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

Ribosomes

“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 

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 

PROTEIN IS HISTONES

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 ARE IN THIS

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-disjunction

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