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21 Cards in this Set

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what is a gene?
all the DNA that encodes the primary sequence of a final gene product
-this includes promotor regions for initiation, distal elements associated with regulation of RNA expression, and anything important for the inheritance of that sequence


keep in mind that the elements that make up a gene do not necessarily all reside in one specific area
prokaryotes don't have introns, how does this help them?
confers them a special benefit in terms of speeding up replication
-a compact, small genome that can be replicated rapidly in changing conditions gives prokaryotes a huge survival advantage
how much of our genome is introns?
around 28.5%
how much of our genome is exons that go on to express proteins?
around 1.5%
number of genes in the human genome
~25,000
average number of exons
10.4
pseudogene
a nucleotide sequence of DNA closely resembling that of a functional gene, but containing numerous mutations that prevent its proper expression

most pseudogenes arise from the duplication of a functional gene followed by the accumulation of damaging mutations in one copy

there are more than 20,000 of these in the human genome
structural components of a chromosome
structural components of a chromosome
in addition to containing an abundance of individual genes, chromosomes also contain structural elements such as centromeres and telomeres

centromeres- involved in cell division and are usually found near the middle of a chromosome

telomeres- repeat nucleotide sequences at the end of chromosomes
telomeres
telomeres
-repeat nucleotide sequences at the end of chromosomes
-largely TG rich
-highly regulated by enzymatic systems
-shorten with each cell division (aging component)
-shortening also seems to be correlated with smoking, obesity, and stress
replication bubbles
replication bubbles
single stranded regions on the chromosome that serve as origins of replication

enzymes attach to these points to begin the building of daughter strands

chromosomes tend to have multiple origins of replication to speed up the process
supercoiling
supercoiling
an intrinsic property of DNA and also a form of potential energy, and results when DNA is subject to some form of structural strain- usually as a result of under winding

plays a role in the compaction of DNA and strand-separation of DNA during replication/transcription

when the axis of the DNA double helix is coiled on itself, it forms a new helix (supercoil)
topology
the study of the properties of an object that do not change under continuous deformations
-for example, in Supercoiling, as we continue to twist and pack DNA, we don't change any of its underlying function in any way
effects of DNA underwinding
effects of DNA underwinding
strain is almost always a result of under winding the DNA in the closed circle
-this means there are fewer helical turns in the DNA than expected.

under winding can make it easier to separate DNA strands! Facilitating strand separation is one important reason for maintaining DNA in an unwound state

Relaxed DNA has 10.5 base pairs per turn and this is very stable

if unwound, the DNA will have more base pairs per turn and will become super unstable

it will deal with this instability in one of 2 different ways
-it can result in strand separation
-or, the strain can be relieved by formation of a supercoil

every cell under winds its DNA with the aid of enzymatic processes, and the resulting strain represents a form of stored energy
linking number
linking number
DNA underwinding is defined by topological linking number as a measure of potential energy
-the link number describes the number of times one strand of DNA crosses another (specifically, how many times it loops around)

we can change the linking number by under winding or overwinding the DNA

changing the linking number, either positively or negatively, introduces strain

under winding results in a negative change in linking number
topoisomers
topoisomers
identical pieces of DNA that differ in topology, or differ in their linking numbers

right handed helixes are usually positive supercoils (overwinding)

left handed helixes usually have a negative linking number
how do you calculate linking number?
how do you calculate linking number?
Linking Number= (# of base pairs)/ 10.5

can't be calculated if there is a break
Specific Linking Difference
length-independent quantity that is a measure of the turns removed relative to those present in relaxed DNA
topoisomerases
enzymes that catalyze changes in the linking number of DNA by breaking and reforming DNA strands

Type 1: break only one strand of DNA and change the Lk in increments of 1

Type 2: do double strand breaks and change the Lk in increments of 2

Type 2 are much more common than Type 1.

Topoisomerases are found at sites of replication and are critical in the condensing of DNA during mitosis/meiosis.
histones
histones
DNA is wound around protein cores called histones, which both protect DNA and make it more accessible

DNA wrapped around a histone cores is called a Nucleosome, which are further combined in forming chromosomes

linker DNA segments bridge neighboring histones and are digested by nucleases, releasing nucleosome core particles

we can dissociate the histone and DNA in a nucleosome using high concentrations of salt
supercoiling and DNA packing around histones
supercoiling and DNA packing around histones
-topoisomerases function mainly during the S phase of interphase
-part of the compaction of DNA is the winding of double-stranded DNA around a histone core to give the structure of a nucleosome
-relaxed DNA is wrapped around a histone in a Negative supercoil manner, and this introduces a positive supercoil in the rest of the DNA.
-Topoisomerases act on the positive supercoil by removing turns and inducing a stress (potential energy) that ultimately allows the DNA to naturally wrap around this histone
compaction of DNA in a eukaryotic chromosome
compaction of DNA in a eukaryotic chromosome
the building of nucleosomes leads to higher order structures like the 30 nm fiber (basically a packaged bundle of nucleosomes), which is wrapped in a right-handed structure around nuclear scaffolds to achieve the classic chromatid structure