Biology Quiz #4

What causes a shift in the translational reading frame within the HIV example? When is a termination codon found? What is the overall result of this? Why does it prove to be a beneficial mutation?

-32 bp (nucleotide) deletion for CCR5 allele→ causes shift in translational reading frame, and all downstream amino acids are incorrect -translation continues for another 26 amino acids, at which point the shifted reading frame encounters a termination codon -virus can't get in as well to T cells → beneficial mutation. Didn't affect people's immune system. benefit=less likely to be infected by HIV

What is emphysema affected by and associated with? What is the main function of how smoking can affect one's genetics? What does cigarette smoking reduce? What is the result? What does PIZ cause?

-80% of all cases associated with cigarette smoking (affects action of enzyme alpha-1-antitrypsin) -main function=inhibit enzyme elastase (which breaks down connective tissue elastin) Overly rapid breakdown usually prevented by inhibition of elastase by alpha-1-antitrypsin, but cigarette smoke reduces enzymes activity -result=excessive destruction of elastin, loss of lung elasticity, emphysema When smoke.... Still being made but not quite bonding to elastases as well PIZ: causes low levels of activity... make protein that has decreases activity. If people with this mutation smoke, get emphysema a lot earlier → mutations can lead to issues

How can DNA from different individuals differ? When PCR is used to amplify a region of the genome from different individuals or from maternal + paternal homologs of the same individual, what may be different? What is this genetic difference called? where are they found and what is their job?

-DNA from different individuals can differ in the distance between adjacent restriction sites or in the presence or absence of a particular restriction site at some location in the genome -when PCR is used to amplify a region of the genome from different individuals or from maternal and paternal homologs of the same individual, the lengths of the resulting DNA fragments may be different, due to different numbers of short repeats in the region -can take parts of our chromosomes and analyze them for differences (amplify piece of it using PCR) -genetic difference= VNTR -found throughout chromosomes, neither benefit nor disadvantages, able to verify differences in people's chromosomes -people vary on number of repeats/sizes

In replication error management, what does DNA polymerase do? Mismatch repair enzymes? What happens if proofreading doesn't catch an error?

-DNA polymerase: proofread work. Mismatch repair enzymes- can fix errors that were missed by the DNA polymerases -if proofreading doesn't catch an error, then mismatch repair enzymes can come in and repair the damage → 2nd line of defense

What makes someone homozygous? heterozygous? What can different alleles lead to? What can a 1 nucleotide change ultimately cause?

-If individual inherits same type of allele from both parents, homozygous for that trait -If they inherit different types of alleles, heterozygous -different alleles can lead to different functionalities of a protein/genotypes -change in protein structure can lead to sickle cell anemia (could clog up some of internal organs)

What happens during P. falciparum immune evasion? What is Pfemp1?

-Our immune system sees the parasite but.....it produces over 2000 different cell surface antigens at varying rates and at varying life stages . Some proteins are secreted to act as "cover" for the eventual parasite to dodge the immune response Pfemp1 --> causes then to stick to red blood vessels -invades immune system, live in red blood cells, carried by mosquitos

Influenza virus: What are viruses? what can they replicate in? what are they classified by? dependent on? What do they do? What is a difference between RNA genome and DNA genome?

-RNA genome of virus bound up with proteins, made up of 8 segments in each virus virus: small infectious agents, only replicate inside of host cells, classified by genome type -completely dependent upon host cell -All attach, inject DNA or RNA, make many more of self (some right away...some much later), lyse cell to infect more cells RNA genome: when infects cells, already have mRNA to get made directly into proteins DNA viruses (genome): start making RNA off of DNA with RNA polymerase, or other options

What is plasmodium falciparum within malaria? what is the life cycle of it? What happens during the red blood cell bursting cycles? What do infected red blood cells stick to?

-Unicellular protozoan parasite -Sporozoites come out of mosquito salivary gland -goes in our liver first -Infect red blood cells -During the red blood cell bursting cycles (where red blood cells burst so can infect more,) cyclic fever is produced in patient.... cycles of fever -Infected red blood cells stick to blood vessel walls (blocks your vessels because "stuck" (depending on how intense infection is) --> affects brain, kidney, liver)

what is MRSA and pathogenesis? what do they adhere to? what do they do at these sites? What does the bacteria do to you? what does S. aureus produce?

-adhere to damage skin, mucosa, or tissue surfaces... at these sites, evade defense mechanisms of the host, colonize and cause tissue damage S. aureus produces disease by: multiplying in tissues, liberating toxins, stimulating inflammation -can overcome it without the use of drugs/antibiotics -S aureus: attach to + break down a lot of different tissues in body (wide range of cell tropism) --> releases different toxins that can lead to toxic shock syndrome

What happens if the bacteria evolve to resist antibiotics?

-bacteria can make an enzyme that breaks down antibiotic (inactivating enzyme) -Eflux pumps: transporters that find antibiotic in cell and pump it back out -decreased uptake -target alterations -can alter how it makes its cell wall (MSRA)... protein that makes it is completely changed so methicillin doesn't work on it anymore

What do T cells become? What do they exhibit? What happens if the system doesn't distinguish self from non-self?

-become MHC restricted, meaning that they interact only with antigens that are associated with MHC proteins - exhibit tolerance—they do not respond to self antigens. -The ability to distinguish self from non-self is critical and failure leads to autoimmune diseases, in which the immune system becomes active against antigens of the host. --> can be debilitating, T cells or antibodies attack cells and organs of the host.

How are insertions and deletions seen at the chromosomal level? what can a deletion result from? How to tell if a chromosome contains a duplication? The larger the deletion...

-chromosome in which region is present twice instead of once contains duplication -deletion=when region of chromosome missing → may result from replication error or joining of breaks that may have occurred on either side of deleted region -since chromosomes occur in homologous pairs, deletion in 1 chromosome can persist in a population → but, in general the larger the deletion, smaller chance of survival

What does genetic variation describe? How can human genetic variation be detected? What are the two common types of genetic variation?

-describes common genetic differences (polymorphisms) among the individuals in a population at any given time -human genetic variation can be detected by DNA typing -two common types of genetic variation are single-nucleotide polymorphisms (SNPs) and copy-number variation (CNV) -chromosomal variants can also occur but are usually harmful

What are drugs in malaria therapeutics known for?

-drugs: cause toxicity to the parasite (will effect cells of pathogens) but not to you (your cells) -look for specific things in pathogen that we don't have -don't affect you, affect pathogen

What are the effects of different mutations? How is this seen within alleles and sickle cell anemia? SS? AS?

-effects of mutations could be beneficial or harmful -when both S alleles inherited from parents, offspring SS (homozygous) for the trait and have sickle-cell anemia -people w disease die before adulthood -if S allele inherited from 1 parent and A allele from other, offspring=AS (heterozygous for sickle-cell anemia) → milder form -AS=mild form of blood disease, but in areas of Africa where malaria widespread, mutation beneficial because provides partial protection against severe malaria

What happens with incomplete penetrance, and what is the result? What is an example of this in real life? Why does incomplete penetrance occur?

-genotype doesn't always produce expected phenotype (just because get dominant genotype, don't necessarily show dominant phenotype) Polydactyly (more fingers): dominant alleles, individuals w dominant allele can occasionally have normal # digits (but have affected children) Penetrance: % of individuals w particular genotype that express expected phenotype In traits with incomplete penetrance, individuals with genotype corresponding to a trait do not actually show the phenotype, either because of environmental effects or because of interactions with other genes

What do the different lines in pedigrees represent? In a pedigree of a dominant allele, for the rare dominant trait, most matings that produce the affected offspring have only.... from mating in which one parent affected...

-horizontal line between individuals=mating. Vertical line leads to progeny. Progeny arranged horizontally, left to right in order of birth. Double line means mating between relatives -for rare dominant trait, most matings that produce affected offspring have only 1 affected parent -from matings in which one parent affected, ½ offspring affected

What is the principle of segregation? What happens when meiosis occurs?

-individuals inherit two copies of each gene, one from mother and one from father, and when individuals form reproductive cells, the two copies separate equally in the eggs and sperm → equal separation of these alleles when meiosis occurs

In the Malaria example, what happens when individuals inherit a C allele from both parents? What do the effects of different mutations depend on? an individual is homozygous for a gene if...

-individuals who inherit C allele from both parents more protected from malaria + have a very mild anemia that often doesn't require medical treatment -effects of different mutations depend on if mutation is homozygous or heterozygous + environment in which mutation is present An individual is homozygous for a gene if: -developed from sperm + egg that carried same allele

What does a mutation in lacl (repressor) cause? How does this affect lacZ and lacY? What happens in cells containing 1 mutant and 1 normal copy of lacl to lacZ and lacY? What does a mutation in lacO (operator) cause? How does this affect lacZ and lacY? What happens in cells containing one mutation and one normal copy of lacO to lacZ and lacY?

-mutation in lacl does not produce functional repressor... lacZ and lacY repressed in presence + absence of lactose -lacZ and lacY expressed only in presence of lactose -mutation in lacO: prevents repressor protein from binding, lacZ + lacY expressed in presence + absence of lactose -1 mutant + 1 normal copy: lacZ and lacY expressed in presence + absence of lactose absence of lactose=repression

What is methylation of DNA? What is the most common chemical modification to DNA? When does this tend to occur? What are the nucleotides abbreviated as, and what are CpG islands? What does the undermethylation of the CpH island allow for?

-not changing sequence of DNA, but adding methyl group... most common chemical modification to DNA=addition of a methyl group to cytosine. -occurs in cytosine bases that are adjacent to guanosine bases on a DNA strand. nucleotides abbreviated CpG, where the "p" represents the phosphate between the two nucleotides... cytosines flanked by guanines CpG sites are often clustered near the promoter of the gene & are called CpG islands. -undermethylation of CpG island allows transcription -when methylated, inhibits transcription

What is immune evasion? what are some of the mechanisms for this? These are counteractions for the immune system!

-over generations, can evolve mechanisms to "get away" antigenic variation: varying antigens (can happen via small mutations in replication of pathogen OR certain pathogens turn on/off different proteins depending on type of infection) Evasion from phagocytes: can prevent lysosome-phagosome action, prevent lysosomal toxic action, escape into cytoplasm, can resist complement lysis immune suppression (suppressing immune response) surface + secreted antioxidant enzymes

In the pedigree of the recessive allele (for example, albinism), what is observed?

-rare recessive trait may skip 1+ generations -females + males equally likely to be affected -individuals have unaffected parents -affected individuals often result from mating between relatives (typically first cousins)

How is the foreign recognized from the self? What is phagocytes role within this? What are toll-like receptors?

-recognize self vs non-self Phagocytes- attack foreign cells that they encounter, leave host cells alone. - able to recognize pathogens by detecting specific surface molecules that are present on pathogens but not on the body's own cells. Toll-like receptors (TLRs)=family of transmembrane receptors present on phagocytes that recognize and bind to molecules on pathogens. -variety, recognize different types of things found on bacteria

What does the segregation of alleles within meiosis effect? Does it happen dependently or independently? Random or non-random? What does it yield?

-segregation reflects the separation of homologous chromosomes during anaphase I of meiosis → segregation happens at random (explaining the ratio of 3:1) -segregation of genes happens independently, always random, gets resultant gamete from each of alleles you have inside

What are antibiotics? when do you take them? What are some of their effects? How do these worked to stop MSRA?

-take when infected by bacteria -some effect cell wall synthesis of bacteria -have different type of ribosome (so our ribosomes not affected) -RNA polymerase different than ours -DNA gyrase: bacterial DNA gyrase different, can bind to/lock in DNA so bacteria can't unwind it

When can an extra copy of a gene become new? What is a gene family and mutated copy?

-when mutation in extra copy of gene beneficial to organism's survival, extra copy can become a new gene -gene family=group of genes with related functions - new mutated copy=new version of gene

What are the 3 steps of transcriptional regulation?

1) ) Regulatory transcription factors bind with a DNA sequence called an enhancer. 2) Binding of regulatory transcription factors recruits the general transcription factors to the promoter of the gene. 3) general transcription factors recruit the components of the RNA polymerase complex, and transcription takes place without transcription factors, aren't making much of gene product or aren't making any... regulate expression of transcription (at transcriptional level)

How did he work to "breed" his peas? (3 step process)

1) Crossing peas- anthers of female parent exposed + cut off to prevent self-fertilization In pea flowers, both female + male organs enclosed together within petals → self-fertilize 2) Mature pollen collected from another flower, deposited on stigma of female parent 3) After fertilization, small cloth bag tied around fertilized flower (so no stray pollen could enter)

What are the steps of transcription?

1) General transcription factors bind to the promoter, and transcriptional activator proteins bind to enhancers. 2) Through looping of DNA, transcriptional activator proteins, mediator complex, RNA Pol II, and general transcription factors are brought into close proximity, allowing transcription to proceed... folds over -level of regulation dealing with transcription factors binding to enhancer sequences

What are the three steps of clonal selection? Population of B cells? Selection? Differentiation?

1) Population of B cells: B cells express a diversity of cell-surface antibodies. 2) Selection: A foreign antigen interacts with one B cell from the population. The B cell divides to form a population of clones. 3) Differentiation: The B-cell clones differentiate into plasma cells that secrete antibodies and memory cells with cell-surface antibodies.

Within X-inactivation, what happens to the Xist gene? How does the Xist noncoding RNA work with this? What is the 4 step process of X-inactivation?

1) The Xist gene (piece RNA made from X chromosomes) is transcribed and the transcript spliced, and Xist noncoding RNA binds with the X-chromosome inactivation center (XIC). 2)Transcription of Xist continues, and the X chromosome becomes coated with Xist RNA 3) Eventually the entire chromosome becomes coated with Xist RNA. 4) Presence of Xist RNA triggers DNA methylation and other changes associated with reduced transcriptional activity -inactivates other X chromosome

what is the operon in the presence of lactose?

1) When operator is not bound by the repressor, the promoter recruits the RNA polymerase complex and transcription of the polycistronic mRNA occurs -repressor protein bound by lactose, can no longer bind to DNA 2) In the presence of lactose, the repressor protein is unable to bind to the operator.

With insertions and deletions, how many nucleotides do they involve? What results in a polypeptide? What eliminates an amino acid? What adds amino acids? how many nucleotides will lead to a new protein or codon?

1)Small insertions/deletions involve several nucleotides .... 3 nucleotides will lead to new protein/codon 2) small deletion or insertion that is an exact multiple of 3 nucleotides results in a polypeptide with as many fewer (in the case of deletion) or more (in case of insertion) amino acids as there are codons deleted or inserted 3) So, deletion of 3 nucleotides eliminates 1 amino acid, + insertion of 6 adds 2 amino acids

What is the 4 step process of inflammation?

1. Bacteria and other pathogens enter a wound. 2. Mast cells release histamine that increases blood flow (causing redness and heat) and makes blood vessels leaky (causing swelling). 3. Immune system cells in the tissue release chemical messengers called cytokines that bind to and recruit phagocytes in nearby blood vessels 4. Phagocytes enter the infected site from the blood and remove pathogens by phagocytosis. cascade of signalling that is occurring

what is the 3 step process of extravasation?

1. Rolling: The phagocyte travels along the inside of the vessel wall. 2. Adhesion: The phagocyte binds to the vessel wall. 3. Extravasation: The phagocyte changes shape, exits the vessel, and enters the surrounding tissue to travel to the site of damage. (phagoctye leaves blood + comes into surrounding tissue in order to fight an infection) look at picture for this! -get inflamed because trying to increase bloodflow to region where infection is... several cells can go in (explaining swelling, heat, color, etc.)

What did early theories of heredity assume? Who started the study of modern transmission genetics? What is the principle of segregation? Independent assortment?

1.Early theories of heredity incorrectly assumed the inheritance of acquired characteristics and blending of parental traits in the offspring. 2.The study of modern transmission genetics =Mendel, garden pea as his experimental organism and studied traits with contrasting characteristics. 3.Principle of segregation-members of a gene pair separate equally into gametes. 4. independent assortment-different gene pairs segregate independently of one another.

what does nondisjunction and first-division nondisjunction result in? What about in second division nondisjunction? What do nondisjunction events lead to?

1st: nondisjunction results in gametes with an extra chromosome and gametes that are missing a chromosome (2 have 2, 2 have 0) 2nd: extra chromosome formed in 1, missing chromosome (empty) in the other 2nd division: cells split fine in meiosis I, but not in meiosis II -nondisjunction events leads to polyploids (many different amounts in chromosomes in final cells)

What is the principle of independent assortment? What does the independent assortment of genes in different chromosomes reflect?

2 copies of each gene segregate into gametes independently of the two copies of another gene → genes are independent of one another, traits independent of one another -independent assortment of genes in different chromosomes reflects the fact that non-homologous chromosomes can orient in either of the two ways that are equally likely

What happened when a population of mosquitos was exposed to a pesticide for several generations? Why is this?

A population of mosquitoes exposed to pesticide for several generations. At the end of that time most individuals in the population are resistant to DDT. The most likely reason is that: Some individuals in the original population had the mutations that lead to resistance. → spontaneous!

What is the principle of segregation ? What is the expected ratio of AA:Aa:aa genotypes? Ratio of dominant:recessive phenotypes? What happens in the F2 generation?

AA + aa (P1 generation) → Aa (F1 generation) Expected ratio of AA:Aa:aa genotypes=1:2:1 Expected ratio of dominant:recessive phenotypes=3:1 F2=mating it to itself (1 in 4 chance to see homozygous recessive traits)

What is the probability that an individual is Aa or AA if his or her parents are both heterozygous for the trait? Why is seeing segregation in alleles not easily observed? What is the best way to look at human patterns of inheritance?

Aa x Aa → ¾ Seeing segregation of alleles in humans is not as easily observed because... don't choose mating partners for convenience of biologists, # of children in human families relatively small (mendelian ratios often obscured by random fluctuations due to chance) -Use pedigrees to look at human patterns of inheritance

What happens when it is necessary to combine probabilities of 2+ possible outcomes of a cross? What are the two rules that prove useful when this case occurs?

Addition rule: when outcomes being considered cannot occur simultaneously, add together their individual probabilities Multiplication rule: when outcomes can occur simultaneously + occurrence of one has no effect on likelihood of other, multiply their individual probabilities LOOK AT EXAMPLE OF THIS PICTURE! IMPORTANT!

What do T cells do? Where do they originate in and then mature in? What is a mature T cell characterized by? What does the binding of TCR trigger? What does the diversity of TCRs among different T cells result from?

All T cells, like B cells, originate in the mammalian bone marrow --> mature in the thymus. -characterized by the presence on the plasma membrane of a T cell receptor (TCR), --> protein receptor that recognizes and binds to the antigen in conjunction with a host molecule (MHC). Binding of TCR triggers the T cell to divide into clones, resulting in a pool of T cells that are each specific for a given antigen. -Like antibodies, the diversity of TCRs among different T cells results from genomic rearrangement. -unlike antibodies, TCRs always stay on the Tcell, not secreted.

In RNA control, what is alternate splicing? RNA editing? What do small regulatory RNAs bind to? What is their effect?

Alternate Splicing: introns & Exons -splice out introns + exons (found inside of RNA before processed + sent out of nucleus) RNA editing: Transcripts from the same gene can produce multiple types of proteins (even in a single cell) Small regulatory RNAs... -bind to transcripts and blocking translation. -bind to transcripts (RNA) and causing degradation --> way to control expression -other RNAs that bind to our RNA

base excision repair?

Base excision repair: individual enzyme cleaves out incorrect nucleotide ONLY, single nucleotide replaced

What are beneficial mutations, and what is an example of this? What is needed for HIV to invade a T cell? What happens after this? When is HIV not able to attach as well to our T cells?

Beneficial mutations: ex: HIV resistance → creates an advantage Look at picture! -for HIV to invade a T cell, must interact with a CD4 receptor (surface protein) and a CCR5 co-receptor -binds to surface protein + binds to CCR4 co-receptor -If CC45 mutates in a certain way, HIV isn't able to attach as well to our T cells

What is blending inheritance? What did Charles Darwin believe? What did he find a problem with blending inheritance to be?

Blending Inheritance, 19th century: traits of offspring resemble average of those in parents. Suggests that variation will be lost over time (not what happens in most populations) → can eventually have rare traits that get "blended out" Charles darwin- believed in natural selection + blending inheritance → understood that conflicted -problem with blending inheritance: rare variants have no opportunity to increase in frequency even if survive + reproduce more (bc gradually disappear over time)

What is Candida auris? What is it related to? who does it infect? What does it lead to?

Candida auris is a fungal pathogen... anti-fungal resistant Distantly related to Saccharomyces cervisiae infects Immuno-compromised patients Fever, chills, bloodstream infection that doesn't respond to anti-fungals. newly discovered

How is chromatin remodeled (histone tail modifications) where does modification usually occur? how do amino acids relate to this/how are they modified ?

Chromatin is remodeled by chemical modification of histones around which DNA is wound. Modification usually occurs on histone tails Individual amino acids in the tails can be modified by the addition (or removal) of different chemical groups including methyl and acetyl. -not changing amino acid sequence, just strapping something else onto amino acid adding something to histone proteins opens up chromatin more

Why is gene regulation simpler in prokaryotes than in eukaryotes? What is the regulation of transcription in prokaryotes? What happens in positive transcriptional regulation? what happens if the repressor proteins binds to the DNA?

DNA is not packaged into chromosomes. mRNA is not processed. there is not a nuclear membrane separating the processes of transcription and translation. 1) positive transcriptional regulation-RNA polymerase can bind to the promoter only if an activator protein binds to a site near the promoter. 2) negative transcriptional regulation- if repressor protein binds to the DNA, it inhibits recruitment of RNA polymerase, and transcription does not occur.

What are epigenetic effects? Can they be inherited? Are they reversible or irreversible? Why is gene regulation by means of epigenetic mechanisms useful to the organism?

Epigenetic effects are... changes that are not to the DNA sequence itself, but to manner in which the DNA is packaged, sometimes causing changes in gene expression. -cause a phenotype even though not changing sequence -changes can be inherited but (since not changing DNA sequence) are often reversible and responsive to changes in the environment. Gene regulation by means of epigenetic mechanisms are useful to the organism: -does not require new mutations. -can quickly be reversed. -can respond rapidly to environmental change.

What is epistasis? What is an example of this? Within the example, what genotypes have colored feathers? What is the F2 ratio of white:colored? Is this expected?

Epistasis: when 1 gene directly affects the phenotype of another gene One gene dominant or recessive for color, one gene just gets rid of all color Only when have CC or C and ii are we able to get a chicken with some form of color.... All came from chickens that had no form of color (13:3)... modified form of expected 9:3:3:1 ex: -white leghorn white because inhibitor allele I blocks expression of pigment allele C -white wyandotte white because pigment allele c does not produce pigment -genotypes C-ii have colored feathers

What happens in chromatin remodeling? what does it allow for? What is Eukaryotic DNA packaged as? What happens when chromatin is coiled (can it be accessed)? What happens during chromosome remodeling?

Eukaryotic DNA packaged as chromatin (complex that gives chromosomes their structure.) When the chromatin is coiled, DNA cannot be accessed --> chromatin must unravel, which is accomplished by chromatin remodeling, RNA polymerase can't start making mRNA During chromosome remodeling, nucleosomes are repositioned to expose different stretches of DNA.

What is the F2 generation, and what did it prove? What is Mendel's process for creating the F2 generation? How is it different from natural self-fertilization?

F2 generation → shows that blended inheritance theory is wrong → mated F1 to F1 Seeds from F1 plants produced from cross of true-breeding yellow-seed and green-seed plants=yellow because yellow is dominant and green is recessive in seed color -peas normally self-fertilizing so, if left alone, pollen produced in each flower fertilizes ovules, producing seed pod whose contents have genotypes that depend on the alleles in that individual flower's pollen and ovules -because fertilization takes place at random, any individual pod can have a ratio of dominant:recessive that deviates from 3:1

Failure of cell division in anaphase in meiosis can result in a: How are chromosomal abnormalities seen within spontaneous abortion? What are polyploid organisms? What do they normally result from?

Failure of cell division in anaphase in meiosis can result in a: diploid gamete and triploid fertilized egg Spontaneous abortion- among fetuses in 100,000 recognized pregnancies, ab 8000 have major chromosomal abnormalities (7500 undergo spontaneous abortion) Polyploid organisms: these karyotypes usually result from a defective spindle apparatus and failure of cell division in anaphase

What do the phagocytes do following the binding of a foreign molecule? How are cytokines relevant? what do they provide?

Following binding of a foreign molecule... phagocytes send a message to the rest of the immune system that the body is under attack by releasing chemical messengers called cytokines -cytokines= recruit other immune cells to the site of injury or infection. provide long-distance communication between cells.

For genes contained on the X chromosome, what is the dosage of genes compared to females vs males? what about the level of expression of X-linked genes? what does this imply? What is dosage compensation? What does dosage compensation occur through?

For genes on the X chromosome, the dosage of genes is twice as great in females (XX) as it is in males (XY), yet the level of expression of X-linked genes is about the same in both sexes. -regulation mechanism of the X chromosome that differs between males and females. -females regulating one of X chromosomes This differential regulation= dosage compensation -inactivation of one of X chromosomes in each of female cells. Dosage compensation occurs through the inactivation of one X chromosome in each cell in females, X-inactivation.

What is gene duplication and evolutionary divergence? What allows divergence to occur? what happens when 1 gene is replicated?

Gene duplication and evolutionary divergence: formation of new genes from duplication of old ones → gene duplication allows for divergence to occur -divergence=slow accumulation of differences between duplicate copies of gene that occurs on evolutionary time scale -when gene duplicated, 1 copies can change without harm to organism because other copy still carries out normal function

What does gene regulation encompass? what are the potential control points for gene expression? What different levels is gene regulation seen at?

Gene regulation encompasses the ways in which cells control gene expression (where genes turned on, when turned on, how much gene product made) Each event that takes place in the expression of a gene is a potential control point for gene expression. -through chemical modification of chromatin or histones, during transcription, during RNA processing, during translation -tighter condensing, DNA less likely to get transcribed. -once leaves nucleus, can control how stable RNA is, how often its made, etc.

What is genetic variation specifically? What is a genotype vs phenotype? What are alleles, and what do they correspond to?

Genetic variation: genetic differences that exist among individuals in a population at a particular point in time → not every difference at genotypic level can be shown at phenotypic level Genotype: the genetic makeup of a cell or organism Phenotype: an individual's observable characteristics alleles=different forms of gene... correspond to different DNA sequences (polymorphisms) in genes

What are harmful mutations, and what are they affected by? Do they stay within generations, or are they eliminated? When do they persist in a population, and what may they depend on?

Harmful mutations → affected by environment -often eliminated after few generations because decrease the survival and reproduction of the individuals who carry them -sometimes harmful mutations (such as mutations that increase risk of emphysema) persist in a pop → may depend on environment in which those harmful mutations exist (increase ability of mutations to hurt people)

What are Helper T cells activated by? What happens when TCR binds to antigen + MHC class II proteins?

Helper T cells are activated by binding to an antigen presented by certain immune system cells that have phagocytosed a pathogen -When TCR binds to antigen and MHC class II proteins.... helper T cells release cytokines that activate other parts of the immune system, including macrophages, B cells, and cytotoxic T cells.

what does heavy methylation of the CpG island inhibit?

In many organisms, some cytosine bases in DNA are changed by enzymes into 5-methyl cytosines. Heavy methylation of the CpG island inhibits transcription.

What do you see in the absence of glucose? What happens if lactose is present? What is lactose is not present?

In the absence of glucose: a.cAMP levels are high. b.cAMP binds to CRP, changing the shape of CRP. c.CRP binds DNA and activates transcription. -lactose present, the repressor cannot bind and the lactose operon is induced. -lactosenot present, the repressor is bound and the lactose operon is not transcribed, even in the presence of the cAMP-CRP complex. presence of glucose: do not get activation. control at level of how much lactose present=negative regulation control at level of how much glucose=positive regulation -lactose utilized only when glucose depleted

What are inversions, and when do they form? What is reciprocal translocation, and what kind of genomes are they seen in?

Inversions: form when the region between two breaks in a chromosome is flipped before the breaks are repaired Reciprocal translocation: join segments from nonhomologous chromosomes -in large genomes, breaks likely to occur in noncoding DNA, so breaks themselves do not usually disrupt gene function (segments joined together, making 2 unique chromosomes. Kind of like crossing over but with nonhomologous chromosomes)

In DNA repair, what recognizes mismatched bases? What are recruited? What removes successive nucleotides? what fills in missing nucleotides + joins backbone?

MutS (initiates repair process!) recognizes mismatched bases in DNA, + initiates repair process MutL and MutH proteins recruited, MutH breaks backbone Exonuclease- removes successive nucleotides, including the one with the mismatched base. DNA polymerase fills in missing nucleotides, DNA ligase joins backbones

What do mutation rates depend on? How are mutations seen within each of these kinds of cells? more DNA (larger genome size)=

Mutation rates depend on cell type: -somatic cells, body Germ cells, reproductive cells -mutations in somatic: passed only to daughter cells in area, not transferred to future generations (cancer) -mutations in germ: passed to new offspring (cystic fibrosis) -mammals: rate mutation per nucleotide per replication in somatic cells much greater than in germ cells -more DNA (larger genome size)=replicate cells a lot more=more mutations (per generation... not rates)

What is a mutation? What do many processes, like DNA replication, transcription, and translation depend on? What do mutations and mistakes and replication lead to? What are not heritable?

Mutation=any heritable (mutation stable, passed on through cell division) change in the genetic material •Many processes (i.e., DNA replication, transcription, translation) depend on reliable pairing of complementary bases, but spontaneous and random mutations also occur •Mistakes/mutations in replication lead to alterations in the nucleotide sequence in the DNA → passed onto daughter cells when the cell divides. •RNAs are not heritable → stability + viruses

what are neutral mutations? What are they typically found in?

Neutral mutations: no effect on organism, often found in noncoding DNA (part of chromosome that doesn't have a gene in it... doesn't encode a protein)

What happens within a nucleotide excision repair? When is this seen? What is used as the template? What is more harmful; duplication or deletion ? LAST SLIDE CHAPTER 14

Nucleotide excision repair: 1+ damaged bases signals repair process, enzyme cleaves the DNA backbone at sites flanking the damage, region with damaged bases removed, gap filled by new DNA synthesis, using ungapped strand as template -DNA damage to the nucleotides, but nucleotides are correct -deletion is more harmful

Nucleotide excision repair?

Nucleotide excision repair: correct nucleotides (just damaged are recognized,) they and surrounding bases are cleaved out and the DNA polymerase/ligase fills in the gap

What is the parental generation, or P1? What is the dominant trait? recessive trait? What are reciprocal crosses?

Plant growth from true-breeding strain w yellow seeds (dominant) and plant grown from true-breeding strain with green seeds (both true-breeding) -true-breeding strains crossed constitute P1, or parental generation trait that appears in F1 generation when plants bred together (yellow seeds)=dominant, and other trait (green seeds)=recessive Reciprocal crosses: interchanged which parent (male or female) exhibited each trait

3 antifungal therapies: What are polyenes? azoles? allyamines? What is the basis of all of these therapies?

Polyenes: amphipathic molecules that bind to ergosterols found only in the membrane of fungi Azoles: Inhibits the an enzyme in fungal synthesis of ergosterols. Allyamines: inhibit a different enzyme in ergosterol synthesis. cell wall synthesis is inhibited within fungi through anti-fungal therapy

What is the positive selection of T cells? What is the negative selection of T cells?

Positive selection: retains T cells that react with self MHC proteins, removes those that do not react with self MHC proteins. Negative selection: removes T cells that react too strongly with self antigens in association with MHC proteins. -T cells only recognize our own MHC proteins (why organ transplants denied a lot)

What is a post-replication mismatch repair? base excision repair? Nucleotide excision repair?

Post-replication mismatch repair: single mispaired base repaired by removing + replacing DNA segment Base excision repair: incorrect base + its surrounding bases excised from the strand, then replaced Nucleotide excision repair: recognizes multiple mismatched bases in a region

what is a post-replication mismatch pair?

Postreplication mismatch repair: Mut proteins recognize mismatch, exonuclease takes out all surrounded bases, DNA polymerase refills/ligase seals

in a postreplication mismatch repair, what happens? What removes the successive nucleotides? In a base excision pair, what in DNA signals the repair process? What cleaves the backbone and removes the sugar?

Postreplication mismatch repair: exonuclease removes successive nucleotides, including the one with the mismatched base → DNA polymerase fills in the missing nucleotides, and a DNA ligase joins backbones Base Excision pair: Uracil in DNA signals repair process, DNA uracil glycosylase cleaves uracil from the deoxyribose sugar -different protein for each different base recognizes mismatch, "pops out" that one base ... those that signal + cleave differ -AP endonuclease cleaves backbone + removes sugar. Other enzymes close the gap by new DNA synthesis, using intact nucleotide opposite the site as a template

In translational regulation, what do proteins bind to? What does the translation machinery assemble on before translation is initiated? What is translation often regulated by? What is translation initiation enhanced by?

Proteins can bind to sequences in the 5' UTR (cap) to transport the mRNA to particular locations in the cell, or can affect translation initiation directly. The translation machinery assembles on the 5' cap often regulated by sequences in the 3' untranslated region (3' UTR), sometimes by binding with specific proteins. initiation is enhanced by a poly(A)-binding protein (tail) that brings the tail into contact with the initiation machinery on the 5' cap. -longer polyA tail=longer RNA sticks around inside cell

In humans, ability to roll tongue ( R) is dominant to being unable to roll ( r). Having freckles (F) is dominant to having no freckles (f). A man heterozygous for both traits marries a woman heterozygous for both traits. What is the probability that they will have a child with freckles ?

Question has NOTHING to do with rolling of tongue... Ff x Ff → ¾ (1:3)

Small RNAs: Once RNAs are made, what do they form? What recognize the folded sRNAs? What do these also do? How is incorporation seen? what protein complex is important in small RNAs?

RNAs are made....but RNA folds back upon itself to form one or more hairpin structures. Enzymes recognize the folded sRNAs and cleave the stems from the hairpin leaving small, double-stranded fragments. One strand of the fragment becomes incorporated into a protein complex called RISC (RNA-induced silencing complex) that base pairs with a region of the target mRNA. Translation is inhibited OR RNA is degraded

When does random X-inactivation occur? What happens in each cell lineage? What is an example of this?

Random X-inactivation in the embryo occurs at about the time of implantation in the uterine wall. -In each cell lineage, the inactivated X remains inactivated. Calico cats (female;) the orange and black fur colors are due to different alleles of a single gene on the X chromosome. -heterozygous female; X-inactivation predicts discrete patches of orange and black -mosaic colors results from x-inactivation

For regulation after mRNA --> protein transition (posttranslational) what is a key regulator or protein activity? What kind of posttranslational controls do we employ?

Reversible addition of a phosphate group to the side groups of amino acids such as serine, threonine, or tyrosine is a key regulator of protein activity. Marking proteins for enzymatic destruction by the addition of chemical groups after translation is also important in controlling their activity. another level of control to see how long protein sticks around + whether or not degraded,etc. controlling proteins activity or controlling length + time protein around, stability of protein, when protein degraded

What is an example of how single missense mutations have incredible effects?

Sickle-Cell anemia: caused by change in single amino acid (Glu replaced by Val in hemoglobin subunit B-globin...nonsynonymous mutation) → leads to misfolding of hemoglobin -individuals who inherit two copies of the mutant B-globin gene have sickle-cell anemia -In this condition: hemoglobin crystallizes in low levels of oxygen, causing cell to collapse

what is a single nucleotide polymorphism? what about a polyploidy?

Single Nucleotide Polymorphism (SNP): changes of just 1 single nucleotide which can lead to different types of phenotypes Polyploidy: difference you can have in genomes, not as common, error in cell splitting/meiosis... end up getting multiple copies of chromosomes (more or less than necessary) inside of the cell

What are small scale mutations? What are examples of these? What are large scale mutations?

Small scale mutations (nucleotide substitution or point mutation) → synonymous (silent) mutations, nonsynonymous (missense) mutations, nonsense mutations, frameshift mutations Large scale (chromosomal mutations) → insertion or deletion ... codons read different, completely changes frame (everything downstream will be different with different codons)

how is specificity seen in the adaptive immune system? How is memory seen in the adaptive immune system? What kind of cells are seen within the adaptive immune system? where do they mature?

Specificity: The adaptive immune system produces an array of molecules, each of which has the potential to target a specific pathogen it has never before encountered. Memory: The adaptive immune system remembers past infections and mounts a stronger response on re-exposure. B lymphocytes, or B cells, and T lymphocytes, or T cells: -In mammals, B cells mature in the bone marrow. -In most vertebrates, T cells mature in the thymus, an organ of the immune system located just behind the sternum, or breastbone.

What is anti-pathogenicity therapy for MSRA? what is a new way to fight antibiotic resistance in the future?

Staph. aureus- gold sheen on bacterium; which is encoded by a gene for fatty acid integration factor in the membrane of the bacterium. Recent studies showed that isolates mutated in the "gold" gene were less able to colonize mice/cause death. Investigation into the pathway which the gold gene is in, revealed that a certain cholesterol inhibitor could act to decrease enzymatic action. Tests confirmed loss of "gold" phenotype when treated with human cholesterol inhibitor. Mice treated with cholesterol inhibitor showed a 100% increase in survival from MRSA infection. use antibiotic against bacteria, selects for mutations (causing bacteria to mutate) use anti-pathogenicity therapy, not putting as hard of selective pressure on bacteria to mutate + be resistant to it.... not killing bacteria, taking away "weapons" so doesn't cause as severe of an infection cholesterol inhibitor causes it to change from gold to white

What does the immune system protect organisms from? What does the innate immune system act as? What does the adaptive immune system include? What have some pathogens evolved to have?

The immune system protects organisms from pathogens. The innate immune system acts generally against a diversity of pathogens. The adaptive immune system includes B cells and T cells. Some pathogens have evolved mechanisms that enable them to evade the immune system.

What is the specificity of the adaptive immune response in part the result of? What is an antibody? What are antigens, and what is the great diversity of antigens on different microorganisms matched by?

The specificity of the adaptive immune system is in part the result of antibodies produced by B cells. antibody=large protein found on the surface of B cells or free in the blood or tissues and binds to molecules on the surface of foreign cells (antigens) antigens: molecules that lead to the production of antibodies. -great diversity of antigens on different microorganisms is matched by a great diversity of antibodies produced by an individual. -estimated that humans produce approximately 10 billion different antibodies, each with the ability to recognize one or a few antigens on microorganisms.

What is transmission genetics? What did Aristotle propose?

Transmission genetics: manner in which genetic differences among individuals passed from generation to generation (each person has own personal genome) -Aristotle: proposed that process of heredity only transmits potential for producing traits/characteristics present in parents (and not traits themselves)

what do two types of granulocyte defend against? What are mast cells and what do they release? Do natural killer cells recognize foreign cells?

Two types of granulocyte, eosinophils and basophils, defend against parasitic infections, but also contribute to allergies. Neutrophils=Bacteria Mast cells- release histamine (contributor to allergic reactions and inflammation) Natural killer cells do not recognize foreign cells, but recognize/kill host cells that are infected by a virus or have become cancerous or otherwise abnormal (recognize when self-cell is infected)

When looking at a gel, what does VNTR provide? What can this then be used for?

Variable Number of Tandem Repeats (VNTR) → each of the different genotypes yields a unique pattern of bands in the gel can check, based on sizes, if people homozygous or heterozygous for different versions of an allele

What is variable expressivity? Is the trait always expressed, or not always? What can variation among individuals in expression of a trait result from?

Variable expressivity: particular phenotype is expressed with a different degree of severity in different individuals -trait always expressed, though severity varies; with incomplete penetrance, trait either expressed or not -variation among individuals in expression of trait can result from action of other genes, from effects of environment, or both

Pedigrees of families affected by brachydactyl suggest that the condition is a dominant trait because....

affected individuals equally likely to be males or females (+ appear in each successive generation), most matings that produce affected offspring have only one affected parent, among matings in which one parent affected, half offspring affected

What are frameshift mutations? Which mutations in an animal somatic cell would be inherited by the next generation?

an insertion or deletion that is not an exact multiple of 3 nucleotides changes the reading frame of translation Since somatic, no cells get passed onto the next generation

antigenic shift vs antigenic drifts?

antigenic shift: when whole, new piece picked up by virus ... H1 changed (to H2) -influenza: whole new RNA chromosome picked up, new re-assorting of genome antigenic drift: little mutations occur that slightly change surface protein (so not recognized as well by antibodies) .... H1 edited

what is the influenza vaccine?

antigenic shifts and drifts can lead to individuals having different reactions to it (sometimes works, sometimes doesn't), or could not cause as deep as an infection, etc.

epigenetic modifications can...

be inherited, reversed, alter gene expression

what is a parasite? what is a difference between it and a virus? What is the vector of malaria?

bigger genomes than virus (so more things encoded on it) -like to go into red blood cells, multiply, and then break out of red blood cells mosquito=vector that is moving infection

Influenza What is the process of this? what is the life-cycle?

binds to cell, induces cell to take it into an endosome -virus then takes in H ions, breaks open, and releases its RNA in cytoplasm--> bought into nucleus of host cell --> replicated --> "steal" 5' cap from host cell/RNAs, allows proteins to be made in cytosol --> translation occurs --> get put onto surface of host cell

Where do T cells mature? Where do B cells mature? What are major sites of the lymphocytes?

both part of the lymph system T cells in thymus, B cells in bone marrow of mammals liver, spleen, lymph nodes (major sites mature lymphocytes)

A man is scratched by his cat. A phagocyte near the scratch site recognizes and engulfs a bacterium. Shortly thereafter, more phagocytes arrive in the tissue surrounding the scratch. How are the additional phagocytes recruited to the site of the scratch?

by cytokines secreted by the initial phagocyte cytokines produced by cells recognizing the pathogen

What are transposable elements, and what are their effects?

can disrupt the normal function of a gene. When transposable element removed, function of original gene can be restored -"jumping genes" → move around from one host piece of DNA to another (can disrupt different genes) -the transposable element (after part removed into another chromosome) is excised/combined afterwards

what is cell tropism? what does it play a role in? within cell tropism, how can HIV invade a T cell?

cell tropism: pathogens do not infect every cell... based on receptors + attachment, have tropism for certain cells (not every cell will get infected) -what cells the virus/bacteria attach to -plays role in adhesion for HIV to invade T cell, must interact with CD4 receptor and CCR5 co-receptor (recognize CD4 surface protein from T cell) -pathogens sense where they are and regulate which surface proteins using in order to bind to correct host + bind to correct cells within the host.

What is a nonsense mutation? small-scale or large-scale changes?

change 1 nucleotide, leads to a stop codon -a nucleotide substitution that creates a stop codon -makes a truncated protein (shorter), which is then usually nonfunctional and unstable -small-scale, single-nucleotide changes

What does S. aureus do within immune evasion and pathogenicity factors?

controls the expression of different things... expresses surface proteins that allow it to bind to different types of host proteins releases coagulase: causes blood to solidify around bacteria (so white blood cells cant get in) later in infection: starts to release toxins (causing immune system to "freak out"), more blood flowing around, more nutrients

The precursors of small regulatory RNAs may be... Where are precursors processed? What happens to them? What are the fragments? What are they incorporated into?

double-stranded RNA or single-stranded RNA that forms hairpin (fold back on themselves) Precursors processed in the cytoplasm and cleaved into small (20-25 nucleotide) fragments. -These fragments=small regulatory RNAs that are incorporated into a RISC complex and target complementary mRNA sequences.

what is an example of negative regulation? What is CRP-cAMP regulation? glucose vs cAMP? What is constitutive expression? What is it generally the result of?

effects of lactose and lacl (repressor) low glucose, high cAMP constitutive expression: when gene made all the time in what ever condition... generally, result of mutation in either repressor no longer working or operator no longer able to be bound by repressor

What is restriction fragment length polymorphism (RFLP)? What indicates an individuals genotype?

estriction enzyme cleaves both DNA samples at all of the sites it recognizes, producing fragments of different lengths. Following electrophoresis, the gels show the position of the fragments to which the probe hybridizes -# and position of bands indicate genotype -can be used for different alleles

What is incomplete dominance? What is the ratio result of segregation? What is the intermediate? What is an example of this? ratio of red:pink:white phenotypes? What are the heterozygotes in the situation of incomplete dominance? In notating incomplete dominance, how should you indicate alleles? What is the genotype and phenotype ratio in the case of incomplete dominance?

example: Red and white flower bred, "daughter"=pink -phenotype of heterozygous CRCw plant is intermediate -result of segregation can be observed directly, because ratio of red:pink:white phenotypes is 1:2:1, which reflects ratio of CRCR:CRCW:CWCW genotypes -heterozygote (strains that have both) are very own phenotypes because of incomplete dominance... not red or white In notating incomplete dominance, use subscripts to indicate alleles (neither allele dominant to other) -in this case, genotype ratio and phenotype ratio both 1:2:1, because each genotype has distinct phenotype

What is genomic rearrangement? The large number of antibodies that can be produced in a single individual is a result of:

forms different antibodies -occurring at DNA level and at mRNA level via RNA processing -once genomic rearrangement has occurred (decided which regions to lock in), that is ALL that that B cell will make -each B cell only makes/secretes 1 type of antibody (specificity) a single B cell producing a unique antibody from all other B cells by genomic rearrangement.

What is the rate of mutation per cycle of DNA replication or rate of mutation per organismal generation in germ-line? somatic? What is most important in germ-line and somatic mutations? For somatic mutations, are they transmitted to future generations?

germ-line=rate of mutation per organismal generation most imp -imp to evolutionary processes... through transmission between generations, may become present in many individuals Somatic mutations=rate of mutation per cycle DNA replication most imp -somatic mutation not transmitted to future generations, but to progeny cells in mitotic divisions

what is a mechanism of methicillin resistance?

horizontal transfer of genomic island SCCmec (contains gene mecA) --> produces PbP2A protein responsible for resistance

What happens with insertions or deletions? What are its effects?

if added, codons read would be different... frame is changed (everything downstream will be different with different codons) -can knock entire gene sequence out of frame so changes entire amino acid sequence (creates completely new protein) → can "knock" everything out of frame

What happens in cystic fibrosis?

in most common mutant proteins, 3 nucleotides deleted in CFTR gene --> missing amino acid at position 508 -mutant CFTR protein unstable + degraded before reaching the membrane -CFTR transporter pumps chloride ions out of the cell

What happens when mutations go without repair? Example: A G is erroneously incorporated into the daughter strand opposite the T and is not corrected by the proofreading function...

in the next round of replication, the G specifies a C on the opposite strand. The new C-G pair is replicated as faithfully as the original T-A pair and the mutation is now present in this cell lineage.

Innate immune system: What does it target? ability to distinguish self from nonself (the person who makes those cells and an invader)? specificity? memory? Organisms: adaptive immune system: What does it target? ability to distinguish self from nonself? specificity? memory? Organisms:

innate: diverse pathogens yes no no all organisms adaptive immune system: diverse pathogens yes yes yes vertebrates

In the lac operon, what is the structural gene for the repressor protein? Why are lacZ and lacY called structural genes? What happens to operon in the absence of lactose?

lacl=structural gene for the repressor protein. can prevent transcription from occurring by binding to operator lacZ and lacY called structural genes because they code for the primary structure of proteins. absence of lactose: repressor protein binds to the operator and prevents transcription from taking place. -in presence of glucose, has its carbon source. when lactose around, repressor protein doesn't make it as much

What are leukocidins?

leukocidins: proteins that kill white blood cells

What is independent assortment? When is it seen? What is the general principle of independent assortment What does hereditary transmission of a gene affect?

more than one gene/trait=independent assortment -principle of independent assortment: states that segregation of one set of alleles of a gene pair is independent of the segregation of another set of alleles of a different gene pair (independent) -hereditary transmission of either gene has no effect on the hereditary transmission of the other example of this: P1 generation: plant grown from true-breeding strain with yellow + wrinkled seeds (AA, bb) + plant grown from true-breeding strain with green + round seeds (aa, BB) --> because of dominance, the seeds in the F1 generation are yellow + round

For mutation rates, do more mutations occur in replication of RNA or replication of DNA? What happens as the genome size?

mutation rates: very small numbers, more mutations can occur in replication of RNA than replication of DNA -as genome size increases, mutation rates seem to decrease

lacI=

negative regulator of transcription

What does innate immunity activation depends on? previous exposure to a foreign antigen. diversity of antibodies in the blood stream. MHC proteins. memory B cells. None of the other answer options is correct.

none of the above... because innate!

Alternative splicing- What is the difference between mRNA in liver and mRNA in skeletal muscle? What are the receptors for insulin affinity?

nucleus... primary transcript liver: make with exon 11 present ... 36 nucleotides constituting exon 11 included in mRNA... receptor w low insulin affinity skeletal: make with exon 11 eliminated ... excises exon 11 along w flanking introns... receptor with high insulin affinity -want insulin more so than want in liver control exactly how that protein is going to work, + controlling which type of receptor will have -based on if exon is kept in or spliced out (with introns)

How do mutations occur? What are they caused by?

occur spontaneously -could have single-stranded breaks in DNA (x-rays), crosslinked thymine bases (UV light), missing base (bleach/hydrogen peroxide. Reactive O species), bulky side group/chain attached to base (chemicals like tobacco), double-stranded break in DNA backbone Mutagen: help causes mutations to occur

What is the lac operon, and what does it contain? lacZ vs lacY? What is an operon?

operon=region of DNA that includes the coding sequence for multiple genes that get transcribed together into a single molecule of mRNA (polycistronic mRNA). -do not exist in eukaryotes The lac operon contains gene coding sequences: -lacZ =gene for β-galactosidase (protein), cleaves the lactose molecule into its glucose and galactose constituents. lacY =gene for lactose permease, which transports lactose from the external medium into the cell. -allows lactose to get into the cell

What is an example of a genotype-by-environment interaction? Who are much more susceptible to developing emphysema? What is the mutant allele? What happens to people who are homozygous for this related mutation?

phenotype (emphysema) is the result of an interplay between genes (alpha-1-antitrypsin) + environment (cigarette smoker) -individuals with mutant gene + that smoke far more susceptible to developing emphysema -individuals who never smoke can also develop by mutation in gene encoding alpha-1-antitrypsin -mutant allele=PiZ -individuals who are homozygous for this mutation produce alpha-1-antitrypsin with reduced activity + therefore have reduced elastase inhibition → severe emphysema

What is a point mutation, and what is an example of this?

point mutations=changes in a single nucleotide (change of 1 single nucleotide to another) -G erroneously incorporated into daughter strand opposite T and is not corrected by proofreading function

microbial mechanism of pathogenicity? what is this pathway? What is cell tropism?

portals of entry --> # of invading microbes and adherence --> penetration or evasion of host defenses --> damage to host cells --> portal of exit pathogenicity: ability of disease agent to cause disease factor: kind of protein produced that can live inside host (+ possibly cause damage) microbes have proteins that can anchor to a host cell (+ penetrate deeper in order to get at more nutrients)

what is a pre-erythrocytic vaccine? blood-stage? transmission blocking?

pre-erythrocytic: prevent infection, reduce disease (trying to make vaccine against proteins expressed in parasite after mosquito bites but before goes into red blood cell) blood stage: antibodies that attach to pathogen as it is breaking out of red blood cells + before gets into new ones prevent disease Transmission blocking: prevent transmission

What is antibody protease?

protease- enzymes that break down proteins -in order to invade host, pathogens can send out protease that will break down antibodies

What is MecA How is this a resistance mechanism/displays how the bacteria is antibiotic resistant?

protein/gene that fills in for some of the other proteins found in MSRA that build the cell wall (regardless of methicillin) -allows it to no longer be effected by other antibiotics that affect cell wall synthesis (can't bind to cell wall) -builds cell wall, not affected by methicillin (cell-wall making enzymes stopped from doing their job by methicillin)

What did Gregor Mendel study? What did he prove? What did he focus on?

proved blending inheritance not correct (genes are transmitted in inheritance, not traits) -studied hybridization (interbreeding) between two different varieties of pea plant → focused on 7 contrasting traits → strains of plants that were true breeding for each trait (physical appearance of offspring in each successive generation is identical to previous one) -ex: if took green-seeded plant and crossed it with itself, saw only green-seeded plant → true-breeding

In all 7 contrasting traits that he studied, what was the ratio of dominant to recessive phenotypes in the F2 generation?

ratio of dominant to recessive phenotypes in F2 generation was 3:1 in all 7 contrasting traits he studied (seed color, shape, pod color, shape, flower color, position, plant height)

In peas, what are the dominant traits? What are the ratio of the phenotypes? How many genotypes and phenotypes are there?

round (not wrinkled)=dominant, yellow=dominant 9 possible genotypes and 4 possible phenotypes.... Ratio of phenotypes=9:3:3:1

What is the history of influenza? What is H? what is N? What is antigenic drift? antigenic shift? both lead to differences in H and N types

subtypes: H stands for HA=hemagglutinin --> surface protein that binds to host cell receptors, helps virus enter N=NA=neuraminidase --> helps virus break free from the infected host cell if get mutations, structure of H and N proteins can change (multiple effects) --> small changes in influenza (bc RNA virus)=antigenic drift (small nucleotide changes) antigenic shift=massive changes --> introducing a whole new surface protein (when have big change)

What does the result of the experiment support?

supported the hypothesis that mutations occur randomly and without regard to the needs of the organism (to survive in an environment containing antibiotics)

What are synonymous/silent mutations? What about nonsynonymous/missense? What can they change?

synonymous/silent mutation: at protein level, don't see it. Nonsynonymous/missense: can change amino acid sequence, and one nucleotide change makes difference at protein level -changes one nucleotide and turns it into another amino acid

RNA editing what does the deamination of adesonine produce? What does the deamination of cytosine produce? What is the difference between the mRNA in the intestine vs the mRNA in the liver? What does this difference show?

take RNA sequence and change it: deaminated: NH2 replaced by oxygen Deamination of adenosine produces inosine. Deamination of cytosine produces uracil liver: unedited mRNA encodes a protein of 4563 amino acids that transports cholesterol in the blood intestine: edited mRNA encodes a protein of 2152 amino acids that absorbs lipids from foods. --> different cell type in intestine deaminates this cystine (changed to uricil). -two totally different proteins made from same transcript (made direct change to transcript sequence) -controls gene expression

where does the regulation of gene expression take place? What happens after mRNA is transcribed + exported to the cytoplasm? how is transcriptional regulation illustrated in bacteria?

takes place at many levels... DNA packaging in chromosomes, transcription, RNA processing After mRNA transcribed + exported to the cytoplasm in eukaryotes, gene expression can be regulated at the level of mRNA stability, translation, and posttranslational modification of proteins. Transcriptional regulation is illustrated in bacteria by the control of the production of proteins needed for the utilization of lactose.

What is a testcross? what does a testcross allow for? recessive:dominant trait ratio?

testcross: by crossing F1 progeny with the true-breeding recessive strain (test crossing), you can learn the genotype of unknown parent -can take strain not sure about and mix it with true-breeding, homozygous recessive → can then look at phenotype coming out to determine what the parent was -saw 1:1 ratio of how much got recessive trait vs how much got dominant trait

What results in malignant colon cancer?

the accumulation of 3 successive mutations in a lineage of colon cells results in malignant colon cancer Mutations occur, build up... develops more and more mutations in different genes → idea=accumulation of mutations (relates to many kinds of cancer)

True or false: F1 generation of cross between two individuals, one that is homozygous dominant for trait + other that homozygous recessive for trait, will yield progeny with the same phenotype What is the phenotype ratio of progeny of cross between 2 individuals with a trait that displays incomplete dominance?

true 1:2:1

What is anti-pathogenicity therapy?

understand the bacteria + how it causes infection... use human immune system either disarm the bacteria (weaken the host but don't kill) or arm the host (vaccinate)

What is an experiment that shows how mutations arise? When would you expect that no antibiotic resistant mutants are there?

use bacteria to show that mutations arise spontaneously... take plate (with no antibiotics) and put bacteria on it, repiclapating moved bacteria directly from this plate to new plate that does have antibiotics, and wanted to see if could grow) -If mutations arise only to response to environment=would expect that no antibiotic-resistant mutants 1) By chance, colony contains a few mutant cells (nonselective medium) 2) Sterile velvet template picks up both mutant + non-mutant cells... incubation allows growth of colonies 3) once mutant cells grow on selective medium, position of colony tells you which colony on the nonselective medium contains the mutant cells 4) mutant colony identified on original plate --> culture diluted + cells spread on selective medium 5) pure culture of antibiotic-resistant bacteria

What are physical barriers? What are phagocytes? What happens in phagocytosis?

very first step in immune system=physical barriers (protect from invading pathogens) phagocytes: designed to "eat up" things and break them down (and maybe recognize that something is a bacteria, so signal other cells to come in) -take up foreign matter + decide if need to alert rest of alert system phagocytosis: recognition: particle binds to receptor Engulfment: neutrophil takes in particle Digestion: lysosomes fuse with vesicle and digest the particle

In his pea plant experiments, what did he figure out is the dominant trait?

yellow seeds dominant, phenotype present in F1 every time