Genetics Exam 1

are all amino acids equally common across all organisms?

no. different organisms have different genomes, so they have different frequencies of codons that specify amino acids. some amino acids are encoded by more codons than others.

key observations from early cell biology

• chromosomes migrate to the daughter cell when a new cell is formed

• nuclei fuse during fertilization

• something inside the nucleus is important in cell functions

purines

adenine and guanine, double ring structure

pyrimidine

cytosine and thymine, single ring structure

Erwin Chargaff

suggested the frequency of A,T,G,C was not identical and different organisms have different compositions of each

sickle-cell hemoglobin

one amino acid (out of 300) in the primary structure is altered. this leads to an exposed hydrophobic region in the beta subunit. the molecules then crystallize into a fiber, and the capacity to carry oxygen is reduced. in normal hemoglobin, the molecules do not associate with one another, each carries oxygen. sickle cell phenotype segregates according with mendelian rules for a single causing gene.

why would GC content vary between species?

phylogenetic signal, different mutation patterns, natural selection, different evolutionary histories

which organisms do you expect to have highest proportion of GC in their genomes?

organisms that live in very hot environments. GC pairs are thermally more stable than AT because they have 3 hydrogen bonds vs 2

where is genetic information stored in prokaryotes?

in the cytoplasm. they are only single-celled organisms

where is genetic information stored in eukaryotes?

the nucleus (linear DNA) with membrane separating single and multi-celled organisms. also stored in the mitochondria and chloroplast (circular DNA)

genome

the full hereditary information for an organism (i.e. a complete set of its DNA)

why is genetic drift more likely on an organelle genome?

random changes in organelle DNA frequencies have a stronger effect because organelle genomes have a smaller effective population size and a more restricted pattern of inheritance (typically only inherited from the mother)

why do mitochondria and chloroplast need their own genomes

they perform different functions. chloroplast DNA is genes involved in photosynthesis. mitochondrial DNA is genes involved in mainly cellular respiration/ energy production

do they DNA differ between the mitochondria and chloroplast of the same organism

yes. and they have different coding genes

how big is an E.coli genome? a human genome?

E. coli: 4639 kb (.006ft)

Human: 3,200,00 kb (6ft)

is DNA positively or negatively charged? polar or non-polar?

negative due to the phosphate. polar

how wide is a DNA molecule

2nm. the volume fits inside a cell/nucleus, but must be carefully packed

positive supercoiling (overwound helices)

DNA twisted tighter than its normal relaxed state

negative supercoiling (underwound helices)

DNA twisted less than its normal, relaxed state → makes DNA easier to separate because the two strands aren’t held together as tightly

what happens to DNA in terms of supercoiling during replication/ transcription

when DNA is being opened for replication or transcription, the DNA ahead of the moving machinery tends to become overwound, and the DNA being opened can become underwound

topoisomerase enzyme

temporarily cuts DNA, allows it to rotate or pass through itself, and then reseals it, helping to control coiling. runs in front of helicase

topoisomerase I

makes transient single-stranded breaks in the DNA double helix and reseals the strand

topoisomerase II

makes double-stranded breaks in the DNA double helix and reseals the strands using ATP. useful when DNA molecules become tangled or intertwined

chromatin

combination of DNA and the proteins (especially histones) that package and organize that DNA inside the cell nucleus

make-up of a chromosome

DNA wraps around histones → which forms nucleosomes → which collectively makes up chromatin → which becomes highly condensed during cell division and forms chromosomes

euchromatin

loosely packed DNA, inferred to be actively being read to produce proteins

heterochromatin

tightly packed DNA. inferred to not being read

histones

proteins that act like spools. DNA wraps around groups of histone proteins to form nucleosomes

when are chromosomes at maximum packaging

during cell division

nucleosome

the basic structural unit of chromatin

nucleosome composition

a core particle (histones and 160 nucleotides), about 40 base pairs of DNA called linker DNA that link adjacent core particles

nucleosome job

regulate gene expression. if DNA is tightly wrapped/ packaged into nucleosomes, transcription proteins have a harder time accessing the DNA, and gene expression decreases. if chromatin is more open and DNA is accessible, gene expression can increase

linker DNA

short stretch of DNA between adjacent nucleosomes. can be more accessible to binding proteins. cells can further compact chromatin, and proteins such as linker histone H1 can bind to linker DNA and help organize/ condense chromosomes

condensin

ring proteins, composed of 5 sub units, that actively form a loop of chromatin to help condense chromosomes for cell division

acetylation of histone proteins

loosens DNA packing

methylation of histone proteins and DNA

tightens DNA packing

what do chromosomes do when cells are not dividing

segregate in distinct neighborhoods. chromatin fibers form discrete chromosome territories. they are correlated with gene densities. territories of chromosome domains that are relatively gene rich tend to be located toward the interior of the nucleus

are histones found in prokaryotes and eukaryotes?

no, only eukaryotes

what can Cp genome mutations cause

lack of chlorophyll production

how are organelles genome inherited?

it is very common for strictly maternal inheritance. species with ISOGAMY have biparental inheritance more often

what parts of chromosomes are condensed at all times

the centromere and telomere

how many chromosomes is the human genome

23

diploid

inside each nucleus of an organism, there are 2 copies of each chromosome

how many chromosomes and how much DNA are in a single, non-dividing human cell?

46 chromosomes, 6.2×10^9 bp of DNA

what ploidy are most bacteria

haploids (1 set of chromosomes)

what ploidy are all mammals?

diploid

what type of organisms are more likely to have the impact of a mutation be seen?

haploid organisms. if an organism has more chromosomes, it is less likely that a mutation will be seen

how does ploidy describe the increase in size of strawberries?

when an organism has more sets of chromosomes, its cells contain more DNA. to accommodate for this, the nucleus must expand, therefore making the cell expand

what are the two main ways polyploids arise

autopolyploids and allopolyploids

autopolyploid

extra chromosome set from the same species. usually from an error in cell division where chromosomes fail to separate properly, producing a gamete or cell with an extra complete chromosome set

allopolyploid

chromosome sets from different species. two different species mate and produce a hybrid. the hybrid undergoes chromosome doubling. the resulting organism has complete chromosome sets from both parent species. it is undivided gametes from 2 different species coming together, their genome is similar, but not identical. the offspring could be fertile.

what percent of adult human hepatocytes (liver cells) are polyploid

40%, up to 90% in rodents

what percent of cells in cancer tumors are polyploid?

36%, as much as 50% of a tumor will be polyploid cells

endopolyploid

localized polyploid cell, unlikely to pass into the next cell. DNA replication → no cell division → DNA replicates again → no cell division … the cell becomes larger and contains more DNA

how many chromatids does a dividing cell of a diploid with a single chromosome genome have?

4

what did Watson and Crick propose in their second paper (1953)?

1. unwinding of double helix exposes bases on each strand

2. each strand acts as a template for synthesis of new strands

3. new strand forms by insertion of complementary base pair

semi-conservative nature of DNA replication

every new molecule has one new chain and one old chain. Meselson and Stahl experiment with Nitrogen

area of nucleation

initial pairing/assembly of molecules at the site where replication begins

how is DNA denatured and reannealed based on sequence, allowing it to restore function?

Duplex DNA → as the temperature is increased, the bases unstack, and hydrogen bonds break → partially unwound DNA (with areas rich in A/T base pairs breaking apart more than G/C) → at higher temperatures, even G/C-rich regions are disrupted → totally denatured DNA (separate strands) → when the solution is returned to lower temperatures, complementary regions on separate strands form base pairs → once nucleation has occurred, renaturation is rapid due to zippering → Duplex DNA

does single strand or double strand DNA absorb more UV light?

single strand

DNA polymerase

can add new nucleotides to the 3’ end of a DNA strand

what powers the connection of the nucleotide to the DNA template strand?

new nucleotides come in as nucleotide triphosphates (like ATP). this loss of two phosphate groups releases energy to power the connection of the nucleotide to the strand

limitations of DNA polymerase

1. they cannot unwind double-stranded DNA

2. they cannot start a chain, they can only add a nucleotide to an existing nucleotide strand

3. they can only add nucleotides to 3’ ends (5’ → 3’ synthesis)

4. they cannot link existing DNA chains to each other

DNA helicase

unwinds double-stranded DNA, but overwinds the DNA in front of it. a beta sub-unit ring that runs in front of replication. only goes across one strand

primase

builds short RNA strands called primers that DNA polymerase can work from to build a DNA strand. can only put a primase once the DNA is opened. it binds to the template strand and synthesizes an RNA primer. when the primer is complete, primase is released. DNA polymerase binds and synthesizes new DNA

leading strand

synthesized toward the replication fork. continuous synthesis. the 3’ end is going into the fork

lagging strand

synthesized away from the replication fork. series of segments (Okazaki fragments). 3’ end facing away from the fork

how does DNA polymerase replace RNA primers with DNA

cuts the RNA off and then inserts the correct base pairs

DNA ligase

connects adjacent strands of DNA together to combine Okazaki fragments to form one continuous new strand

end replication problem

eukaryote’s linear chromosomes can never be fully replicated due to lagging strand dynamics. chromosomes shorten during each replicative cycle. the final Okazaki fragment requires an RNA primer near the chromosome’s end. after that primer is removed, there is a gap. there is no DNA beyond the end of the chromosome to provide the template/starting point needed to make the final piece. there is no DNA with a free 3’ OH group for DNA polymerase to extend from, so it cannot fill this gap

telomere

repetitive DNA sequences at the end of chromosomes. they protect the important genetic information from being lost or damaged

telomerase

a protein RNA complex in eukaryotes that maintains telomere length in stem and germline cells. can extend the telomeres, providing extra DNA that can solve the end-replication problem

how does telomerase operate in cancer cells

it is inappropriately activated in as many as 90% of human cancers. in a normal cell, telomeres shorten and eventually the cell stops dividing. in cancer cells, activation of telomerase allows for the telomeres to be maintained/ lengthened, and the cell can keep dividing.

mitosis

cell division that preserves the number and kinds of chromosomes (somatic cells)

meiosis

cell divisions that lead to the creation of gametes, allowing chromosomes number reduction (germ cells)

is there a pathway for genetic information to flow from somatic cells into germ cells in animals?

no, early on in development, the germline and soma are physically separated

mutations in somatic cells

confined to that cell. there is no way for a mutation that arises in a somatic cell to migrate into a germ cell

how do mutations get passed from parent to offspring?

if a mutation arises during DNA replication that produces sperm or egg precursors, or if it was already present in the primordial germ cells from early development, that can end up in a gamete and be passed to offspring

do plants set aside special germ cells at the embryo stage?

no. instead, germ cells are derived from somatic cells late in development. germ cell formation isn’t a one-time developmental event from a reserved lineage like in animal cells. it is a repeated process that happens over and over throughout the plant’s life. therefore, mutations that arise in “somatic” plant cells can end up in gametes and be inherited

somatic cells

skin, muscles, neurons, etc. genetic dead end that doesn’t get passed on from one generation to the next

germ cells

the cells in mammals that give rise to gametes (sperm and eggs) and are the lineage responsible for transmitting genetic information from one generation to the next. they are set aside early in development specifically to produce the next generation

does DNA replication occur in meiosis or mitosis?

BOTH

recombination

only happens in meiosis.

1. during prophase I, each chromosome finds its homologous partner (the maternal and paternal copies of that chromosome) and they pair up tightly.

2. an enzyme called SpoII introduces double-strand breaks in the DNA of one of the paired homologs

3. the broken DNA invades the DNA of the homologous chromosome (not the sister chromatid) and uses it as a repair template. this creates a physical connection between the two homologs

4. some of these repair intermediates get resolved in a way that results in actual reciprocal exchange of chromosome segments between the homologs.

chiasma

the physical site where DNA recombination occurs

G1 phase of mitosis

interphase, gap before duplication

S phase of mitosis

DNA synthesis and chromosome duplication

G2 phase of mitosis

interphase, chromosomes are duplicated, gap before mitosis

M phase of mitosis

mitosis (separating the chromosomes), cytokinesis (splitting the cell)

external checkpoints that control the cell cycle

growth factors, nutrient availability, space/contact

internal checkpoints that control the cell cycle

DNA damage survey, proper chromosome alignment

what in the cell cycle can cause tumors?

breakdown of the control patterns

mitosis prophase

chromosomes condensed, spindles form, nucleous breakdown

pro metaphase

spindles attach to centromeres

metaphase

chromosomes line up

pro prophase

centrosomes start migrating

anaphase

chromatids separate, spindles retract

telophase and cytokinesis

spindles disappear, chromosomes separate, cell splits into two, nucleous reformed

does meiosis lead to an increase or reduction in ploidy

reduction

what is the main use of meiosis 1

provides a checkpoint to make sure each chromosome is paired up before the chromosome divides

does meiosis 2 have duplication?

no