Genes & Chromosomes
Composition of the Human Genome
Introns 內含子
Transposons
Extrons外含子
“satellite” DNA
DNA Supercoiling
(Is the Coiling of a Coil)
Purpose
access of proteins to read the information in DNA sequence
packing of large DNA molecules within the cells
Classification
依旋轉方向
依形成結構
Characteristics
DNA of underwinding
(fewer helical turns )
Purpose
Describe
Superhelical Density
LK (linking number )
Facilitates Additional DNA Structural Changes.makes later separation of the strands easier.
Topoisomers拓撲異構物
（Same # bp, same sequence but different degree of supercoiling)
Structure of chromosome
Chromatin
Organization of information in chromosomes
Central Dogma
Replication
Transcription
Translation
DNA
Viral Genomes
are regions of genes that are transcribed but not translated.— do not encode polypeptide sequence.
are expressed sequences (translated into amino acid sequence).— account for only 1.5% of human DNA!
are removed after transcription and the exon
mRNA sequences are spliced together.
creates “mature transcripts”
Functions
In bacteria
In phage
they interrupt mainly tRNA sequences,do not interrupt protein-coding sequences
interrupt protein-coding sequences.
Many bacterial introns encode catalytic RNA sequences that have the ability to insert and reverse transcribe themselves into the genomic DNA.
Functions (account for
~50% of the human genome)
can move around within the genome of a single cell.
the end of transposons: contain terminal repeats,and hybridize with complementary regions
of target DNA during insertion.
Highly Repetitive DNA (Repeated millions of times)or Simple Sequence Repeats (SSRs)
Associated with
centromeres 著絲點
telomeres 端粒
Have AT-rich repeated sequences of ~130 bp. Essential for equal distribution of chromosome sets to daughter cells
Region where the chromatids are held together during mitosis.(after DNA replication but before cell division)
keep DNA ends from unraveling
Are Associated with Cellular Aging, telomeres are shortened after each round of replication in many tissues.具有保護生物體基因的功能，但無法防止DNA分子因連續多回複製而縮短，只能延緩DNA分子末端基因被侵蝕
Positive supercoils(+)
Negative supercoils(-)
Plectonemic
Toroid/Solenoid
involves a right-hand superhelix with terminal loops in plasmids.
provides more compaction, involves tight left-hand turns, in chromatin
has great influence on transcription and replication of DNA.
can be highly regulated.
Nonsupercoiled DNA is called relaxed.
(Closed circular DNA is rarely relaxed)
In longer DNAs and higher levels of DNA underwinding ,the effect of underwinding is important. Because the hydrogen-bonded base pairs would generally preclude strand separation over such a short distance
Expresses change in LK in a quantity independent of DNA length
Lk is an integer for closed-circular DNA and is (+), reflecting a right-handed helix.
Formula
Linking number in relaxed DNA:
Lk = total of bp / (10.5bp/turn)
Lk = Tw + Wr
Twist (Tw)
Underwind by removing two helical turns: if原本的 Lk = 198
Lk = 198 – 200 = –2
Writhe(Wr)
is the # twists or turns of the helix (+)
is the # coils (-)
Example
若有一個LK=20的 relaxed DNA，remove 4 turns and rejoin，則有兩種可能：
LK=16
Tw=16
Wr=0
LK=16
Tw=20
Wr=-4
Underwinding of the DNA facilitates the partial strand separation needed to promote cruciform formation at appropriate sequences.
Helps to maintain structure of cruciforms at palindromes (next slide)
Note that negatively supercoiled DNA (more compact) travels faster in an agarose gel electrophoresis experiment than relaxed or nicked DNA do.
Chromatin fiber
Nucleosomes
Histones(共有8個)
DNA
H2A, H2B, H3, H4 各乘以2
H1
Amino-terminal tails of histones stick out, form sites for covalent modification, and form important contacts between nucleosomes.(The amino-terminal tails of one nucleosome extrude from the particle and interact with adjacent nucleosomes, helping to define higher-order DNA packaging.)
It forms a left-hand solenoid.
is a “linker” DNA and bound to histone H
Wrapping DNA around the histone core requires removal of one helical turn.
The underwinding occurs without a strand break, so a compensatory (+) supercoil forms.
consists of fibers of protein and DNA and a small amount of RNA.
Chromosome Structure Changes over the Course of a Cell Cycle
Interphase 間期
Mitosis 有絲分裂期
S (synthesis) phase
G2 (gap) phase
G1 (gap) phase
中期
後期
末期
前期
染色質變染色體(二分體)、核膜核仁消失、中心粒形成紡錘體
有些紡錘絲連結於染色體中節的著絲點上、染色體隨意排列在紡錘體中央
個染色體的中節分裂為二、姐妹染色體分離向兩極移動
細胞膜內凹陷、細胞一分為二、染色體變成染色質、核膜核仁出現
Topoisomerases 拓撲異構酶
Function
are required for DNA unwinding and rewinding during transcription and replication,which Change Lk
Reason
超螺旋的發生是因為有結構性張力被引入DNA而導致：為了疏解張力，所以進一步纏繞成為雙螺旋。至於結構性張力被引入的原因，是因為有拓撲異構酶的存在。拓撲酶的作用原理是：對於放鬆狀態的DNA進行切割後，移位，再粘回去，從而將張力引入螺旋之中，導致超螺旋的形成。
Topoisomerase Inhibitors used as
Chemotherapy Agents
Chemotherapy Drugs
Antibiotics
Types
Type I
Type II
make a transient cut in one DNA strand, changes Lk by 1
make a transient cut in both DNA strands, change Lk in steps of 2
The Topoisomerases Types in
E. Coli
Eukaryotic
Topo I and IIIare Type I
Topo II is called DNA gyrase
remove negative supercoils to relax DNA,and increase Lk. use single-stranded breaks.
看圖 First nucleophilic attack by the active-site Tyr residue breaks one DNA strand. The ends are ligated by a second nucleophilic attack. At each step, one high-energy bond replaces another.
introduces negative supercoils,and decreases Lk. uses ATP and double-stranded breaks
Topo I and III are Type I (As in E.coli)
Type IIA and Type IIB
can relax both positive and negative supercoils
Mechanism of a Eukaryotic Type IIa Topoisomerase 看圖
Coumarins(inhibit bacterial Type II topoisomerases from binding ATP), Quinolones(inhibit the last step, which is resealing the DNA strand breaks),Nalidixic acid,Ciprofloxacin,Irinotecan, Topotecan
Eukaryotic Type I topoisomerase inhibitors
Eukaryotic Type II topoisomerase inhibitors
captothecin, irinotecan (Campto), topotecan (Hycamtin)
doxorubicin (Adriamycin), etoposide (Etopophos), ellipticine
Doxorubicin, Etoposide, Ellipticine
one strand of double-stranded DNA acts as the molecular template for RNA synthesis (DNA ->messenger RNA).
Proteins (determines its biological function ) are synthesized based on the information stored in ribonucleotide triplets in RNA. the triplets of nucleotides in mRNA bind to complementary triplets in tRNA.
DNA in a cell is organized into compact forms, typically via coiling and association with proteins. Eukaryote DNA Is in Multiple Discrete Chromosomes. Human somatic (non-sex) cells have 46 chromosomes.
RNA genomes may be small and single-stranded
Genomes may change from circular to linear, and so on, during the life cycle.
Many viruses: only RNA or DNA surrounded by protein coat (They use the host’s genes when they infect a plant, animal, or bacterium)
Telomerase 端粒酶
真核生物的生殖細胞為避免染色體DNA越來越短，以致其上基因消失，故具有端粒酶以催化端粒延長，以恢復DNA的長度
端粒和癌細胞
癌化的體細胞中發現端粒酶的活性較高，使癌細胞可無限制的進行細胞分裂。
P.s 一般細胞不具有端粒酶，故細胞複製的次數有限，當DNA過短則使細胞進行凋亡