DNA to DNA
In DNA Replication, you go from _____________ to _____________
DNA to RNA
In Transcription, you go from _____________ to ______________
RNA to protein
In Translation, you go from _______________ to ______________
prokaryotic
-large, circular chromosomes
-no histones, but still complexed with proteins to form large twisted loops
-in nucleoid
-1 ori site
eukaryotic
-linear chromosomes
-chromatin change locally as genes are transcribed and changes all during cell cycle
-wrap around histones
-located in nucleus
-multiple ori sites
chromatin
Eukaryotic Chromosome:
DNA + associated proteins (Scaffold-SARS, kinetochore, telomere caps, histones)
euchromatin
relatively uncondensed chromatin that is always ready for transcription
heterochromatin
condensed chromatin that is never transcribed
-for functional structures
constitutive heterochromatin
chromatin that is always condensed, found in centromeres and telomeres
telomeres, centromeres, barr body
3 things heterochromatin is for
facultative euchromatin
chromatin that goes back and forth between a condensed and uncondensed state depending on whether that area of DNA is being transcribed or not
tertiary structure
How does DNA pack into a small nucleus?
supercoiling
Packing DNA into Small Spaces:
either remove some coiling or add some; one form of tertiary structure
-found in bacterial chromosomes, plasmids, even portions of linear DNA
topoisomerase type I
Packing DNA into Small Spaces:
Supercoiling:
enzyme that breaks one strand of the double stranded DNA so supercoiling can be released and molecule can get closer to relaxed state; then the enzyme re-glues the strands back together
topoisomerase type II (gyrase)
Packing DNA into Small Spaces:
Supercoiling:
breaks both strands of DNA to either relax or cause supercoiling; then the enzyme re-glues the strands together once the supercoiling is relaxed
scaffold proteins
proteins detached from chromosomes, histones removed
-these allow DNA to attach
scaffold attachment region (SAR)
area where DNA and scaffold proteins are attached
histones
Eukaryotic Chromosome:
Chromatin:
Proteins:
-most abundant protein
H1, H2A, H2B, H3, H4
nonhistone chromosomal proteins
Eukaryotic Chromosome:
Chromatin:
-either act as structural or processing (TC or replication) proteins
Scaffold proteins
Kinetochore
Telomere caps
Molecular motors to move chromosomes during mitosis/meiosis
nucleosome
Eukaryotic Chromosome:
core particle consisting of DNA wrapped 2 times around a histone octamer
H2A, H2B, H3, H4 all x2
Histone octamer is made of:
H1
Eukaryotic Chromosome:
Nucleosome:
acts as a clamp to lock nucleosomes in place
chromatosome
Eukaryotic Chromosome:
Nucleosome:
nucleosomes plus H1
Linker DNA
Eukaryotic Chromosome:
Nucleosome:
DNA found between chromosomes
solenoid
Eukaryotic Chromosome:
the 30nm strand, spiral of nucleosomes
scaffolding proteins, scaffold attachment regions (SARs)
Eukaryotic Chromosome:
30nm strands loop back and forth to attach to _________________________ by means of _________________________ on the DNA
polytene chromosomes
Eukaryotic Chromosome:
Changes in Chromatin Structure:
-you can see how the chromatin periodically RELAXES to allow TC and replication in these
-these chromosomes are only found in flies and only in their salivary glands and footpads
-chromosomes are very
chromosome puff
Region on a polytene chromosome that is a TC site
epigenetics
stable alterations of chromatin structure that may be passed on to cells or individual organisms
centromeres
structure critical for chromosome movement during mitosis and meiosis
-inhibit anaphase until spindle fibers form the poles attach
-not defined by DNA sequence but by epigenetic changes in chromatin structure
point centromeres
Type of Centromere:
-Saccharomyces = 125bp
-relatively small; repeated several times in centromeric region
regional centromeres
Type of Centromere:
-in fission yeast, central core of 4000-7000bp flanked by blocks of centromere-specific, often tandem repeat, sequences
-in humans, there are hundreds of thousands of repeats
telomeres
-structure that provides stability against degradation of the chromosome
-critical in replication b/c last few nucleotides on ends are unable to be replicated
-so chromosome gets shorter every time cell divides
telomerase
enzymes that prevents shortening of telomeres
-found in germ cells and single celled organisms
tandem repeats
telomeres consist of _________________ (human one is TTAGGG repeated 250-1500 times)
-number of repeats depends on the cell type and the chromosome
shelterin
multi protein complex which binds to mammalian chromosome telomeres so they won't be repaired as a double-stranded DNA break would
tandem repeats
3 Types of DNA Sequences in Eukaryotes:
Moderately Repetitive DNA:
short sequences that are repeated over and over again
artificial chromosomes
Chromosomes that can replace a bad chromosome
-can be created to try new gene flavors
-human proteins usu. need stuff added
-plants can do that!
-ex: vaccinations in bananas
C value
Variation in Eukaryotic DNA Sequence:
haploid amount of nuclear DNA per cell
-doesn't always equate with complexity of organism
denature
heating the DNA molecules enough that H bonds break between the 2 strands
-now have single stranded DNA
-aka "melting" the DNA
renaturation
reannealing of two DNA strands by cooling it down
hybridization
when 2 ssDNA molecules from different sources anneal b/c they are complementary
nonrepetitive unique sequence DNA
3 Types of DNA Sequences in Eukaryotes:
-includes protein coding genes & gene families; only show up once to a few times in the genome
moderately repetitive DNA
3 Types of DNA Sequences in Eukaryotes:
150-300bp long generally
-thousands of times repeated (tandem or interspersed)
-can be functional or nonfunctional (LINES, SINES, viral retrotransposons, transposons)
interspersed repeat
3 Types of DNA Sequences in Eukaryotes:
Moderately Repetitive DNA:
repeat is scattered throughout genome
tRNA, rRNA, histones
3 Types of DNA Sequences in Eukaryotes:
Moderately Repetitive DNA:
3 types of functional moderately repetitive DNA
LINES, SINES, viral retrotransposons, transposons
3 Types of DNA Sequences in Eukaryotes:
Moderately Repetitive DNA:
4 types of nonfunctional moderately repetitive DNA
LINES
3 Types of DNA Sequences in Eukaryotes:
Moderately Repetitive DNA:
Nonfunctional:
-retrotransposon
rTn>>TC>>RT>>inserted in another place
-encodes RNA binding protein
-have their own TC and RT
-encodes RT homologue with endonuclease activity (ability to c
SINES
3 Types of DNA Sequences in Eukaryotes:
Moderately Repetitive DNA:
Nonfunctional:
-retrotransposon
rTn>>TC>>RT>>inserted in another place
-borrow TC from our cells
-Alu sequence - has All restriction site in it; ~11% of human DNA
-average size is 300bp lo
viral retrotransposons
3 Types of DNA Sequences in Eukaryotes:
Moderately Repetitive DNA:
Nonfunctional:
-encode all viral protein but envelope protein so can't bud from cell
-integrase & reverse transcriptase proteins allow it to move in the genome
-TERRIBLE if these move in e
gag pol env
Keys for identifying retroviruses, nonfunctional
transposons
3 Types of DNA Sequences in Eukaryotes:
Moderately Repetitive DNA:
Nonfunctional:
gene that can move in the genome if active, but it usually can't do anything
highly repetitive DNA (satellite DNA)
3 Types of DNA Sequences in Eukaryotes:
-often <10bp repeats
-hundreds of thousands to millions of copies
-tandem or dispersed into clusters
-usu. has no known function
(centromeric DNA, telomeric DNA, micro satellite repeats, VNTR DNA/minisatellite repea
centromeric DNA, telomeric DNA (satellite DNA)
2 functional types of highly repetitive DNA sequences
VNTR (mini satellite DNA), dinucleotide repeats (micro satellite DNA)
2 nonfunctional types of highly repetitive DNA sequences
move, mutations
The Nature of Transposable Elements:
~45% of human DNA
-able to _______ around the genome
-may cause _______________ by inserting within a gene or by promoting DNA rearrangement
-have short direct flanking repeats and may have terminal inverted repeats
short direct flanking repeats
The Nature of Transposable Elements:
-due to insertion process; not part of transposon
terminal inverted repeats
The Nature of Transposable Elements:
recognition sequence of transposases
transposition
movement of transposable element from one location to another
DNA, transposase, homologue, prokaryotes
Mechanisms of Transposition:
Transposons:
-transpose via __________ intermediates
-those that still move, encode own ___________________ and may have other genes
-either replicative or non replicative
-even 2nd version results in increase of # of copies o
replicative transposition
Mechanisms of Transposition:
Transposons:
new copy of transposon introduced at new site while old copy stays at old site
nonreplicative transposition
Mechanisms of Transposition:
Transposons:
-transposon excises self from one site and moves to another
RNA, not, viral, eukaryotes
Mechanisms of Transposition:
Retrotransposons:
transpose via _________ intermediates
-do ________ encode own transposase but may have _________ genes like RT
-most common in _____________________
1 centromere, 2 telomeres, ori site
3 things a chromosome needs
attracted to CenH3 (H3 histone) on centromere
Why do kinetochore proteins attach at the centromere