Gentics Exam 1

Bacteriophages: viruses that specifically infect bacteria, proteins can be labeled w/ radioactive sulfur and DNA w/ radioactive phosphorus 

Nucleotide: comprised of a sugar base, and phosphate group 

DNA: double helix composed of two intertwined strands, each has a partially (directionality(, forms right-handed helix, antiparallel (strands go in opposite directions) 

↳ double-stranded DNA has complementary base pairing . (A→T , C→G)
↳ only have hydrogen bonds (No covalent), makes it so DNA can easily come apart 

↳ strands of original (parental) DNA separate to replicate

↳ each serves as a template strand to make a complimentary daughter strand through  A-T, G-C base pairing 

 ↳proteins are more complex, DNA is more simple 

For problems, be careful with whether you are starting with 3’ or 5’ strand 

The two strands in DNA are: complimentary 

DNA uses RNA as: an intermediate to generate proteins, DNA does NOT generate proteins directly, RNA pairs U with A 

Transcription: produces RNA from DNA templates, produces RNA molecules, reads 3’ to 5’, producing a transcribed 5’ to 3’ 

Translation: producers proteins from single stranded mRNA, takes place in ribosome (where all 3 forms of RNA work together) 

• Sequence of bases in the RNA code for the sequence of the amino acids in the polypeptide 

• mRNA is translated codon to codon by means of tRNA molecules, each having a different base sequence 

Ribosome: “scans” mRNA for start codon (AUG)

Messenger RNA (mRNA): carries genetic information from the DNA and is used for protein synthesis → modified and exported from nucleus for translation in ribosomes 

• Is translates in non-overlapping groups of 3 bases (codons) → each coding for a specific amino acid

• The coding sequence in mRNA specifies the amino acid of a polypeptide chain 

Ribosomal RNA (rRNA): major constituents for ribosomes

Transfer RNA (tRNA): 45 different ones total, carrying a particular amino acid for translation 

• Carries anticodons which are complementary to codons in the mRNA, other end of tRNA carries amino acid specified by the codons 

• Complementary base pair UAC first gets integrated in the genome, this consists of the amino acid methionine and as the chain of amino acids grown they become linked 

Key principle of central dogma: complementary base pairing, due to this, DNA sequence tells you the sequence of your RNA 

RNA: uses ribose as sugar, usually single-stranded but can form double-stranded structure, uses U instead of T, not deoxyribose as it has an oxygen in it 

Start codon: AUG *translation ONLY starts with this 

Stop codon: UGA, UAA, UAG

NOT all DNA codes for proteins, only a small amount of it which are called: genes = areas of DNA that encode for proteins 

Gene: a region of DNA containing genetic information, usually transcribed into RNA molecule that is processed and usually translated into proteins, these also code for enzymes 

Neurospora: easy to grow, haploid )only 1 set of chromosomes) , useful  for complementation tests 

mutation: change in a DNA sequence, can be generated by x-rays or by UV light 

Complementation: brings two mutant genes together in the same cell 

↳ when cell is non-mutant (behaves like wild type), then the mutations complete each other → different genes (this can create a functional copy of each of the 2 genes) 

↳ 

When cell is mutant and fails to compliment each other → mutations are on same gene 

↳  mutations can be in different gene and still not complement each other → this is when you have 2 copies of the SAME mutation 

ALternative definition of gene: set of mutant alleles that make up one complementation group, mutant phenotypes result when pair of mutant alleles fail to complement each other 

True breeding: only produces progeny like parent 

Phenotype: observable property of an organism caused by one or more mutations of a gene → alleles, mutations can also in some cases cause a change in genotype and not phenotype 

Genotype: the genetic constitution of an organism 

Polymerase chain reaction (PCR): followed by a gel electrophoresis, allowing to separate DNA fragments by size

• Allows you to amplify a specific region of a genome 

• One PCR generates billions of copies of a region 

• DNA is (-) charged 

• Smaller fragments of DNA travel farther down gel 

Transposable elements: DNA sequences capable of moving (transposition) from one location to another

• There needs to be a transposable region that fits the certain shape of these elements 

When amplifying a gene in a mutant: you are also amplifying the DNA from the transposable element , therefore amplifying more DNA , bigger DNA fragment = higher on gel 

• A band for a mutant fragment is HIGHER than normal 

Law of segregationL when reproducing 2 alleles from each gene, separate so you can only inherit 1 allele from each parent 

Testcross: a cross between an organism of dominant phenotype (genotype unknown) and an organism of recessive genotype 

Law of independent assortment (law of reassortment) : alleles of different genes segregate independent of one another during gametogenesis and are distributed independently of one another in the next generation 

Linked genes:  genes on same chromosome, independent assortment may not happens as genes are on same chromosome and super close to each other 

Complete linkage: when genes are too close to each other and cant be independently assorted 

Incomplete dominance: phenotype of heterozygous genotype is between the two genotypes, ex. red+white = pink

Codominance: heterozygous genotype exhibits both traits associated with both homozygous genotypes, ex. Red+white = mixture of red and white (not pink), more frequent in molecular traits like blood 

epistasis: a phenotype can be hidden by mutations, there can be a dihybrid cross in which a mutation can block phenotype of another, only type of gene interaction that results in F2 dihybrid ratio of 9:3:3:1 being modified into some other ration, one gene is masking the expression of another 

In a dihybrid cross, this ratio indicates independent assortment: 9:3:3:1

Variable expressivity: genes that are expressed to different degrees in different organisms 

Penetrance: proportion of organisms whose phenotype matches genotype for a given train 

• A genotype that is always expressed has a penetrance of 100% 

Mitosis: process of nuclear division ensuring that two daughter cells receive a diploid complement of chromosomes that are identical with the diploid complement of the parent cell

• Daughter cells are identical genetic copies 

• Usually accompanied by cytokinesis 

Cytokinesis: process in which cell divides itself to yield 2 daughter cells 

S-phase of mitosis: synthesis phase

• Genetic material is replicated (duplicated) 

• DNA/chromosomes replicate

• Creates duplicate amount of chromosomes/DNA (3x amount  per normal cell) 

Mitosis: distribution of DNA into 2 daughter cells 

•  PMATC (NOT interphase) 

Interphase: anything that is not mitosis  

Prophase: chromosomes condense, each chromosome is longitudinally double, consisting of 2 subunits called chromatids 

• Each chromosome pair is a result of duplication in S-phase 

• Chromosomes are held together by centromere (this can be in center or closer to one end) 

Chromosome: thread like structures made of protein and a single DNA molecule which carries genetic information 

• Located in nucleus of cells 

• Humans have 46 chromosomes → 23 pairs 

Diploid: cells containing 2 copies of the same chromosome pair (2 pairs) → 4 of the same chromatids total 

Metaphase: mitotic spindle forms (a bipolar structure  arching between centrosomes which contain microtubules) 

•  Spindle fibers attach to kinetochore 

• Chromosomes move toward center of cell until all kinetochores lie on an imaginary plate equidistant from spindle poles, this is called the metaphase plate 

Kinetochore: the region of the centromere on the chromosomes that the spindle fibers attach to, when 2 chromatids are attached = 1 chromosome 

Anaphase: centromeres divide longitudinally 

• 2 sister chromatids separate, moving toward opposite poles of a cell 

• Once chromatids separate, they are individual chromosomes 

Telophase: nuclear envelope forms over teh 2 divided groups of chromosomes

• Nucleoli form, spindle disappears 

• Chromosomes decondense until they are no longer visible as discrete entities 

• Two daughter nuclei assume typical interphase appearance 

• Cytokinesis → separation of cytoplasm 

G2 phase: after s-phase and before mitosis 

• Cells check that s-phase has properly replicated DNA 

• Check for DNA damage 

• If not properly replicated, won’t go into mitosis

G1 phase: after mitosis and before DNA replication starts again 

• Entering cell cycle is regulated by external growth factors 

• If growth factors aren’t present, cell stops at restriction point and enters G0

G0: quiescent stage 

• Cells in this stage are metabolically active and can stay in this for a while 

• Here they are not going through the cell cycle 

• Rather than arrest, still doing same normal functions of the cell, but isn’t actively dividing 

Growth factors: take cell out of G0 phase and back into synthesis phase 

• These are essential for wound healing 

Gametes: to generate gametes, number of chromosomes is divided in half → haploid

• One set of chromosomes 

• One member of each of the pairs 

• Haploid gametes unite in fertilization to produce diploid somatic cell

• Chromosomes are then in pairs again after fertilization, one maternal and one paternal copy 

Meiosis: process of creating gametes, takes A LOT longer than mitosis, taking days to weeks 

• Takes place in meiocytes (tissues in which meiosis is happening) 

• Oocytes= egg cell, spermatocytes= sperm cell 

• In females, only 1 out of these 4 products form into a functional cell (other 3 disintegrate) 

Homologous chromosomes: before each nuclear division homologous chromosomes pair with each other 

• Each member in a pair of homologs consists of 2 sister chromatids  joined at the centromere (two chromosome pairs) resulting in a 4-stranded structure 

First meiotic division: homologs pair and condense 

• Then they separate with one member (1 pair consisting of 2 chromatids) going to opposite poles of the spindle 

• 2 nuclei form, each containing replicated chromosomes 

Second meiotic division: resembles a mitotic division without DNA replication

• At metaphase chromosomes align, anaphase separates them into opposite daughter nuclei, as cell divides twice, there are 4 haploid daughter cells at the end of the second division 

Prophase of meiosis consists of 5 substages: leptotene, zygotene, pachytene, diplotene, and diakinesis 

Leptotene: chromosomes become visible as thread-like structures 

• First stage of condensation 

Zygotene: lateral paring (synapsis) of homologous chromosomes, beginning at the tip 

• Synapsis continues to form along the whole chromosome 

• Bivalent = pair of homologous chromosomes, each consisting if 2 chromatids during meiosis 1

Pachytene: chromosomes continue to shorten and thicken 

• Sometimes= tetrad of the four chromosomes 

• Usually = chromosomes are very close to each other 

• crossing-over  (exchange of genetic information) happens here 

Diplotene: synapse chromosomes begin to separate 

• Homologous chromosomes held together by cross-connections (chiasma)

Diakinesis: homologous chromosomes appear to repel each other 

• Only sections with chiasmata stay close together 

• Nuclear envelope breaks down 

• Spindle is formed 

Metaphase I: the bivalents positioned with the centromeres of the two homologs on opposite sides of the metaphase plate 

• As each bivalent moves onto the metaphase plate, its centromeres are oriented at random with respect to the poles of the spindle 

• * there is independent assortment of genes on NONhomologous chromosomes that are touching each other

Anaphase 1: homologous chromosomes, each composed of two chromatids joined at an undivided centromere, separate from one another and move to opposite poles of the spindle

• The physical separation of the homologous chromosomes in anaphase I ii the physical basis of Mende’s principle of segregation

• Recombination of chromosomes can happen here 

• One spindle is going on each centromere of the chromosomes and are pulling the chromosome pairs apart 

Recombination: chromosomes can overlap and exchange genetic information with each other

Telophase I: A haploid set of chromosomes consisting of one hololog from each bivalent is located near each pole of the spindle 

• The spindle breaks down; the chromosomes enter the second meiotic division after only a limited uncoiling 

• Chromosome replication never takes place between the two divisions 

The second meiotic (equational) division: the second nuclear division resembles a mitotic division, but there is NO DNA replication 

• At metaphase, the chromosomes align on the metaphase plate, and at anaphase, the chromatids are separated into opposite daughter nuclei

• The net effect of the two divisions is the creation of 4 haploid nuclei 

Prophase II: formation of a second division spindles

Metaphase II centromeres of the chromosomes in each nucleus become aligned on the central plane of the spindle at metaphase II 

anaphase II: the centromeres divide and the chromatids of each chromosome move to opposite poles of spindle, once centromere has split, each chromatid is considered a separate chromosome

Telophase II: a transition to the interphase condition of the chromosomes in the four haploid nuclei, accompanied by a division of the cytoplasm 

Meiosis vs mitosis: 

• Meiosis produces 4 haploid cells, each containing 1 copy of each pair of homologous chromosomes, which are usually not genetically identical because of crossing over associated with the formation of chiasmata during the prophase of the first division 

• Mitosis produces 2 diploid cells that both contain both members of each pair of homologous chromosomes, which are genetically identical 

Eukaryotic chromosomes: highly-coiled and stable complexes of DNA and protein called chromatin 

• Each contains a single DNA molecule of enormous length (X-chromosome = 155 million nucleotides) 

• Some proteins present in chromatin determine chromosome structure and structural changes during cell cycle 

• Other chromatin proteins have role in regulating chromosome functions 

Nucleosome: the basic structural unit of chromatin

• Eacn nucleosome is composed of a core particle (histones and 145 nucleotides), ~55 base pairs of DNA called linker DNA that link adjacent core particles 

• You can view these through electron microscopy

Histones: small proteins that are highly conserved among different organisms 

• They have an internal structure of 2xH2s, 2xH2B, 2xH3, 2xH4

Determination of DNA within one nucleosomes: 

• short term treatment only breaks the connection between nucleosomes → length of DNA in nucleosome and linker DNA 

• Long Term treatment mostly degrades linker DNA (DNA bound to histones partially protected by degradation) → DNA in nucleosome 

• Excessive treatment will degrade all DNA, so timing is important 

Linker DNA between nucleosomes: is straight and bridges between adjacent nucleosomes on opposite sides of 30 nm fiber

“Typical” chromosome shape: not visible in non-dividing cells 

• Chromosomes are not intermingles when going into mitosis

• In nucleus of non-dividing cell, chromosome fibers form discrete chromosome territories (these are correlated with gene densities) 

• Gene-rich territories are located more towards interior of nucleus 

Metaphase chromosomes: have several layers of condensation 

• 30 nm fiber gets coiled into 300 nm chromatin 

• Coiled coil of 700 nm on the next level 

• Metaphase chromosomes end with 1400 nm diameter 

• IMPORTANT: single DNA strand stays intact during entire process (does not break or knot) 

Giemsa stain: stain used to visualize chromosomes 

• For ex they can show typical “X” shape chromosome during metaphase

• Different parts of chromosome are differently stained 

Heterochromatin: compact and heavily stained regions of chromatin

•  mainly consist of highly repeated NONCODING DNA sequences (satellite DNA) (LESS G-C) MORE A-T

• small amount of genes are here compared to euchromatin

• Contain centromere 

• Telomeres are also made of this 

Euchromatin: part of chromosome that is not heterochromatin which becomes only visible after chromosome condensation in mitosis or meiosis, 

• This is G-C rich 

• A large amount of genes are here compared to heterochromatin 

Centromere: the point of constriction on the chromosome that binds specific proteins, which in turn make up a disk-like structure called the kinetochore 

• Primary constriction of the condensed chromosome 

• Primarily made of AT-rich genomic regions → heterochromatin 

Kinetochore: Disk shaped protein complexes which are closely associated with centromere, site of assembly and disassembly of microtubules

• One of the key molecules for pulling chromosomes into different directions 

• When chromosomes move farther apart from center, kinetochore microtubules aren’t moving

• Assembly and disassembly of microtubules and kinetochore allows chromosomes to move 

Bleaching experiment: proved how microtubules aren’t moving when chromosomes move farther apart from the center 

• Microtubules break down/get disassembled 

• Motor proteins then bring chromosomes up the microtubule 

• Thai breaking down of microtubules is not at the upper part but is occurring near the chromosomes themselves 

End problem: ends of chromosomes get shorter with every cycle of replication 

• DNA replication machinery works in 5’ to 3’ direction 

• Primers are needed for the enzyme to synthesize the new strand of DNA 

• Primers usually get replaced with new DNA, this is not possible on the 3’ end 

• This results in single stranded overhangs that are prone to degradation and if these aren’t fixed, DNA gets shorter with each cell division

Telomeres: essential for stability of chromosome tip, these require a special mechanism to restore DNA in telomeres in each cycle of replication called telomerase

• Consist of telomeric repeated sequences, not possible for DNA polymerase to replicate 3’ end of DNA

telomerase: adds more DNA, giving DNA primase an area to synthesize, therefore chromosomes aren’t shortening 

Mandelian rules predict a male to female ratio to be: 1:1

Y-chromosome: much shorter than x-chromosome, key genes are on y chromosome are important for testis development, may carry some sex-specific traits 

X-linked inheritance: rare traits linked to recessive allele, affected individuals are ONLY males and females are carriers 

• Affected males have normal sons as the X-chromosomes come from mother, so if X-chromosome has mutation, men will have it 

• A woman whose father was affected has normal sones and effected sons in a ratio of 1:1

• Mating progeny (of all kids, not just sons) results in 3:1 ratio 

Non-disjonction: failure of chromosomes to separate and move to opposite poles of the division spindle; the result is a loss or gain of a chromosome 

• Cells can sometimes make a mistake during meiosis with 2 chromatids not separate therefore making 3X chromosomes, so XXX

Drosophila special in sex determination: presence of Y-chromosome does not lead to development of male features but to male fertility 

Law of independent assortment suggests that there is what likelihood of getting one of 2 alleles: 50% likelihood as the alleles of different genes segregate independently of one another during gametogenesis and are distributed independently of one another in the next generation

Gene linkage can be investigated using: genes with observable phenotypes in different model organisms 

cis(coupling) configuration: mutant alleles of both genes are on the same chromosome = ab/AB (big on one side, little on the other) 

Trans(repulsion) configuration: mutant alleles are on different homologues of the same chromosome = Ab/aB (big and little each on a side) 

Allele: alternative forms of a given gene 

Crossing over (or recombination): leads to the exchange if DNA from one homologue (like chromosomes 1 switches with chromosome 1, they each have the same sequences as each other) with chromosome to another 

• If the chromosomes carried different alleles to a specific gene, a recombinant is formed 

• Parental combinations are  usually in higher numbers of gametes 

Linkage is measured as: the frequency of recombination 

Calculation of recombination rate: the sum of all recombinant types divides by the sum of all progeny (offspring) 

Linked genes: genes with recombination frequencies less than 50% are on the same chromosome

Linkage group: all known genes on a chromosome

Unlinked genes: two genes that undergo independent assortment have a recombination frequency of 50^ and are located in nonhomologous chromosomes or far apart on the same chromosome 

Frequency of recombination always depends on: the genes investigated 

• The smaller the recombination rate, the closest together two genes are on a chromosome

• The MAXIMUM recombination rate is 50% (independent assortment) 

• Recombination frequencies are the same in cis and trans configuration 

1% recombination is equal to: 1 in 50 meiotic cells showing recombination

One event of recombination generates: r recombinant genes 

• 2 cells have 1 piece of recombinant DNA 

• This is because they only overlap in one spot, and the two other chromosomes are unaffected 

As the distance between genes on a chromosome increases: so does the recombination fraction 

• Distance measurement (recombination) 1 map unit = 1 percent recombination (true for short distances_ = 1 centimorgan 

• Genes closer together are less likely to overlap so therefore have a low recombination frequency 

• Genes farther apart are more likely to overlap and they therefore have a more likely recombination frequency 

Genetic map: shows the distance between two genes, this does NOT tell you which comes first and which comes second, rather just telling you the distance between the two 

Multiple crossovers: when genes are far apart from each other, multiple crossovers can happen

• These can undo the exchange of alleles that a single cross would cause 

• General rule: when recombination rate between genes A bad B is below 10%, the double cross overs are highly unlikely as it is too close for it to happen 

  
  

Nonrecombinant: the two most frequent types of gametes in any genetic cross, these provide the linkage phase (cis vs trans) of the alleles in the multiply heterozygous parent 

Double-recombinant gametes: the rarest classes in a genetic cross 

• The effect of double crossing over is exchange of members of the MIDDLE PAIR  of alleles between the chromosomes 

• Middle gene exchange search for the gene that is different compared to the parental genotypes in the rarest cases → the middle gene 

Numbers of recombinants allow for the calculation of: the distance between the genes