first half Flashcards
What are the characteristics of eukaryotes
- Genome larger and linear
- much more complex
- DNA in nucleus
What are the characteristics of prokaryotes
- Genome small and circular
- DNA in cytoplasm
- No defined nucleus
What is the cell cycle? Characteristics? Stages?
- 24hr cycle → most of time spent in interphase preparing for mitosis; only a few hrs spent in mitosis
- G 1 phase → growth,prepare cells for cytokinesis and mitosis
- s phase (synthesis)→DNA replication
- g2 phase → preparation for mitosis
- M phase (mitosis) →chromosomal separation and cytokinesis
- interphase → time between mitosises
- Go→ cells can exit the cell cycles enter a quiescent state
What is a diploid cell
A cell than has 2 complete sets of chromosomes → one from mother and one from father
What is a haploid
A cell with one complete set of chromosomes
What occurs during prophase (mitosis)
- Chromosomes condense
- Centrosomes radiate micro-tubules and migrate to opposites
What are kinetochores
attach to the centromeres of the chromosomes and the microtubule spindles to split the sister chromatids
What occurs during metaphase (mitosis)
the chromosomes line up in the centre of the cell
What occurs during anaphase (mitosis)
The chromatids are separated and pulled to opposite poles by the microtubule spindles
What occurs during telophase (mitosis)
- the nuclear envelope begins to reform
- the chromosomes decondense
What occurs during cytokinesis (mitosis)
- a contractile ring constricts to separate the daughter cells
- reforming of the nucleus
why is it important to regulate the cell cycle
- uncontrolled and contact cell divisions is dangerous and can lead to cancer
- controlled by proteins and enzymes that also appear and disappear in cycles
how do cyclins regulate the cell cycle
- cyclins bind to and activate CDK (cyclin-dependant kinases)
- cyclin-CDK complexes phosphorylate target proteins that promote cell division
which CDK helps at each stage
- G1/S cyclin-CDK occurs in G1 phases and helps prepare for DNA replication
- S cyclin-CDK occurs in S phase and helps initiate DNA synthesis
- M cyclin-CDK occurs in M phase and helps prepare for mitosis
what are cell-cycle checkpoints
places where cells pause within the cell cycle is something is not correct before they progress to the next stage
where is the DNA replication checkpoint? what does it check for?
- the end of G2
- checks for the presence of unreplicated DNA
Where is the DNA damage checkpoint? what does it check for?
- before the cell enters S phase/end of G1
- checks for damaged DNA ( damaged DNA will cause mutated cells)
Where is the spindle assembly checkpoint? what does it check for?
- beginning of mitosis
- checks for all chromosomes being attached to the spindle
what results from mitosis
2 diploid daughter cells that are identical
what results from meiosis
4 haploid daughter cells that are each genetically unique
what occurs during prophase I (meiosis)
- chromosomes condense and undergo synapsis (gene-for-gene pairing)
- chromosomes forms a bivalent, each chromosome consists of 2 sister chromatids
- nuclear envelope begins to break down
what is cross over
when the chromatids of 2 non sister chromatids cross over and exchange genetic information with each other
what occurs during prometaphase I (meiosis)
the spindles attach to the kinetochores on the chromosomes
what occurs during metaphase I (meiosis)
the homologous Pairs line up in the centre of the cells
what occurs during anaphase I ( meiosis)
homologous chromosomes separate (sister chromatids do not)
what occurs during telophase I and cytokinesis
daughter cells form and prepare to move to prophase II
What is Meiosis II? what occurs that is different than mitosis?
- the second half of the meiosis process, VERY similar to mitosis
- the daughter cells produced only contain 1/2 the DNA
What is nondisjunction
The failure of a pair of chromosomes to separate during anaphase of cell division
What results from a disjunction
one daughter cell receives an extra copy of that chromosome and the other daughter cell receives no cope of the chromosome
What were the benefits of mendels experiments
- The pea’s were tightly inbred
- The structure promotes self-fertilization
- The traits could be studies one at a time
- peas grow rapidly, which allow him to complete an entire generation in a growing season
What is a gene
a inherited factor that helps determine a characteristic
What is an allele
one of 2+ alternate 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
a individual organism possessing 2 of the same alleles at a locus
what is a heterozygote
an individual organism possessing 2 different alleles at a locus
what is a phenotype
the appearance or manifestation of a genotype
what is a monohybrid cross
crosses between 2 parents that differed in a single characteristic
what is the principle of segregation
each individual diploid organism possesses 2 alleles for any particuar characteristic
what is the concept of dominance
when 2 different alleles are present in a genotype, only one characteristic will appear in the phenotype
multiplicative rule
the probability that 2 events occur together is the product of their individual probabilities of occurrence
additive rule
the probability that a least one of multiple events occur is the sum of their individual probabilities
conditional probability
additional information that modifies the conditional probability
what is the binomial expansion
(p+q)^n
calculates the probability of the events occurring together.
p is the probability of one event
q is the probability of the other event
n is the number of times the event occurs
what is a test cross
one individual of unknown genotype is crossed with another individual with a homozygous recessive genotype
reveals the genotype of the first individual
when it is preformed, any recessive allele in the unknown genotype will be expressed in the progeny
What are dihybrid crosses
crossed varieties that differ in 2 characteristics
principle of independent assortment
alleles at different loci separate independently of one another
an extension of the principle of the segregation
applies to characteristics encoded by loci located on different chromosomes
the arrangement of different tetrads is random and all combinations are equally likely
what are the challenges of human genetics
- humans have a long generation time, about 20 years in humans
- controlled matings are not possible
- human family size is generally small
what is a pedigree
a pictorial representation of a family history, outlines the inheritance of one or more characteristics
analysis of a pedigree
mendelian ratios are impossible to discern in a single pedigree
certain patterns may exclude the possibility of a particular mode of inheritance
what are autosomal recessive traits
- normally appear with equal frequency in men and women
- appears only when a person inherits 2 alleles of a trait
- is a trait is uncommon then most parents are heterozygous and unaffected
- seems to skip generations
what is consanguinity
mating between relatives
what are autosomal dominant traits
- appear in both sexes equally
- both sexes are capable of transmitting the diseases equally
- do not skip generations
what are X-linked recessive traits
- have a distinctive pattern if inheritance
- traits appear more frequently in males, males only need to inherit a single copy of the allele to display the trait
- affected males are usually born from unaffected mothers
- not passed from father to son
- all daughters of affected males will be carriers
what is a obligate carriers
- people with heterozygous genotypes can be definitively determined from the pedigree
what are X-linked dominant traits
- appear in both males and females, appear more frequently in females
- do not skip generations
- affected men pass the trait to all their daughters and none of their sons
- affected women pass the trait to about half their sones and half their daughters
what are Y-linked traits
- easily recognized patterns of inheritance
- only males are effected, its passed from father to son
- if a male is affected than all male offspring will be affected
- do not skip generations
- neither dominant or recessive
what is the chromosome segregation in sex chromosomes
MALES; segregation of the X chromosome from the Y chromosome, resulting in half the sperm with X chromosome and half the sperm with Y chromosome
FEMALES; each egg contains a X chromosome
what is criss cross inheritance
- X chromosome present in the male in once generation mush be transferred to the female in the next generation, which can then be transferred back to the male
- X chromosomes alternate between the sexes in successive generations
what is a nucleotide
- subunit of DNA
- composed of a phosphate group, a five-carbon sugar and 1/4 cyclic nitrogenous bases
what are the 4 nitrogenous bases in DNA
adenosine, guanosine, thymidine, cytidine
what is the structure of a polynucleotide chain
- 3’ to 5’ phosphodiester bonds
- polarity has a direction of 5’-to-3’
- 5’ end has a free phosphate group
- 3’ end has a free hydroxyl group
what is the structure of a double helix
- the strands are antiparallel
- most commonly a right-handed double helix
- hydrogen bonging between the bases
- hydrophobic interactions between the “stacked” bases
- opposite strands are complementary
- A double bonded to T
- G triple bonded to C
what is B form DNA
- most common DNA
- right-handed double helix
- major groove and minor groove
- every turn has 10 nucleotides
What is A form DNA
- compacted right-hand double helix
- every turn has 11 nucleotides
What is Z form DNA
- most uncommon, most unknown
- left-hand double helix
what is the first level of DNA condensation
- packing the DNA into nucleosomes
- the highly positive histones are wrapped in highly negative DNA strands
- wrapped around a core of 8 histone proteins (2 each of H2A,H2B,H3,H4)
- anchored by a H1 histone
- 10nm fibre
what is the second level of DNA condensation
- additional folding/supercoiling
- becomes a 30nm fibre
what is the third level of DNA condensation
- condenses even further
- attachment of the 30nm fibre at many places
- becomes a 300nm fibre
what function do telomeres serve
- protect the end of chromosomes
- resist degration
- prevent fusion
- facilitate replication
what is the composition of RNA
- a phosphate group, a ribose sugar, and 1/4 nitrogenous bases
what is a nucleoside
- a covalent bond between a nitrogenous base and the 1’-carbon atom from the sugar
what is a phosphodiester linkage
- the bonds that connect nucleotides
- strong covalent bonds
What is topoisomerase II
- breaks the double-helix, rotates the ends and seals the break
what are supercoils
- the DNA coils in on itself
- allows all the base pairs to form
- under-winding supercoils; result from under-winding the DNA, negative supercoils, most common
overwinding supercoils; result from overwinding the DNA, positive supercoils
what is a nucleoid
- the supercoils of DNA form a structure with multiple loops
- bound together by proteins
What is chromatin
- complex of DNA and proteins
- not random; has a fundamental repeating structure
What are the 2 types of chromatin
- euchromatin; undergoes the normal processes of condensation and decondensation, majority of chromosomal material, where most transcription takes place
- heterochromatin; remains in a highly condensed state throughout the entire cell cycle, permanent heterochromatin at the centromeres and the telomeres, can occur for periods of time during development stages, lack of transcription, absence of crossing over and late replication
What are histones
- positively charged proteins
- 5 major types; H1,H2,H2B,H3 and H4
- attract the negative charges on the phosphates
- H1 is not part of the histone core, binds to the DNA where it joins and leaves the octamer, lock the DNA in place
what are nonhistone chromosomal proteins
- varient histones
- amino acid groups are incorporated into the chromatin structure instead of one of the major histones
- changes chromatin structure and function
What is a nucleosome
- simplest level of chromatin structure
- a core particle consisting of DNA wrapped around 8 histone proteins
- positively charges amino acids on the histones interact with the negative charges on the phosphates of DNA
What is linker DNA
- varies in size
- seperates nucleosomes
- associated with nonhistone chromosomal DNA
How does archaea differ in histones
- does not have histone proteins
- instead has its own histones that are similar to H3 and H4
- in groups of 4; tetramer
What is the higher order chromatin structure
-nucleosomes continue to fold on themselves in order to form denser, more tightly packed structures
What are topically associated domains (TADs)
- large regions of chromatin from spatially interacting regions
- within a TAD the chromatin is tightly packed and interacts with each other
- the TADs are far enough however that they do not interact with each other
What are polytene chromosomes
- giant chromosomes
- occurs when DNA replication occurs without cell division, results in thousands of copies of DNA lined up
What are chromosome puffs
- localized swelling of a region of the chromosome
- the region where active DNA transcription is occurring
- occurs partly due to the histones loosing their grip on the surrounding DNA
What is acetylation
- an enzyme called acetyltransferases attach acetyl groups to lysine amino acids that are on the histone tails
- reduces the positive charges and destabilizes the nucleosome structure
- histones hold the DNA less tightly
What are epigenetic changes
- stable iterations of chromatin structure that may be passed on to descendant cells or individuals
- changes that do not alter the DNA sequence
What is the centromere
- a constricted region of the chromosome that is the attachment site for kinetochore and for spindle microtubules
- necessary for proper chromosome movement in mitosis and meiosis
- span hundreds of thousands of base pairs
- made of heterochromatin
- no specific sequence makes up a centromere; most centromeres are defined by the chromatin structure and not the DNA sequence
what is CENP-A
- a variant histone protein present in the nucleosomes of centromere which takes the place of the H3 histone
- necessary for the assembly of proteins associated with the kinetochore
- alters the nucleosome and chromatin structure which allows the kinetochore proteins to bind and spindle microtubules to attach
What are telomeres
- the natural ends of a chromosome
- serve as caps to stabilize chromosomes and prevent them from degradation
- in somatic cells, they shorten with each round of cell division
what are telometric sequences
- consist of repeating units of a series of adenine or thymine
- always oriented with a string of Gs and Cs at the end of a chromosome
- proteins bind to the sting of Gs in order to protect the telomeres from degradation and prevent the chromosome ends from sticking together
What are shelterin
- binds to telomeres and protects the ends of the DNA from being repaired
What is telomerase
- an enzyme that lengthens the telomeres
prevents chromosome shortening
What are ribozymes
- catalytic RNA molecules that can cut out part of their own sequences, connect some RNA together, replicate others and catalyze the formation of peptide bonds between amino acids
what is RNA involved in
- many biological processes
- transcription, replication, RNA processing and translation
What is RNA
- polymer of nucleotides
- containing a sugar, a phosphate group and a nitrogenous base
- joined by phosphodiester bonds
- contain ribose sugars which contain a free hydroxyl group on the 2’-carbon
- less stable than DNA
- contains pyrimidine in replacement of thymine
- consists of a single polynucleotide strand
What is the secondary structure of RNA
- short, complementary regions within the strand pair and form secondary structure
- called hairpins
- paired regions are antiparallel
- determined by the base sequence of the nucleotide strand
- different RNA strands form different structures
- structure determines function
What is ribosomal RNA (rRNA)
- makes up the ribosome
- site of protein assembly
What is messenger RNA (mRNA)
- carries the coding instructions for the polypeptide chain from the DNA to the ribosome
- specifies the sequence of the amino acids in a polypeptide chain
- provides a template for the joining of the amino acids
What is pre-messenger RNA (pre-mRNA)
- the immediate products of transcription
- modified extensively before they become mRNA
What is transfer RNA (tRNA)
- the link between the coding sequence of nucleotides in the mRNA and the amino acids
- incorporate the amino acids into the polypeptide chains
What is small nuclear RNAs (snRNAs)
- combine with small proteins to for small nuclear ribsomucleoproteins (snRNPs)
- participate in the processing of RNA, converting pre-mRNA to mRNA
What are microsRNAs and small interfering RNAs
- located in the cytoplasm
- carry out RNA interference
- trigger the degradation of mRNA
What are piwi-interacting RNAs
- have a role in suppressing the expression of transposable elements in reproductive cells
what is long noncoding RNAs
- does not code for proteins
- provide a variety of functions, including regulation of gene expression
What is CRISPR RNAs
- aid in the destruction of foreign DNA molecules
What is transcription
- cellular RNA is synthesized from DNA templates
- only parts of the DNA molecule are transcribed into RNA
- highly selective process
- individual genes are transcribed only when they are needed
- requires 3 major components; a DNA template, raw materials, and a transcription apparatus ( proteins necessary for catalyzing the synthesis of RNA)
What is the template for RNA synthesis
- a single strand of a DNA double helix
- takes place on only one of the 2 nucleotide strands
- the strand used it the template strand while the other is the contemplate strand
What occurs during RNA synthesis
- the RNA strand is complementary and antiparallel to the transcribing DNA strand
- has the same polarity and base sequence as the nontemplating strand other than the replacement of U for T
what is the transcription unit
- a stretch of DNA that encodes the RNA molecule and the sequences that are necessary for transcription
- includes 3 critical regions; the promoter, the RNA-coding regions and the terminator
What is the promoter
- a DNA sequence that the transcription apparatus recognizes and attaches to
- indicates which of the 2 DNA strands is the template strand
- determines the way that the DNA is read
- determines the transcription start cite
What is the RNA-coding regions
- a sequence of DNA nucleotides that is copied into an RNA molecule
What is a terminator
- a sequence of nucleotides that signals where transcription ends
- usually part of the RNA coding regions
What is ribonucleoside triphosphate
- RNA is synthesized from
- consisting of a ribose sugar and a base attached to 3 phosphate groups
- during DNA synthesis, nucleotides are added, 2 of the phosphate groups are then removed and the remaining one participates in a phosphodiester bond that connects it to the RNA molecule
What is RNA polymerase
- carries out all the required steps
- enhanced by a number of accessory proteins that join and leave the polymerase at different stages
What is core enzyme
- makes up most bacterial RNA polymerases
- 2 copies of alpha and a single copies of beta, beta prime and omega
- sigma bond controls the binding of the RNA polymerase to the promoter
What are the types of RNA polymerase
- RNA polymerase I; transcribes rRNA
- RNA polymerase II; transcribes pre-mRNAs, snoRNAs, miRNAs, and snRNAs
- RNA polymerase III; transcribes other small RNAs
- RNA polymerase IV; transcribes siRNAs
- RNA polymerase V; transcribes siRNAs
What is the underlying principle of the one gene, one enzyme hypothesis
- an auxotropthic mutant cannot from on a compound that comes before a step that is blocked my a mutation in the pathway
What is the one gene, one enzyme hypothesis
- genes function by encoding enzymes and each gene encodes a separate enzyme
- each step in the pathway is controlled by a different enzyme
- demonstrate that mutations affecting any one step aways occurred at the same chromosomal location
- mutations affecting a particular biochemical step occurred at a single locus that encoded a particular enzyme
What is a amino acid
- the building blocks of proteins
- composed of a central atom bonded to an amino group, a hydrogen atom, a carboxyl group and a R group that differs for each
- the R group helps to determine the chemical properties of each group
- joined by peptide bonds
What is a peptide bond
- join together to form amino acids
- join to create polypeptide chains
What is a polypeptide bond
- have polarity
- consist of a free amino group on one end and a free carboxyl group on the other end
What is the primary protein structure
- a sequence of amino acids
What is the secondary structure of proteins
- the interactions between neighbouring amino acids
- causes the polypeptide chain to fold and twist
- beta pleated sheets or alpha helix
What is the tertiary structure of proteins
- folding of the secondary structures
- creates a 3-D shape of the protein
What is the quaternary structure of proteins
- occurs in proteins that have 2 or more polypeptide chains that associate together
What is a codon
- the set of nucleotides that are read together to form a amino acid
- must contain a minimum if 3 nucleotides (triplet codons)
- formed by A,G,C and U
what are sense codons
- the 61 codons that actually code amino acids
What is degenerate
- multiple physical states that have equivalent meaning
- amino acids that are coded by multiple codons
What are synonymous codons
- codons that specify the same amino acids
What are isoaccepting tRNAs
- different tRNAs that accept the same amino acids but have different anticodons
What is a wobble in pairing
- flexibility in the pairing of the 3rd codon
- caused by the fact that some nonstandard pairings of bases can take place in the 3rd codon
what is the initiation codon
- the first codon of mRNA to specify an amino acid
- most often AUG
- it marks the beginning of translation but also codes an amino acid
what is a termination codon
- 3 codons that do not encode amino acids
- UAA,UAG and UGA
- signal the end of translation
What is a mutation
- an inherited change in the DNA sequence of genetic material
- descendants that inherit the change can be cells or organisms
- the source of all genetic variation
What are somatic mutations
- arise in somatic tissues
- do not produce gametes
- passed to the daughter cells when the somatic cell divides
- many have no obvious effect on the phenotype of the organism
- the function is usually taken over by the functioning cells around it or the mutant cell dies
What are germ-line mutations
- arise in cells that ultimately produce gametes
- can be passed to future generations, producing offspring that carry the mutation
- gene mutations vs chromosome mutations
What is a base substitution mutation
- the alteration of a single nucleotide
- transition; a purine is replaced by a different purine or a pyrimidine is replaced by another pyrimidine
- transversion; a purine is replaced by a pyrimidine or vice versa
What is a insertion or deletion mutation
- the addition or subtraction of one or more nucleotide pairs
What is a frameshift mutation
- changes in the reading frame
- alter all of the amino acids following the mutation
- can introduce premature stop codons
What are expanding nucleotide repeats
- the number of copies of a set of nucleotides increases
- most commonly caused by the CNG combination; N can be any codon
- stability and severity depends on the number of repetitions
What is a forward mutation
- a mutation that alters the wild-type phenotype
What is a reverse mutation
- changes a mutant phenotype back into the wild type
What is a silent mutation
- changes the codon to a synonymous codon
- some alter nucleotides that serve as binding sites for regulatory proteins or alter sequences that affect mRNA splicing
What is a neutral mutation
- a missense mutation that alters the amino aid but does not significantly change the function
- the amino acid is replaced by one that is chemically similar
What is a loss-of-function mutation
- complete or partial absence of normal protein function
- alters the structure of the protein so that it no longer works correctly or affects the transcription, translation and splicing
What is a gain-of-function mutation
- causes the cell to produce a protein or gene that causes a function that is not normally present
What is a conditional mutation
- mutations that are expressed only under certain conditions
What is a surpressor mutation
- a genetic change that hides the effect of another mutation
- occurs at a site distinct from the site of the original mutation
What is a intragenic suppressor mutation
- takes place in the same gene that contains the gene being suppressed
- may change another codon in the affected triplet in order to correct the change in coding
- may surprise a frameshift mutation
what is a intergeneric suppressor mutation
- occurs in a gene other than the one bearing the original mutation that it surpresses
- change the way that the mRNA is translated
What is a mutation rate
- the frequency with which a wild-type allele at a locus changes to a mutant allele
- expressed as the number of mutations per cell division, per gamete or per round of replication
- how often a mutation arises
What are the factors affecting mutation rate
- the frequency with which changes in the DNA take place
- the probability that when a alteration takes place, it will be repaired
- the probability that a mutation will be detected
What causes differences in mutation rates
- ability to repair mutations, unequal exposures to mutagens or biological differences in rates of spontaneous mutation
- fewer mutations occur in DNA sequences that are associated with nucleosomes
What is an adaptive mutation
- mutations that occur due to increased stress in the environment
What are spontaneous mutations
- result from both internal and external factors under normal conditions
What are induced mutations
- result from changes in environmental chemicals or radiation
What are tautomeric shifts
- primary cause of spontaneous replication errors
- positions of protons in the DNA bases change
What are mispairings
- mispairing between bases in DNA can arise through a wobble
What are incorporated errors
- a base substitution causes a mispaired base to be incorporated into a newly synthesized nucleotide chain
what is strand slippage
- occur when one nucleotide strand forms a small loop
- produces insertions and deletions from uneven crossover
What is depuration
- the loss of a purine base from a nucleotide
- common cause of spontaneous mutation
What is deamination
- the loss of a amino group from a base
What is a mutagen
any environmental agent the significantly increases the rate of mutation above the spontaneous rate
What are base analogs
- chemical structures similar to those of any of the 4 standard nitrogenous bases of DNA
- if any base analogs are present during replication, they may be incorporated into newly synthesized DNA
- mutations caused by base analogs can be reversed by treatment with the same or different analogs
What are alkylating agents
- chemicals that donate alkyl groups
- mutations cued by EMS can be reversed with more EMS
what is hydroxylamine
- a very specific base-modifying mutagen that adds a hydroxyl group to cytosine, converting it into hyroxylaminocytosine
- increases the frequency if a rare tautomer that pairs with adenine instead of guanine
What are oxidative radicals
- reactive forms of oxygen
- produced in the course of normal aerobic metabolism
- damage DNA and induce mutations
What are intercalating agents
- proflavin, acridine orange, ethidium bromide and dioxin
- produce mutations by sandwiching themselves between adjacent bases in DNA, distorting its 3-D shape
- causing single-nucleotide insertions and deletions in replication –> frequently produce frameshift mutations
- can reverse themselves
What is radiation mutations
- greatly increase mutation rates in all organisms
- dislodge electrons from the atoms that they encounter, changing stable molecules into free radicals and reactive ions; alter the structures of bases and break phosphodiester bonds
What are pyrimidine dimers
bulky lesions that distort the configuration of DNA and block replication
What is the SOS system
- a system that overcomes these blocks and allows replication to proceed even with pyrimidine dimers present
