genomes and chromosomes

Question 1

why are stomach microbes important?

Answer 1

the microbes found in the intestinal tract are important because they contain thousands more genes than are possessed in the entire human genome

Question 2

what is the difference between vertical and horizontal gene transfer

Answer 2

vertical gene transfer refers to the passing of genetic information from parents to children whereas horizontal gene transfer refers to the transfer of genetic material between two fully developed microbes

Question 3

what are structural genes and control sequences?

Answer 3

structural genes are genes that actually get transcribed to form fully functional pieces of RNA whereas control sequences are pieces of DNA that regulate the expression of structural genes

Question 4

what is conjugation and why was it important in determining bacterial chromosome structure

Answer 4

conjugation is a form of horizontal gene transfer which requires cell to cell contact. since this process takes place over time by measuring how long it took for certain genes to be exchanged it was possible to map how close genes were relative to one another

Question 5

what is recombination

Answer 5

recombination is when a transferred gene replaces the original gene from a cell showing new expression

Question 6

what is the shape of bacterial chromosomes?

Answer 6

there are linear and circular chromosomes dependent upon the species under study`

Question 7

what are the big differences between bacterial DNA and eukaryotic DNA

Answer 7

in eukaryotes there is a much larger genome consisting of many times more base-pairs than are found in prokaryotic organisms also there is much more viral and non-coding DNA incorporated into the human genome than there s in bacterial genomes

Question 8

how much of human DNA is non-coding?

Answer 8

over 90%

Question 9

what is the difference between enhancers and promoters

Answer 9

enhancers are regions of DNA that drive transcription of promoters and can be far away from the genes they regulate whereas promoters are right next door and activate coding regions

Question 10

what is the term for RNA that is produced by a gene that stands alone

Answer 10

monocystronic

Question 11

what is the term for when genes work together to produce RNA products?

Answer 11

operons- an operon though a group of genes is regulated by a single promoter region

Question 12

a collection of genes and operons found at separate cites on a chromosome that regulate the same thing is known as a

Answer 12

regulon- a regulon also uses only one promoter region for activation

Question 13

how do we know that dna is not parallel

Answer 13

because base pairing cannot occur in models where the two strands run parallel

Question 14

what are purines?

Answer 14

nuleotides with bicyclic bases adenine and guanine

Question 15

what are pyrimidines?

Answer 15

monocyclic base nucleotides thymine or cytosine

Question 16

what is a nucleoid

Answer 16

a nucleoid is the area within bacterial cells that contains their DNA this area is kept free of ribosomes and is distributed throughout the nucleus

Question 17

bacterial cells use histone like anchoring proteins to…

Answer 17

anchor DNA so it can be super coiled

Question 18

how do we know that DNA coiling is a process independent of each separate coil structure

Answer 18

if a nick is created in one piece of coiled DNA only DNA associated with the same anchor protein will unwind

Question 19

explain positive and negative supercoiling

Answer 19

positive super coiling is when DNA tries to coil in the same direction as it is wound this creates stress because the coils try to unwind thus causing over coiling. the DNA negative super coiling on the other hand relieves stress by twisting in the opposite direction the DNA just becomes more tightly wound.

Question 20

is it easier to separate negatively or positively super-coiled DNA

Answer 20

it is easier to separate negatively super-coiled DNA which is another reason it is used by most higher organisms (usually only organisms in harsh environments rely on positive super-coiling)

Question 21

what are topoisomerases

Answer 21

topoisomerases are enzymes which add or relieve stress in DNA group 1 enzymes are used to relieve stress whereas group 2 enzymes are used to add stress

Question 22

what is the notable difference between group one and group two topoisomerases?

Answer 22

group one topoisomerases have only a single sub unit where as group two enzymes are made up of multiple subunits

Question 23

how is DNA super coiling useful when coming up with drugs to combat bacterial pathogens?

Answer 23

many classes of drugs directly target the enzymes responsible for DNA coiling. for example quinolone antibiotics target group two topoisomerases to prevent cells from being able to coil DNA

Question 24

in which direction does DNA replication occur

Answer 24

always in the 5’ to 3’ direction

Question 25

what are the three steps of DNA replication

Answer 25

initiation- unwinding the DNA and inserting polymerases
elongation- addition of nucleotides to the new strand followed by strand proofreading
termination- DNA is replicated and supercoiling is reinstated

Question 26

how is bacterial DNA replication different from DNA replication in other organisms

Answer 26

since bacterial DNA is circular bacteria have a single origin and a single termination point for replication versus other organisms which may have many per chromosome

Question 27

it takes ecoli 40 minutes to copy its genome about how long does replication take

Answer 27

about 20 minutes many bacterium can divide even before it’s entire genome is done being copied

Question 28

how does replication initiation occur in bacterial cells

Answer 28

in bacterial cells there is a specific cite on each chromosome which acts as the origin of replication and is initiated by DNA polymerases. to prevent the cell from dividing to early there are two regulatory proteins DNAa which encourages replication and SEQa which discourages replication by bonding to the origin cite of DNA. SEQ bind to the origin cite right after DNA replication starts because during that period of time the DNA is unmethylated which causes SEQa to bond more readily. once methylation is fully achieved SEQa disassociates

Question 29

how does DNAa help to control replication of DNA?

Answer 29

DNAa bons to the origin point of replication to initiate the copying of the DNA as the cell grows the level of DNAa increases eventually leading to initiation of cell division

Question 30

explain how initiation begins

Answer 30

DNAa leads to strand separation allowing DNA helicase to bind and start unwinding the double helix. dna primer bonds to the unwound dna and lays down a short rna sequence where dna synthesis can begin. a sliding clamp protein then binds to the dna to keep dna polymerase from falling off the dna as new strands are synthesized then finally dna polymerase 3 binds and begins synthesis of a leading strand

Question 31

what is a replisome

Answer 31

a replisome is the combination of the primase helicases and DNA polymerases responsible for replication

Question 32

how is the lagging strand protected

Answer 32

single stranded binding protiens

Question 33

true or false replisomes move along the length of dna during replication

Answer 33

false replisomes remain stationary

Question 34

there are two functions of DNA polymerase three what are they

Answer 34

synthesis of a new strand of DNA and proofreading for incorrectly placed pairs via excess motility of nucleotides

Question 35

what is the function of DNA polymerase 1

Answer 35

DNA polymerase one comes back through after RNA segments are cleaves by RNase and synthesises DNA to replace the RNA strands that were removed. it also removes and resynthesises the first 5’ nucleotide it encounters

Question 36

what is the function of DNA ligase

Answer 36

DNA ligase goes through and creates phosphodiester bonds in the DNA backbone where unbonded RNA primers once existed

Question 37

DNA forms positive supercoils during replication how is stress on the DNA prevented?

Answer 37

DNA gyrase sits at the head of each strand and uncoils the positive super coils as they form

Question 38

what is tus (terminus utilization substance)

Answer 38

tus is a protein which bonds to DNA and acts as an antihelicase causing helicase to disassociate and the DNA to remain together this is how replication terminates

Question 39

what is a catenane

Answer 39

two interlocking molecular rings after replication this is the appearance plasmids take on. topoisomerase 4 a group two topoisomerase then comes in and resolves this structure

Question 40

plasmids are not chromosomes but small circular pieces of DNA found in prokaryotes and archea which generally code for only one gene how do they replicate?

Answer 40

generally plasmids replicate using the bacterial cell’s protiens and enzymes but can replicateeith bidirectionally or unidirectionaly via rolling cycle replication

Question 41

what are addiction modules

Answer 41

addiction modules are genes found on some plasmids which force cells to either keep the plasmid or die

Question 42

there are two ways that plasmids ensure that daughter cells retain copies of plasmids what are they

Answer 42

the first is that high copy number plasmids make many copies of themselves in order to ensure that by random chance all daughter cells will receive at least one copy low copy number plasmids make fairly few copies of the plasmid but have partitioning genes to ensure each daughter cell recieves a plasmid

Question 43

what is another way plasmids ensure their proliferation

Answer 43

some plasmids contain genes which are essential for a cell to survive in the environment thus loss of the plasmid leads to cell death

Question 44

why are plasmids essential to bacterial evolution

Answer 44

plasmids can be easily transferred from one cell to another making it easy for bacteria to transfer genes essential for survival. plasmids can also be absorbed from dead bacteria (transformation) or transferred via accidental uptake by bacteriaphages (transduction)

Question 45

introns are?

Answer 45

non-coding segments of eukaryotic genes

Question 46

what are restriction endonucleases?

Answer 46

they are proteins found in bacteria used to clip the DNA of foreign bodies