Exam 3- Chapter 13, 14, 15 Flashcards
Describe Griffith’s experiment
-Experimented with streptococcus pneumoniae
-Used virulent S strain and nonvirulent R strain
-Mice injected w/ live S cells died
-Mice injected w live R cells lived
-Mice injected with heat-killed S cells lived
-Mice injected with killed S cells and live R cells lived
Conclusion: some molecule released from S cells transformed the R cells into their virulent form– “tranfroming principle” present
Avery’s Experiment
-Identified the chemical nature of the transforming principle
-Degraded either protein, DNA, and RNA in heat killed S cells
- If proteins or RNA were destroyed, the S still transformed R cells
Conclusion: DNA is the transforming principle
Hershey-Chase experiment
-Established definitively that DNA is the hereditary molecule using E.coli and the bacteriophage T2
-Radioactively labeled DNA with 32P and proteins with 35S
-Found that labeled DNA entered the cell and was present in progeny phages
-There was also little radioactivity inside the E.coli cell for radioactive protein
Structure of a nucleotide
-5 carbon sugar (deoxyribose)
-phosphate group attached to 5’ side and 3’ side to link nucleotides together
-nucleotide (A,C,G, or T) attached to 1’ side
Purines
Adenine and Guanine
Pyrimidines
Thymine and Cytosine (also Uracil)
How many bonds do C and G form?
3
How many bonds do A and T form?
2
How many rings in A and G?
Two
How many rings in C and T?
One
What is Chargaff’s rule?
- Amount of purines=amount of pyrimidines (adenine=thymine, guanine=cytosine)
- Ratio of guanine+cytosine:adenine+thymine is species specific
What bond links adjacent nucleotides together?
Phosphodiester bond
Where is the hydroxyl end of a sugar?
The 3’ end
What did Wilkins and Franklin discover?
They used X-ray diffraction to find the double helical structure of DNA
DNA diameter
2 nm
Length between base pairs
.34 nm
Number of base pairs in one twist
10
Length of one helical twist
3.4 nm
Double-helix model
- DNA is double stranded and right-handed, forming a double helix 2 nm in diameter
- Sugar-phosphate backbones are on the outside of the helix, with base pairs on the inside
- Two strands are antiparallel
- Base pairs connect the sugar-phosphate backbones
- Base pairs lie flat and perpendicular to the long axis of the DNA molecule
- DNA has major and minor grooves
What model of replication did Watson and Crick propose for DNA replication?
Semiconservative replication
Semiconservative replication
Two parental strands of DNA unwind, and each is a template for a new strand. Each new DNA molecule has 1 parental and 1 new strand
Conservative replication
Parental strands of DNA unwind, each is a template, and parental strands pair up again. No new DNA is mixed with the old DNA
Dispersive replication
Double helix splits into segments and intersperse with old and new
Which end does DNA polymerase add on to?
3’ end only (synthesizes new strands in 5’ to 3’ direction)
Which direction does DNA polymerase read the template in?
3’ to 5’
Sliding clamp
A protein that encircles DNA and binds to the rear of DNA polymerase, anchoring the DNA polymerase to the template
What would happen without the sliding clamp?
DNA polymerase would detach only after a few polymerizations
Topoisomerase
Cuts DNA ahead of replication fork to prevent twisting
RNA primers
Synthesized by primase, gives DNA polymerase a free 3’ end to add onto
Okazaki fragments
Short lengths produced by discontinuous replication in opposite direction to unwinding, gradually as the DNA unwinds since DNA polymerase can only synthesize in the 5’ to 3’ direction (occurs on the lagging strand)
DNA polymerase III
Main polymerase- extends primer by adding DNA nucleotides
DNA polymerase I
Removes RNA primer at 5’ end of previous newly synthesized okazaki fragment, replacing it with DNA nucleotides
DNA helicase
unwinds the DNA
T or F: the lagging strand uses more than one primer
T
When does new DNA synthesis stop on the lagging strand?
When the polymerase reaches the 5’ end of the previously synthesized okazaki fragment
T or F: DNA polymerase has 5’ to 3’ exonuclease activity and 5’ to 3’ polymerizing activity
T
DNA ligase
Seals space between adjacent fragments
DNA polymerase 1
Acts on lagging strand to remove primers and replace them with DNA- has 5’ to 3’ exonuclease activity
DNA polymerase II
DNA repair
DNA polymerase III
Main replication enzyme
All three DNA polymerases have what activity
3’ to 5’ exonuclease activity (proofreading)
Why does the lagging strand loop around
So that primase can synthesize the primer for the next fragment- this loop becomes smaller as replication proceeds
Replisome components
Primosome- primase, helicase, SSB, topoisomerase
2 DNA POL III
How many replication forks happen in a bacterial chromosome?
Two, proceeding bidirectionally away from eachother
How many oris present in eukaryotes?
multiple
Why is the RNA primer a problem for linear chromosome replication?
New DNA synthesis on the 3’ to 5’ template starts with a primer and is removed, but this leaves a region at the 5’ end after it leaves. DNA polymerase cannot add onto this region . THis creates a shortened chromosome
Telomeres
Repeated DNA sequences (5’ TTAGG 3’ on the template strand. It binds to the single stranded 3’ end of the chromosome via complementary base pariing and synthesizes new telomere DNA using telomerase RNA as the template. 3’ end hangs over 5’ end
What enzyme makes telomeres?
Telomerase (stops shortening of chromosome ends by adding on telomere repeats)
Do telomeres shorten with age?
Yes
How to tell cancer cells apart from others?
Telomerase is upregulated so chromosome length is preserved, allowing for indefinite division
Nucleosomes in DNA replication
Nucleosomes first disassemble as replication fork passes, then reassembles into nucleosomes (mix of new and parental histones)
Types of repair mechanisms
- Proofreading- corrects errors made by dna polymerase during replication
- mismatch repair- occurs after proofreading
excision repair- corrects dna damage such as those caused by chemicals and radiation
What is the most common error for DNA polymerase?
base-pair mismatches
what happens if an error occurs in proofreading?
DNA polymerase reverses using 3’ to 5’ exonuclease activity to remove incorrect nucleotide, adds correct one, then resumes
Proofreadinf leaves about ___ in 107 erorrs, and mismatch repair corrects about ____%
1, 99
How does a postreplication error become corrected after proofreading?
mispaired base detected, DNA is cut on either side of the mismatch and removed, and DNA pol 1 fills in the new gab with DNA, and sealed with DNA ligase
Nonbulky damage
No DNA bulging
Base excision repair
removes erroneous base and replaces it with the correct one, is the most important fixing mechanism after proofreading
Bulky distorsions
UV light causes adjacent thymines to form dimers, which bulge out and affect DNA synthesis. Nucleotide excision repairs remove the segment and replace it with new DNA (XP) is caused by a defect in excision repair, causing sensitivity to UV light
Mutations
Replication errors and DNA damage that remain unrepaited
George Beadle and Edward Tatum hypothesis
Neurospora uses chemicals in MM to synthesize more complex molecules
Auxotrophs
Mutant strains that require a nutrient supplement in the MM to grow
Srb and Horowitz experiment
3 arginine auxotrophs- found that each of the three arg genes encoded an enzyme that controls a different step in the arginine pathway
wildtype grew on all four
arg-1 grows on mm+arginine but not on mm+ citrulline or ornithine
arg-2 grows on mm+arginine or citrulline but not on ornithine
arg-4 grows on all except mm+nothing
what was the one-gene-one enzyme hypothesis later modified to?
one gene one polypeptide
Transcription
genetic info in DNA transferred to RNA
translation
use of info encoded in RNA to assemble amino acids into a polypeptide
central dogma
dna, rna, polypeptide
What enzyme copies DNA into RNA?
RNA polymerase
Difference between replication and transcription
Only 3’ to 5’ strand is used and only a small part of a gene is copied at any time
T or F: transcription and translition only occur in some organism
F
What makes eukaryotic transcription different?
A precursor mrna is produced, and extra segments are removed by RNA processing, after which mrna exits nucleus and is translated in cytoplasm
where does transcription occur in bacteria
cytoplasm
Codon
a 3-letter triplet of the code
which strand of DNA does RNA polymerase read?
the 3’ to 5’ nucleotide sequence
features of the genetic code
3-letter code, commaless, universal, and degenerate, with stop and start codons
Stop codons
UAA, UAG, and UGA
start codon
aug- methionine
how many codons specify amino acids?
61/64 (methionine and tryptophan only coded by one)
hammerling experiment
-cells of green alga cut into pieces and observed, discovered that hereditary information is stored in cell’s nucleus (nucleus in base determines type of cap regenerated)
Promoter
a control sequence for transcription (TATA box- TATAAT), 25-35 base pairs upstream of transcription start point
Transcription unit
section of gene that is copied into an RNA molecule
which rna polymerase is involved in transcription?
rna polymerase 2
consensus promoters
-10: tataat
-35: ttgaca
initiation
transcription factors bind to promoter area of tata box, and recruit RNA pol II. dna is unwound ahead of rna polymerase 2 to expose the template, tf’s are released
elongation
rna polymerase proceeds in the 5-3 direction
difference between eukaryotes and bacterial genes
in bacteria, rna polymerase directly binds, and in bacteria, specific dna sequences called terminators end the transcription of the gene
rna polymerase 3
transcribes trna and 1/4 rrnas
rna polymerase 1
transcribes 3 other r rna genes
pre-mrna
typical eukaryotic protein coding gene is transcribed into a precursor mrna, which then undergoes processing
introns
non-protein coding regions
is there a terminator in eukaryotic dna
no; transcription continues past end of gene and eventually stop
what is at the 5’ end of a pre-mrna?
a modified gtp molecule called 5’ cap added soon after rna pol 2 begins transcription and remains when premrna is converted to mrna. this is where a ribosome binds at the start of translation
polyadenylation signal
near 3’ end of gene, is transcribed into premrna, and proteins bind and cleave just downstream. then polyA polymerase ads 50-250 adenine nucleotides to form a poly-A tail
what do the 5’ cap and the 3’ poly-A-tail do>
prevent digestion
exons
protein coding sequences- include the 3’ and 5’ untranslated regions
prokaryotic transcription
single rna polymerase exists as core and holoenzyme
- core: 2 alpha, 1 beta, one beta prime
-holo enxyme: core+sigms subunit (during transcription, sigma dissociates, since it is the one that recognizes promoters)
betas are active site, alphas hold complex together
mrna splicing
removes introns from pre-mrnas - takes place in a spliceosome, which is a complex formed between premrna and small nuclear ribonucleoprotein (snrna bound to proteins)
how does splicing happen?
snrnas bind to specific sequences at 5’ and 3’ ends defining juncitons and cleaves it to release mrna (the complex loops out the intron and brings exon ends close togenter, then cleavage occurs and intron loops in a lariat structure while exons join together
alternative splicing
exons joined in different combinations to produce different mrnas from a single gene- increases number and variety without increasing genome size- 95% of human genes
what percent of mutations in protein coding genes adversely affect splicing?
35
alpha-tropomyosin gene
undergoes alternative splicing in smooth muscle, skeletal muscle, liver, and brain (exons 2 and 12 in smooth, 3, 10, and 11 in striated)
exon shuffling
exons of 2+genes to produce a gene encoding a protein with unprecedented function
what did transcriptonomics in encode teach us
pervasive transcription (74%)
variable expression of protein-coding genes to produce gene isoforms
translation
reading of mrna to create a polypeptide chain
tRNAs bring amino acids to complex to be joined into polypeptide chain
what direction is mrna read in
5-3
what direction is polypeptide assembled in?
n terminal to c terminal
tRNA structure
70-90 nucleotides, cloverleaf shape where tip of one helical segment is anticodon, and the other end is amino acid corresponding to anticodon; amino acid binds to 3’ end
how do codon and anticodon pair?
antiparallel manner
wobble base pairing-
pairing between 3’ base of codon and 5’ base of anticodon is less stringent, so less accurate base pairing ; a trna can read more than one codon so fewer trnas can accommodate all codons
anticodon- g can pair with u or c in codon
u can bind with a or g
i can bind with a, u, or c
where is peptidyl transferase activity formed
lsu of ribosome- alows peptide bond formatio between amino acids
A site
where incoming trna with amino acid joins
p site
where trna with polypeptide chain is bound
e site
trna emptied binds here and leaves
translation initiation
components assemble on start codon of mrna
translation elongation
amino acids are joined into polypeptide
translation termination
complex disassembles
how is translation fueled
gtp hydrolysis
polysomes
entire structure of mrna and multiple ribosomes attached
T or F: most proteins are inactive after translation
T- finished forms may include amino acid removal, addition of carb or lipids, or combination with other polypeptides
pepsin has inactive precursor called pepsinogen, acidity removes a segment of amino acids and converts the enzyme into active form- this protects other cells from being degraded
where are proteins sorted?
cytosol (free ribosomes), endomembrane system, or other organelles (free ribosomes)
base pair/point mutation
change of single base pair in genetic material
missense mutation
sense codon changed to one coding for another amino acid (hemoglobin- glutamic acid to valine, leading to nonpolar beta sites that are stickly and form sickle cell shape)
nonsense mutation
sense codon changed to stop codon
silent mutation
no change in amino acid
drame shift
insertion or deletion
spontaneous mutations
suddenly occur naturally in cell- replication or chemical activity
induced mutations
organism exposed to physical or chemical agent, occurs much more commonly. can replace a base in dna, alters a base, or damages a base (radiation and chemical mutagens)
UV light is nonionizing radiation, all forms of ionizing radiations can cause mutations. chemical mutagens are naturally ocurring and synthetic, - food, cosmetics, environment (benzpyrene becomes a mutagen after metabolism)
sex-linked genes
genes on chromosomes that are different in males and females
autosomes
genes on chromosomes other than sex chromosomes
why is the female the homogametic sex?
she has only one type of gamete with respect to the sex chromosomes. the male has two (x or y) so sperm can either be x or y
other sex chromosome arrangements
xx females, xo males in some insects
zz males, zw females in reptiles, birds, butterflies
bees and wasps: diploid is female, haploid is male
yeast has two sex types, a and alpha
what does human sex determination depend on?
the y chromosome, which contains the SRY gene that switches development towards maleness (x chromosome is mainly nonsexual). this means that originally the reproductive organs are similar, then sry activates and stimulates testes formation. this degenerates the ovaries. in females, male structures degenerate
T or F: a particular gene on the y chromosome is key to human sex determination . this means that genes for sex development are inherited in both males and females, but only certain genes are expressed due to regulation
T
What features cause sex linkage?
alleles on x chromosome occur twice on females but only once on males, and alleles on y chromosomes are not present on females
Morgan sex linkage experiment
Red eyes (dominant) female with white eye male produced all red eyed progeny (Females are XRXW and males are XRY)
when this generation reproduced, progeny were XRXR, XRY, XRXW, XWY so all red eyed females and 1/2 red, 1/2 white eyed females, indicating white-eye chromosome is on x (3/4 red, 1/4 white)
With white female and red male, 1/2 of F1 and F2 generations were red or white
crisscross inheritance
x-linked allele from a parent of one sex to a child of opposite sex to grandchild of first sex
x-linked inheritance
pattern of inheritance of a x-linked gene
what is an indicator of x-linked inheritance of a recessive trait?
all male offspring have the mutant phenotype if their mother has the mutation
queen victoria hemophilia
heterozygous for recessive hemophilia allele,
how are the activities of x genes equalized in males and females?
x chromosome inactivation- folding and packing of chromatin of one of the x chromosomes into a condensed, inactive state called a barr body (visible as a mass of heterochromatin) occurs early in embryonic development. same x chromosome will be deactivated in all descendants of the cell
how is an x chromsome inactivated?
xist- expressed by inactivated x, creating an rna that will not be translated, this rna coats the x chromosome and inactivates it
what happens if two x chromosomes carry different alleles of a gene?
inactivation may produce recognizably different effects
in calico cats, o allele on x chromosome is for orange, and b gene on autosome is for black. if o on x chromosome is active, b gene is masked, but if o allele is inactive because its x chromosome is inactive, b gene will be expressed
anhidrotic ectodermal dysplasia (patchy sweat glands)
deletion
broken segment lost from a chromosome (deletion of chromosome 5 is cri-du-chat)
duplication
segment transferred from one chromosome and inserted into homolog so homolog has inserted fragment twice
can be beneficial since mutations have less efffect (may happen during crossing over)
translocation
broken segment attached to different nonhomologous chromosome- common in cancer where philadelphia chromosome and causes uncontrolled cell growth
inversion
broken segment reattaches to same chromosome but reversed
nondisjunction in first meotic division
both chromosomes of one pair pulled to both sides, causing two gametes with extra and two gametes with not enough chromosomes
nondisjunction in second division
one cell has 3 homologs, one has 1, other two are normal
aneuploids
individual with extra or missing chromosomes
down syndrome
nondisjunction in chromosome 21 (risk increases with age of mother)
XO
turner syndrome- sterile, normal indelligence, underdeveloped
XXY
klinefelter syndrome- male genitalia
XXX
triple x syndrome- slight cognitive impairment
XYY
normal but taller than average
T or F: people with a Y chromosome are externally male even if a X chromosome is present
T
Monoploid
one set of chromosomes
autosomal recessive inheritance
phenylketonuria, sickle cell anemia, cystig fibrosis- autosomal recessive inheritance, homozygous for recessive allele show trait
Phenylketonuria- cannot convert phenylalanine to tyrosine, leadning to buildup causing mental retardation (cannot consume aspartame)
- most affected individuals have 2 noemal parents
may skip generations
autosomal dominant
does not skip generations
at least one parent of affected child must be affected
achondroplasia (dwarfism)
progeria
duchenne muscular dystrophy
x-linked recessive
x-linked recessive
-more males than females, all sons of affected mother should be affected
x-linked dominant
enamel hypoplasia, constitutional thrombopathy
more in females
males with x dominant pass it on to all daughters
genetic counseling
counselors can predict likelihood of children with the disease
prenatal diagnosis
amniotic fluid or cells tested (amniocentesis) or chorionic villus sampling
where does mitochondria come from
mother (uniparental)
cytoplasmic inheritance
inheritance follows that of genes in cytoplasmic organelles
