Exam 2

Griffith's Experiments

There is a transforming principle that caused the conversion of rough to smooth

Avery, MacCleoud, McCarty Experiment

If they see transformation, then transforming principle was not destroyed.

Transformed bacteria fremained virulent in subsequent generations so transformed traits are heritable.

Hershey & Chase experiments

phosphorous was in pellet -> DNA is genetic material

structure of nucleotide

consists of sugar, phosphate, and base

structure of deoxyribose

C2 has H
C5 has phosphate attached
C1 has N-base attached

Chargaff's Rules

total pyrimidine (T+C)=total purine (A+G)
T=A and G=C but A+T/=G+C

Rosalind Franklin & Maurice Wilkins

studied X-ray diffraction of DNA

DNA is made of 2 parallel parts
DNA is helical
helix contains 10nt per turn
measured helix diameter

DNA structure important for replication

1. complementary strands -> each strand could be template for the other
2. specific base-pairing -> only one sequence is possible from a template

conservative DNA replication

2 strands original 2 strands new

semi-conservative

uses 1 strand original one strand new

dispersive

2 strands mixed

A form

-less hydrtaed
-more compact (10.9 bp/turn)
-right handed
-seen under high salt conditions

B form

-more hydrated
-less compact (10 bp/turn)
-right-handed
-typically found in vivo
-proposed by Watson & Crick

Z form

-left-handed
-zig zag sugar phosphate backbone
-seen in short DNA pieces with alternating purine/pyrimidine

oligonucleotide

short chain of nucleotides
single-stranded DNA

denaturing

separating 2 strands of DNA by melting, breaking H bonds between strains. G/C has higher melting temp due to its 3 hydrogen bonds

annealing

when 2 complementary single strands of DNA hydrogen bond back together

stem

hairpin with no loop

differences between DNA and RNA

deoxribose vs ribose, thymine vs uracil, double stranded vs single stranded, DNA more stable RNA less stable

hairpin

-sequences on same strand are inverted complements
-sequences between inverted repeats forms loop

Meselson-Stahl experiment

After first round, 1 band in between weight (LH)- eliminated conservative replication. After second round, 2 band one LL one LH- eliminated dispersive replication. Proved semi-conservative replication

Taylor Experiment

after S phase autoradiography produces 2 crossed patterns which eliminates conservative replication. After mitosis and S phase under no radioactivity conditions, autoradiography produces 2 strands instead of crossed pattern which eliminates dispersive replication

direction of DNA synthesis

5' -> 3'

Theta replication

DNA replication in prokaryotes

starts at oriC, initiator proteins melt DNA so single strands can act as template
- 1 replication bubble with 2 replication forks
-DNA synthesis happens simulataneously in both directions
-product= 2 circular chromosomes

eukaryotic replication

1 bubble (2 forks) from each origin
Bidirectional DNA synthesis
final product=2 linear chromosomes

lagging strand

made discontinuously, contains Okazaki fragments

DNA helicase

bind after DNA melts and continues denaturing

SSBs

keep DNA melted

topoisomerase

works ahead of replication fork to reduce strain due to helix unwinding

primase

makes an RNA primer using ssDNA as template, short oligonucleotide that provides free 3'-OH for DNA polymerase to add onto

DNA polymerase III

elongates RNA primer by adding new DNA , has 3' -> 5' exonuclease activity to correct mistakes

DNA polymerase I

has 5' -> 3' exonuclease activity to remove RNA primer
has 5' -> 3' polymerase activity to replace RNA primer with DNA
has 3' -> 5' exonuclease activity for proofreading

DNA ligase

seals final hole (nick) in sugar/phosphate backbone

Replication Licensing Factor (RLF)

controls timing of replication initiation in eukaryotes

telomerase

extends DNA at chromosome ends protein part synthesizes new DNA RNA part acts as template for DNA synthesis
expressed in germ cells and stem cells

Chromatin

DNA + proteins

chromosome

chromatin that is highly condensed

heterochromatin

highly condensed (tightly packed) throughout cell cycle- no gene expression

constitutive heterochromatin

always condensed
ex centromeres, telomeres

facultative heterochromatin

condensed at certain times
ex inactivated X chromosome

euchromatin

packaging changes during cell cycle, contains expressed genes

POT proteins

bind single stranded overhang- provide stability and prevent ends from degrading or sticking together

nucleosome

8 histones + DNA

histone proteins

small, positively charged- Arg & Lys amino acids that bind tightly to DNA

linker histone

H1

core histones

H2A H2B H3 H4 (all +2 charge)

epigenetics

study of phenotypic variation caused by variation in gene expression (changes in chromatin structure)

How is level of DNA methylation maintained after DNA replication

*DNA replication
*both DNA molecules are hemimethylated
-methylated on 1 DNA strand
*special methyltransferase enzymes recognize hemimethylated DNA

methylation of nucleotide bases

mostly cytosine, frequently CpG dinucleotides and both strands of DNA are modified

How DNA methylation down-regulates gene expression

1. methyl group in major groove prevents binding of transcription factors
2. creates binding site for histone deacetylase enzymes

acetylation (histone)

masks positive charges, makes binding to DNA weaker

methylation (histone)

creates binding sites for transcription factors- stimulates gene expression or can mark an area for increased or decreased gene expression

DNA methylation in Honeybees

queen is the only one that eats royal jelly, Dnmt3 gene repressed- codes for methyltransferase enzyme > less methylation in genome leads to increased gene expression

X-ist gene

encodes long RNA that does not code for protein, binds X-chromosome from which it was made, attracts protein complexes that methylate histones to turn off gene expression

Tsix gene

keeps active X chromosome from being inactivated
encodes long RNA that does not code for protein- antisense to Xist RNA- prevents Xist expression on activated X

X-inactivation Center

segment of X-chromosme where inactivation begins

Jpx gene

encodes long RNA that does not code for protein- stimulates synthesis of Xist on inactive chromosome

Xite gene

encodes long RNA that does not code for protein-sustains Tsix expression on active X chromsome

genomic imprinting

gene expression affected by whether gene comes from Mom or Dad- results in autosomal traits that show different results for reciprocal crosses

gene conflict hypothesis

explains genomic imprinting

maternal behavior

in rats, when a mom licks and grooms their child, it results in different patterns of DNA methylation which alters expression of stress-response genes and makes them less fearful as adults

chronic stress

male mice exposed to chronic stress produced offspring with blunted hormonal response in HPA axis and expression of genes in stress response. caused by miRNAs in stressed fathers' sperm

cognition

acetylation of histone proteins improved learning and memory in mice with Alzheimers- acetylation decreases with age ->diminished gene expression

euploid

vary by # of complete sets of chromosomes present

aneuploids

vary by # of individual chromosomes present

Intercalary deletion

deletion of internal region

Terminal Deletion

deletion of end of chromosome

psuedodominance

deleting dominant allele -> expression of recessive allele

haploinsufficiency

deleting an allele can lead to gene dosage effects

chromosomal deletion

loss of chromosomal segment, break and then degradation

duplication

2 copies of a chromosomal segment

tandem duplication

chromosome is duplicated and second copy is inserted right after original copy

displaced duplication

copied original chromosome but inserted in a different place

reverse tandem duplication

inserted next to original in different orientation

inversions

chromosomal segment is turned around

paracentric inversion

region inverted does not include centromere
can result in chromatids with 2 or no centromeres

pericentric inversion

region inverted includes centromere
can result in chromatids with duplications & deletions

position effect

effect of a chromosomal inversion in which gene expression is altered because position of regulatory genes are moved

translocation

movement of DNA between non-homologous chromosomes

reciprocal translocation

piece of chromosome moves and gets exchanged

simple translocation

piece of chromosome gets moved to different chromosome

unbalanced translocation

DNA is deleted after break and before translocation happens

balanced translocation

no DNA is deleted after break and before translocation happens

Robertsonian translocation

result from fusion of 2 acrocentric chromosomes
ex. familial Down syndrome

somy

number of copies of a particular chromosome

autopolyploid

same species contributes all chromosome sets, chromosomes are homologous

allopolyploid

different species contribute chromosome sets, chromosomes are homeologous

unreduced gametes

increase in chromosome # happens during meiosis, happens in plants 1-40% of the time, forms autopolyploids

endoreduplication

mitosis where chromosomes replicate but cell doesn't divide

nondisjunction during Meiosis I

results in 2 n+1 gametes and 2 n-1 gametes

nondisjunction during Meiosis II

results in 1 n+1 gamete 1 n-1 gamete and 2 n gametes

nondisjunction during mitosis

results in 2n-1 and 2n+1

Turner syndrome

monosomic for X chromsome (XO)

Triple X Syndrome

trisomic for X chromosome (XXX)

Klinefelter Syndrome

disomic for X chromosome (XXY)

XYY

disomic for Y chromsome (XYY)

Patau Syndrome

trisomic for chromosome 13

Edwards Syndrome

trisomic for chromosome 18

Trisomy 8

trisomic for chromosome 8

Down syndrome

trisomic for chromosome 21