Chapters 16-22 Flashcards
Where is the regulatory sequence, and what is located here?
generally in 5’ region. promoter is located here
What is the function of transcription factors?
affect RNA polymerase’s ability to bind can bind within regulatory region can help or hurt RNA polymerase
What are the two main motifs that recognize where to attach to DNA?
DNA binding motif leucine zipper motif
What is the DNA binding motif?
repeated structure in the protein EX. helix-turn-helix
What is the leucine zipper motif?
found repeatedly on proteins contains a zipper like protein
What is an operon?
grouping of proteins found only in prokaryotes genes necessary to make the enzymes necessary for a particular product
What is trp operon?
gene necessary to make the enzymes to make the amino acid tryptophan
What is the structure of trp operon?
coding region regulatory region
What is the regulatory region in a trp operon?
Contains a promoter
What sits on the promoter in trp operon?
RNA polymerase
What is an operator?
Binding site for a transcription factor
How does this operon work? When is it on, when is it off?
If tryptophan is absent the cell needs it - promoter is unoccupied and operon is on If tryptophan is present- promoter is occupied and the operon is off
What does the lac operon do?
produces the necessary enzymes to digest loctose
Is the lac operon a weak promoter or a strong promoter?
Weak promoter
What does CAP stand for?
Catabolite activator protein
What happens when glucose is low in a bacteria?
Bacteria must use a different sugar like lactose
What are the three things that happen in bacteria when glucose is low?
Then [cAMP] is increase, cAMP binds to CAP CAP binds to DNA allowing RNA polymerase to bind to lac operon
What is cAMP?
little molecule that is like ATP
What are the three genes within the coding region of a lac operon?
Z, Y, A
What are the three sections of the regulatory region in the lac operon?
Promoter operator CAP binding site
What happens if [glucose] is low and [lactose] is high?
RNA polymerase attaches to promoter and transcription occurs
What happens if [glucose] is low and [lactose] is low?
repressor attaches to operator
What must happen in order to for the lac operon to be on?
[glucose] low, and [lactose] higher
What are specific transcription factors?
they stick out of general transcription factors and attach to other parts of DNA called enhancers
What is development?
process that determines form and function of organisms
What are the three multicellular kingdoms?
Kingdom Fungi, Kingdom Viridiplantae, Kingdom Animalia
What is the kingdom fungi?
less complicated minimal development
What is Kingdom viridiplantae?
plant kingdom does have development- specialized cells flexible development
what is kingdom animalia?
animal kingdom most complex kingdom
What are the four model organisms?
Mouse- Mus musculus Fruit Fly- Drosophila Plant- Arabidopsis Insect- C. elegans
What is Mus musculus?
mouse vertebrate and mammal
What is totipotency?
up to 8-cell stage, any cell could produce a normal adult
What is Drosophila?
fruit fly has a short generation time and small and simple nutrient needs and enough complexity to be of interest goes through metamorphosis does 12 rounds of mitosis before any cytokinesis
What is metamorphosis?
different stages you go through as you grow EX, egg, larva, pupa, adult
What is it called when there are multiple rounds of mitosis before any cytokinesis?
syncytial blastoderm
What genes place appendages in correct place?
homeotic genes
What is Arabidopsis?
a plant mustard family easy to grow and small and self-pollinate
What is the development of the Arabidopsis?
Fertilized eggs under goes mitosis ball of cells differentiation into three layers this becomes three tissue systems ball changes shape into two cotyledons first root forms packaged into seed if conditions are right, undergoes germination grows into seedling
What are cotyledons?
1st leaves of a plant
What are meristems?
points of growth in plants the shoot and root
What are C. elegans?
round worm= nematodes 1 mm long and transparent always have over 959 cells
What are the 6 stages of vertebrate development?
Fertilization cleavage gastrulation neuralation organogenesis morphogenesis
What is the front of a sperm called?
acrosome or a modified lysosome
What is the use of an acrosome on sperm?
to digest its way through the stuff around the egg
What are the three steps of fertilization of vertebrate development?
Penetration activation nuclear fusion
What is penetration that happens during fertilization
the sperm gets through egg membrane by fusing with it
What happens during activation during fertilization?
egg cell membrane changes increase in protein synthesis cytoplasmic movement
What happens during cleavage during vertebrate development?
rapid cell division not getting bigger just getting more cells that are tinnier and tinnier
What is a blastula?
a hallow ball of cells 500-2000 cells. has fluid that accumulates in center of the ball (morula)
What happens during the gastrulation phase of vertebrate development?
lots of cell movement when tissue types are formed varies between animal groups in form
What does the endoderm cells become in the blastula?
lining of digestive and respiratory tracts
What does the ectoderm become in the blastula?
skin, nervous system, sense organs
What does the mesoderm form in the blastula?
skeleton, muscles, blood vessels, heart, blood, gonads, kidneys
When does gastrulation happen?
3 weeks after fertilization
What happens in the neuralation stage of vertebrate development?
beginning of the formation of the nervous system first steps or organogenesis
What happens in the organogenesis stage of vertebrate fertilization
making organs
When does organogenesis happen?
4th week after fertilization
What happens during morphogenesis in vertebrate development?
change in form like limbs cells dividing cells growing cells moving cells dying
What is induction?
one cell switches its developmental pathway because of an interaction with another cell
What must a cell be able to do in order to move?
cells must become less bound before it can move, then it must rebind itself to its new neighbors
What is determination and differentiation?
First cll can develop into anything as time goes on certain genes are turned off it is determined through the turning off of genes differentiation happens later when the cell forms into what it is becoming
What is a genome?
an entire genetic sequence of an organism
What is genomics?
study of genomes
What are some physical maps of genomes?
DNA sequence human genome project banding patterns on chromosomes restriction sites
What is the human genome project?
starts in 1990 attempt to map the human genome by 2001 the overall idea figured out
What is a genetic map?
genes are mapped onto the chromosomes can look for stop and start codons can look at linkage
How much of DNA actually codes for protein?
1 to 1.5%
What are the four types of DNA that does code for protein?
Single-copy genes segmental duplications multi-gene family Tandem cluster
What are single-copy genes?
25,000 of them 90,000 to 100,000 proteins made from them done by alternative splicing
What is segmental duplications?
gene group on more than one chromosome functional
What is multi-gene family?
collection of similar genes EX hemoglobin - 2 alpha 2 beta
What is a tandem cluster?
group of identical genes
What are the 6 types of DNA that does not code for protein?
Introns structural DNA simple sequence repeats segmental duplications pseudogenes transposable elements
What are introns?
intervening sequences of DNA snipped out of primary mRNA 24% of total DNA
What are the two controls for transcriptional regulation
Regulatory sequence on DNA Transcription factors
What is the structural DNA?
20% of DNA concentrated near centromere area does not uncoil or copy also found at ends of chromosomes-telomeres
What are simple sequence repeats?
3% of DNA 1-6 nucleotides long like stutters some are associated with mutations
What are segmental duplications?
chuncks of DNA found in more than one place does not make a message or protein
What are pseudogenes?
inactive genes a mutation happens and cannot work anymore 2% of DNA
What are transposable elements?
Transposons jumping genes ability to randomly move found in prokaryotes and eukaryotes stretch of DNA that can move
Who first discovered transposable elements?
McClintock found these in Indian Corn in 1950s
What is SNP?
single nucleotide polymorphism the fact that a single nucleotide in our genome is variable
What is comparative genomics?
genomes of different species are compared field of study more similar genomes = more common ancestor
How similar are drosophila and humans?
50% of Drosophila genes have a human counterpart
How are similar are humans and chimps?
have only 1.2% difference in nucleotide sequence
How similar are mice and humans?
both have 25,000 genes share 99% of genes
What is synteny?
degree of similarity between different organisms
What is proteomics?
study of cell’s proteins
What is bioinformatics?
integration of biology, math and computers
What is functional genomics?
Field looking at the function of genes instead of the structure
What are somatic cells?
cells of the body
What is teh basal lamina?
membrane that protects the organs, a-cellular
What is metastasize?
When secondary tumors appear from cancer cells moving throughout the body When cancer cells go from a primary location to a secondary location
What is epidemiology?
study of how to prevent cancer
What do cancer cells contain on the chromosomal level?
highly abnormal chromosomes, reflecting genetic instability trasnlocation
What is chromosomal painting?
a new version of karyotyping?
How do tumors evolve?
by repeated rounds of mutation and proliferation
What happens to the cancer cells after each evolutionary step?
gains a new mutation that enhances its ability to proliferate, survive, so that its progeny become the dominant clone in the tumor
What are some competitive advantages of cancer cells?
reduced dependence on signals from other cells less prone to apoptosis cancer cells can proliferate indefinitely genetic instability abnormally invasive lack of cell adhesion molecules can survive in foreign tissues
What are the two classes of cancer genes?
oncogene and tumor suppressor gene
What is oncogene?
Dominant mutation gain of a function activating mutation enables oncogene to stimulate cell curvival and proliferation
What is the tumor suppressor gene?
recessive mutation loss of function two inactivating mutations functionally eliminate the tumor suppressor gene, stimulating cell survival and proliferation
What three kinds of genetic changes that can convert a proto-oncogene into an oncogene?
mutation i coding sequence gene amplification chromosome rearrangement
What type of mutation in the coding sequence creates oncogene?
hyperactive protein made in normal amounts
What gene amplification turns on the oncogene?
normal protein greatly overproduced
What chromosome rearrangement creates oncogene?
nearby regulatory DNA sequence causes normal protein to be overproduced fusion to actively transcribed gene produces hyperactive fusion protein
What is biotechnology?
moving genes for our own benefit
What is genetic engineering?
the cutting of DNA -basic technique -cut into specific pieces -rearranged for a practical purpose
What is the enzyme called that cuts DNA? And where does it cut it?
restriction endonucleases and cut at the restriction site
Where was restriction endonucleases found at?
in bacteria
Where does the restriction endonuclease cut at?
When a nucleotide sequence reads forwards and backwards the same
Why does the Restriction endonuclease cut at a palindrome?
to create a sticky end
What is a vector?
carries foreign DNA into another cell
What are the three most common vectors and where do they carry too?
Plasmids- carry into bacteria and plants Animal virus- carry into animal cells Bacteriophage- virus that infects bacteria
What is gel electrophoresis?
a method to separate molecules
What is the end product of gel electrophoresis?
DNA, mRNA
What is the process of gel electrophoresis with DNA?
-have a mixture made of DNA fragments -set up slap of gel with negative charge and positive on other side -load mixtures on negative side -submerge in liquid -turn on current -molecules move towards positive end
What molecules are going to be closest to the positive side?
the smaller molecules
What is gel electrophoresis used in?
crime scenes
What is the process of getting a gene from one organism to another?
-cutting the DNA -mix the two DNA sources -get plasmids back into first organism -grow each organism separate -screen for the clone
When cutting the DNA to put a gene from one organism to another, what must be done?
Have to do it to both organisms have to use the same restriction endonuclease
How do you mix the two DNA sources in order to get a gene from one organism to another?
sticking together- recombinant DNA all fragments together are called a library
What are two ways toe get the plasmids back into the first organism when transferring genes?
Gene gun- little pellets coated with DNA gets shot in and some get rid of DNA Solubilize wall of bacteria- plasmids get taken back in
What are the 5 processes of hybridization or screening for the clone that contains the gene of interest
-make a copy of clones -add a solution that denatures the DNA from double to single stranded -add a solution that contains a probe -probe will bind to the colony that has the gene of interest -take correct colony and grow it for the gene product.
What is a probe?
a single stranded radioactively label DNA of the gene of interest
What is cDNA?
Complementary DNA
What is cDNA used in?
used in a technique that drastically shortens the experiment of moving one gene from an organism to another
What is the shorter process of moving one gene from an organism to another?
-extract mRNA from a cell that makes what you want -an enzyme called reverse transcriptase is used -take mRNA and go backwards -makes cDNA -put cDNA into a bacteria to make a product
What is PCR?
polymerase chain reaction
What is PCR used for?
used to make a lot of copies of a DNA piece quickly
What is PCR used in?
-Crime scene -pre-natal DNA -fossils
What do you need in order to do PCR
-original piece of DNA -DNA polymerase -nucleotides -short DNA primer -thermal cycler
How do you do PCR?
Denaturation- double stranded DNA changes to single stranded Annealing- primer attaches Synthesis- When DNA is actually copied
What is Southern Blotting and RFLP analysis used for?
to make a DNA fingerprint more commonly called DNA profiling
How is DNA profiling done?
-cut DNA with restriction endonuclease -separate fragments by gel electrophoresis -take gel and transfer onto special paper -place paper in basic solution -apply to multiple probes -repeat until you can say that two are similar
What does RFLP stand for?
Restriction fragment length polymorphism we all have different fragment lengths
What are the uses of PCR?
DNA fingerprinting, identification of disease carriers, paternity testing
What does STR mean?
short tandem repeat
What are the medical reasons for using DNA sequencing?
If you know nucleotide sequence -> know amino acid sequence -> know 3D structure -> know how protein works -> know if there is a mutation -> find a pharmaceutical solution to mutation
What are the forensic uses of DNA sequencing?
Can be used to identify remains
What are some medical application off using DNA sequencing?
diagnosis of a disease, Human gene therapy, pharmaceutical products
How can DNA sequencing help in diagnosing a disease?
using PCR to amplify DNA look for foreign DNA in cell Identify a carrier of a disease
How can DNA sequencing help in Human gene therapy?
Placement in a person’s cells of a function allele
What are some uses of DNA sequencing in plants?
Herbicide resistance in crops. drought resistant genes, frost resistant genes, increase nutritional value of a crop, N- fixation, Biopharming
What are the results about adding herbicide resistance in crops?
Weeds are gaining resistance to herbicide neighboring farms may or may not like it
Has animal bio-engineering worked?
NO
What are some example of attempted genetically modified animals?
Salmon- AquAdvantage
What are some bad things of genetically modified food/organisms?
might transfer genes into natural populations, people might be allergic to it might hurt organic farms increasing resistance of weeds to herbicides
What is some environmental applications of genetic engineering?
bacteria can help break down oil from an oil spill e coli and yeast can make crude oil
Who is Charles Darwin?
1809-1882 English 1861-1866- naturalist on HMS Beagle Compared artificial selection to natural selection
Who were the two people that Darwin communicated with?
Thomas Malthus- 1798- essay on principle of population Charles Lyell- 1830- book that talked about age of earth
What happened in 1842?
Darwin writes essay of 1842 butt does not publish it
What happens in 1858?
Darwin gets a letter from Alfred Russel Wallace. Decided that Wallace and Darwin should present papers at the same meeting
What happens in 1859?
Darwin published origin of species
What did Darwin theorized?
World is not static but it is changing evolution is gradual natural selection is a process and it results in evolution
What is genotype?
genetic makeup
what is phenothpe
physical appearance
what is population
individuals of one species that live together and are able to interbreed
what is phenotype
physical appearance
what is population
individuals of one species that live together and are able to interbreed
What is gene pool
all genes in a population
what is environment
total situation an organism lives in
what is biotic
factors that are living in the environment
What is abiotic
factors that arre nonlivinng in the envrionment
What is natural selection?
differential perpetuation of genotypes
Why is Natural selection necessary?
organisms are capable of sexual reproduction exists inheritable differences organisms are tested by environment
What is the result of Natural selection?
microevolution
What is microevolution
a result of natural selection that is a change in allele frequencies
What type of natural selection is this?
Stabilizing Natural Selection
What type of natu ral selection?
Directional
What type of Natural Selection is this?
Disruptive
What is adaptation?
Changes of organism to get use to environment
natural selection produces adaptations
What is Micro Evolution?
Change in allele frequency
natural selection produces micro evolution
What is co evolution
Evolution that uses two species
What is Morphological variation?
Variation you can see
What are Allozymes?
alternate forms of an enzyme that are coded for by the same locus
How can you tell allozymes apart?
by gel eletrophoresis because they differ in size and or charge
How do you quantify Allozymes?
H= Heteroozygosity
the percent of the loci that are in a heterozygous form in an individual (avergae)
P= polymorphism
The percent of the loci that are in a polymorphic form in a population (average)
What is the percent of H in humans?
7%
what is the percent of P in humans?
38%
Where is most of the variability in DNA?
Non-coding
What is the neutral theory?
Mutations that are neither positive nor negative
What is evidence of the Neutral theory?
genetic codon- takes 3 nucleotides and makes 1 amino acid, less likely to have a mutation that changes protein all together
ABO blood types, no advantage to havinng the,
Where are enzymes less variable?
At the active site, more neutral
What is population geneticists?
study by looking at allele and genotype frequencies in populations and how they change
What are the two most important agents of change that can change allele frequency?
Natural selection is the most important
migration is another one
What are 4 basic assumptions of organisms?
Individuals are diploid, undergo meiosis
individuals mate randomly
no net mutation, no immigration, no natural selection
population is statistically large
What is Panmixis?
Individuals mate randomly
What happens if the 4 assumptions are true?
the distribution of ggenotypes and gametes will stay th esame generration to generation
What is the Hardy-Weinberg equilibrium?
If there is no change there will be no resulting change
How do you calculate genotype frequency?
Consider Locus A, a
Number of possible genotypes- AA, Aa, aa
number of AA individuals= N(AA)
total population size= N
frequency of genotype= f(AA) = N(AA)/N =.5
How do you calculate allele frequency?
total number of alleles in a population at a locus= 2n or 2 times the total population
f(A)=(2*N(AA)+1*N(Aa))/2n
If there is a mutation does it change allele frequency?
rates -0.001 to -0.00001 mutation per locus in a generation
What is a mutation from A to a symbolized by?
What is a mutation from a to A symbolized by?
What are the reasons that random mating does not exist?
organisms often mate with a neighbor
organisms sometimes mate with an individual more like themselves
what is the result with inbreeding?
increase of homozygosity
Why are there not a lot of large population size?
Most are in a small group
Genetic Drift- Changes in allele frequency due to chance. Deals in small population size
What are the two different species concepts?
Morphological species concept
Biological species concept
What is the morphological species concept?
organism that look different enough are put in different species
What is the biological species concept?
interbreeding individuals are in the same species
What is speciation?
Appearance/production of a species
What is geographical isolation?
a population has to become discontinuous
2 separate populations start with slightly different gene pools
experience different environments
leads to natural selection
What is adaptive radiation?
When one species creates many
What are reproductive isolating mechanisms?
biological properites of organisms that prevent interbreeding
What are the three types of RIM?
Ecological RIM
Temporal RIM
Behavioral RIM
What are ecological RIM?
Potentional mates do not meet each other
they are in different sup-sections of their habitat
What are temporal RIM?
Reproduce at different times
frequent in insectts and plants
What are Behavioral RIM?
Potential mates meet but don’t mate
have different signaling
frequent in animals
What is hybridization?
interbreeding between two species
Why are hybrids sterile
Genome of hybrid is AB
cannot create homologous pairs
What are someways hybrids can reporduce?
if asexual reproductioin is possible
become polyploidy
What is polyploidy?
more than 2 sets of chromosomes
Where do polyploidy come from?
from a hybrid individual
error in meiosis or mitosis
What happens if you get an odd polyploidy?
Triploid is not successful
What are fossils?
any preserved sign of life?
What does homologous fossils mean?
assumed to come from a common ancestor and are therefore similar
What are analogous fossils mean?
Similarity are due to common function
Why is ciochemical date used?
can look at DNA nucleotide or amino acid sequences
What does biochemical dating do?
compare organisms and count number of differences or similarities betwen both fo them
What is gradualism?
A group of organisms change gradually through time
What is punctuated equilibrium?
alternation between rapid change and equilibrium
What are some examples of rapid change?
genetic drift
polyploidy
developmental change
What is extinction?
disappearance of some taxonomic
what is taxonomic?
a named group
What are some causes of extinction
both abiotic and biotic can cause it
Is extinction continuously happening?
yes
What are mass extinctions?
extinction that happens at higher rates
