Final Exam Flashcards
What is a diploid organism, and what are homologous chromosomes
A diploid organism has two sets of chromosomes organized as homologous pairs.
Chromosomes of a homologous pair are usually alike in structure and size, and each carries genetic information from the same set of hereditary characteristics
What are sister chromatids
sister chromatids are identical copies of a chromosome. Each sister chromatid consists of a single molecule of DNA.
what are the four different types of eukaryotic chromosomes and what do they look like
submetacentric: centromere located near the center (slightly above)
metacentric: centromere located at the center
telocentric: located at one end
acrocentric: centromere is super close to one end
Draw the cell cylce and what occurs at each stage
G1: cell grows
G0: non-dividing phase
G1/S checkpoint:
S phase: DNA duplicates
G2 phase: cell prepares for mitosis
G2/M checkpoint
Mitosis
What happens in each stage of mitosis and what does the cell look like in each stage
interphase: nuclear membrane is present and chromosomes are relaxed
prophase: chromosomes condense. Each chromosome possesses two chromatids. The mitotic spindle forms
prometaphase: the nuclear membrane disintegrates. Spindle microtubules attach to chromatids
metaphase: chromosomes line up on metaphase plate
anaphase: sister chromatids separate and move toward opposite poles
telophase: chromosomes arrive at spindle poles. The nuclear membrane re-forms and the chromosomes relax
what is the purpose of mitosis
to develop two genetically identical cells
what is the purpose of meiosis
also called gametogenesis; to create gametes for sexual reproduction
what are the results of meiosis
four genetically variable cells whose chromosome number has been halved
what is the difference between the two divisions that occur in meiosis
reduction division (chromosome number reduced by half) and equational division (similar to mitosis)
what is the order of the stages of meiosis
Meiosis 1: Prophase 1, Metaphase 1, Anaphase 1, Telophase 1
Meiosis II: Prophase II, Metaphase II, Anaphase II, Telophase II –> products
what occurs during prophase I
Chromosomes begin to condense and the spindle forms. Homologous chromosomes pair. Crossing over takes place, and the nuclear membrane breaks down.
what occurs during metaphase I
Homologous pairs of chromosomes line up along the metaphase plate
what occurs during anaphase I
The two chromosomes (each with two chromatids) of a homologous pair separate and move toward opposite poles
what occurs during telophase I
Chromosomes arrive at the spindle poles
What happens during interkinesis
In some types of cells, the spindle breaks down, chromosomes relax, and a nuclear membrane re-forms, but no DNA synthesis takes place.
what occurs in prophase II
Chromosomes condense, the spindle forms, and the nuclear membrane disintegrates
what occurs during metaphase II
Individual chromosomes line up on the metaphase plate
What occurs during anaphase II
Sister chromatids separate and move as individual chromosomes toward opposite spindle poles
what occurs during telophase II
Chromosomes arrive at the spindle poles; the spindle breaks down and a nuclear envelope reforms
compare and contrast the events of mitosis and meiosis
Mitosis: cell division, NO reduction in chromosome number, NO genetic variation, NO crossing over, NO random distribution
Meiosis I: cell division, reduction in chromosome number, genetic variation, crossing over, random distribution
Meiosis II: cell division, NO reduction in chromosome number, NO genetic variation, NO crossing over, NO random distribution
Metaphase in mitosis and meiosis II: individual chromosomes line up
Metaphase in meiosis I: homologous pairs line up
Anaphase in mitosis and meiosis II: chromatids separate
Anaphase in meiosis I: homologous chromosomes seperate
How is genetic variation created in meiosis
crossing over which occurs in prophase I and it is the exchange of genetic material between non-sister chromatids
Random separation of homologous chromosomes occurs in anaphase I after random alignment during metaphase I.
how are gametes formed in humans
- male spermatogenesis occurs from puberty through adulthood. Produces 4 sperm cells for each round of meiosis
- female oogenesis actually begins prior to birth and is not complete until after fertilization. Only one egg is produced for each round of meiosis
what is a gene
an inherited factor (encoded in the DNA) that helps determine a characteristic
What is an allele
one of two or more alternative forms of a gene
what is a locus
a specific place on a chromosome occupied by an allele
what is a genotype
a set of alleles possessed by an individual organism
what is a homozygote
an individual organism possessing 2 of the same alleles at a locus
what is a heterozygote
an individual organism possessing two different alleles at a locus
what is a characteristic/character
am attribute or feature possessed by an organism
what is a phenotype/trait
the appearance or manifestation of a characteristic
what is the concept of dominance
when two different alleles are present in a genotype, only the trait encoded by one of them — the “dominant” allele is observed in the phenotype
define the principle of segregation
(Mendel’s first law) each individual diploid organism possesses two alleles for any particular characteristic, one inherited from mom and one from dad. These two alleles segregate (separate) when gametes are formed and one allele goes into each gamete
how/when do you use the multiplication rule
the multiplication rule states that the probability of two or more independent events taking place together is calculated by multiplying their independent probabilities.
The key indicator for applying this rule is the word and; additionally, the two events must be independent meaning the outcome of one will not influence the outcome of the other
how/when do you use the addition rule
the addition rule states that the probability of any two or more mutually exclusive events is calculated by adding the probabilities of the events.
the key indicator of this rule are the words either and or. For this rule to be valid the events of must be mutually exclusive meaning that one event excludes the outcome of the other
what is a testcross and how is it used
a testcross is used to analyze genetic crosses. One individual of an unknown genotype is crossed with an individual who is homozygous recessive for the trait in question. The testcross reveals the genotype of the unknown individual.
what is the principle of independent assortment
(Mendel’s second law) states that the alleles at different loci separate independently from one another.
This is an extension of the principle of segregation. The separation is independent of the separation of alleles other loci
what is the Chi-square goodness of fit test
it is used to evaluate the role of chance in producing deviations between observed and expected values. It indicates that the probability that the difference between the observed and expected value is due to chance. It must always be applied to numbers of progeny not proportions or percentages.
what is the purpose of the p-value (P)
P= probability that the deviation between expected and observed values are due to chance.
high p= chance alone produced the differences in observed and expected numbers
low p= some other factor produced the differences in observed and expected numbers
what is the difference between sex chromosomes and autosomes
sex chromosomes differ between males and females
autosomes are non sex chromosomes and they are the same between males and females
how are the x and y chromosomes able to pair up in meiosis
Even though they are different in size and content they are homologous at their pseudoautosomal regions which allows them to find each other and pair up during Prophase I
How is sex determined in humans
it is determined by the SRY gene on Y chromosome (not by the whole Y chromosome). Without the SRY gene the gonads will develop into ovaries
what are the following sex anomalies in humans: Klinefelter, turner, triple x, xyy male
Klinefelter syndrome: xxy; phenotype: male
Turner syndrome: xo; phenotype: female
Triple-X: xxx; phenotype: female
XYY male: xyy; phenotype: male
what is the cause of androgen insensitivity syndrome
women with androgen insensitivity syndrome have x and y chromosomes. Testosterone must bind to an androgen receptor in order to stimulate the development of male characteristics, but with the absence of testosterone female characteristics develop. In androgen insensitivity there is nothing for the testosterone to bind to so the body develops as a female.
what is the difference between x linked and y linked traits
x linked traits: genes on the x chromosome that determine specific characteristics
y linked traits: genes on the y chromosome that determine specific characteristics. will only ever be present in males and always inherited from the father
what is a reciprocal cross and how does it apply to sex-linked traits
a reciprocal cross crosses a male and female with different phenotypes and then does it again with the phenotypes corresponding to the opposite sex. This will help indicate if a trait is sex linked or not.
what is nondisjunction
failure of chromosomes to separate properly during anaphase
what is dosage compensation
only 1 x chromosome is expressed in each cell of female mammals. Which X is inactivated is random and set early in development. In cells with more than 2 X chromosomes, all but one X will become inactivated
what is a barr body
Inactivated X chromosome that appears as a condensed, darkly staining body in the nuclei of most cells of female placental mammals.
How are heterozygous females mosaics for x-linked traits such as the tortoiseshell cat/rabbit
Xa or XA depending on which X gets inactivated, some cells express a, others A
what are the different types of dominance
complete dominance: phenotype of the heterozygote is the same as the phenotype of one of the homozygotes
incomplete dominance: phenotype of the heterozygote is intermediate (falls within the range) between the phenotypes of the two homozygotes
Codominance: phenotype of the heterozygote includes the phenotype of both the homozygotes
what is penetrance
percent of individuals having a particular genotype that express the expected phenotype
what is expressivity
degree to which the phenotype is expressed
what are lethal alleles
alleles that cause death at an early stage of development
what are multiple alleles
more than two alleles are present within a group of organisms
What are ABO blood types and their corresponding genotypes
ABO blood group is a multi allele system.
AA or Ai= blood type A (anti-B)
BB or Bi= blood type B (anti-A)
AB= blood type AB (universal receiver)
ii= blood type O (anti-A anti-B)
What is gene interaction
the effects of genes at one locus depend on the presence of genes at other loci.
what is gene interaction with epistatsis
one gene masks or hides the effect of another gene at a different locus
what is dominant epistasis and recessive epistatsis
recessive epistasis needs both epistatic genes present in order to mask
dominant epistasis needs one epistatic gene present in order to mask
what is a sex influenced trait
sex influenced characteristics are determined by autosomal genes and are inherited according to Mendel’s principles, but they are expressed differently in males and females (the trait has higher penetrance in one of the sexes)
what are sex limited traits
sex limited characterisitics are encoded by autosomal genes that are expressed in only one sex; the trait has zero penetrance in the other sex.
what is cytoplasmic inheritance
characteristics encoded by genes located in the cytoplasm exhibit cytoplasmic inheritance.
cytoplasmic genes come from only one gamete and it is usually the egg.
most cytoplasmically inherited traits are present in both males and females and are passed from mother to offspring, never from father to offspring.
There is no mechanism to ensure cytoplasmic genes are evenly distributed during cell division so different cells and different individual offspring will contain various proportions of cytoplasmic genes
what is genetic maternal effect
the phenotype of the offspring is determined by the genotype of the mother. The offpsrings phenotype is determined not by its genotype but by the genotype of the mother
what is genomic imprinting
differential expression of genetic material depending on whether it is inherited from the male or female parent
what is the difference between the following sex influences on heredity:
- sex linked characteristic
- sex influenced trait
- sex limited characteristic
- genetic maternal effect
- cytoplasmic inheritance
- genomic imprinting
- sex linked characteristic: genes located on the sex chromosomes
- sex influenced traits: autosomal genes that are more readily expressed on one sex
- sex limited characteristic: autosomal genes whose expression is limited to one sex
- genetic maternal effect: nuclear genotype of the maternal parent
- cytoplasmic inheritance: cytoplasmic genes, which are usually inherited from only one parent
- genomic imprinting: genes whose expression is affected by the sex of the transmitting parent
what is anticipation
a genetic trait becomes more strongly expressed, or is expressed at an earlier age, as it is passed from generation to generation
can environmental factors influence phenotype
yes
what is a phenocopy
a phenotype that is produced by environmental factors alone but it is the same phenotype produced by a genotype
what is the difference between polygenic and pleiotropy
characteristics encoded by genes at many loci are polygenic characteristics
pleiotropy is when one gene affects multiple characteristics (inverse of polygenic)
what are characteristics of autosomal recessive traits
- usually appears in both sexes with equal frequency
- tends to skip generations
- affected offspring are usually born to unaffected parents
- when both parents are heterozygous approximately 1/4 of the offspring will be affected
- appears more frequently in children of consanguineous marriages
what are characteristics of autosomal dominant traits
- usually appears in both sexes with equal frequency
- both sexes transmit the trait to their offspring
- does not skip generations
- affected offspring must have an affected parent unless they possess a new mutation
- when one parent is affected (heterozygous) and the other parent is unaffected, approximately half the offspring will be affected
- unaffected parents do not transmit the trait
what are some characteristics of x-linked recessive traits
- usually more males than females are affected
- affected sons are usually born to unaffected mothers; thus, the trait skips generations
- approximately half of carrier (heterozygous) mothers sons are unaffected
- never passed from father to son
- all daughters of affected fathers are carries
what are some characteristics of x-linked dominant traits
- both males and females are usually affected: often, more females than males
- does not skip generations. Affected sons must have an affected mother; affected daughters must have either an affected mother or an affected father
- affected fathers pass the trait to all their daughters
- affected mothers (if heterozygous) pass the trait to half of their sons and half of their daughters
what are some characteristics of y-linked traits
- only males are affected
- passed from father to all sons
- does not skip generations
what is quantitative genetics
the genetic analysis of complex characteristics
what is the difference between continuous and discontinuous traits
continuous traits: also called qualitative traits, vary continuously on a scale of measurement exhibiting many overlapping phenotypes
discontinuous traits: possess only a few distinct phenotypes
why are some characteristics continuous
- many are polygenic (influenced from genes at many loci.)
- often arise when environmental factors affect the phenotype because environmental variation results in a single genotype producing a range of phenotypes.
most continuous traits are both polygenic and influence by environmental factors
what are meristic characteristics and why are they considered continuous traits even though there is not an infinite number of phenotypes
meristic characteristics are measured in whole numbers (like litter size) but they are considered quantitative because they are determined by multiple genetic and environmental factors
what are threshold characteristics and why are they considered quantitative traits even though there are only 2 phenotypes (you have it or you don’t)
threshold characteristics are either present or absent. they are considered quantitative because they are determined by multiple genetic and environmental factors. the expression of the characteristic depends on an underlying susceptibility that varies continuously
what is a karyotype
the complete set of chromosomes possessed by an organism
what is chromosome rearrangement
they alter the structure of chromosomes: a piece of chromosome may be added duplicated, deleted or inverted
what is aneuploidy
the number of chromosomes is altered: one or more individual chromosomes are added or deleted
what is polyploidy
one or more complete sets of chromosomes are added. a polyploid is an organism that has more than two sets of chromosomes
what do duplications cause
unbalanced gene dosage
what are the effects of an inversion
inversions often have pronounced phenotypic effects.
it may break a gene into two parts with one part moving to a new location and destroying the function of that gene
what is Robertsonian translocation
the short arm of one acrocentric chromosome is exchanged with the longer arm of another creating a large metacentric chromosome and a fragment that often fails to segregate is lost
this results in an overall reduction in chromosome number - they are the cause of some cases of downsyndrome
what is monosomy
the loss of a single chromosome. it is represented as 2n-1
what is trisomy
the gain of a single chromosome represented as 2n +1. The gain of a chromosome means that there are three homologous copies of one chromosome. Most cases of downsyndrome are a result of trisomy of chromosome 21
what is nullisomy
the loss of both members of a homologous pair of chromosomes. It is represented as 2n-2 where n refers to the haploid number of chromosomes
what is tetrasomy
the gain of two homologous chromosomes represented as 2n + 2. It is not the gain of any 2 homologous chromosomes but the gain of two homologous chromosomes, so that there are four homologous copies of a particular chromosome
how can robertsonian translocations lead to aneuploidy
familial downsyndrome arises in offspring whose parents are carriers of a chromosome that has undergone a robertsonian translocation usually between chromosome 14 and 21.
the long arm of 21 and the short arm of 14 exchange places. The exchange results in one chromosome that includes the long arms of 14 and 21 and another very small chromosome that contains the short arms, which generally is lost after several cell divisions
how can aneuploidy arise through nondisjunction
nondisjunction is the failure of homologous chromosomes or sister chromatids to separate in meiosis or mitosis. nondisjunction leads to some gametes or cells that contain an extra chromosome and other gametes or cells that are missing a chromosome
what are the 2 different types of down syndrome and how
There is familial Down syndrome and primary Down syndrome.
Familial Down syndrome has a tendency to run in families and it is a result of a Robertsonian translocation, it has the same phenotypic characteristics as primary downsyndrome
Primary down syndrome is also known as trisomy 21 and it is a result of a spontaneous nondisjunction during egg formation. about 75% of nondisjunction events that cause downsyndrome are of maternal origin mostly arising during meiosis 1
Why are sex chromosome aneuploidies more tolerated in humans than autosomal anueploidies
there is no mechanism of dosage compensation for autosomes most embryos with autosomal aneuploidies are spontaneously aborted
most commonly seen autosomal aneuploidy is downsydrome which is likely because chromosome 21 is relatively small and carries relativity few genes, so the presence of extra copies is less detrimental
What is genetic mosaicism and how does it arise?
Genetic mosaicism is nondisjunction in mitotic division that generates patches of cells in which every cell has a chromosome abnormality and other patches in which every cell has a normal karyotype. This type of nondisjunction leads to regions of tissue with different chromosome constitutions.
what is polyploidy and what is the difference between autopolyploidy and allopolyploidy
polyploids are organisms that possess two or more sets of chromosomes
autopolyploidy: all chromosome sets are from a single species
allopolyploidy: chromosome sets are from two or more species (hybridization between two species)
what are chargaffs rules
DNA from different organisms vary significantly in base compositions, but between each organism, there is regularity in the ratios of the bases:
A=T and G=C
what was Griffiths experiment and the conclusion that was drawn from it
Griffith discovered the phenomenon of transformation. (discovered that transformation existed BUT NOT WHAT the transformation factor is)
Experiment:
virulent bacteria injected into a mouse –> mouse died
nonvirulent bacteria injected into a mouse –> mouse lived
heat killed virulent bacteria injected into a mouse –> mouse lived
mixture of virulent and heat killed viruletn injected into a mouse –> mouse died
conclusion: a substance in the heat-killed virulent bacteria genetically transformed the nonvirulent bacteria into live virulent bacteria.
what was Avery, MacLeod, and McCarty’s experiment and what conclusion did they draw from it
They identified WHAT the transforming substance was (DNA is)
Experiment:
they took virulent material and used heat to to kill it. They then separated it into three samples one with RNase (destroys RNA), one with protease (destroys proteins), and one with DNase (destroys DNA)
They added all the treated samples to cultures of nonvirulent DNA. Cultures treated with protease or RNase contained transformed bacteria but the culture with DNase did not
Conclusion: because only DNase destroyed the transforming substance, the transforming substance is DNA
Describe the Hershey-Chase experiment and the conclusion that was drawn from it
worked with T2 bacteriophage to determine what part of the phage served as genetic material
Phage genome is DNA. All other parts of the bacteriophage are protein. Phage attaches to E. coli and injects its chromosome. Bacterial chromosome breaks down, and the phage chromosome replicates. Expression of phage genes produces phage structural components. Progeny phage particles assemble. Bacterial wall lyses, releasing progeny phages.
Experiment:
ingect E.coli grown in medium containing sulfur marker and one grown in medium with a phosphorus marker.
sulfur marker is taken up in phage protein which contains S but not P. Phosophurs marker is takin up in phage DNA, whihc contains p but not s.
phages with s and p marker infect unlabled E.coli
shear off protein coats and separate protein from cells by centrifuging.
Results: S is recovered in fluid containing virus coats and infected bacter form a pellet containing P at the bottom of the tube. Progengy phages are radioactive indicating that DNA has been transmitted to the progeny phages
Conclusion: DNA (not protein) is the genetic material in bacteriophages
describe the Fraenkel-Conrat and singer experiment and what conclusion was drawn from it
question: what substance- RNA or protein - carries the genetic material in tobacco mosaic virus (TMV)
Experiment
Have 2 types of TMV (type A and type B) degrade both types to yield RNA and coat proteins. Mix RNA of one type with protein of the other to create hybrid viruses. Infect tobacco with the hybrids
Results: the type of RNA in the hybrid parent TMV determines the RNA and protein of the progeny viruses
Conclusion: RNA is the genetic material of TMV
what is a nucleotide and what are the three main parts that make up a nucleotide
a nucleotide contains a sugar, a phosphate, and a nitrogen containing base
DNA consists of a large number of linked repeating units (nucleotides)
describe the structure of DNA
DNA runs in opposite directions; antiparallel
DNA has deoxyribes sugar (missing an oxygen compared to RNA).
composed of polynucleotide strands
CG pairs have three hydrogen bonds and TA pairs have two hydrogen bonds
A phosphodiester linkage connects the 5’- phosphate group and the the 3’ OH group of adjoining nucleotides
Describe the structure of RNA
also composed of polynucleotide strands
Uracil (U) replaces thymine (T)
RNA has a ribose sugar (an OH group where DNA just has an H)
what is chromatin
Eukaryotic DNA in the cells is closely associated with proteins. The complex of DNA and proteins is called chromatin
what is euchromation
euchromatin undergoes the normal process of condensation and decondensation in the cell cycle
what is heterochromatin
heterochromatin remains in a highly condensed state throughout the cell cycle, even during interphase.
what are the difference between euchromatin and heterochromatin
euchromatin constitutes the majority of the chromosomal material and is where most transcription takes place
all chromosomes have permanent heterochromatin at the centromeres and telomeres; the y chromosome consists largely of constitutive heterochromatin
heterochromatin may also occur during certain developmental stages
heterochromatin is also characterized by a general lack of transcription, the absence of crossing over, and replication late in the S phase
what are histone proteins and what are the five main types
must abundant proteins in chromatin are the histones, which are small, positively charged proteins of five major types: H1, H2A, H2B, H3, and H4
all histones have a % of bargaining and lysine which gives them their net positive charge. These positive charges attack the negative charges on the phosphates of DNA; this attraction holds the DNA in contact with the histones.
why is it important for histone proteins to have a positive charge
the positive charges attract the negative charges on the phosphates of DNA, which holds the DNA in contact with the histones
what is the makeup of the nucleosome with respect to the histone proteins and the DNA
The core of protein and DNA produced by digestion with nuclease enzymes is the simplest level of chromatin structure (the nucleosome)
The nucleosome is a core particle consisting of DNA wrapped about two times around an octamer of eight histone proteins (2 copies each of H2A, H2B, H3, and H4)
each of the histone proteins that make up the nucleosome particle has a flexible “tail”
positively charged amino acids in the tails of the histones interact with negative charges of the phosphates on the DNA, keeping the DNA and histones tightly associated
how are mitochondrial and chloroplast DNA inherited differently than nuclear DNA
mitochondrial and chloroplast DNA is inherited through replicative segregation
what is the endosymbiotic theory
around 1 billion years ago an anaerbic cell engulfed an aerobic bacterium through endocytosis. The aerobic endosymbiont evolved into mitochondria. Endocytosis of a photosynthesizing bacterium led to the evolution of modern eukaryotic cells with mitochondria and chloroplasts
The endosymbiotic theory proposes that mitochondria and chloroplasts in eukaryotic cells arose from bacteria
what is replicative segregation
a heteroplasmic cell has two distinct varieties of DNA contained in its organelles
the organelles segregate randomly in cell division, replicate, and again segregate random in cell division and organelles replicate again this happens a total of three times.
cell division –> replication of mitochondria –> cell division –> replication of mitochondria
most of the resulting cells are heteroplasmic, but, just by chance, some cells may receive only one type of organelle
describe the Meselson and Stahl experiment and how did they interpret their results
the goal was determine what model of replication of DNA was accurate
filled a centrifuge tube with a heavy salt solution and DNA fragments then spun the centrifuge for several days
a density gradient developed and heavy DNA (15n marker) moved toward the bottom and light DNA (14n marker) moved toward the top
After one round of replication, DNA appeared as a single band at intermediate weight
after a second round of replication, DNA appeared as two bands 1 light and the other intermediate
conclusion: DNA replication in E.coli is semiconservative
differentiate between the structures of DNA and RNA
DNA:
composed of nucleotides
deoxyribose sugar
no 2’ OH group
nucleotides are joined by phosphodiester bonds
usually double stranded
secondary structure is a double helix
stable
RNA:
composed of nucleotides
ribose sugar
has a 2’ OH group
nucleotides are joined by phosphodiester bonds
usually single stranded
many types of secondary structures
easily degradable
what is the location and function of rRNA
Cell type: prokaryotic and eukaryotic
Location of function in eukaryotic cells: cytoplasm
Function: structural and functional components of the ribosome
what is the location and function of mRNA
Cell type: prokaryotic and eukaryotic
Location of function in eukaryotic cells: nucleus and cytoplasm
Function: carries genetic code for proteins
What is the location and function of tRNA
Cell type: prokaryotic and eukaryoitc
Location and Function in Eukaryotic cells: cytoplasm
Function: helps incorporate amino acids into polypeptide chain
what is transcription and the general steps of the process
Transcription: synthesis of an RNA molecule from a DNA template
RNA synthesis is complementary and antiparallel to template strand
Only certain regions of the DNA are transcribed (mostly gene regions) rather than the entire chromosome
Only 1 of the 2 DNA strands is transcribed for each gene
Nucleotides are added to the 3’ end of the RNA molecule so the direction of synthesis is 5’-3’
* refer to Fig 13.8
describe the bacterial transcription apparatus
Bacterial cells only possess one type of RNA polymerase, which catalyzes the synthesis of all classes of bacterial RNA.
5 sub units make up the core enzyme: 2 copies of alpha, 1 beta, 1 beta prime, 1 omega
The core enzyme catalyzes the elongation of RNA molecules by the addition of RNA nucleotides.
The sigma factor controls the binding of RNA polymerase to the promoter forming a holoenzyme.
It is said to move downstream during transcription: it binds to the promoter and moves toward the terminator.
differentiate between bacterial RNA polymerase and eukaryotic RNA polymerase
bacteria only have one RNA polymerse that transcribes all RNA, eukaryotes have many RNA polymerases (named with roman numerals) that transcribe different RNAs
know that in eukaryotes there are different RNA polymerases that transcribe different types of RNA
RNA pol II transcribes pre-mRNA
define promoter and what is its function
the promoter is a DNA sequence that the transcription factor recognizes and binds. It indicates which of the 2 DNA strands is to be read as the template and the direction of transcription. In most cases, the promoter is located next to the transcription start site but is not itself transcribed
what is a consensus sequence and why is it important within the promoter
A consensus sequence is the set of most commonly encountered nucleotides among sequences that possess considerable similarity, or consensus. The presence of a consensus within a set of nucleotides usually implies that the sequence is associated with an important function.
The holoenzyme initially binds weakly to the promoter but then undergoes a change in structure that allows it to bing more tightly and unwind the double stranded DNA
what are the steps of bacterial transcription
Initiation (fig 13.12):
- sigma and core RNA polymerase bind to promoter
- unwinds DNA
- nucleotides incorporated – no primer required
- 2 phosphates cleaved for each new nucleotide added
- sigma released
Elongation:
- RNA polymerase continues adding nucleotides
- unwinding at front of bubble and rewinding behind bubble
- proofreading
Termination- different genes can use different termination mechanism
1. RNA polymerase transcribes a terminator sequence, which consists pf a sequence that forms a hairpin structure in the RNA followed by several uracils in the RNA
2. the hairpin structure causes the RNA polymerase to pause
3. at this point, only A-U bonds (weak bonds) are holding DNA and RNA together – DNA and RNA separate (13.14)
what is the difference between general transcription factors and other transcription factors
general transcription factors combine with RNA polymerase to form basal transcription factors. It is needed to initiate minimal levels of transcription
other transcription factors bind to other DNA sequences and bring about higher levels of transcription by stimulating the assembly of the basal transcription apparatus at the start site
What is the difference between a core promoter and a regulatory promoter within eukaryotes (fig 13.15)
Core Promoter:
- immediately upstream of a gene
- basal transcription apparatus binds here, which is required for transcription
- there are several consensus sequences within the core promoter that are recognized by many different proteins, but the important one to remember is the TATA box at -25
Regulatory Promoter:
- immediately upstream of core promoter
- affects rate of transcription
- not required for transcription
What are the steps of eukaryotic transcription (for RNA polymerase II)
Initiation (fig 13.6):
- TFIID contains a TATA-binding protein (TBP) which binds to the TATA box within the core promoter
- General TFs + RNA pol + mediator bind to the core promoter via TFIID
- TBP of TFIID positions active site of RNA polymerase over the start site
- other transcription factors: may bind to regulatory promoter, may bind to enhancers, affect transcription rate by interacting with the basal transcription apparatus via the mediator
Elongation (fog 13.80:
- similar to bacterial elongation
Termination:
- there are proteins that assist to remove the RNA polymerase and the RNA transcript from the DNA
what is the difference between an intron and an exon
exons are RNA coding regions, and the noncoding regions are called introns. All the introns and exons are initially transcribed into RNA but during or after transcription the introns are removed and the exons are joined to yield mature RNA.
what organisms are introns common within and what organisms are they rare within
common in eukaryotic genes but rare in bacterial genes
introns have been observed in archaea, bacteriophages, and some bacteria
present in mitochondrial and chloroplast genes as well as in the nuclear genes of eukaryotes.
Draw and label the structure of a mature mRNA (fig 14.5)
What are the three main steps in pre-mRNA processing
- Addition of the 5-cap
- Addition of the poly(A) tail
- RNA splicing
what type of cells does pre-mRNA processing occur in and where inside the cell
it occurs in eukaryotic cells within the nucleus
Describe how the 5’ cap is added and its function
It is a guanine nucleotide added backwards (5’ to 5’ bond) to the 5’ end of the mRNA.
then methyl groups are added to the mRNA
Function:
1. assist with binding of ribosome to mRNA for translation
2. stabilizes mRNA
how is the poly(A) tail added and what is its function
How:
cleavage 11-30 nucleotides downstream of AAUAA consensus near 3’ end
Polyadenylation: many adenines are added
Function:
increases stability of mRNA
required for ribosome binding to 5’ cap
what is splicing
RNA splicing is the removal of introns. This takes place in the nucleus before the RNA moves to the cytoplasm. Splicing requires the presence of of 3 seuqneces in the intron ( 5’ splice site, 3’ splice site, and branch point)
what is a splicesome and what is its makeup
splicesome is a large complex where splicing occurs
consists of several snRNPs ( ‘snurps’ )
snRNP= 1 snRNA + proteins
each snRNP plays a different role in the splicing process
what is alternative splicing (fig 14.12a)
alternative splicing is when the same pre-mRNA can be spliced in more than one way to yield different mRNAs that are translated into different amino acid sequences thus different proteins. Alternative splicing uses different combinations of exons
explain multiple 3’ cleavage sites (fig 14.12b)
Two or more potential sites for cleavage and polyadenylation are present in pre-mRNA. mRNA products of different lengths are produced after splicing
*the calcitonin gene is a good example but it doesn’t need to be memorized
What is the purpose of RNA interference (RNAi)
defense mechanism against viruses
regulation of gene expression
*RNAi is only found in eukaryotes
Describe how RNAi works
Double-stranded RNA gets chopped up by the enzyme dicer
The resulting RNA pieces are called microRNAs (miRNAs) or small interfering RNAs (siRNAs)
miRNAs/siRNAs form a complex with proteins- this complex is called RISC
RISC pairs with the target mRNA (because the miRNA/siRNA is complementary to the target mRNA)
The target mRNA can no longer be translated
Thus the mRNA has been ‘interefered’ with so that the gene that the mRNA came from will no longer be expressed (no protein produced)
what is the purpose of CRISPR RNA (crRNA)
it is like the immune system of prokaryotes
they defend prokaryotic cells against invasion of foreign DNA (DNA from bacteriophages and plasmids)
What is the action of CRISPR RNAs
- Foreign DNA (ie phage DNA) gets incorporated into the bacterial DNA – specifically it is inserted into a CRISPR array region of the bacterial genome
- The CRISPR array gets expressed (transcribed into crRNA)
- the crRNA and CAS protein form a complex
- now when the foreign DNA enters the cell again, the crRNA-CAS complex will bind to it (because the crRNA is complementary to it) and CAS cuts the foreign DNA rendering it non functional
What is codon
a set of nucleotides that encodes a single amino acid. They are the basic unit of genetic code.
what is meant by the degeneracy of code
genetic code is redundant: amino acids may be specified by more than one codon. Because there are 64 codons but only 20 amino acids; 1 amino acid may be specified by more than one codon
what is meant by wobble in the code (fig 15.11 and table 15.2)
there are 61 different sense codons, but there are less than 61 different tRNAs. Wobble is a non standard base pairing at the third position of the codon (3’) and it allows 1 anti codon to pair with more than one codon
what is translation
translation is how amino acids are assembled into proteins.
Only mRNAs are translated into proteins
where does translation occur within the cell
Translation takes place on the ribosomes. Ribosomes can be thought of as moving protein-synthesis machines.
explain the process of translation initiation in prokaryotes (fig 15.16, 15.17)
- IF-3 bind to small ribosomal subunit
- IF-3/small subunit bind to mRNA
- the rRNA in the small subunit is complementary to Shine-Dalgarno sequence
- tRNA carrying n-formyl methionine + IF-2 + GTP all come in together and and anticodon binds to start codon
- IF-1 joins this complex
- GTP is hydrolyzed to GDP and all IF’s leave the complex
- Large subunits join
explain the process of translation elongation (fig 15.19)
- after initiation, the fMet-tRNA is in the P site of the ribosome
- EF-Tu + GTP + charged tRNA enter A site
- GTP hydrolyzed to GDP and EF-Tu/GDP leaves
- peptide bind forms between amino acids in P and A sites (peptidyl transferase is the enzyme that does this)
- tRNA in P site releases its amino acid so now the peptide chain is entirely on the tRNA at the A site
- ribosome shifts down by one codon (translocation) with the help of EF-G and GTP
- tRNA that was at the P site is now in the E site and then immediately leaves
- A site in now available to receive the next charged tRNA and the cycle continues
Explain the process of translation termination (fig 15.20)
- when a stop codon is in the A site, a release factor comes to the A site
- another release factor joins the ribosome and all components are released
explain simultaneous transcription and translation and state whether this occurs in prokaryotic or eukaryotic cells
in prokaryotic cells transcription and translation are simultaneous; multiple ribosomes may be attached to the 5’ end of the mRNA while transcription is still taking place at the 3’ end.
(mRNA molecules are translated simultaneously in both prokaryotes and eukaryotes but that is different)
explain polyribosomes and state whether they occur in prokaryotic or eukaryotic cells
an mRNA with several ribosomes attached is a polyribosome this occurs in both prokaryotes and eukaryotes
explain the relationship between how tightly packaged DNA is and whether transcription occurs or not
transcription can not take place when DNA is wrapped tightly around histone proteins because there is no room for the transcription machinery to fit and get by. Before transcription, chromatin structure changes so that DNA becomes more accessible to transcription machinery
what are 2 ways that histones can be modified and describe the effects of these modifications as well as the enzymes involved (fig 17.2)
- Methylation of histones:
- the addition of methyl groups to the tails of histone proteins. This results in activation or repression depending on which histone is modified.
- Enzymes called histone methyltransferases add methyl groups to specific amino acids of histones.
- enzymes called histone demethylases, remove methyl groups from histones. - Acetylation of histones:
- the addition of acetyl groups to histones. This usually stimulates transcription
- in general, acetyl groups destabilize chromatin structure allowing transcription to take place.
- acetyl groups are added to the histones through acetyltransferase enzymes.
- deacetylases strip acetyl groups from histones and restore chromatin structure, which represses transcription
how is DNA methylation associated with gene regulation. What gets methylated and how does this result in gene regulation
DNA methylation is most common on cytosine bases adjacent to guanine nucleotides.
-heavily methylated DNA is associated with the repression of transcription
- when genes are not being transcribed CpG islands are often methylated, but the methyl groups are removed before the initiation of transcription. CpG methylation is also associated with long-term gene repression
what are CpG islands
DNA regions with many CpG sequences and they are commonly found near transcription start sites.
what are general transcription factors
General transcription factors: bind to the core promoter and are part of the basal transcription apparatus. These are required for transcription
what are other transcription factors
bind to regulatory promoter which is located upstream of the core promoter. They bring about higher levels of transcription by stimulating the assembly of the basal transcription apparatus at the start site
define basal transcription apparatus
a group of proteins that assembles near the transcription start site and is sufficient to initiate minimal levels of transcription
define core promoter
Core promoter: located immediately upstream of a gene and is capable of minimal levels of transcription
define regulatory promoter
Regulatory promoter: others transcription factors bind here and it is located upstream of the core promoter.
what is the difference between silencers and enhancers? What type of transcription factors bind to these? Where are silencers and enhancers located with respect to a gene (fig 17.5)
Enhancers are regulatory elements that affect the transcription of distant genes. In many eukaryotes, enhances are highly abundant. Enhancers usually regulate genes in a cell type specific manner- they turn on different sets of genes in different cell types and help establish the traits that characterize cells of different tissues.
Silencers have an inhibitory effect on the transcription of distant genes.
how are regulatory promoters and mediators associated with eukaryotic gene regulation? where are these located with respect to a gene? (fig 17.5)
- Regulatory promoters typically contain several different consensus sequences to which different transcription factors . Each promoter is regulated by a unique combo of transcription factors
- The binding of transcription factors to the consensus sequences in the regulatory promoter affects the assembly or stability of the basal transcription apparatus at the core promoter
- The mediator is a component of the basal transcription apparatus; it is a complex of proteins that interacts with RNA polymerase. Transcription factors that bind to sequences in the regulatory promoter (or enhancer) make contact with the mediator and affect the rate at which transcription is initiated
what is the purpose of an insulator and how do they work (fig 17.8)
insulators are DNA sequences that block the effect of enhancers in a position-dependent manner. If an insulator lies between an enhancer and a promoter, it blocks the action of the enhancer, but if it lies outside that region it has no effect.
Insulators are important because most enhancers are capable of stimulating any promoter in their vacinity
what is mutation
an inherited change in the DNA sequence of genetic information
define base substitution
an alteration of a single nucleotide in the DNA. It can be a transition or a transversion
what is the difference between transitions and transversions
transitions are when a purine is replaced by a different purine or a pyrimidine is replaced by a different pyrimidine.
transversions are when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine.
Transitions are more likely to happen than transversions
define insertions and deletions and describe what type of mutations they cause (fig 18.2b, c)
insertions and deletions are collectively called indels
insertions and deletions are the addition or removal of one or more nucleotide pairs.
these can cause frameshift mutations: changes in the reading frame of the gene. Frameshift mutations usually alter all amino acids encoded by the nucleotides following the mutation.
define in-frame insertions and deletions and describe how they arise
insertions or deletions consisting of any multiple of 3 nucleotides leaves the reading frame intact.
define expanding nucleotide repeats
mutations in which the number of copies of a set of nucleotides increases
explain how strand slippage can cause expansion of nucleotide repeats (fig 18.5)
strand slippage is the misalignment of the sequences or stalling of replication.
If a DNA molecule has 8 copies of a CAG repeat, the two strands separate and replicate. In the course of replication, a hairpin forms on the newly synthesized strand, causing part of the template to be replicated twice and increasing the number of repeats on the newly synthesized strand, causing part of the template to be replicated twice and increasing the number of repeats on the newly synthesized strand. The 2 new strands of the new DNA molecule separate. The strand with the extra CAG copies serves as a template for replication. The resulting DNA molecule contains five additional copies of the CAG repeats.
explain how expanding nucleotide repeats correspond to anticipation
Number of copies of the repeat also correlates with its instability: when more repeats are present, the probability of expansion is more to even more repeats increases.
diseases caused by expanding nucleotide repeats gets more severe with each generation (attenuation)
define and describe 3 effects base substitutions can have on the amino acid sequence (fig 18.6)
Missense mutation: the new codon encodes a different amino acid; there is a change in amino acid sequence
Nonsense mutation: The new codon is a stop codon; there is a premature termination of translation
Silent mutation: The new codon encodes the same amino acid; there is no change in amino acid sequence
differentiate between forward mutation and reverse mutation (fig 18.7)
a forward mutation alters the wild-type phenotype to a mutant
a reverse mutation changes a mutant phenotype back into the wild type.
define neutral mutation
a missense mutation that alters the amino acid sequence of a protein but does not significantly alter its function.
define loss of function mutation
these are mutations that cause partial or complete loss of normal protein function. This mutation alters the structure of the protein that the protein no longer works anymore.
define gain of function mutation
this mutation causes the cell to produce a protein or gene product whose function is not normally present. Gain of function mutations are frequently dominant in their expression because a single copy of the mutation leads to the presence of a new gene product.
define conditional mutation
conditional mutations are expressed only under certain conditions
define lethal mutations
mutations that cause premature death.
define suppressor mutation (fig 18.7)
It is a genetic change that hides or suppresses the effect of another mutation. A suppressor mutation occurs at a site distinct from the site of the original mutation; thus an individual with a suppressor mutation is a double mutant, possessing both the original mutation and the suppressor mutation
this mutation can either be intragenic or intergenic
differentiate between intragenic and intergenic suppressor mutations and give an example of how each may occur (fig 18.8, 18.9)
An intragenic mutation takes place in the same gene that contains the mutation being suppressed. This may work by the suppressor changing a second nucleotide in the same codon altered by the original mutation, producing a codon that specifies the same amino acid that was specified by the original, nonmutated codon. They can also work by suppressing frameshift mutation. Lastly, it may work by making compensatory changes in the protein.
An intergenic mutation occurs in a gene other than the one bearing the original mutation that it suppresses. They sometimes work by changing the way the mRNA is translated. They can also work through gene interactions.
differentiate between spontaneous and induced mutations
spontaneous mutations result under normal conditions
induced mutations results from changes caused by environmental chemicals
how can strand slippage cause insertions and deletions and nucleotide repeat expansion
Strand slippage occurs when one nucleotide strand forms a small loop.
If the looped-out nucleotides are on the newly synthesized strand, it will cause an insertion.
If the looped-out nucleotides are on the template strand, it will cause a deletion.
Nucleotide repeat expansion occurs when repeats of nucleotides cause a hairpin structure to form on the newly synthesized strand (strand slippage). The more strand slippage happens, the more likely it is to occur again, causing expanding nucleotide repeats.
how can unequal crossing over cause insertions and deletions (fig 18.4)
Misaligned pairing can cause unequal crossing over that results in one DNA molecule with an insertion and the other with a deletion.
how can depurination cause base substitutions (fig 18.5)
depurination is the loss of a purine base form a nucleotide. This creates an apurinic site. In the absence of a base an incorrect nucleotide is incorporated into the newly synthesized DNA (usually adenine)
how can base analogs cause mispairing during replication (fig 18.8)
base analogs are a class of chemical mutagens with chemical structures similar to those of any of the 4 standard bases of DNA. If base analogs are present during replication, they may be incorporated into newly synthesized DNA molecules. If incorporated, it will pair with the wrong base, and then in the next replication, it will lead to a permanent mutation.
name the two types of radiation and briefly explain the types of mutations they cause (fig 18.22)
Ionizing radiation (X-rays, gamma rays, and cosmic rays): dislodge electrons from the atoms they encounter, changing stable molecules into free radicals and reactive ions, which alter the structures of bases and break phosphodiester bonds in DNA. It also frequently results in double-stranded breaks in DNA
UV light: pyrimidine bases readily absorb UV light causing chemical bonds to form between adjacent pyrimidines on the same strand of DNA, creating pyrimidine dimers. These are bulky lesions that distort the configuration of DNA and often block replication.
how do intercalating agents result in frameshift mutations. What is an example of an intercalating agent
intercalating agents produce mutations by sandwiching (intercalating) themselves between adjacent bases in DNA. This distorts the 3D structure of the DNA helix causing single nucleotide insertions and deletions in replication. These often produce frame shift mutations (since only one base is added or deleted)
Ethidium bromide is an intercalating agent
what are transposable elements (aka transposons)
DNA sequences that can move about the genome and they are often causes of mutations. Because they can move around they are also called jumping genes.
Cause gene mutations and chromosome rearrangements
There are _________ _________ that repair errors and there is __________ between the mechanisms with respect to the types of ________ they repair.
There are several mechanisms that repair errors and there is overlap between the mechanisms with respect to the types of mutations they repair.
describe how restriction enzymes can be used to create recombinant DNA (fig 19.2b)
DNA molecules cut with the same restriction enzyme have complementary sticky ends that pair if fragments are mixed together
Nicks in the sugar-phosphate backbone of the two fragments can be sealed by DNA ligase
Describe how CRISPR-Cas9 is used for genome editing (fig 19.3)
- Scientists have engineered crRNA from bacteria with a sequence that is specific to the target sequence of interest
- The other part of the crRNA contains a sequence that pairs with CAS9 protein which creates a crRNA/Cas9 complex
- This complex finds and binds to to the target DNA sequence
- Cas9 makes double-stranded cuts within the target DNA sequence
The cells DNA repair mechanisms kick in to try and repair the cut– 2 things can happen
1. Nonhomologous end joining is a repair pathway that repairs chromosome breaks but often causes insertions/deletions within the process – this would inactivate the gene
2. Donor DNA can be inserted into the cell with ends complementary to the break sequence– homologous recombination would insert this sequence to repair the gene
how can gel electrophoresis be used to separate DNA fragments by size (fig 19.4)
Gel electrophoresis separates molecules on a basis of size and electrical charge. DNA fragments are placed in the wells of the gel and an electrical current is passed through the gel (negative next to DNA positive at the bottom)
DNA fragments move toward the positive end of the gel (because DNA is negatively charged). The smaller the DNA fragment the faster it moves.
List the 5 components of a PCR reaction
- Taq polymerase (DNA polymerase)
- dNTPs
- Template DNA
- Primers
- Magnesium ions (to mimic cellular conditions)
Explain the steps in a PCR cycle (fig 19.5)
- DNA is heated to 90-100 C to separate the two strands
- The DNA is quickly cooled to 30-65 C to allow short single-stranded primers to anneal to their complementary sequences
- The solution is heated to 72 C; DNA polymerase synthesizes new strands, creating two new double-stranded DNA molecules
- The entire cycle is repeated. Each time the cycle is repeated the amount of target DNA doubles
define gene cloning. what is the process for gene cloning in bacteria
Produces identical copies of genes.
Process:
plasmid –> digest with restriction enzyme —> join with DNA ligase —> recombinant plasmid
how can a foreign DNA fragment can be inserted into a DNA plasmid (fig 19.9)
- the plasmid and foreign DNA are cute by the same restriction enzyme
- when mixed, the sticky ends anneal, joining the foreign DNA and plasmid
- nicks in the sugar-phosphate bonds are sealed by DNA ligase
what is transformation
the mechanism where bacterial cells take up DNA from the external environment. Inside the cell, the plasmids replicate and multiply as the cells themselves multiply
explain how to use selectable markers to identify recombinant cells (fig 19.9)
bacteria with an original (nonrecombinant) plasmid produce B-gal, which cleaves X-gal and makes the colonies blue
Bacteria with a recombinant plasmid do not synthesize B-gal. Their colonies remain white
Bacteria without a plasmid will not grow
how does next-generation sequencing work, specifically Illumina sequencing (fig 19.19)
Most next-generation sequencing technologies do sequencing in parallel, meaning millions of DNA fragments can be sequenced simultaneously.
Illumina sequencing is the most widely used sequencing technology today.
1. Primers, DNA polymerase, and dNTPs are added to the flow cell. The primer attaches to the template
2. The first nucleotide is incorporated into the new strand. The tag is excited with a laser and fluoresces
3. The fluorescence is recorded by a computer. Thousands of fragments are sequenced and imaged simultaneously.
4. The tag and the terminator are removed
5. New dNTPs and polymerase are added
6. The next nucleotide is incorporated and excited with a laser
Define DNA fingerprinting
It is a technique used to identify individuals by examining their DNA sequences.
what type of sequence is analyzed in DNA fingerprinting
Most DNA fingerprinting uses microsatellites or short tandem repeats (STRs)
how does DNA fingerprinting work (fig 19.22)
DNA samples are collected and subjected to PCR. The fragments are separated by gel electrophoresis. Different-sized fragments appear as different bands.
13 core STRs are used for DNA fingerprinting
describe how RNAi could be used to turn off a gene
RNAi can be used to silence genes by 1. designing siRNAs that will be recognized and cleaved by Dicer. The complementary sequence must be unique to the target mRNA and must not be found on other mRNAs. Next, the double-stranded siRNA is delivered to the target cells. The RNAi sequence has the potential to become a permanent part of the cell’s genome and be passed on to progeny
what is the difference between genetic maps and physical maps
genetic maps provide a rough approximation of the locations of genes relative to the locations of other known genes.
they are based on the process of recombination. They are measured in centimorgans
genetic maps are low in details and they do not always correspond to physical distances between genes (there are sometimes discrepancies.
Physical maps are based on the direct analysis of DNA and they place genes in relation to distances measured in number of base pairs. They generally have higher resolution and are more accurate than genetic maps.
what are some problems associated with sequencing an entire genome
only small fragments (500-700 bp) can be sequenced at a time.
must fragment the genome into millions of small overlapping fragments for sequencing.
difficulty ordering the sequenced genome
define single nucleotide polymorphisms and haplotype (fig 20.8)
single nucleotide polymorphism is a site in the genome where individual members of a species differ in a single base pair (SNP)
The specific set of SNPs and other genetic variants observed on a single chromosome or part of a chromosome is called a haplotype
Explain how SNPs can be used for genome-wide association studies
genome-wide association studies use numerous SNPs scattered across the genome to find genes of interest. SNPs have been used in genome-wide association studies to successfully locate genes that influence many additional traits, such as height, body mass index, the age of puberty, etc.
The genes identified often explain only a modest proportion of the genetic influence on the trait.
describe how bioinformatics can be used to identify a gene
ab initio approach scans the sequence, looking for features that are usually found within a gene. Specific sequences mark the splice sites at the beginnings and ends of introns; other specific sequences are present in promoters immediately upstream of start codons. It looks for similarities between a new sequence and a sequence of all known genes.
define annotation as it applies to bioinformatics
annotation means linking its sequence information to other information about its function and expression, the protein it encodes, and similar genes in other species.
define metagenomics and briefly describe why this exists
metagenomics is an emerging field in which the genome sequences of an entire group of organisms that inhabit a common environment are sampled and determined.
it mostly applies to microbial communities. It provides the ability 1) the identification and study of microbes that cannot be cultured in the laboratory and 2) the study of the community structure of microorganisms.
define homology search and explain how this can be used to understand the function of a gene
homology search is used to determine gene function. It relies on comparisons of DNA and protein sequences from the same species and from different species. Homologous genes are genetically related genes
differentiate between ortholog and paralog (fig 20.9)
orthologs are homologous genes found in different species that evolved from the same gene in a common ancestor
paralogs are homologous genes in the same species
list 2 techniques that can be used to study the expression of a gene
Microarrays: rely on nucleic acid hybridization
RNA sequencing: provides detailed information about gene expression, including the types and number of RNA molecules produced by transcription, the presence of alternatively processed RNA molecules, differential expression of the two alleles in a diploid individual, and different RNA molecules generated by bidirectional or overlapping transcription of DNA sequences.
describe how microarrays can be used to examine gene expression (fig 20.10)
used with cDNA, microarrays can provide information about the expression of thousands of genes, enabling scientists to determine which genes are active in particular tissues.
A microarray consists of DNA probes fixed to a solid support, such as nylon. Each spot consists of a different DNA probe. Cancer and noncancer cells are removed from 78 women with breast cancer cells. mRNA from the cells is converted into cDNA and labeled with red or green nucleotides. The cDNAs are mixed and hybridized to DNA probes on a chip. The chip is scanned by spot. Yellow indicates equal expression of the gene in both types of cells.
The microarray scan is converted to a heat map. Each spot represents the expression of one gene in one patient’s tumor compared with the expression of that gene in noncancer cells.
Describe the process of RNA sequencing (fig 20.12)
- collect total RNA from cells
- isolate mRNA
-reverse transcribed into cDNA - fragment cDNA
- sequence with next-gen sequencing
- assemble sequences into RNA transcripts
define evolution and explain the two steps involved
biological evolution refers only to a specific type of change: genetic change happening taking place in a group of organisms. This includes only genetic change and it takes place in groups never just an individual
step one: genetic variation arises
second step: change in the frequencies of genetic variants
Explain how we observe genetic variation today.
molecular variation: we can investigate evolutionary change directly by analyzing protein and nucleic acid sequences. Variation in protein and nucleic acid sequence is has a clear genetic basis and is easy to interpret.All organisms have certain molecular traits in common. These molecules offer a valid basis for comparisons among all organisms.
Molecular data is quantifiable, which facilitates the objective assessment of evolutionary relationships. It can also reveal clues about the process of evolution
Describe the biological species concept.
it is a widely used definition of a species. It defines species as a group of organisms whose members are capable of interbreeding with one another but are reproductively isolated from the members of other species.
TLDR; members of the same species have the biological potential to exchange genes, and members of other different species cannot exchange genes. Because different species do not exchange genes, each species evolves independently
define reproductive isolating mechanisms
any biological factor mechanism that prevents gene exchange
Differentiate between Prezygotic and postzygotic reproductive isolating mechanisms.
Prezygotic: prevent gametes from two different species from fusing and forming a hybrid zygote. Includes 5 different types
Postzygotic: gametes of two species may fuse and form a zygote, but there is no gene flow between the two species, either because resulting hybrids are inviable/sterile or because reproduction breaks down in subsequent generations. 3 different types
list and describe the five types of prezygotic reproductive isolating mechanisms (table 26.1)
- Ecological isolation: members of 2 species do not encounter each other so they do not reproduce with each other (dif ecological niches)
- Behavioral isolation: differences in behavior prevent interbreeding (ex: dif mating calls)
- Temporal isolation: reproduction in different species takes place at different times of year
- Mechanical isolation: results from anatomical differences that prevent successful exchange of gametes
- Gametic isolation: mating between individuals of different species may take place, but the gametes do not form zygotes
List and describe the three types of postzygotic reproductive isolating mechanisms. (table 26.1)
- Hybrid inviability: incompatibility between the genomes of the two species prevents the hybrid zygote from developing. (ex: gamete forms but resulting embryos never complete development)
- Hybrid sterility: hybrid embryos complete development but are sterile, so that genes are not passed between the two parental species. (ex: donkeys and horses make mules but mules are sterile)
- Hybrid breakdown: species are able to mate and produce viable and fertile F1 progeny but further crossing of the hybrids produces enviable or sterile offspring
Define speciation
the process by which new species arise. It comes through the evolution of reproductive isolating mechanisms
List and define the two principal modes of speciation (fig 26.5, 26.10)
Allopatric speciation: occurs when a geographic barrier splits the population into two groups and blocks the exchange of genes between them
Sympatric speciation: speciation that arises in the absence of any external barrier to gene flow, reproductive isolating mechanisms evolve within a single population
What is phylogeny, phylogenetic tree, branches, nodes, rooted, and gene tree
Phylogeny: evolutionary relationships among a group of organisms
Phylogenetic tree: a graphical representation of phylogeny
Branches: evolutionary connections between organisms
Nodes: points where the branches split, representing a common ancestor that existed before divergence took place
Rooted: A tree is rooted when one node represents a common ancestor to all other nodes on the tree
Gene tree: shows evolutionary relationship among prolactin and somatropin genes in vertebrates (evolutionary relationship among a group of genes)
cancer cells _____ respond to normal cell cylce controls
they do what to healthy tissues
They do not respond to normal cell cycle controls
They rob healthy tissues of nutrients
Define tumor
distinct mass of abnormal cells.
Define benign
When the tumor cells remain localized
Define malignant
When the tumor cells invade other tissues
Define metastasis.
When the tumor cells have traveled to other sites in the body and established secondary tumors.
explain why cancer can be described as both a genetic disease and not a genetic disease
- Genetic disease: cancer cells arise from defects of DNA
- Not genetic disease: if cancer is inherited, every cell in body should have the cancer-causing gene
and every cell should become cancerous; however, tumors typically appear only in certain tissues - Not a genetic disease: many cancers do not run in families
- Not a genetic disease: huge environmental influence
Explain Knudsen’s “two-hit hypothesis” as it applies to retinoblastoma (fig 23.3)
Suggests that cancer is the result of a multi-step process that requires several mutations. If one or more of the required mutations are inherited, fewer additional mutations are required to produce cancer and the cancer tends to run in families.
In retinoblastoma, only two mutations are necessary to cause the tumor. In the case of retinoblastoma, the two required mutations occur at the same locus, but mutations at different loci are required for the development of many other cancers.
explain the concept of clonal evolution of tumor cells (fig 23.4)
- as cells acquire more mutations, they become the dominant cell type within the tumor
- examples of these mutations:
- DNA repair pathway
- chromosome segregation (many cancer cells are aneuploids)
- structural change that allows cell to invade other tissues
what is the role of environmental factors in cancer
- Chemical mutagens and radiation can mutate genes that predispose a cell to cancer (we talked
about how these environmental factors cause mutations in Ch 18) - Environmental factors can interact with genetic predispositions to cancer; ie some people carry a
genetic variant of a gene that predisposes them to lung cancer, so smoking would further increase
the chance for these people to develop lung cancer
What are some of the many different types of genes that contribute to cancer when mutated?
- Oncogenes and tumor-suppressor genes
- Genes that control the cell cycle
- DNA repair genes
- Telomerase
- Genes that promote vascularization and tumor spread
- miRNAs
Define proto-oncogenes
Normal cellular genes are called proto-oncogenes. They are responsible for basic cellular function or normal cells, but when mutated, they become oncogenes that contribute to the development of cancer.
Define oncogenes
proto-oncogenes that have been mutated that contribute to the development of cancer
Define tumor-suppressor genes
Genes that inhibit cancer and are recessive. Both alleles must be mutated before the inhibition of cell division is removed. Because the failure of their function promotes cell proliferation, tumor suppressor genes cannot be identified by adding them to cells and looking for cancer.
Defects in both copies of a tumor suppressor gene are usually required to cause cancer.
The cell cylce needs ______ and _______ signals to function properly
the cell cycle needs stimulatory (proto-oncogenes) and inhibitory (tumor-suppressor genes) signals to function properly
What is the relationship between mutant DNA repair pathway genes and mutant proto-oncognees/tumor suppressor genes.
Car has accelerator (proto-oncogene) and brake (tumor-suppressor gene). The car will be uncontrollable if the accelerator becomes hyperactive or if the brake does not work. A bad mechanic (defective DNA repair pathway) would not be able to fix the accelerator/brake
Understand how genes that control the cell cycle can play a role in cancer. (fig 23.8 and 23.9)
- cyclins and CDKs are proteins that regulate checkpoints of the cell cycle; mutations in the genes that encode these proteins can cause the disruptions in normal cell cycle control, leading to cancer
- external signals (hormones and growth factors) trigger a cascade of intracellular reactions that ultimately stimulate/inhibit cell cycle (signal transduction pathway); a mutation in genes that play a role in any of these reactions can lead to cancer
Explain how telomerase is related to cancer
Activation of the enzyme telomerase can contribute to the progression of cancer.
Telomerase becomes shorter with each cell division. The shortening eventually leads to the destruction of the chromosomes and cell death.
In many tumor cells, sequences that regulate the expression of the telomerase gene are mutated, allowing the enzyme to be expressed and the cell is capable of unlimited cell division. This allows cancer cells to divide indefinitely.
Explain how mutant genes that promote vascularization and tumor spread can lead to cancer.
Oxygen and nutrients are essential to the survival and growth of tumors are supplied by blood vessels, and the growth of new blood vessels (angiogenesis) is important to tumor progression.
In tumor cells, genes encoding these proteins are often overexpressed compared with normal cells and inhibitors of angiogenesis-promoting factors may be inactive or under-expressed.
How can mutant miRNAs lead to cancer?
miRNAs are important in controlling gene expression and development. Many tumor cells exhibit widespread reduction in the expression of many miRNAs
Lowered levels of miRNAs may contribute to cancer by allowing oncogenes that are normally controlled by the miRNAs to be expressed at high levels.
Overexpression of miRNAs can also be associated with cancer. Several miRNAs have been implicated in the process of metastasis
Describe how epigenetic changes are associated with cancer
- hypomethylation may activate oncogenes
- hypermethylation may silence tumor-suppressor genes
many cancers arise through the _____ of a number of genes
many cancers arise through the sequential mutation of a number of genes. An example of this is seen with colon cancer (Fig 23.10—don’t memorize this figure)
many cancer cells have __________ mutations. Are these mutations a cause or effect of cancer (fig 23.13)
Many cancer cells have chromosomal mutations.
- Cause: some cancers are associated with specific chromosome mutations
- Effect: most cancer cells have chromosomal mutations that result from the cancer
List three types of chromosomal mutations that are associated with cancer
- Deletion of tumor-suppressor gene
- Inversions
- Translocations
Describe how inversions and translocations are associated with cancer.
- Both of these require breaks within the chromosome. Cancer may result if the breakpoints lie within a tumor-suppressor gene, which would mutate the tumor-suppressor gene
- Both of these can rearrange the chromosome and may bring together sequences that stimulate
cancer
- For example, the rearrangement may place a cancer-causing gene under a different regulatory sequence that would upregulate its expression (Fig 23.11 and 23.12 give
examples but don’t memorize these)
Describe how viruses are associated with cancer.
- Most cancer-causing viruses are retroviruses but some are also DNA viruses
Describe how retroviruses can cause cancer (fig 23.14)
Two different ways: mutating or rearranging proto-oncogenes or by inserting strong promoters near proto-oncogenes
Mutating or rearranging proto-oncogenes:
1. A retrovirus inserts its RNA into the cell. The viral RNA undergoes reverse transcription and inserts into the host chromosome next to a proto-oncogene.
2. When the virus reproduces, the proto-oncogene is incorporated into the virus.
3. After repeated rounds of viral infection and reproduction, the proto-oncogene becomes rearranged or mutated or both, producing an oncogene that is inserted back into the host chromosome.
Inserting strong promoters near proto-oncogenes
Retrovirus infects the cell and the provirus inserts near a proto-oncogene. The strong viral promoter stimulates overexpression of the proto oncogene.
Briefly describe the three models of semiconservative replication.
- Theta model: common in bacteria (fig 12.4)
- Rolling circle model: some viruses and bacteria (12.5)
- Linear model: eukaryotic chromosomes (fig 12.6)
Define dNTP (fig 12.7a)
New DNA is synthesized from deoxyribonucleicoside triphosphates (dNTPs)
List the four substrates required for DNA replication.
dATP
dTTP
dGTP
dCTP
Explain how dNTPs are added to a growing DNA chain. (fig 12.7b)
- In replication, the 3’-OH group of the last nucleotide on the strand attacks the 5’-phosphate group of the incoming dNTP.
- Two phosphates are cleaved off.
- Phosphodiester bond forms between the two nucleotides.
What is the direction of DNA synthesis?
Nucleotides added to 3’-OH of growing chain; so chain grows in a 5’ to 3’ direction.
Template strand is read in a 3’ to 5’ direction because it is antiparallel to the new strand.
Explain how 5’ to 3’ replication can occur simultaneously on 2 antiparallel strands. (fig 12.8, 12.9)
- Because two template strands are antiparallel, and DNA synthesis is always 5’ to 3’. DNA synthesis proceeds from right to left on one strand and from the left to right on the other strand.
- On the lower template strand, DNA synthesis proceeds continuously in the 5’ to 3’ direction (the same way it is unwinding) - On the upper template strand, DNA synthesis begins at the fork and proceeds in the direction opposite of unwinding, so it soon runs out of template. DNA synthesis starts again at the fork on the upper strand, each time proceeding away from the fork. DNA synthesis on this strand is discontinuous
Explain in detail how replication occurs in bacteria.
1) initiation (Fig 12.11)
2) unwinding (Fig 12.12)
– Helicase
– SSBs
– Gyrase (topoisomerase)
3) elongation (Fig 12.13, 12.14)
- DNA polymerase: requires 3’ OH in order to add a nucleotide
- DNA polymerases in bacteria:
- *DNA Polymerase III - synthesizes DNA from primers:
*- 5’→ 3’ polymerase activity (DNA synthesis),
*- 3’→ 5’ exonuclease activity (proofreading),
- High processivity: can add many nucleotides,
- DNA Polymerase I - removes and replaces primers:
*- 5’ → 3’ polymerase activity,
*- 3’ → 5’ exonuclease activity,
*- 5’ → 3’ exonuclease activity (remove primers),
*- DNA Polymerase II, IV, V - DNA repair
- Primase: creates primer (RNA) to initiate DNA synthesis
- Primase = RNA polymerase; does not require 3’ OH
- Ligase
4) termination
- Usually occurs when replication forks run into each other
State telomerase present in germ cells, somatic cells and cancer cells?
telomerase is present in single-celled eukaryotes, germ cells, early ebryonic cells, and certain proliferative somatice cells, all of which must undergo continuous cell division
Most somatic cells have little or no telomerase activity; these cells are capable of only a limited number of cell divisions
Telomerase appears to play a role in cancer. cancer cells have the capactiy to divide indefiniely and telomerase is expressed in 90% of all cancers
Explain how the telomeres are replicated with the help of telomerase. (fig 12.18)
- The telomere has a protruding end with a G-rich repeated sequence
- The RNA part of telomerase is complementary to the G-rich strand aand it pairs with it, providing a template for the synthesis of copies of teh repeats
- nucleotides are aded to the 3’ end of teh G-rich strand
- After several nucleotides have been added, the RNA template moves along the DNA
- more nucloeitdes are added
- the telomerase is removed
- synthesis takes place on the complementary strand, filling the gap due to the removal of the RNA primer at the end
