BSCI222 Exam 2

what is the molecular basis of chromosomes in both prokaryotes and eukaryotes?

double stranded DNA made of nucleotide sequences of A T C and G

what is the physical conformation of the DNA double helix in both prokaryotes and eukaryotes?

B-DNA which is the normal right handed helix

how do both prokaryotes and eukaryotes fit massive amounts of DNA into small cellular spaces?

both use proteins to wind up DNA and employ topoisomerase enzymes to create compact supercoiling

what is supercoiling in DNA?

overwinding or under winding of the DNA double helix creating strain and compacting the molecule

what are topoisomerase enzymes?

enzymes that mediate supercoiling of DNA

what is the structure of prokaryotic chromosomes?

singular circular chromosomes

what is the structure of eukaryotic chromosomes?

multiple linear chromosomes

what specific proteins organize DNA in prokaryotes?

nucleoid associated proteins aka NAPs to anchor DNA in loops

what specific proteins organize DNA in eukaryotes?

histones to wrap DNA intro structures called nucleosomes

do prokaryotes or eukaryotes have more DNA?

eukaryotes bc they contain 10 million to 100 billion base pairs

where are chromosomes found in the cell for prokaryotes?

within the cytoplasm in the nucleoid

where are chromosomes found in the cell for eukaryotes?

in the nucleus

which chromosome type contains centromeres and telomeres?

eukaryotic chromosomes

what are centromeres?

large span of heterochromatin

why are centromeres important?

they connect sister chromatids and serve as attachment points for spindle microtubules after DNA replication

what are telomeres and why are they important?

repetitive sequences at ends of DNA to protect them from shortening

what are plasmids?

DNA molecules that replicate independently of the main chromosome

where are plasmids found?

in prokaryotes

how many origins of replication do prokaryotic chromosomes have?

a single origin

how many origins of replication do eukaryotic chromosomes have?

multiple origins per chromosome

what is the function of histones in eukaryotic cells?

bind to DNA to help keep it compacted, organized, and to regulate gene expression

why do histones have a strong attraction to DNA molecules?

they are rich in amino acids arginine and lysine which give them a net positive charge and attracts the negative charges on the DNA phosphate backbone

how many histone proteins are there?

8

what are the major histone proteins?

H2A, H2B, H3, and H4

what is a nucleosome?

fundamental unit of chromatin

how are nucleosomes structured?

about 200 base pairs of DNA coiled around a core of 8 histone proteins

what does histone H1 do for nucleosomes?

acts as a lock to anchor the DNA onto the nucleosome core

what is euchromatin?

decondensed genetic information that is available for transcription aka genetically active

what is heterochromatin?

highly condensed genetic information that is not transcribed aka genetically inactive

is euchromatin involved in crossing over?

yes

is heterochromatin involved in crossing over?

no

what are the two types of heterochromatin?

constitutive and facultative

what is constitutive heterochromatin?

permanently compacted genetic information that is inactive aka centromeres and telomeres

what is facultative heterochromatin?

developmentally regulated meaning it can be condensed or relaxed depending on cells needs aka barr bodies

what is histone methylation?

reduces overall charge on nucleosome, condensing nucleosomes together through hydrophobic forces

what does histone methylation result in?

prevents transcription

what is histone acetylation?

reduces positive charge on histone tails and loosens their interaction with DNA

what does histone acetylation result in?

allows transcription by making genes more accessible

what is histone deacetylation?

removal of acetyl groups causing histone tails to regain their positive charge and leads to stronger interaction with DNA

what does histone deacetylation result in?

prevents transcription

what is a telocentric centromere?

joins chromatids at tips

what is a acrocentric centromere?

joins chromatids near tips

what is a submetacentric centromere?

joins chromatids near center

what is a metacentric centromere?

joins chromatids at center making them arms symmetrical

what does the position of centromeres influence?

rate of crossing over during meiosis

what are telomeres?

sequence repeats on ends of linear chromosomes

what is the structure of telomeres?

has a G rich 3’ overhang that binds proteins and protects ends of chromosomes

why are telomeres referred to as a “buffer” for DNA replication?

chromosomes shorten with each round of replication so the telomeres ensure that genetic info is not lost during the process

what enzyme is responsible for maintaining and lengthening telomeres?

telomerase enzyme

in what specific context does telomere lengthening occur?

in gametic cells

what is linkage?

genes that are physically close together in the same chromosome and do not segregate independently

what is the rate of recombination for linked genes?

low

what does recombination frequency indicate?

rate of recombination is proportional to the distance btwn genes on a chromosome

what is a linkage group?

cluster of genes aka loci that are located on the same chromosome

what are the expected phenotypic results for unlinked genes in a dihybrid F2 generation (F1 self fertilized) cross?

9;3;3;1 due to independent assortment

what are the expected phenotypic results for linked genes in a dihybrid F2 generation (F1 self fertilized) cross?

parental phenotypes appear in excess and recombinant phenotypes are fewer than expected

what are the expected results for unlinked genes in a dihybrid test cross (AaBb x aabb)?

a 1:1:1:1 ratio is expected resulting in 50% parental and 50% recombinant genotypes

what are the expected results for linked genes in a dihybrid test cross (AaBb x aabb)?

parental phenotypes will be in excess so more than 50% and recombinant phenotypes will be less than 50%

how are linked genes identified and analyzed in a trihybrid test cross?

the two most common phenotypes among the offspring are the non recombinants aka parental types and the two least common will be the double cross over progeny

what is the rate of recombination proportional to?

the physical distance btwn genes on a chromosome

how does physical distance btwn genes affect the expectation of linkage?

genes that are very far aka more than 50 cM on the same chromosome cannot be distinguished from genes on different chromosomes and are considered effectively unlinked

what is the physical process of crossing over during meiosis?

when homologous chromatids exchanged pieces of DNA which results in the recombination of linked alleles

what is a coupling arrangement?

aka cis configuration meaning that dominant alleles are linked on one chromosome and the recessive alleles on the other (AB - ab)

what is a repulsion arrangement?

aka trans configuration meaning that each chromosome carries one dominant and one recessive allele (Ab - aB)

how do you predict the gametes for a double heterozygote in coupling (AB - ab) after a single cross over?

parental games will be AB ab and recombinant gametes produced will Ab and aB

what are the consequences of a double crossover in a three point test cross?

double crossovers are the least common phenotypes bc it would require two rare events to happen

why do double crossovers often lead to an underestimation of map distances?

if two crossovers happen btwn two far genes, the second crossover can switch the alleles back to their original parental arrangement making the recombination undetectable

what is the maximum expected frequency of recombinant offspring in any cross?

50%

why is the maximum frequency of recombinant offspring 50%?

bc if they’re on different chromosomes or far apart on the same chromosome then they follow independent assortment

what is interference in the context of crossovers?

when one crossover event inhibits a second crossover from happening in the same chromosomal region

what is the coefficient of coincidence?

the ratio of observed to expected double crossovers

what happens if the interference number is high?

there will be fewer double crossovers

what is the formula for interference?

1 - coefficient of coincidence

what happens during a double crossover btwn three genes?

outer genes stay the same and only middle gene switches

what is the null hypothesis in a chi-square test for genetic crosses?

observed data fits expected ratios

what does it mean to reject the null hypothesis?

the observed results are significantly DIFFERENT from expected data

if the null hypothesis is accepted, what does that mean in terms of linkage?

genes assorted independently and genes are not linked

if the null hypothesis is rejected, what does that mean in terms of linkage?

genes may be linked

what is the formula for chi square test?

(O-E)²/E

how to calculate expected values?

total offspring divided by amount of categories in ratio

how to find degrees of freedom (df)?

number of categories - 1

what is the typical significance value used?

0.05

if x² is greater than critical value, what happens?

reject null hypothesis aka genes are linked

if x² is less than critical value, what happens?

fail to reject null hypothesis aka genes are not linked

how to calculate linkage distance in dihybrid cross?

recombinants divided by total offspring times 100

how to calculate linkage distance in trihybrid cross?

single plus double crossovers divided by total offspring times 100

how do you find the middle gene in gene order?

the gene that flips is in the middle

when does DNA replication occur in the cell cycle?

during the S phase aka synthesis phase and before mitosis occurs

what is semi conservative synthesis in DNA replication?

when the DNA double helix unwinds at the origin of replication to serve as single stranded templates for the creation of new DNA

what is the outcome of semi conservative synthesis in DNA replication?

two DNA molecules are produced each consisting of one original parental strand and one newly synthesized daughter strand

what is a replicon?

unit of DNA that is replicated from a single origin of replication

what is the primary function of the origin of replication?

where the DNA double helix unwinds to create a replication bubble with two forks allowing for the synthesis of new daughter strands

how many replicons do prokaryotic cells have?

one single replicon

how many replicons does a eukaryotic cell have?

multiple replicons per chromosome

what is the direction of DNA synthesis?

5’ to 3’

what initiates replication at the prokaryotic region?

DnaA initiator proteins bind to DnaA boxes to trigger strand separation at AT-rich DNA unwinding elements aka DUEs

what initiates DNA replication in eukaryotes?

origin recognition complex aka ORC proteins recruit helicase at the origin of replication

why do eukaryotes require to have thousand of replicons?

bc they are linear and larger so they require multiple origins of replication

how to draw a replication bubble?

two horizontal lines in from of an oval bubble and mark the origin of replication in the middle