Bio Exam 2

two events must take place to ensure that the protein that is made is the one specified by the mRNA

1) a tRNA must chemically read each mRNA codon correctly 2) the tRNA must deliver the amino acid that corresponds to the mRNA codon once these things occur, ribosomes catalyze the formation of peptide bonds between the amino acids

Chromatin packaging is heavily influenced by two alterations

1) chemical modification of histone proteins 2) methylation of bases in the DNA molecule these alterations can be passed on to daughter cells but are easily reversible

DNA replication involves several different steps

1) initiation: unwinding the double helix of DNA to separate the two strands, and synthesizing RNA primers 2) elongation: synthesizing new strands of DNA starting from RNA primers and using the parental strands as templates 3) termination: synthesis ends after the region has been replicated during DNA replication, each nucleotide is convalently attached to the growing nucleic acid chain by a phospodiester bond synthesis proceeds 5' to 3' by adding nucleotides in the 3' end growing strand and the template strand is always read in the 3' to 5' direction

Implications of the cross breeding flower color experiment

1) missing (white) trait was present in F1, it was just not visible 2) all characters obey the same transmission rules 3) parents contribute equally Mendel reasoned that characters were determined by pairs (now known as genes) we now know that different traits arise because the DNA sequences of a gene for a particular character can vary with a paricular sequence resulting in one trait and a slightly different sequence resulting in another trait

viruses shut down host genes using three mechanisms

1) production of new sigma factors so the RNA polymerase no longer recognizes bacterial promoters 2) posttranscriptional mechanisms such as a virus-encoded nucleus that degrades host RNA before it can be translated 3) a viral encoded DNA nuclease that digests host chromosomes

4 events must occur for cell division/asexual reproduction

1)Reproductive signal: Can be in or out of the cell. To initiate cell division. 2)Replication: Make two copies of DNA so that each cell will a full complement of genetic info. 3)Segregation: Distribution of the DNA into the two daughter cells so that each receives a copy of the chromosome. 4)Cytokinesis: Separation of the two cells (cytoplasm, cell walls...)

Eukaryotic Viruses

Eukaryotes are susceptible to infections by various kinds of viruses that have a variety of life cycle strategies some eukaryotic viral life cycles can be quite complex

Eukaryotic cell cycle is regulated internally

G1 to S transition is the restriction point, and usually means the cell will proceed with the rest of the cell cycle and divide cell cycle reponds to external signals to progress through the r point, and then from there the internal signals take over for the rest of the progression

hybrid

Offspring of crosses between organisms that differ in one or more characters single-factor crosses: monohybrid crosses, Mendel did this for 7 pea characteristics

Meiosis I

Two characteristics of Meiosis I 1. Homologous chromosomes pair in the middle 2. No centromere division occurs and instead the homologous chromosome pairs separate during Anaphase I Goes from diploid of replicated chromosomes to haploid number of replicated chromosomes

one gene can affect multiple characters and one character can be affected my multiple genes

a single gene can produce a protein that functions in many different parts of an organism (pleiotropid genes), mutant alleles of the genes can have phenotypic effects on multiple characters epistasis: proteins interact with one another in a variety of ways e.x they catalyze different steps of the same pathway, or are subunits of a larger protein. these interactions cause the phenotypic expression of particular genotypes at one gene to be affected by the genotypes present at a second gene in a phenomenon known as epistasis e.x of epistasis: Lab dogs, two genes determines coat color (pigment gene AND deposition gene, if no deposition gene than pigment gene does not matter)

aesexual reproduction

a single organism reproducing without the aid of another offspring from aesexual reproduction are clones, and are genetically identical to themselves and their parents any genetic variations are called mutations (rare genetic changes that alter DNA sequences)

DNA ligase

a special DNA polymerase replaces the RNA primers, in addition to removing the strand (this is not the ligase) there is unbonded break between the DNA that replaced the RNA and the first formed DNA, which is fixed by the ligase enzyme by catalyzing the formation of the phosphodiester bond

Structural Gene

a structural gene is any gene that encodes a protein not involved in gene regulation

Sigma 70

abundant under optimal conditions promoter sequence: TTGACA directs RNA polymerase to bind to a promoter sequence that is shared by a large number of housekeeping genes involved in growth and division

Conditional Mutations

affect phenotype only under certain environmental conditions many are temperature-sensitive

drug-resistance bacteria and public health concerns

antibiotics prevent assembly of the bacteria cell wall overtimes mutations occur in bacteria that render them resistant to the drug new antibiotics are made in response but then new mutations form again that are insensitive to that new drug superbugs are resistant to many current antibiotics and are increasing a lot bacteria are able to evolve quickly because of the resistance gene in the plasmids, when a mutation occurs on this DNA it can spread rapidly by conjugation to other bacteria

human immunodeficiency virus (HIV)

causes AIDS in humans infects only cells of the immune system that express of surface receptor called CD4 proteins in the membrane of the virus, encoded by the viral genome, are involved in the infection of new host cells which HIV enters by direct fusion of the viral envelope with the host cell's membrane HIV is limited to those cells in the body that have receptors in which HIV can bind HIV is a retrovirus: the genome is a single-stranded RNA and carries within the virion an enzyme called reverse transcriptase (makes a DNA strand that is complementary to the RNA, while at the same tie degrading the RNA and making a second DNA strand that is complementary to the first, the resulting DNA strand becomes integrated into the host's chromosome aka a provirus) the provirus resides in the host's chromosomes and can remain inactive for years, transcription of the viral DNA is initiated but host cell proteins prevent elongation under some circumstances, the rate of transcription increases and some viral RNA is made, which encoded a protein called Tat which binds to the 5' end of the viral RNA to prevent the prevention of elongation, allows rest of the viral cycle to proceed

cell division is abnormal in cancer cells

can migrate from original location and grow in other locations of the body can divide without restraint no external signals needed to initiate the cell division arise from DNA mutations that encode normal functions

Histone Deacteylase

can remove the acetyl groups from histones to repress transcription

Demethylase

catalyzes the removal of the methyl groups

In between Meiosis I and II

chromosomes become uncondensed no DNA replication occurs!! centrosome replication does occur so spindles can be formed

sex chromosomes

chromosomes involved in sex determination that differ in numbers between males and females do not always occur in homologous pairs XX-female XY-male

Codons and DNA reading

codons are mRNA so the base sequence of the template DNA strand is complementary and anti-parallel to these codons

Can epigenetic changes be inherited?

epigenetic changes can be passed from mother to daughter cells in mitosis can they be passed from generations? Unlikely because... 1) epigenetic responses would have to occur in the germline that produces gametes 2) when gametes formed, histone modifications are removed and methylation of genes is largely removed as well plant germ cells are derived from tissues later in plant growth and epigenetic changes are not erased in the germline

Different sexual life cycles

evolution has generated many different versions of the sexual life cycle: 1) haplontic: diploid zygote immediately undergoes meiosis and spends all of life as a haploid, diploid zygote (2n) forms and undergoes meiosis to produce haploid spores. Spores (n) divide by mitosis to produce the mature organism. 2) diplontic: haploid gametes immedietly udnergo fertilization and spends all of life as a diploid, gametes are the only haploid cells in the life cycle and its somatic (body) cells are diploid 3) haplo-diplontic: spend significant amount of time in both stages, a multicellular haploid stage and a multicellular diploid stage

Mutations of Codons

examination of the genetic code reveals that base-pair substitution (point mutations) can have a variety of affects on protein sequence silent mutations: occur when a DNA substitution alters the genetic codon but does not alter the encoded amino acids, will not cause change to the amino acids missense mutations: occur when DNA substitution alters the codon so it encodes a different amino acid and changes the protein, if the missense mutations occurs at the start of the codon the effect is more severe nonsense/stop mutations: results in a change from a sense codon to a stop codon, causing premature termination of translation, likely to be loss-of-function mutations loss-of-stop mutations: result in change from a stop codon to a sense codon, causing additional amino acids to be added to the end of a protein, the effect depends on how many amino acids are added to the protein frame-shift mutations: insertion or deletion of one more base pairs (not a multiple of three), causes the reading frame to be out of register, leading to different multiple of three being read and leading to alter shifts of amino acids and proteins, if insertion or deletion were in multiples of three it would just result in additional or less amino acid which is not a fame shift mutation

The genetic code is universal among species

exceptions: mitochondria and chloroplasts a few codons differ. Mostly universal, indicating life came from one ancestor. transgenic organisms: organisms engineered to express a gene from another organism, universal code makes this process easier

Phenylketonuria (PKU)

involves the same pathway as alkaptonuria the enzyme that converts phenylalanine to tyrosine is nonfunctional, causing buildup up phenylalanine causes intellectual disabilities can be avoided with a diet low in phenylalanine

Fidelity function

function of ribosome to ensure that the right anticodon and codon match up any tRNA that does not form hydrogen bonds with all three bases of the codon is ejected from the ribosome

Asexual multicelluar organisms

fungi and plants virtually identical genetically, all the plants are the same and reproduction is asexual

Haploid cells

gametes contain only a single set of chromosomes, means they are haploid

Recombinant

gametes from meiosis that differs from the two gametes that fused to make the heterzygote because homologuous chromosomes can physically exchange corresponding segments during phophase I of meiosis by crossing over, involved 2 of the 4 chromatids which both break and then reform which then both become recombinant probability of obtaining recombinant gametes is lower for genes that are physically closer together than from genes further apart on the chromosome

Parental

gametes from meiosis that have the same genotype as the gametes of the individual parents that fused to make the heterzygote

11.1 Transcriptional regulation conserves energy

gene expression often occurs at the level of transcription because it allows cells to conserve resources (every step after transcription involves energy input, makes sense to shut off a gene before going through trouble to make the protein)

Alleles encode different versions of the same protein

genes determine phenotype by encoding proteins with particular functions the dominant gene is expressed the recessive gene is changed in order to no longer be expressed or it encodes a nonfunctional protein genes are subject to mutations (rare, stable, inherited changes in the DNA), an allele can mutate into another allele geneticists define one allele of a gene as the wild type, this is the allele that is present in most individuals in nature. other alleles of that gene are usually called mutant alleles and they may produce different phenotypes, re both inherited according to mendelian laws wild type that is present less than 99 percent of the time is said to be polymorphic, wild type and dominant are not the same thing

Double-helical structure of DNA is essential to its function

genetic material stores heritable information, the bases contain info that is passed from parent to offspring the helical structure suggested a way in which info in DNA might be replicated so it could be passed down the info contained in a DNA molecule is fully contained in each of the two strands, thus knowing the identity of a particular base on one strand means you know the bases for the other strand DNA replication could be as simple as unzipping a DNA molecule into two strands that could be used as templates for synthesizing new strands

Apoptosis

genetically programmed cell death why? 1) no longer functioning appropriately and are replaced 2) no longer needed by organism 3) cells have reached limit in how many times they can reproduce because of chromosome shortening (Hayflick limit) 4) the cell is reponsing to an infection, prevents infection from spreading events: cell becomes detached from neighbors, hydrolyzes its DNA into smaller bits, forms membrane blebs, break into cell fragments, surrounding cells ingest remains by phagocytosis or lysosomes to be recycled. for plant cells blebs do not form an instead they digest their own components in the vacuole to be released into the vascular system

structure of DNA

important as the shape of DNA provides insight into: 1) how DNA is replicated between cell divisions 2) how protein sequence information is encoded chemical composition of DNA provided important clues to its structure knew that DNA is a very long polymer of 4 different nucleotides, each of these nucleotides contains a molecule of the sugar deoxyribose, a phosphate group, and a nitrogen-containing base, the only difference among the 4 nucleotides is their nitrogen bases: double-ring purines A and G and the single ring pyrimidines C and T

Probability in Inheritance

in a heterozygote x heterozygote cross, 3/4 will have dominant phenotype, 1/4 recessive phenotype in a hetero x homo, half dominant phenotype, half recessive phenotype probabilities are expected outcomes, it is not the guaranteed outcome, the more the probability actually plays out the more close to the expected outcome

homologuos pair

in diploid cells, the two chromosomes in each pair are identical in length and DNA sequence making them homologuos pairs, each chromosome of the pair is called a homolog

Necrosis

in multicellular organisms when a cell is damaged or starved swell up and burst results in inflamation surrounding tissue

single vs multi celled organisms cell division

in single-celled organisms, cell division and reproduction are the same thing in multi-celled organisms, many rounds of cell division occur before reproduction, and only a subset of cells are involved in reproduction, cell division is important for maintaining integrity and replacing dead or damaged cells

Alternative Splicing

most primary mRNA transcript in multicellular Eukaryotes contain several introns alternative splicing: particular exons of a gene may be excluded from the final mRNA transcript, allowing different proteins to be produce from the gene can result in the same gene producing different proteins

Mutations can have various phenotypic effects

mutations can occur in somatic cells which are not passed to offspring, or to gametes which can be passed to offspring somatic mutations have consequences for the phenotype of the individual, gamete mutations can have consequences for future generations some sequences that do not encode proteins regulate which protein-coding genes are expressed at a certain time, so that mutations in these regions may have phenotypic effects, but much of the DNA in non-expressed regions has no real function and mutations here have little to no phenotypic effects mutations than occur in functions regions may or may not have phenotypic effects mutations in the region encoding the amino acid sequences in protein-coding genes may 1) not alter the amino acid sequence without altering the function of the protein 2) alter the amino acid sequence and the function of the protein

Gain-of-function

mutations lead to proteins with altered function, usually show dominant inheritance, common in cancer

Sexual reproduction

involves the production of specialized cells called gametes which fuse to produce offspring that differ genetically from one another and the parents DNA is halved during the cell life cycle before being fused to another gamete

Character

observable, physical feature pea plants have easily scored and variable characteristics

Chromosomal Translocation Mutation

occur when segment of chromosome breaks off and become joined to different chromosomes many involve reciprocal exchanges if the break points occur do not occur within a gene, it is not likely to affect the phenotype because all genes are present in the appropriate number of copies its just the location that has changes some occur such that a gene is inserted next to a control region that alter its expression chromosomal rearrangments involved double-stranded breaks, in some cases it occurs in crossing over in other cases, chromosome breaks represent NDA damage caused by radiation or chemicals a double-stranded break often triggers a repair pathway to rejoin the broekn chromosomes together

Crossing Over

occurs during prophase I during which the homologous chromosomes pair, an exchange between nonsister pairs occurs chromatids are broken and reattached eventually they repel each other but remain attached at the centromere, giving the X-shape called the chiasmata Chiasma is the point were a chromatid breaks and rejoins to a nonsister chromatid results in recombinant chromatids

Termination

occurs when replication forks that are moving towards one another meet, proteins bind to the sequences to prevent the forks from going into regions already replicated

Positive Regulation

occurs when the regulatory protein is an activator that increases transcription when it binds

a single gene can have multiple alleles

often a gene has multiple alleles, however a diploid can only carry two of them, shows a hierarchy of dominance, new phenotypes can result from different combinations of alleles (like rabbit fur color!)

Errors during Cell Division or Fertilization

result in incorrect number of chromosomes in cells nondisjunction: occurs in mitosis or meiosis when a pair of homologuous pairs (meiosis I) or sister chromatids (meiosis II or mitosis) fail to seperate, resulting in one cell having a missing and one having an extra chromosome aneuploidy: a cell having an unequal number of copies of each chromosome, in a diploid is would be nullisomic (no copies), monosomic (one copy)... a nullisomic cell dies when it is formed, monosomic and up have an unequal balance which can caused significant problems (cancer) Nondisjunction in Meiosis leads to aneuploidy gametes, meaning upon fertilization the resulting zygote will also be aneuploidy, most do not survive Trisomy 21 = Down Syndrome (distinctive facial and intellectual characteristics)

chromosome behavior of meiosis is consistent with mendel's laws

separation of homologs in anaphase I result in equal segregation of alleles, law of segregation is true at every single meiotic cell division meiosis also explains the independent assortment of alleles for two genes residing on different chromosomes. independent assortment is caused by independent alignment of different pairs of homologous chromosomes. If the two alignments are equally likely, then four possible gametes will occur, explains Mendel's law of independent assortment. 2nd law does not apply to genes that are close together on the same chromosome, because the two possible alignments are no longer equally likely

Several ribosomes can translate an mRNA

several ribosomes can simulataneously translate a single mRNA molecule, making multiple polypeptides at the same time

Gregor Mendel

showed that inheritance was particulate, passed without alteration from one generation to the next

Mitosis

single-celled Eukaryote, asexual production of cells produces two identical daughter cell used to add new cells to a multi-cellular Eukaryote

Diploid cell

somatic cell containing two (paired) sets of chromosomes

3 types of RNA

some RNAs do not encode proteins 1) messenger RNA: encode protein information. the two strands of DNA unwind and separate into a coding strand and a template strand, the template strand is transcribed to produce a single-stranded mRNA molecule that is complementary to the template strand. processed in the nucleus and then moves to the cytosol where it is translated (in eukaryotes). mRNA determines the ordered sequence of amino acids in the polypeptide chain, which is built by a ribosome 2) ribosomal RNA: make up ribosomes, make the proteins, catalyses peptide bond formation between amino acids to make polypeptides 3) transfer RNA: bind to both amino acids and recognize sequences of nucleotides in mRNA. recognize which amino acid should be added next to the growing polypeptide chain.

DNA replicates semiconservatively

structure of DNA gave obvious suggestions of how DNA replicates each strand of DNA double helix could be used as a template to make a new strand using complementary pairing, according to Watson and Crick 3 models for how replication would work: 1) Semiconservative: each strand of the parental DNA could be used as a template for synthesis of a new strand 2) Conservative: two parental strands remain together and is the template for another 2 strand daughter molecule 3) Dispersive: parental molecule ends up dispersed among both strands of the two daughter molecules semiconservative seems to be most likely way as Watson and Crick suggested

Chargaff's Rule

the amount of A equaled amount of T The amount of G equaled amount of C amount of pruines equals the amount of pyramides

11.1 positive regulation

transcription factors bind to a specific site to increase transcription, activator

11.1 negative regulation

transcription factors bind to a specific site to reduce transcription, repressor

Codons/Genetic Code

translation of the nucleotide sequence of an mRNA into the amino acid sequence occurs within the ribosome codons: genetic information in an mRNA molecule, non-overlapping 3 letter "words", the letters are three adjacent ribonucleotide bases in the mRNA, discovered as a three-letter code because it was the shortest combination that could account for all 20 amino acids genetic code: relates codons to specific amino acids

blending inheritance

19th century, that offspring are a blend of the characteristics of their parents, not viable for many characteristics

11.1 expression of a gene is influenced by both internal and external factors

3 examples 1) diet causes enzymes to be up or down regulated 2) extracellular signal binds to its receptor on a Eukaryotic cell, it sets in motion a signal transduction pathway that ends with some genes being activated and others being repressed 3) during the cell cycle, cyclin proteins are synthesized only a specific stages gene expression is highly regulated, thousands of genes not all are expressed at the same time

11.1 Repressible genes

A gene that can be turned off by repressors, usually on except when an environmental factor change causes it to turn off, controls anabolic pathways (turns on until concentration of substate is sufficient)

Targeting to a location may occur during or after translation

After: for other proteins, translation is completed in the cytosol and then a signal sequence is bound by other proteins that direct the translated protein to the correct organelle common for mitochondria, plastids and the nucleus less commonly for the endomembrane system

???

Among genes transcribed by an RNA polymerase bound to a sigma factor, some are inducible and some are repressible The high mRNA level depends on the presence of lactose because if lactose is removed the mRNA level goes down, the response of the bacteria to lactose is clearly at the level of transcription

Sigma 32

At elevated temperatures, directs RNA polymerase to several genes that share a common promoter sequence (CCTT-GAA) that encodes proteins involved in responding to heat stress

11.1 Repressors

Compounds that reduce transcription of a gene

11.1 Induces

Compounds that stimulate the transcription of specific genes

Targeting to a location may occur during or after translation

During: some signal sequences are bound to a signal-recognition particle as soon as they exit the ribosome this binding halts translation and picks up again once the signal recognition particle binds to its specific receptor protein at the surface of the RER as translation proceeds in the RER an enzyme cuts off the signal sequence, thus the targetted proteins are in the RER the membrane or lumen as they proteins are being translated proteins are in the RER to be retained there or move somewhere else in the endomembrane system

lytic cycle steps

Early Stage: upon infection, a set of early viral promoters are bound to the host RNA polymerase and then transcribe Middle and Late Phase: resulting viral proteins have several effects including shutting down expression of host genes, viral genome replication, and activating transcription of viral middle and late genes

11.1 Inducible genes

Genes that can be activated by inducers, usually off except when an environmental factor change causes it to turn on, control catabolic pathways (turned on only when substrate is available)

Prokaryotes: genes share a promoter

Genes that encode the 3 proteins for processing lactose in E. colo lie adjacent to one another, only the first contains a promoter How are the other two transcribed? The set of genes share a single promoter and their DNA is transcribed into a single continuous molecule of mRNA that contains the coding regions for the three proteins either none or all the enzymes are made at a time

For transcription to occur, DNA must be accessible

In eukaryotes, DNA is packaged with various proteins (histones), to form chromatin If the packaging is tight, it is hard for transcription factors to access the DNA and assemble the BTA (chromatin is closed) Transcription requires open chromatin, which is less tightly packaged

Transcription occurs in 3 steps

Initiation: Requires promoter (special region of DNA which RNA polymerase binds tightly to, tells RNA polymerase where to begin transcription and on which DNA strand to transcribe, contains start site and short sequences to facilitate binding, promoters are variable in sequence) At the end of initiation, RNA polymerase is tightly bound to promotor region and the DNA is locally unwound and enters elongation phase Elongation: reads DNA 3' to 5' and making RNA 5' to 3', antiparallel to DNA template strand and complementary (uracil exception, instead of T), RNA polymerase catalyzes formation of phosphodiester bonds, releasing pyrophosphate in process, as transcription progresses, the DNA strands are rewounded RNA polymerases have proofreading mechanisms as well, not as efficient of the DNA ones, but it is less problematic that RNA polymerases are less efficient in spotting errors because DNAs are shorter than DNA and errors are not heritble for RNA and has short life span Termination: in eukaeyotes, multiple proteins recognize termination and seperating the newly formed RNA from the DNA and the RNA polymerase

Crossing Over

Mendel's Law of Segregation always held true, but in dihydrbid crosses sometimes yeilded phenotypic ratios that were not predicted by Mende's Law of Independent Assortment some traits seem to be more common together than others, possibility that the two loci are on the same chromosome and unable to assort independently because they are physically linked together

Cytokenesis

Mitosis is only the division of the nucleas, where as cytokenesis is the split of the cytoplasm Animals: furrowing of cell membrane by a ring made actin and myosin microfilaments and other proteins Plants: as the spindle breaks down after mitosis vesicles from the golgi apparatus appear between the two cells to fuse and form a new membrane and cell wall

Basal Transcription Apparatus

RNA polymerase II binds only after several other proteins have bound to the complex RNA polymerase and general transcription factors make up the BTA if only the BTA binds to the core promoter, the rate of transcription is quite low

General Transcription Factors

RNA polymerase II is the polymerase that transcribes the protein-coding genes in eukaryotes it does so after various general transcription factors (regulatory proteins that affect transcription) bind to the core promoter general transcription factors bind to most promoters and are distinct from transcription factors that have specific regulatory effects only at certain promoters act like the sigma factors of prokaryotic transcription

Transcription

Transcription (forming specific RNA sequence from DNA sequence) is performed by a DNA dependent RNA polymerase mRNAs, tRNAs, rRNAs are all encoded by specific genes

RB protein

an inhibitor of the cell cycle at R, to go into S phase a cell must overcome the RB block G1/S cyclin bound to its CDK catalyzes the addition of phosphate to RB which causes a change in the RB shape to inactivate it

11.1 How transcription factors recognize nucleotide sequences of DNA

atoms in the bases of DNA that are available for hydrogen bonding but are not involved in base pairing interact with the transcription factors, van der Waals interactions stabilize binding once their is an induced fit between the protein and the DNA, the protein undergoes conformational change allowing it to bind to specific DNA sequence and not others

bacteria exchange chromosomal genes by conjugation

bacteria are able to exchange genetic material present on their main chromosome during conjugation happends when the DNA strand is a part of the bacterial chromosome and large pieces of the chromosomal DNA travels through conjugation tubes undergoes two crossover events to swap out alleles, if only one crossover events occured it would result in a large linear molecule which would kill the cell

tRNA (transfer RNA)

because the translation of mRNA into proteins requires molecules that can link the info in each mRNA codon with an amino acid, tRNAs performs this function

Recombination frequency

calculated by dividing the number of recombinant progeny by the total number of progeny, to estimate how far apart the genes are on the chromosome can be converted to a genetic map distance in map unit cM (1 map unit cM = 1% recombination frequency) the frequency of recombinant gametes is always less than or equal to the frequency of parental gametes

histone acetyltransferase

can add acetyl groups to the positive amino acids to neutralize them this reduces the affinity of the histone tails for the DNA, loosening the compact, and facilitating the binding if regulatry proteins promotes both initiation and elongation as the enzyme can be found near promoters and coding regions can be recruited to promoters by transcription factors

During/After translation protein modifications

during translation: removal of the initiator methionine posttranslational modifications: 1) proteolysis: cutting of the polypeptide chain by enzymes called proteases, this is because some mature proteins are made from polyproteins (contained sequences of multiple proteins) which need to be cut up to make distinct proteins 2) glycosylation: addition of carbohydrates to proteins (forms glycoproteins), essential for directing proteins to lysosomes, protein conformation, cell recognition functions, or stabilizing proteins (like in the extracellular matrix) 3) phosphorylation: addition of phosphate groups to proteins (catalyzed by protein kinases), changes the conformation of the protein to expose an active site of an enzyme or binding site of another protein, important for cell signaling

Primase/Initiation

eukaryotic chromosomes have multiple oris scattered at intervals of tens of thousands of base pairs to shorten replication time several proteins are involved in controlling the inititation of replication at ori to ensrure it only occurs once per round following the denature of the ori, initiation proceeds with the synthesis of short RNA molecules called primers, they are complementary to the DNA template strand and is synthesized by the primase enzyme

Trp Operon, Repressible Genes in Negative Regulation

has a promoter and an operator and encodes 5 enzymes that catalyze the synthesis of tryptophan from a precursor molecule the operon is repressible, meaning it is usually transcribed except when tryptophan levels are high the repressible trp operon is switched off when its repressor is bound to the operator, like in the lac operon in this case, however, the repressor binds to the DNA only in the presence of a co-repressor (tryptophan), a molecule that binds to the repressor which causes it to change shape and bind to the operator, thereby inhibiting transcription (allosteric regulation)

Binary Fission

how single-cell prokaryotic cells reproduce a type of asexual cell-division that produce two symmetrical daughter cells from a parent cell is single-cell production, and is the prokaryotic equivalent to the eukaryotic asexual reproduction of mitosis -Products identical to the 'mother cell'

Chromosomal Inversion Mutation

in which a segment of a chromosome is flipped, so that its base sequence reads in reverse likely to cause loss-of-function mutation of that gene

Meiosis II

indistinguishable from Mitosis: replicated chromosomes condense and attach to the spindle by their kinetochores (prophase II), the chromosomes allign (metaphase II), centromeres divide and the sister chromatids move to the opposite ends (anaphase II), nuclea envelope reforms and chromosomes uncondense (telophase II)

Lac Operon, Inducible Genes in Negative Regulation

is transcribed at high levels only when the predominant sugar in the cell's environment is a B-galactoside such as lactose allactose is a structural isomer of lactose that, when converted from lactose, is the inducer that switches on the expression of the lac operon in absence of allactose, a repressor protein binds to the operator and prevents the RNA polymerase from binding when allactose is present, the repressor detaches which allows the RNA polymerase to bind the repressor protein has two binding sites, one is a DNA binding site and the other is an allosteric binding site for the inducer, when the inducer (allactose) binds to the repressor it changes shape so it can no longer bind to the DNA

Eukaryotic cell cycle is controlled by cyclin-dependent kinases

kinases involved in cell cycle regulation are called cyclin-dependent kinases (CDKs), which catalyze the phosphorylation of target proteins that regulate the cell cycle, they are activated by binding to cyclin, which then changes shape of the CDK to open an active site CDKs serve as cell cycle checkpoints, here progress of the cell cycle is regulate by the activity of specific CDKs, these CDKs phosphorolate several target proteins (active or inactivate) to regulate each phase 3 checkpoints (where the cell cycle will stop) 1) r point (G1 to S), stops if DNA damage 2) S checkpoint (DNA damage/incomplete replication) 3) G2 checkpoint (DNA damage) 4) metaphase checkpoint (chromosomes fail to attach to spindle) each CDK has a cyclin to activate it, after the CDK acts the cyclin is broken down by protease (hydrolyzes proteins) cyclins are synthesized in reponse to growth factors etc.

Evolutionary Explanation for Codon Patterns

most amino acids have more than 1 codon that codes into them, these codons differ by just 1 letter (other two are the same) evolutionary explanation: the patterns serve to minimize DNA mutations (if a base is messed up at one base, it still makes the same amino acid!)

Induced Mutations

most cancer-causing mutations are caused by mutagens, substances that chemically alter DNA and lead to induced mutations mutagens often cause DNA damage, so that it has a chemical structure not normally found in DNA radiation can also damage DNA a third DNA repair mechanism, called excision repair, which removes damaged nucleotides and replaces them with normal ones, the excision repair proteins recognize damaged DNA and remove the fragment, then DNA polymrase and ligase fill the gap sometimes repair does not occur and damaged bases give rise to mutations that can affect various cellular processes

autosomes

non sex chromosomes, always appear in two copies regardless of the sec of the organism

Errors in cytokineses or fertilization can affect ALL chromosomes

organisms can have additional set of chromosomes and be triploid (3n) polyploidy: possession of more than two entire sets of chromosomes, can be caused by two things 1)failure of spindle formation, all chromosomes remain in one part of the cell and not separated with cytokenesis (4n, tetraploid) 2) failure of cytokeniesis to occur, two nuclei remain in the same cell, fuse, and the cell becomes 4n, tetraploid Polyspermy: when more than one male gamete fetilizses

Traits

particular form of a character (round vs wrinkled seeds) true-breeding varieties yield offspring with the same traits as the parent, Mendel said that they would be uniform in their underlying heritable makeup

self-fertilization/selfing

pollen is placed manually into the same plant, stamens of receiving plant is removed to prevent selfing during cross-fertilization

cross-fertilizations

pollen removed from stamens and places into pistils of another plant

Signal sequences

protein synthesis always begins on free chromosomes in the cytosol, the default location for a protein however, some polypeptides contain a signal sequence consisting of short stretches of amino acids that indicates where in the cell the polypeptide belongs proteins with different locations have different signal sequences

Proteins without signal sequences

proteins without signal sequences are secreted from the cell with vesicles that fuse in the cell membrane

11.1 Regulatory Networks

regulation of gene expression often involves multiple regulators, and the regulators can also be subject to regulation collections of interacting regulators that determine the expression level of a gene

Components of Ribosome/3 sites

ribosome is the machine where translation occurs the ribosome is made of two subunits in eukaryotes the large subunit consists of 3 rRNAs and 49 protein molecules and the small subunit consists of 1 rRNA molecule and 33 proteins these two subunits interact noncovalently, when not active in translation the ribosome exists as two separate subunits on the large subunit there are 3 places for tRNA to bind to, the ribosome moves along the mRNA in the 3' direction and as it does so a charged tRNA moves in the three sites starts from A site to P site to E site A (amino site): site where the charged tRNA anticodon binds to the mRNA codon P (polypeptide site): site where the tRNA adds its amino acid to the polypeptide chain E (exit) site: site whereth tRNA, with not amino acid now, resides before being released from the ribosome, reenters ribosome once recharged

polyribosome

ribosomes and their growing polypeptide chains

circumstantial evenidence for DNA being genetic material

scientists found that DNA is 1) present in the cell nucleus and in condensed chromosomes 2) doubles in abundance in the cell during S phase of the cell cycle 3) is twice as abundant in the diploid cells as into the haploid cells of a given organism DNA was first isolated by Miescher, he chemically treated nuclei and saw that a fibrous substance came out of the solution which he called nuclein, he boldly proposed that nuclein was the genetic material S, G2, and M phases of the cell cycle had twice as much DNA as most of the other cells in G1, found using dyes that would bind to DNA, this supported two other predictions for DNA 1) virtually all nondividing somatic cells of a particular organism have the same amount of nuclear DNA 2) cells resulting from meiosis have half the amount of nuclear DNA as somatic cells

Sense and Nonsense codons

sense codons: 61/64 codons encode amino acids, almost all amino acids are encoded by at least two codons stop, nonsense codons: do not encoded amino acids, cause termination of translation (UAA, UAG, and UGA) start codon: AUG which codes for methionine, initiations signal for translation

Epigenetics

the study of environmental influences on gene expression that occur without a DNA change

Meiosis

type of cell division that results in the production of daughter cells (gametes) that contain only half of the DNA of the original cell increases genetic diversity only occurs in eukaryotes

George Beadle and Edward Tatum

used bread mold as model organism used a mutation that knocked out (blocked gene expression of) certain metabolic pathways within the bread mold showed that knockout mutations encoding a single enzyme was inherited in a Mendelian manner suggests that enzyme knockouts are nonfunctional alleles at genes that encode them led to "one gene-one enzyme" hypothesis

Methyltransferase

when DNA is replicated, a maintenance methyltransferase catalyzes the methylation of the Cs in the new DNA strands it is able to identify and methylate other GcP in a hemimethylated GcP methylation patterns can be passed but are also reversible

Loss-of-function

when a mutation causes a change in the phenotype, the change can be subtle or large, occur either because the expression of the gene is too low or because a nonfunctional protein is produced, almost always show recessive inheritance in a diploid organism

DNA and Chromosomes during Eukaroytic Cell Cycle

•Interphase: DNA exists as long, threadlike "chromatin" •G1: each chromosome consists of 1 DNA (1 double helix) in a long linear sequence. To fit into the nucleus, the DNA is heavily compacted by being wrapped by special proteins called histones (amino acids with positive sides to interact with negative DNA) forming chromatin. It does not fully condense until M phase. •S: DNA replication produces two identical DNA molecules (sister chromatids) for each chromosome •G2: each chromosome consists of two associated DNA molecules (sister chromatids) •M-phase: chromosomes become visible as dense, compact rods, each consisting of 2 chromatids held together at the centromere (until separation) to orient during cell division. Each portion of DNA on a side of the centromere is called a chromosome arm (2 if unreplicated, 4 if replicated). The identical DNA (2) are called sister chromatids which are separated into two chromosomes later in M phase. The number and sizes of the condensed chromosomes is the karyotype.

asymmetric cell division

Cell division in which one daughter cell receives more cytoplasm than the other during mitosis, can see visible differences between mother and daughter in size, the mother cell produces the aughter cell and reminas unchanged e.x yeast, and in more complex eukaryotes

Translation termination

Elongation continues until the ribosome shifts and a stop codon enters the A site no tRNAs can bond with a stop codon so translation terminates the stop codon can bind a protein release factor which causes hydrolysis of the bond between the polypeptide chain and the tRNA in the P site

Transcription

Information in a DNA sequence (a gene) is copied by base-pairing into complementary RNA sequence

Time of Mitosis vs Meiosis

Mitosis is about an hour Meiosis: much longer

Translation

RNA sequence is used to synthesize the amino acid sequence of a polypeptide

Eukaryotic promoter/TATA Box

a eukaryotic promoter is a region of DNA near the 5' end of a gene where an RNA polymerase binds and initiates transcription they are very diverse but each contains a core promoter sequence to which the RNA polymerase binds the core promoters of many genes contain a DNA sequence known as the TATA box

Somatic cell

any cell of a living organism other than the reproductive cells, derived by mitosis

Hemizygous

any gene present as a single copy in a diploid organism, a male will express only allele of his one chromosomes whether that allele is dominant or not

Chromosomal Duplication Mutation

in which a segment of a chromosome is repeated, resulting in multiple copies of that segment mechanism: occurs in homologous chromosomes break at different positions and then reconnect to the wrong partner, a crossing over error in this case, one chromosome will lack a segment (deletion) and one will have two tandem copies (duplication) often leads to overexpression of that gene in those regions

Mendel and Test Crosses

mendel verified equal segregation by performing test crosses (crossing a plant with the dominant phenotype with an unknown genotype to a recessive individual)

histones can also be modified with phosphorylation and methylation

methylation: can activate/inactivate depending on which lysine residue is methylated phosphorylation: involved in chromosome condensation during cell division as well as affecting gene regulation all are reversible

Gregor Mendel continued

performed crosses of pea plants to find principles of inhertiance, ignored by mainstream science until 1900 when chromosomes were found to be carriers of genes established how inheritance experiments should be performed 1) variable, scorable traits 2) large family sizes 3) short generation times 4) controlled matings 5) grown easily and cheaply peas are helpful because they have male and female organs (bearing male and female gametes)

multiplcation rule

probability of two events occurring independently at the same time can be obtained by multiplying their individual probabilities e.x Ww x Ww, egg is one half likely to have W and so if sperm, so probability of having WW phenotype is 1/2x1/2 = 1/4

Independent Assortment

the cells formed after meiosis differ from one another because of the random alignment of homologous chromosomes on the metaphase I plate, it is random which member of the pair attaches to the spindle fibers for a pole, when the chromosomes split in anaphase I they are independent of the maternal and paternal) the more chromosomes there are, the lower probability that a product of meiosis will have all of the chromosomes that were present in one of the parental gametes *genetic variance can also be due to mutations

4 Stages of Mitosis

Cell division in Eukaryotes occurs in the context of a cell cycle Cell division signals: undergoes division when environmental conditions are appropriate, as well as internal environment. When the environment is suitable for a multicellular organism, it does not mean the cells will divide, because cells are related to function in a multicellular organism. In multi-cellular eukaryotes, signals for cell division are related to the needs of the entire organism and are part of the developmental process. Most cells of a fully developed multicellular organism are specialized and seldom undergo cell division. DNA replication: Eukaryotes have more than one chromosome, it has numerous origins of replication and does not overlap with DNA segregation DNA segregation: one copy of each chromosome in the parent cell (after DNA replication) must end up in each new cell. chromosomes become highly condensed before they segregate in order to move to the two nuclei faster. spindles (cytoskeleton microtubules) move the chromosomes during segregation. Cytokinesis: different in plants than in animals

DNA methylation

DNA methylation DNA is covalently methylated by methyl group (-CH3) to form 5-methylcytosine this reaction is catalyzed by DNA methyltransferase often it is cytosine bases that are methylated, occurs on cytosines adjacent to guanines, called CpG sites (p=phosphaste backbone) each site is paired with a GpC dinucleotide on the other strand, if CpG site has a methylated C on both strands = methylated (1=hemi) GpC sites are often methylated except when near active promoters, promoters have GpC islands (rich in GpC sites), if unmethylated the gene is expressed methylated DNA binds specific proteins involved in gene expression repression, some of the proteins increase compaction of chromatin DNA methylation is more long term and stable to histone acetylation

Epigenetics and the Environment ******

DNA methylation and histone modification are reset both in the germline and again in early development Implies that epigenetic modifications of DNA and histones early in development should be very similar/identical among individuals However, epigenetic modifications in individuals often differ. How much of this is because of gnome differences? Identical twins come from a single fertilized egg that divides to produce two separate individuals with identical genomes DNA methylation patterns are virtually the same amongst twins, but in older age, the patterns are very different Environment plays an important role in epigenetic changes i.e diet, chemicals, and stress

Eukaryotic cell cycle

Distinct phases of the cell cycle, divided into interphase and mitosis: Interphase: Begins after cytokinesis and ends when mitosis starts. The cell nucleus is visible and cell functions including DNA replication occur. Interphase divided into three subphases: G1, S, and G2 defined by DNA replication status. G1 (G0): preparing to undergo cell division, where most cells are found and carry out normal functions. If not dividing, they are in G0. Stay in this phase unless recieve signal to divide. S: replicating DNA G2: prepare for mitosis, build what is needed for the dividing M: when DNA segregation and mitosis occur M phase: nuclear membrane dissolves, DNA condenses and divides; division of the cytoplasm Non-dividing cells usually arrested in G0

Cell cycle regulation differs in eukaryotic and prokayotic cells

Eukaryotes: cell cycle will not commence unless entire cell cycle can be completed. G1, cell is preparing enough resources to make it through an entire cell cycle. Unicellular is often initiated by environmental signals. Multicellular is at different times and in different conditions. Mammals produce growth factors that stimulate cell division and differentiation.

Viruses and Gene Regulation

For bacteriophage, once of virus's genetic material is in a host cell, it often turns that cell into a virus factory involves radical changes in the expression of numerous host cell genes viruses are not cells, they are dependent on living host cells viruses may consist of double or single-stranded DNA or RNA

Meiosis

Gives rise to haploid cells, which is required for sexual reproduction (fuse during fertilization) -DNA copied, followed by two rounds of nuclear segregation -DNA content reduced by ½ and each product is unique Split into Meiosis I and II, which results in 4 nuclei with DNA being replicated only once during S phase The cells are genetically different in the resulting cells

Stages of Mitosis

M Phase of Cell Cycle Prophase: chromosomes begin to condense (compaction of replicated DNA into visible chromosomes), specialized protein structures (kineochores) appear on each side of the centromere and are attachment sites for microtubules making them important for chromosome movement, centrosome (required for spindle formation and orient a both ends of the cell for the chromosomes move to, a centrosome is a pair of centrioles which are formed by microtubules and they become duplicated into 2 during the S phase, position of centrosomes determine how a cell divides, each centrosome is a pole from where tubulin dimers aggregate into microtubules that extend from the poles into the middle region which forms the spindle, the microtubules are unstable until they come into contact with the other half's spindle) orientation and spindle formation also occur Prometaphase: spindle becomes fully formed, nuclear envelope breaks down, replicated chromosomes become attached from their kinetochore (located on both sides of the centromere) to the microtubules •Polar microtubules—form spindle; overlap in center •Kinetochore microtubules—attach to kinetochores on the chromatids. Sister chromatids attach to opposite halves of the spindle Metaphase: microtubules has aligned the chromosomes on the metaphase plate at the cell's midline, each microtubule pulls into a stalemate until aligned Anaphase: separation of sister chromatids into separate chromosomes each with a centromere (now are daughter chromosomes). the movement is facilitated by kinetochores which contain molecular motor proteins (use ATP) and the microtubules shortening towards the poles Telophase: nuclear envelope forms around each new set of chromosomes and less become less compact, spindle disappears

Lin-14 and Lin-4

Mutation of the lin-14 gene cause larvae to skip the first larval stage mutations of the lin-4 gene cause certain cells in later larval stages to repeat stage 1 development patterns so the nomral role of the lin-4 gene is to trun off expression of lin-14 so cells can progress to the next stage showsed that lin-14 encodes a transcription factor that affects transcription of genes in larval cell progression, lin-4 encodeds a miRNA that inhibits lin-14 expression post-transcriptionally by binding to its mRNA any mRNAs that are complementary to the miRNA will degrade, has to be perfect complementary but can still reduce translation if not perfect

Nirenberg and Matthaei

Nirenberg and Matthaei made the first decoding breakthrough when they discovered they could synthesize a protein in a test tube using a simple artificial RNA as a template for polypeptide synthesis, as a way to identify which amino acids were being made into the polypeptide led to the identification of the first codons Their main obstacle was synthesizing artificial RNA templates of a known sequence using more than one kind of nucleotide. Another breakthrough was that scientists discovered that an artificial mRNA only three nucleotides long could bind to a ribosome. Using the test tube methods, scientists could make ay triplet codon and see which amino acid would form. With this discovery, the deciphering of the genetic code quickly occurred.

Cell Division

Process by which a cell divides into two new daughter cells, may be symmetrical or asymmetrical DNA replication lies ar heart of cell division DNA is the 'recipe' for cellular function, so cell division mostly concerns duplicating the chromosome(s) completely and sorting a copy to each daughter cell.

4 Stages of Binary Fission

Prokaryotic cells: 1) Cell division signals: External factors are common signals. Nutrient availability and environmental conditions are the reproductive signals that initiate prokaryotic cell division. 2) DNA Replication: Most prokaryotes have one chromosome, a single molecule of DNA—usually circular. Two important regions in DNA replication: ori—where replication starts ter—where replication ends 3) DNA Segregation: Begins near center of cell (ori region) and move towards opposite ends of the cell. Replication and segregation co-occur. DNA binds to proteins essential for segregation. Cytoskeleton is also involved in segregation, provides filaments where the ori proteins can move along. 4) Cytokinesis: Z-ring causes contractions which pinches the cell membrane, as DNA segregation proceeds, the cell pinches more. If it is a plant, cell walls are deposited.

Prokaryotes express multiple genes in response to their environment

RNA polymerase binds to specific DNA sequences at the promoter to initiate transcription For prokaryotes, this binding is facilitated by transcription factors (sigma factors) Different sigma factors may be present under different environmental conditions Genes that encode proteins with related functions have the same promoter sequence which allows them to be expressed at the same time and under the same conditions

Central Dogma of Molecular Biology

Replication->DNA->Transcription->RNA->translation->protein

RNA polymerase

Require a single-stranded template (read in 3' to 5' direction and synthesize RNA in 5' to 3') Use one of the four ribonucleotide triphosphates (ATP, GTP, CTP, UTP) to add to growing RNA strand RNA polymerases do not need a primer to begin polymerization DNA sequences adjacent to genes guide RNA polymerases to specific locations to initiate transcription One kind of RNA polymerase in bacteria/archaea, multiple in eukaryotes

Coding Regions

Sequences within a DNA molecule that are eventually translated as proteins, is transcribed into a complementary mRNA molecule prokaryotes are mostly coding regions which is not the case for eukaryotes prokaryotes and viruses have several adjacent genes that often share one promoter eukaryotes present noncoding sequences (introns) and transcribed regions (extrons) both introns and extrons appear in the primary mRNA transcript (pre-mRNA) but the introns are removed once the mRNA leaves the nucleus

Sexual Life Cycle of Eukaryotes

Sexual Reproduction: -Systematic joining of gametes to produce a diploid phase of the life cycle, coupled with meiosis that reduces chromosome number in the haploid phase. -Meiosis is a specialized cell division where a single round of DNA synthesis is followed by two stages of chromosome segregation. •Diploid mother cell (pairs of chromosomes) à haploid daughter cells (each with one of each kind of chromosome) -Shuffles Genetic Variation •Offspring are not identical to parents or to each other •Exceptions: identical twins, polyembryony (armadillos) Three main variations in this cycle Diplontic Haplontic Alternation of Generations Differ by the presence of mitosis in diploid phase, haploid phase, or both!

Epigenetic gene regulation can occur via alteration of chromatin structure

The basic unit of DNA packaging in Eukaryotes is the nucleosome (a core of 8 + charged histone proteins around which DNA is wound) Each histone protein has a tail of 20 amino acids at its N terminus, usually positively charged lysine Usually, there is a strong ionic attraction between the negative DNA and the positive tail because of this attraction, DNA wound on the nucleosomes forms inaccessible closed chromatin (not transcribed)

Archibald Garrod

The first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell. Reported Alkaptonuria as the first human example of what is now known as Mendelian inheritance. Discovered that a protein is the expressed phenotypic product of a gene Saw children with a rare disease called Alkaptoruria, black urine when exposed to air was a symptom, saw that it was inherited recessively, saw that homogentisic acid accumulated in their blood, joints, and urine. Proposed that in healthy people the acid was converted to a harmless product by an enzyme and that enzyme was missing/nonfunctional in people with the disease, and that the enzyme being active is determined by a dominant wild-type gene ...later the enzyme was identified as homogentisic acid oxidase ...and even later, the DNA mutation leading to this disease was also identified: homogentisic acid is a part of a catabolic pathway that breaks down the amino acid phenylalanine and tyrosine

sex chromosomes in meiosis

X chromosomes in females behave just like a pair of autosomes in meiosis, every egg ends up with one copy of the X chromosomes in males, the X and Y chromosomes do pair with one another and align together at the metaphase I plate and separate at anaphase I, resulting in half the gametes having X and half having Y fertilization of X egg and X sperm = XX fertilization of X egg anf Y sperm = XY

Operon

a cluster of genes with a single promoter the operon that encodes the three lactose proteins is the lac operon

Chemistry of DNA synthesis

a free nucleotide can have 1-3 phosphate groups attached to its pentose sugar nucleotides for DNA synthesis have 3 attached at the 5' carbon of the deoxyribose (thus are called dNTPs, deoxyribose nucleoside tripohosphates) when added to the growing strand, the two outer phosphate groups are released as pyrophophate as the resulting monophosphate (dAMP, dGMP, dCMP or dTMP) is added to the growing chain the release of the two phosphates provides energy for the formation of the phosphodiester bond between the incoming nucleotide and the 3' carbon on the deoxyribose end of the chain

symmetrical cell division

a mother cell divides and produces two daughter cells that are identical e.x bacteria, single-celled eukaryotes

Translation Elongation

after initiation, synthesis of the peptide can occur charged tRNA whose anticodon is complementary to the second of the mRNA now enters the A site the large subunit catalyzes two reactions: 1) breaks the bond between methionine and its tRNA in the P site 2) catalyzes the formation of peptide bond between methionine and amino acid in A site, catalyzed by ribozymes methionine becomes the amino (N) terminus of the new protein (polypeptides grow amino to carboxyl direction) and the second amino acid is bound to the methionine but it still attached to the tRNA in the A site the first tRNA then moves three bases down to the E site and the second tRNA holds two amino acids and the A site gets a new charged tRNA the uncharged tRNA dissociates and moves to the cytosol, the uncharged tRNA of the P site then goes to the E site

Results of crossing true breeding purple and true breeding white

all F1 offspring had purple flowers, the white did not show however, when F1 self-pollinated = 3 purple: 1 white the white flowers produced only white flower offspring in F3 where as the purple ones made the 3:1 ratio again *1/4 true breeding purple, 2/4 purple, 1/4 true breeding white

genotype

allele makeup of an individual

Telomers/End-replication problem

are not fully replicated in eukaryotic cells in the lagging strand, because the replication forks moves opposite of the replication, there is an an RNA primer at the 5' end of the new strand there are enzymes that can remove this primer, however no DNA can synthesized to replace the resulting gap, so the new new chromosome has a short region of single stranded DNA overhang this activates a mechanism for cutting off the single stranded region, this the chromosome becomes shorter with every cell division (end-replication problem) to avoid disappearing, chromosomes have mechanisms to extend themselves, the ends of chromosomes have teomers which are DNA sequences that do not encode protein and instead protect the important protein encoding DNA from being lost, the sequence tends to be TTAGGG, the number of telomer repeats is reduced at one end of the chromosome, the telomerase enzyme adds the DNA repeats (example of DNA polymerase as it uses RNA remplate to synthesize new DNA), telomers have another important function of signaling repair pathways when a chromosome breaks double-stranded, special proteins bind to the telomer repeats so they are not recognized as chromosome breaks after 20-30 rounds of cell division, the chromosome becomes too short and apoptosis occurs the more cell divisions, the shorter its telomers cancer cells express telomerase, allowing them to undergo many more rounds of cell division that normal cells

prokaryotes generate genetic diversity bacteria transfer plasmid genes by bacterial conjugation

bacteria harbor addition, smaller, circular DNA molecules called plasmids that replicate independently of the main chromosome, often containing few genes and mostly for antibiotic resistence transfer genes from one to another without sexual meiotic production is called lateral gene transfer contact is initiated by a sex pilus (a thin projection composed of proteins and phosporolipids that extend from a cell) which attaches to another cell to draw the two cells together and triggers formation of a thin cytoplasmic bridge (the conjugation tube) the genetic material can then pass from one cell to another through the conjugation tube

Chemical changes in bases can lead to DNA mutations

bases in DNA constantly undergo spontaneous chemical changes (at a low rate) than can alter base-pairing properties and result in point-mutations e.x bases can exist as structural isomers, called tautomers (rare), they can pair with a different base leading to a mismatch which produces a mutation e.x occasional removal of an amino group in cytosine which produces uracil, leading to a mismatch and a mutation called spontaneous mutations and cannot be avoided

Protein stability can be regulated/Ubiquitin

certain proteins can be targeted for destruction in a chain of events that begins when an enzyme attaches an amino acid called ubiquitin to one of its lysine residues to be destroyed other ubquitins then attach to the primary one, forming a polyubiquitin chain this then binds to a huge protein complex called proteasome upon entering the proteasome, the polyubiquitin is removed and ATP energy is used to unfold the protein which is then digested

tRNA synthetase

charges tRNA (attaches amino acid correctly with tRNA) highly specific, one amino per tRNA uses energy in ATP to form high energy bond between amino acid and tRNA which later used in formation of peptide bonds in growing peptide chain

sex-linked inhertiance

defines inheritance of a gene that is carried on a sex chromosome a white-eyes female (XwXw) was mated with a red-eyed male (XwY) and all the male offspring had white eyes and all of the females has red eyes, sons inherited only their X chromosome from their mother and were therefore hemizygous for the white allele, the daughters got both the red-eye X and white eye X from each parents making them heterozygotes most sex-linked characters involve a rare X-linked recessive trait, which reveals the following pattern 1) recessive phenotype appears much more often in males, because only one copy of the allele is needed 2) an affected male passes the mutation to all of his daughters but non of his sons because they get the Y chromosome 3) daughters who receive one X-linked mutation are heterozygote carriers, but are phenotypically normal but they pass the mutant allele to half their sons and daughters 4) affected sons often have affected maternal grandfather

Experimentally determining signal sequence identity

determining the identity of a signal sequence involves adding/removing the sequence and seeing if targeting is affected

allele

different DNA sequences of the same gene, one allele is inherited from the male gamete and one from the female gamete (equally) if alleles at a locus are same = homozygous genotype if alleles at locus are different = heterozygous genotype heterozygous individuals carry both alleles but exhibit only one of them, dominate (uppercase) = one that is expressed, recessive (lowercase) = one not expressed *only if a individual is homozygous for the recessive gene will it be expressed

some phenotypes of continuous

discrete traits: easily distinguished from one another an occur in two or few categories quanititive traits: vary within a range, height, weight, etc., often influenced by many genes, and not all the genes associated with these traits influence the trait to the same degree, all genes do still act in a Mendelian manner however

some bacteria recombine with DNA taken up from their environment

do so by transporting double-stranded DNA molecule through a large protein complex, requires energy the DNA is then hydrolyzed to nucleotides for use by the cell duing DNA synthesis sometimes the DNA instead can be recombined and exchanges sequences with the recipient cell's chromosome if there are regions of homology if two crossovers occur, then new gene combinations can be produced in a process can transformation

epigenetic changes are reset in the germ line and in early development

done in 2 steps for DNA methylation 1) first, the existing methyl groups are removed by demethylase (erasure) 2) DNA methylase adds new methyl groups to new Cs ensures that the appropriate pattern of gene expression for normal development will occur

Cell Differentiation/Specialization

during development of a complex organism, cells become more and more differentiated differentiation is brought about in many cases by changes in gene expression, resulting from the activation/inactivation of transcription factors all differentiated cells contain the entire genome, their specific characteristics must arise from differences in gene expression

Mendel's First Law (of Segregation)

during gamete formation, each allele segregates equally from one another. half gametes have one, half have the other use a punnett square to predict genotypes if gametes come together law of segregation: when an individual produces gametes, the two alleles of each pair separate equally so half the gametes receive one allele of every gene and half receive the other allele

Fertilization

during sexual reproduction, two gametes/haploid cells fuse to form a diploid zygote in multi-cellular eukaryotic organisms, the zygote then undergoes mitosis division until the organism is mature

Experiemtnal evidence confirmed that DNA is the genetic material

experimental evidence was needed to confirm the circumstantial evidence chromosomes contain DNA but also proteins bound in DNA so it was hard to rule out proteins as the genetic material in bacteria, it was shown that transformation occurs when a bacterium alters its genetic makeup by taking DNA from its environment, it was concluded that the ability to cause a heritable change in this bacterium was due to information carried on DNA viruses, such as bacteriophages, are composed of DNA and only one or few proteins, realized that a virus contains information that is used to make more viruses but it was known if the protein or the DNA had that information. Hershey and Chase showed that when bacteriophage infects a bacterial cell, it injects only viral DNA, and that DNA makes others bacteriophages implying that the information to do so is on DNA

11.1 Constitutive genes

expressed most of the time at a constant rate

phenotype

expression of the genotype

Human Pedigrees

family trees that show the occurrence of inherited phenotypes in several generations of related individuals do not show clear proportions for humans because they do not have many offspring two features can be seen: 1) every affected person has an affected parent, do not skip generations 2) half the offspring of an affected heterzygote will be affected inheritance of a recessive gene: 1) affected individuals most often have two unaffected parents 2) only a small proportion of people are affected

Genetics

field of biology concerned with inheritance and has been around for a long time

Mendel's Experiment

first he crossed plants that were true-breeding for different traits, he used a male and a female, this was called a reciprocal cross and these plants are called the Parental/P generation the plants from the P plants are called the first filial generation, which were selfed to produce F2/second filial generation

Assembly of the transcription complex at a promoter containing a TATA box

first the protein TFID (TF=transcription factor) binds to the TATA box this binding changes its shape and that shape of the DNA, presenting new surfaces for other transcription factors

Genomic Imprinting

for a few genes, specific patterns on methylation develop in each sex during gamete formation, are retained in the chromosome of offspring after fertilization the pattern differs in males and female gametes either the maternal or paternal is transcriptionally active (called genomic imprinting) while the other is inactive most imprinting genes are involved in embryonic development, must have paternally and maternally imprinting gene patterns to develop properly males and females may produce genetically similar gametes (minus Y chromosome) however, their gametes differ epigenetically

Translation Initiation

initiation complex: consists of a charged tRNA and a small ribosomal subunit, both bound to the mRNA, for prokaryotes, a short sequence of RNA of the mRNA binds to an rRNA molecule in the small subunit in eukaryotes, a complex of proteins including the small subunit binds to the 5' cap and then moves down the mRNA until it reaches the start codon in both cases, once the small subunit is in the needed location, the anticodon of the methionine charged tRNA binds to the start codon to complete the initiation complex once the methionine-charge tRNA has bound to the mRNA the large subunit joins the complex, at this point the ribosome is fully assembled the methionine charged tRNA is in the P site of the large subunit and the A site is aligned with the second mRNA codon assembly is facilitated by initiation factors

DNA replication involves several proteins

initiation: begings when DNA unwinds, so that replication machinery can access it, occurs when a large protein complex binds to specific DAN chromosomes called ori, the unwinding of the DNA at the oris resulting in replication bubbles (each consisting of two replication forks that move away from the ori to provide access to the proteins to perform DNA replication) the seperation of the two strands of DNA at each fork is catalyzed by helicase enzyme, and is thought of as a wedge that is driven between the two strands the strands are prevented form reforming hydrogen bonds by proteins that bind to the strands seperation causes the strands to twist additionally which is revealed by the topoismerase enzyme, which works by breaking the sugar phosphate backbone and rejoining after they untwist

RNA interference

introduction of double-stranded RNA into a cell to inhibit gene expression ??

one gene-one polypeptide hypothesis

it was assumed that a mutant phenotype arises from a change in the protein's amino acid sequence later when it was known that genes could encode non-enzyme proteins, Beadle and Tantum's hypothesis was rephrased to "one gene-one polypeptide" because proteins are composed of more than one polypeptide (and therefore are encoded by more than one gene)

Operator

lac operon contains a short sequence of DNA sequence called an operator, which is near the promoter and controls transcription of the lac genes an operator is a transcription factor binding site that when bound to a repressor reduces the rate of transcription (negative regulation)

Chromosomal Methylation

large stretches/entire chromosomes can be methylated euchromatin: appears diffuse and lightly stains, lower DNA methylation levels heterochromatin: condensed and stains darkly, heavily methylated Barr Body: a condensed X chromosome

Lytic Cycle

lytic cycle: the host cell immediately begins to produce many new viral particles which are released as the cell breaks open some viruses are reproduced by lysogeny: a process in which the viral genome becomes incorporated into the host cell genome and is replicated along with the host genome the cell is unaffected, but at some point a signal can cause the host cell to enter the lytic cycle and produce viruses

Regulation of mRNA stability

mRNA's are degraded by RNA nucleases in the cytosol some sites of mRNA are particularly susceptible to nucleases one method for altering the stability is to produce a protein that binds to the mRNA in a way that nuclease recognition sites are more or less available for nuclease digestion another way is via regulatory RNA's, genomes contain genes that encode other functional RNA's which can regulate gene expression e.x microRNAs which reduce gene expression in Eukaryotes

dominance is not always complete

many genes have alleles that are neither fully dominant or recessive heterzygotes show an intermediate phenotype, called incomplete dominance 1:2:1 phenotype (purple:violet:white) sometimes two alleles of a gene both produce phenotypes when present in a heterzygote, called codominace e.x blood: blood group can be A, B, AB, or O. Gene I determines blood group by encoding an enzyme involved in the attachment of sugars to the glyocproteins. the alleles of the Gene I (I^A, I^B, or ii) I^A and I^B are dominant to i, so if both I^A and I^B are present, you get AB blood groups

Eukaryotic genes scripts are modified before processing

once pre-mRNA is made, introns are removed (if not non-functional proteins would be made) RNA splicing: removes introns and splices extrons together, this requires that introns have consensus sequences (short stretches of DNA that appear with little variation), most common type of GU at 5' end of intron, AG at 3' end and A followed by CG at the branch point (interior of intron), these sequences are bound by small nuclear ribonucleoprotein particles (snRNPs) which make the protein complex spliceosome, spliceosomes remove introns in two steps 1) 5' end of intron is cut and joined to branch site 2) then 3' end is cut and the 2 extrons are joined some gene mutations occur at consensus sequences two additional pre-mRNA processing steps: 1) at the 5' end a cap is added, cap is made of GTP that is methylated and added in a backward orientation (5' phosphate to 5' phosphate) to facilitate binding of mRNA to the ribosome for translation and protects from being digested by ribonucleases 2) at the 3' end a poly-A tail made of 100-300 adenine nucleotides is added which assists in the export of mRNA from nucleus, binding of proteins, and stability

DNA of eukaryotic cells

organized into multiple structures called chromosomes consists of a double-stranded molecule of DNA and associated proteins all cells in a multi-cellular organism contain DNA

locus

particular position of a gene on a chromosome, different DNA sequences at a locus are termed alleles

environment can affect gene action

phenotypic plasticity: when the phenotype expressed by a particular genotype is different in different environments, quantitative traits are often affected by changes in the environment (but single gene alleles can be too) leads to two important realizations: 1) because some phenotypic variation present within a population will be nongenetic, it will respond less well to natural selection 2) an individual's phenotype is determined not by genotype alone but also by the environment across lifespan epinegenetics!

Elongation

polymerase is an enzyme that synthesizes nucelic acid polymers, primase is an RNA polymerase DNA polymerase catalyzes the addition of deoxyribose nucleotides to synthesize a new DNA strand priming with a short RNA strand is required because DNA polymerase cannot start synthesis without two strands RNA polymerases: dont need a primer DNA polymerase: needs a primer during elongation, the replication fork moves to open up the DNA double helix one of the strands is the leading strand: synthesized continually, other strand is the lagging strand: synthesized discontinually, this is because the strands run antiparrallel bu the polymerase synthesizes from 5' to 3', so the leading strand is oriented so that the DNA polymerase can add the nucleotides from 5' to 3' in the same direction the fork is moving where as the the lagging strand has DNA polymerase adding from its 5' to 3' end with the fork moving in the opposite direction so each fragment must be primed serperately due to it being synthesized discontinually lagging strand is synthesized in short fragents called Okazaki fragments, the laggin strand initially contains multiple RNA primers, but before the end of replicatin, these trands are removedand replaced with DNA

Mutations through Replication Errors

polymerases occasionally make mistakes incorporation error rate: the probability an incorrect base will be inserted into the new strand, 10E-5 for DNA polymerases results in a mismatch between complementary strands most of the errors are repaired because of two things 1) proofreading: if a DNA polymerase recognizes that it has made a mismatch, it stops, backs up, removes the base, and recommences polymerization, 00% are recognized 2) mismatch repair: occurs after DA has been replicated, scans the new molecule and looks for mismatched pairs, recognizes it by the abnormal hydrogen bondings and the altered width of the molecule, if a mismatch is found repair proteins make two-stranded cuts and remove the fragment which is then resynthesized by a DNA polymerase and NDA ligase seals the break, 99% of these errors are fixed a few mismatches will lead to base-pair mutations, a type of point mutation (a mutation that substitutes, deletes, or inserts a single base pair in a DNA molecule), the result is hat the incorrect base in the new strand gets used as a template for further DNA synthesis

11.1 Transcription factors

regulatory proteins that control whether or not a gene is active, two types (repressors and activators) repressors: transcription factor that reduces gene expression activators: transcription factor that increases gene expression bind to specific DNA sequences to increase or decrease the rate of transcription

X-ray crystallography/Rosalind Franklin

provided crucial evidence fr the 3D shape of DNA chemical substances are made into crystals and the positions of the atoms can be inferred from the diffraction pattern of X rays passing through the substance Rosalind Franklin obtained a diffraction pattern that provided insight into the #D structure of DNA suggested that the DNA molecule was long, helical, thin, constant of thickness, and insisting 2-3 polymers with nitrogenous bases on the interior

why there are less anticodons than codons

the cell would have to produce 61 anticodons to match the 61 codons of mRNA, but there are fewer because the base pairing at the 3rd position (3' end of codon and 5' of anticodon) is not strictly complementary 3rd position exhibits "wobble" in which certain bases in 3rd position are able to pair with more than just their normal partner in addition, the third position of the anticodon can contain the nucleotide base "hypoxanthine (I)", a purine that can pair with A,C and U

Regulatory Gene

the gene for the lac repressor is upstream from the operon, is referred to as a regulatory gene because it encodes a regulatory protein

Chromosomal Deletion Mutation

the loss of a chromosome segment, can be severe or even fatal mechanism: a DNA molecule might at two point and the two end pieces might rejoin, leaving out a DNA

11.1 Regulation occurs at all possible steps of gene expression

the rate of RNA synthesis is influenced by the accessibility of gene's DNA (pre-transcriptional) and by the rate of transcription posttranscriptional regulation occurs before translation and effects how RNA processing proceeds translation regulation affects how mRNA is translated, post-translation regulation affects how proteins are folded

Translation can be regulated

the rate of translation of mRNAs can also alter levels of proteins found in a cell three ways in which translation can be regulated: 1) binding of complementary RNA to mRNA, interferes with translation e.x antisense RNA to prevent ribosome binding 2) modification of the 5' cap, an mRNA usuually has a chemically midified molecule of GTP at its 5' end, if not it is not translated 3) inhibition of translation by protein binding to mRNAs and either preventing attachment to the ribosome or interferring with ribosome movement along the mRNA

Modifying Transcription Rates

the rates of the BTA are modified with the binding of specific transcription factors to other sequences close to the core promoter (regulatory promoter) specific transcription factors interact with a protein complex called mediator, which facilitates the interaction between specific transcription factors and the basal transcription apparatus DNA binding sites for transcription factors that are not in the core of regulatory promoters are called enhancers if binding increases transcription or silencers if binding decreases transcription combination of factors present determines whether transcription is initiated

Mendel's Second Law (of Independent Assortment)

the rules of inheritance for more than one allele dihybrid cross: uses 2 characteristics the two characteristics are inherited independently of one another ratio: 9:3:3:1 dom.dom, dom.rec., rec.dom, rec.rec alleles assort independently of one another during gamete formation exception: if two genes are located near one another on the same chromosome, their alleles do not assort independently (linkage)

3 function of tRNA

there is at least one tRNA molecule for each of the 20 amino acids, each tRNA has three functions: 1) tRNAs bind to a specific enzyme that attaches to only 1 of the 20 amino acids, tRNA becomes charged (tRNA becomes attached to amino acids, at the 3' end of tRNA) 2) at the midpoint of tRNA there is a triplet of bases called the anticodon which is complementary to the mRNA, the codon and anticodon bind together with hydrogen bonds (tRNA binds to mRNA) 3) ribosomes have sites on it surface to fit the tRNA noncovelently (tRNA interacts with ribosome)

Watson and Crick

used model building to solve the structure of DNA, obeyed Chargaff's Rule, Franklin's diffraction, and the known chemical properties of DNA it immediately suggested explanations for DNA's biological functions DNA is double-stranded, with each strand consisting of nucleotides joined by a phosphodiester bond between the 5' phosphate on one deoxyribose and the hydroxyl at the 3' position of the next ribose the deoxyribose and the phosphate are involved in the covalent linkages between the nucleotides making the sugar-phosphate backbone the two strands run anti-parallel, clockwise helix, a complete twist occurs every 10 nucleotides the two strands are held together by hydrogen bonds (AT 2, CG 3, complementary base pairs involving a pyrimidine and a purine to give constant thickness) the bases are perpendicular to the antiparallel strands the two phosphate backbones are closer together on one side of the helix than on the other, narrow side makes minor groove, and the wider side makes the major groove some of the O, N, and H atoms in the bases are involved in hydrogen bonding between the bases other atoms on the outer edges of the bases are accessible for additional hydrogen bonding, the arrangement of these unpaired atoms are different for AT bonds and CG bonds, thus the surfaces of the base pairs are chemically distinct from one another in both identity and spatial orientation allowing other molecules to recognize different base pair sequences and bind to them atoms of the major groove are more accessible and tend to bind to other molecules rather than those in the minor groove, this binding of proteins to specific base-pair sequences is ket to protein-DNA interactions and is necessary for the replication and expression of the genetic information of DNA

Meselson and Stahl

verified semiconversative replication grew bacteria in 15N isotope and transferred them into a medium containing only 14N isotope to undergo DNA replication if DNA replicated semiconversatively, one strand would be with 15N and one would be with 14N, making it have an intermediate density determined the DNA density by measuring how far it traveled in a salt gradient, moved farther = higher density

Lac Operon Postive Regulation

when glucose is in a bacterial cell environment, the lac operon is not transcribed at high levels transcription of the lac operon is reduced because transcription factor that binds the lac operon promoter can only so do in absence of glucose when glucose is absent, the transcription factor binds to the promoter to facilitate RNA polymerase binding thus, the lac operon is under negative and positive regulation

Progression through binary fission is regulated in prokaryotes

when sufficient resources have been accumulated, cells begin the cell cycle by initiating DNA replication at the ori site of the chromosome DNA replication is the main control point determining whether the cell cycle will begin a DNA-binding protein (DnaA) binds to ori and initiates DNA replication immedietly after inititation, the DnaA levels are low Z-ring (cytokeniesis) is stimulated by the termination of DNA replication (upon replication of the ter site) cell cycle can cause DNA replication if starvation, and -ring formation if DNA damage

addition rule

when two events are mutually exclusive, the probability that either will occur is the sum of the probability of each event e.x. likeness of a heterozygote is sum of each way to form a heterozygote (Ww or WW) 1/4+1/4=1/2

Chromosomal mutations are extensive change in the genetic material

while point mutations only affect one nucleotide in a gene sequence, other kinds of mutations affect longer sequences of DNA, the most dramatic ones being chromosomal mutations chromosomal rearrangements: deletions, duplications, inversions, and translocations