video CRISPR Gene-Editing Reality Check, what is one of the limitations of using CRISPR within humans?
normally function in tiny bacteria, have to move from bacteria to a human cell, have t get crispr in there and template DNA, sometimes crispr will produce inaccurate changes in DNA which lead to disaster
- Which statement describes a way CRISPR/cas9 can be utilized? (we discussed a few answers to this question in class)
Defective or mutilated allele: you can literally remove it
HIV possibilities: cure it by inserting a gene that tells the HIV to not go into the DNA of the host and become spreadable. 2 people in London were able to be cured.
Genetic diseases
Oncogenes: things being worked on to individually try genetic therapies on varying cancers
- How do we know (through experimentation) that there are similarities between nuclear genomes of different species?
Similar to instructions set, only introns are different
- A ___________ is one that has had a gene inactivated so that the function of the gene is lost. Fill in the blank.
knockout animal
- How are using knockout animals during genetic research useful?
Able to inactivate something to see what it is used for and give insight on what the problem is if something is lost or wrong
- A _____________ has a normal allele replaced with an allele that has a specific genetic alteration (i.e. a mutation). Fill in the blank.
knockin mice
- How are using knockin animals (specifically mice) during genetic research useful?
Mutations can be put in to see what would happen: test for loss of function, partial loss of function, or gain of a function of some kind
- How can transgenic plants be created (we discussed four different ways in class)?
Electroporation
Physical Bombardment
Chemical Treatment
Bacterial Transfer: growing genes and bacteria, taking out copies, and putting them into the plant
- Know this diagram and we able to describe what is going on within the different steps of this process.
- Why do human create transgenic plants (i.e. how are they useful)?
Multiple reasons. Increase resistance to frost, withstand high flood or drought conditions, and add high vitamin and nutrient loads.
- How can recombinant DNA help cure some diseases?
Important proteins can be produced using recombinant DNA.
- How can we create needed human proteins with recombinant DNA?
If you use recombinant DNA, take genes you want from one species and take and put them in another.
- How can recombinant DNA help cure some diseases (know the examples discussed in class)?
Important proteins can be produced using recombinant DNA.
- How can we create missing proteins within the human body with recombinant DNA (know the examples discussed in class)?
If you use recombinant DNA, take genes you want from one species and take and put them in another.
- There is growing evidence that stem cell therapy has the potential to treat a variety of chronic diseases. However, which statement describe one of the current problems with using this technology?
Can take 10 years minimum of research to get one tiny piece of stem cells approved and costs over 1 billion dollars
Patient recruitment is very difficult, not a lot are willing to give stem cells
Regulator agencies like FDA have very extensive oversight, which delays everything getting done
Public perception of the use of stem cells
- _______ are fuels derived from biomass made from recently fixed carbon sources, as opposed to fuels derived from fossil fuels. Fill in the blank.
Biofuels
- What part of the algae are you using to create biofuels?
lipids, fats
- Why is genetically engineered microalgae better than using regularly grown algae for biofuel production?
Can make it into something that is a less expensive gas
- How can algae biofuel production lead to cogeneration systems being implemented (i.e. why are they are green energy source monetarily and figuratively)?
C02 emits and algae grow to power the factories
- What is the one main problem, currently, with trying to produce biofuels?
Cost, if gas and oil prices raise then the production of biofuels will start
- The degradation or metabolism of hydrocarbons pollutants by microorganisms is called ____________. Fill in the blank.
bioremediation
- What affects the degradation rates of hydrocarbons by microorganisms?
Gigantic amount of variables because you are releasing a living thing into the environment. Temperature, physical and chemical properties of actual setting, need to know how much oxygen and pH available, salinity, organism predator, and nutrient availability.
- What is the one main problem, currently, with trying to use large quantities of microorganisms to degrade hydrocarbons in the environment?
Works great in the lab, but doesn’t do so well in the real world
- Why are genetically engineered plant and animals becoming very popular within the agricultural industry?
Can create things you’ve never created before
- Which statement describes a benefit to creating and utilizing GMOs (only know the examples discussed in class)?
Pest resistant
Nutrient Needs: can grow in areas where nothing could be grown there before
Vitamins: can say how many vitamins you want
Soil Needs: can make it to grow in anything possible
Medicines and Vaccines: choose what type of medication you want to make and now extract medication from it
Nutrients in Products: you can enable it to add or take away nutrients
- Which statement describes a negative aspect of creating and utilizing GMOs (only know the examples discussed in class)
Pesticides = problems, lawyers and money, and other things that come with eating GM crops like pests
- How does one map a genome? (i.e. what do they use to create one)
Looking at genetic markers in different ways
- What is the difference between genetic maps and physical maps?
Genetic maps: maps that look at genetic markers on chromosomes, look for chromosomes recombination frequency
Physical maps: looking at entire genome sequence, in the genome complete DNA sequence
- Why do we complete genomic studies?
Evolutionary relationships
Genetic susceptibility to disease (like breast cancer genes)
Development (embryonic stages)
- What is the difference between the ability to create physical genome maps now (i.e. 2022) and forty years ago?
To map your own genome it takes 2-3 hours. We are at the point where we are spending under $2.7 billion (under $300 now) and doesn’t take 23 years.
- The Human Genome Project began in the 1980s, what was accomplished by 1995? When was the entire genome completely sequenced?
1995: 94% of human genome completely done
2003: finished the project
- How easy it is now to map our own individual genome?
A few hundred dollars (much cheaper)
- After the Human Genome Project was completed, it was found the number of genes in the human genome was ______ genes. This represents only about 1.5 times as many genes as ______ and nearly half as many genes as ______. Fill in the blank.
20,000
fruit flies
rice
- Humans, _______, and _______ all have about the same number of genes, it just matters how they are expressed that make us different. Fill in the blanks.
mice
puffer fish
- According to the video How to Sequence the Human Genome, what is the goal of genome sequencing?
knowing the sequence of the billions of letters that make up your genome
- According to the video How to Sequence the Human Genome, which of these statements do not describe a step of genome sequencing?
packed together in a clump
- According to the video How to Sequence the Human Genome, how do we decipher what the genetic sequence means (in theory)?]
Scientists still aren’t sure
- The Cancer Genome Project seeks the genetic basis of cancer. They have identified two categories of gene involved: oncogenes and tumor-suppressor genes. What occurs when (a) oncogenes or (b) tumor-suppressor genes mutate?
Oncogenes: bad, turn cancerous, GAIN OF FUNCTION (bad=cancer)
Tumor Suppressor genes: good, doesn’t allow cancer to happen, LOSS OF FUNCTION (bad)
- Genomics have helped to fill out a cancer framework by comparing tumor genomes with the genomes of matched normal tissue. Mutations that are found in a tumor genome are divided into “driver” and “passenger” mutations. What is the difference between these two mutation types?
Driver mutations are bad and lean towards getting cancer overtime
Passenger mutations might end up in a benign tumor, but that’s it (won’t harm you)
- Genomics have helped to fill out a cancer framework by comparing tumor genomes with the genomes of matched normal tissue. When certain genetic mutations occur, what do the “driver” type of genes affect?
Signal transduction pathway
Control of gene expression
Chromatin structure
Metabolism
- Genomics have helped to fill out a cancer framework by comparing tumor genomes with the genomes of matched normal tissue, however, what is the problem with using genomics as “cure-all” model for cancer treatments?
Database is not large enough yet
- Genomes contain coding and noncoding sequences. ______________ (the intron section of DNA) constitutes around 24% of the genome (exon around 1-1.5%). Fill in the blank.
noncoding DNA within genes
- Genomes contain coding and noncoding sequences. ___________ are some regions of the chromosomes which remain highly condensed, tightly coiled, and untranscribed. Fill in the blank.
structural DNA
- Genomes contain coding and noncoding sequences. ______________ regions tend to be localized around the centromere or near the end of the chromosome (at the telomeres). Fill in the blank.
constitutive heterochromatin
- Genomes contain coding and noncoding sequences. ______________ are scattered within the genome and are usually 1 to 5 nucleotides such as CA or CGG repeated thousands of times. Fill in the blank.
simple sequence repeats
- Genomes contain coding and noncoding sequences. _________________ are blocks of genomic sequences of 10,000 to 30,000 bp that have been duplicated and moved either within chromosomes or to a nonhomologous chromosome. Fill in the blank.
segmental duplications
- Genomes contain coding and noncoding sequences. ______________ are inactive genes which may have lost function due to mutations. Fill in the blank.
pseudogenes
- Genomes contain coding and noncoding sequences. _________________ are 45% of the human genome and consists of DNA sequences that can move from in the genome to another (some have the ability to transcribe proteins as well). Fill in the blank.
transposable elements
- Genomes contain coding and noncoding sequences. _________________ are 45% of the human genome and consists of DNA sequences that can move from in the genome to another (some have the ability to transcribe proteins as well). Fill in the blank.
transposable elements
- Genomes contain coding and noncoding sequences. ____________ are miRNA that regulate some of the complex developmental processes in eukaryotes by down-regulating translation (i.e. does not allow it to occur if present). Fill in the blank.
microRNA genes
- Genomes contain coding and noncoding sequences. _____________ are noncoding RNA strands which also regulate gene expression and are important in the physiology and development of eukaryotes. Fill in the blank.
long, noncoding RNA
- Are introns really “junk” DNA?
NO, we don’t really know too much about how much is junk DNA.
- The Encyclopedia of DNA elements (ENCODE) Project has now determined that _______________ (percent) of the human genome is functional. Of that percentage though, only ___________ (percent) is defined as transcriptionally active, but serve no function (i.e. what they transcribe does not affect your body). Fill in the blanks.
80%
63%
- Which statement does not describe ENCODE’s definition of a functional element?
DNA sequence that results in protein production
Can be transcribed
Distinct + reproducible biochemical signature
- What is the scientific consensus regarding ENCODE’s findings regarding “junk” DNA?
No scientific consensus, all the numbers mean nothing, 20-80% estimate of junk DNA
- According to the video Epigenome The Symphony in Your Cells, what is an epigenome?
changes that affect gene expression that aren’t changes to the DNA itself
- According to the video Epigenome The Symphony in Your Cells, what are epigenomic changes?
chemical tweaks to DNA and to the proteins that package our DNA
- According to the video Epigenome The Symphony in Your Cells, what happens during methylation?
when a chemical gets added to the DNA and it prime’s a gene to be turned off
- According to the video Epigenome The Symphony in Your Cells, when does methylation seem to occur more within human cells?
older brains
- What is the definition of bioinformatics?
Is the application of computer programming, mathematics, modeling to the analysis of large sets of biological data
- What can you do with the information from bioinformatics?
Looking at the structure and function of a protein
- What equipment is needed to complete bioinformatics?
Mass spectroscopy + protein chips
- What can you predict with the information from bioinformatics?
structure and function of a protein
- What findings were discovered, after completing the human genome project, regarding mammal genome size?
all similar
- What was another big genetic surprise discovered after the completion of the human genome project?
Large number of unfamiliar protein and coding genes that we don’t know what they’re making
- Some plants have many more genes than humans and mammals. Why?
Plants have more duplications in their genes, plants can do polyploidy and survive, we don’t know why
- Many duplications (to make the genome longer) have arose during the evolution of plants. Why?
polyploidy
- Why do some animals, which we would deem “less-complex” contain more genes than ourselves?
Complexity does not mean we are more genetically complex than a plant. The number of genes doesn’t determine the complexity of an organism.
- Humans, mice, chimps, and gorillas are all very genetically identical, so what makes us different?
We are all very similar but we aren’t the size of a mouse or chirp like a bird. The expression of the genes make us different.
- Humans with a single-point mutation in the transcription factor gene _____________ have impaired speech and grammar but not impaired language comprehension. Fill in the blank.
FOXP2
- Which animals contain the FOXP2 gene and what does this gene normally control (i.e. code for within your cells)?
Mouse, chimpanzee, gorillas, orangutan. Controls motor function in brain and coordination that makes those things happen.
- What is the difference between the FOXP2 gene for humans, mice and primates?
Humans- only differ by 3 amino acids between humans and mice, 2 amino acids between humans and primates
Mice- only differ by 3 amino acids between humans and mice, single amino acid difference between primates and mice
Primates- single amino acid difference between primates and mice, 2 amino acids between humans and primates
- The FOXP2 mutation in humans allows for what to occur compared to other organisms?
If it mutates it doesn’t work. But if it mutates it allows the larynx brain and mouth work in combination to produce speech.
- According to the video FOXP2 Gene Linked to Language, what happened to the one family member when they had a FOXP2 mutation? What happened to a songbird when they had the same mutation?
Had trouble making complex syllables
The males couldn’t properly sing
- According to the video FOXP2 Gene Linked to Language, how did the FOXP2 mutation affect the song of the twin mice?
First one made more complex pitches, second mice produced more simple sounds/sequences
