General Genetics Exam 2
Hershey & Chase concluded DNA was the genetic material in part because they found: A. Avirulent Diplococcus would kill a mouse when mixed with heat-killed virulent bacteria. B. RNase failed to prevent the transformation of a rough colony of Streptococcus into a smooth one. C. 35S from viruses entered cells. D. The nucleotide composition of ox thymus was the same as that of ox spleen. E. Bacteriophage coats/ghosts contained no DNA.
E. Bacteriophage coats/ghosts contained no DNA.
prokaryotic core promoter sequences
E. coli core promoters - two consensus sequences in core promoter - located at -10bp and -35bp upstream from the transcription start site
GTP is
ENERGY
how is it replicated?
- semiconservative mode (DNA) --> Meselsohn + Stahl experiment - from replication origins - replicons - DNA is replicated semidiscontinuous mode --> Okazaki fragments - bidirectional mode
after termination (eukaryote): 5' capping mRNA capping
1. cleave phosphate 5' nucleotide 2. GMP 5'-5' phosphodiester bond (phosphatase) 3. add methyl group - methylation (methyl transferase) **IN NUCLEUS
Which enzyme fills in small regions of DNA where the RNA primers were located? DNA primase DNA polymerase III topoisomerase DNA ligase DNA polymerase I
DNA polymerase I
Which enzyme synthesizes the lagging strand of the DNA? DNA primase topoisomerase DNA ligase DNA polymerase I DNA polymerase III
DNA polymerase III
DNA Pol II (pro)
DNA repair
DNA recombination definition
DNA strands are cut and rejoined with different straands
translation 16s binds to
Shine-Dalgarno sequence
T/F An example of RNA editing by deamination is the removal of an amino group from cytosine via cytidine deaminase thereby creating uracil.
True
genetic coding: stop
UAA, UAG, UGA
Antibiotics: Chloramphenicol
blocks the peptidyl transferase reaction on ribosomes - STOPS TRANSLATION
helicases
break hydrogen bonds
RNA pol III
core promoter binds general transcription factors TFIII
proteins in E. coli DNA replication: DNA ligase
covalently attaches adjacent Okazaki fragments
three point cross
cross between an individual heterozygous at three loci and an individual homozygous for recessive alleles at those loci (AaBbCcxaabbcc = AaBbCc x abc)
topoisomerase
cuts DNA to reduce torsional stress (torsional = pull apart for replication fork)
The recombinant gremlins of the F2 generation were produced by crossing over that occurred:
during spermatogenesis in the F1 males.
differences in replication of pro and eukaryotes
linear chromosomes DNA + histone = chromatin - DNA is negatively charged wrapped in proteins called histone (+ charged) for compaction/condensation/wrapping
eukaryotic termination
linear chromosomes = ENDS - telomeres
differences in translation
location - pro: nucleoid - eu: cytoplasm rRNA + ribosomal subunit sizes different peptidyl transferase activity docking sequence - PRO: SHINE-DALGARNO - EU: KOZAK SEQUENCE - initial AA - inititation/elongation/release factors
An organism with one less chromosome, (2n-1) is
monosomic
ribonucleotides are more/less stable in triphosphate state?
more
Transcription in Eukaryotes
more complex
RNA pol II
most complicated - mRNA is translated into proteins
general RNA synthesis formula
n(XTP) --> (XMP)n + nPPi (pyrophosphate - disphosphate) - synthesized 5'-3' - phosphodiester bonds (5'-3' bond)
DNA joined via a phosphodiester bonds
n(dXTP) --> (dXMP)n + nPPi
Met
n-terminal end
calculation of interference: # observed d/co > # expected d/co
negative interference
calculation of interference: #observed d/co = # expected d/co
no interference
prokaryote polymerase properties: initiation of chain synthesis
no polymerase
termination - stop codon
no tRNA 1. tRNA and polypeptide chain released 2. GTP dependent termination factors stimulate the release of tRNA and the dissociation of the ribosomal subunits, polypeptide folds into a protein
Elizabeth Blackburn, UCSF
nobel prize in physiology or medicine 2009 - repetitive sequence
B-DNA
predominant form in living cells - right hand double helix - 10 bp/turn - bases are relatively perpendicular to central axis
why exploit differences in translation for pro and eu?
prevent illness from mistakes
central dogma: transcription
produces an RNA copy of a gene
apoptosis
programmed cell death
discovery of DNA structure: Rosalind Franklin + Maurice Wilkins
proivded data for DNA strucutre through x-ray diffraction studies
-10bp pribnow sequence
prokaryotes
RNA pol I
promoter - core promoter = core element -1 to -45 bp (-) is upstream - regulator sequence, UCE (upstream control element) -107 to -156 bp
DNA Pol I (pro)
proof reading, removes primer, fills gap
discovery of DNA structure: Linus Pauling
proposed alpha-helical structure for proteins, and pioneered the use of physical model
lifecycle of bacteriophages
protein and DNA - lytic cycle
prokaryote replication: additional requirements
proteins
polyribosomes
proteins - amino terminal end + caroxyterminal end
players in translation
rRNA + ribosomal proteins = small and large ribosomal subunits
Hershey-Chase Experiment labeling
radioactive labeling of molecules labeled DNA-nucleotides with radioactive phosphorous (32P) DNA 32P - nucleotide protein 35S - some amino acids
5' capping
refers to the attachment of a 7-methylguanosine (m7G) to the 5' end of mRNA which plays a role in the splicing of introns, the exit of mRNA from the nucleus, and the binding of mRNA to the ribosome.
3' poly A tailing
refers to the attachment of a string of adenine-containing nucleotides to the 3' end of mRNA which is important for RNA stability and translation in eukaryotes.
RNA processing
refers to the cleavage of a large RNA transcript into smaller pieces which produces one or more smaller functional RNA molecules.
base modification
refers to the covalent modification of a base within an RNA molecule; such as the methylation or acetylation of a base.
snRNA
small nuclear RNA is necessaary in the splicing of eukaryotic pre-mRNA, are components of a spliceosome, which is composed of both snRNAs and proteins subunits
rRNA is measured in S unites
small ribosomal units + large units = ribosome
translation in eukaryotes: transcription and translation
spatially separated - transcription - nucleus (all RNAs must be transported out of the nucleus) - translation - cytoplasm polyribosomes
microRNA (miRNA), telomeric RNA (telomerase), small nuclear RNA (snRNA)
splicing
eukaryotic translation termination
stop codon (no complementary tRNA) = release factors
chromosomal DNA
stores information in units called genes
Nucleotides are linked together in a linear manner to form a...of DNA
strand
ionic concentrations
stress forces cells into different pH ranges
DNA is negatively charged
surrounded (wrapped) in positively charge proteins (in nucleus) --> pH factor (ionic concentrations)
polymerases (holoenzymes - many different activities)
synthesis, endonuclease/exonuclease activity
primases
synthesize RNA
leading strands
synthesized continuously in 5' to 3' direction
proteins in E. coli DNA replication: primase
sythesizes short RNA primers
reverse transciptase activity is a property...
telomerase
mRNA transcription is based on
template strand
What enzyme relaxes supercoiling ahead of the replication fork? DNA primase DNA ligase DNA polymerase III topoisomerase DNA polymerase I
topoisomerase
prokaryote replication: accessory enzymes
topoisomerases, helicases, ligases etc.
tRNA
transfer RNA is necessary for the translation of mRNA
Frederick Griffith is responsible for discovering what process? transmission transformation replication transduction
transformation
Griffith's experiment
transformation experiment conclusion: some "transforming principle" something from dead IIIs bacteria transformed live IIR bacteria into live IIIs bacteria
movement along the ribosome along mRNA is called
translocation
An organism with three sets of chromosomes (3n) is
triploid
An organism with one extra chromosome, (2n+1) is
trisomic
Humans normally have two sets of 23 chromosomes for a total of 46. Individuals with Down syndrome have an extra chromosome 21, and thus have 47 chromosomes. How would this chromosomal anomaly be classified?
trisomy
abnormalities in autosomes: Patau syndrome
trisomy 13 (47)
abnormalities in autosomes: edward syndrome
trisomy 18 (47)
abnormalities in autosomes: down syndrome
trisomy 21 (47)
After the action of the helicase, single-stranded binding proteins keep the parental DNA strands from reforming a double helix. True False
true
Basal transcription in eukaryotes involves the action of only the core promoter. True False
true
T/F A crossover involving a paracentric inversion produces a dicentric chromosome.
true
T/F An individual carrying one copy of a normal chromosome and one copy of an inverted chromosome is known as an inversion heterozygote.
true
T/F Certain RNA molecules such as rRNAs and tRNAs are processed to smaller, functional molecules via cleavage.
true
T/F In order for an inversion heterozygote to undergo crossing over, an inversion loop must form so that the homologous genes on both chromosomes align next to each other despite the inverted sequence.
true
T/F The 5' 7-methylguanosine cap is required for the proper exit of most mRNAs from the nucleus, is recognized by translational initiation factors, and may be important in the efficient splicing of introns.
true
T/F When a pre-mRNA has multiple introns, variation may occur in the pattern of splicing, so the resulting mRNAs contain alternative combinations of exons, a phenomenon known as alternative splicing.
true
The ability of the DNA polymerase to remove mismatched bases is called exonuclease cleavage (proofreading). True False
true
translation can start before transcription ends true false
true - ribosome already at Shine-Dalgarno
mRNA can be translated continuously true false
true polyribosomes
DNA replication process
two DNA strands come apart each serves as a template for synthesis of new strands two newly-made strands = daughter strands/new strands originals (2x) - parental strands
reciprocal translocation in the allele
two parallel strands translocate in the next system: AB/HI --> HI/AB - nonhomologous
puring
two ring = guanine, adenine
promoter sequence
upstream of transcription start site, but not transcribed = 5' of transcription start site called +1
to extend the 3' ss overhang
use telomerase enzyme - binds to 3' G rich tail
helix specifics
width = 2nm = 20 Ang one turn = 3.4 nm = 34 Ang (10 bp/turn) one turn has a major and minor groove two strands are antiparallel
distance between all genes
work out RF between each gene, convert to distance
abnormalities in sex chromosome #: triple x
xxx (47) female
can we exploit the differences between replication in prokaryotes vs eukaryotes?
yes - targeted antibiotics
ARS
autonomosly replicated sequences (efficient)
abnormalities in sex chromosome
due to non-disjunction in meiotic cell cycle
replication of DNA 2. daughter DNAs
duplexes/new and old/template strands
endonuclease
"within" "degrade" nucleic acid = cut within polynucleotide
prokaryote RNA transcription initiation
+ DNA (Closed primer) + RNA pol enzyme + general transcription factors = sigma factors = RNA polymerase holoenzyme
transcription start site
+1, bases preceding this are numbered in a negative direction (no # zero) - bases to the right are numbered as positive
eukaryotic translation initiation
- 40s small ribosomal subunit - mRNA (5' capped) - initiator tRNA (charged with methionine --> P site) - initiation factors (GTP) - docking of mRNA in the small subunits
prokaryote initiation
- ONE origin of replication (circular chromosome) - specific DNA sequence - rich in AT = AT rich oriC = 2 hydrogen bonds (amount of energy needed to open replication bubble is less than if it was packed with G/C
transcription
- RNA is a single stranded molecule non-coding RNAs - tRNA + rRNA
tRNA = transfer RNA
- adapter molecule - b/c one end must recognize the mRNA other end must interact with amino acid
summary of recombination
- alignment - nicking/single strands reaks in chromosomes - crossing over, sealing of DNA strands - strand invasion - chi structure + resolution of chi structure - same strand nicking = two heteroduplex DNAs + different strand nicking - two recombinant DNAs
DNA recombination
- between sister chromatids - prophase I of Meiosis I - genetic maps - crossing over - levels of chromosomes (non-sister chromatids)
enhacer/activator sequence
- binds activator (specific) transcription factors - increase rate of transcription
repressor/operator sequence
- binds repressor (specific) transcription factors - decrease rate of transcription
replication in pro and eukaryotes - differences
- circular/linear chromosomes - naked DNA/chromatin +initiation - naked DNA, one origin/chromatin, many origins + elongation - DNA pol - I,II,III/Greek letters + termination - Ter and Tus/telomerase
tRNA structure
- clover leaf structure - folds upon itself - by base pairing - processed - RNA processing - modified bases - RNA editing
DNA nucleotides
- covalently linked together by a phosphodiester linkage = stable in triphosphate deoxyadenylic acid (dAMP), deoxycytidlyic acid (dCMP), deoxyguanylic acid (dGMP), deoxythymidylic acid (dTMP)
hybridization experiments
- denature of DNA - separate the 2 strands - SS DNA will hybridize to MATURE RNA - proves the presence of precursor RNA (hnRNA)
after termination (eukaryote): splicing
- intron + exon DNA sequences - introns and exons DNA are transcribed *introns spliced out, exons stitched in - self-splicing - ribozymes - evidence of splicing - template SS dna and mature mRNA molecules **IN NUCLEUS
eu - RNA pol I
- nucleolus transcribes rRNA (28s, 18s, 5.8s rRNA)
transcription in prokaryotes
- one cell organism - occurs in cytoplasm/nucleoid - naked DNA - only 1 RNA polymerase
transcription - gene expression
- process of making a copy - refers to the copying of a DNA sequence into an RNA sequence -RNA polymerases- RNA pol - the sequence of DNA is not altered as a result of this process
how are RNA pol + transcription factors + specific DNA sequences related?
- promoter sequence (core promoter) - regulatory sequences/elements
post-traditional modification in eukaryotes
- removal of N-terminal methionine - addition of glycan groups (glycoproteins) --> sugars to proteins - organelles - golgi, RER, ER (NOT IN PROKARYOTES)
two types of termination - prokaryotes
- rho-dependent (rho protein) - rho-independent (other proteins and RNA sequence
similarities in translation
- ribosomes - small + large subunits - tRNA (amino acyl) - mRNA - GTP - energy - elongation - termination - 1 post-traditional modification
replication in pro and eukaryotes - similarities
- semi-conservatice - semi-discontinuous - replicons - bi-directional + initiation = replicons, consensus DNA sequences and specific DNA binding proteins + elongation = DNA pol + termination = termination sequences
pribnow box
-10bp site, (TATAAT)
DNA double helix structure
-anti-parallel strands one 5'->3' other 3'->5' - right handed helix - 10 BASES AND 3.4NM PER COMPLETE TWIST - bases are perpendicular to backbone - sugar phosphate backbone -stabilized by hydrogen bonds between nitrogenous bases -built 5'->3' because nucleotides come from nucleoside triphosphates and favour the open 3' ends OH -loss of 2 phosphate groups is favourable (negativity of phosphate groups increase PE)
DNA nucleosides
-no phosphate group deoxyadenosine, deoxyguanosine, deoxycytidine, deoxythymidine
interference
1- observed # of d/co/expected # of d/co
Avery, McCarty, MacLeod steps
1. IIIS cells in liquid culture centrifuge 2. IIIs cells spun to bottom of bottle heat-kill 3. homogenize cells - recover IIIS filtrate extract lipids 4. carbohydrate proteins, DNA, RNA ? 5. Treat with protease (transformation) active factor NOT PROTEIN 6. treat with ribnoculease (transformation) active factor NOT RNA 7. treat with deoxyribonuclease (no transformation) active factor DNA
3 stages of transcription
1. Initiation - RNA polymerase binds to DNA 2. Elongation - RNA polymerase synthesizes RNA 3. Termination - RNA polymerase stops sythesizing RNA
transcription enzymes
1. RNA polymerase 2. transcription factors (TFs) - proteins
similarities in transcription
1. RNA polymerase enzymes (3) 2. general transcription factors (basal) - specific transcription factors - change rate (activators bind the enhancer sequences and repressors bind the operator/silencer sequences) 3. promoter sequence (core) and regulatory sequences (enhancer and operator/silencer/repressor sequences)
differences between RNA + DNA
1. Uracil (RNA) = Thymine (DNA) 2. ribose/deoxyribose 3. DNA is double stranded - if single stranded = degraded in cell 4. RNA shapes
resolving of chi structures in 1 of 2 directions
1. a second nick is created in the strands involved in crossing over and sealing - two heteroduplex DNA molecules - minimal exchange 2. a nick is created in the strands not involved in crossing over and sealing - resolve the chi structure - two recombinant DNA molecules - maximum exchange
initiation in eukaryotes
1. chromatin remodeling complex (CRC) - disrupt nucleosome structure 2. many origins of replication (replicons) on linear chromosomes - ARS -specific DNA initiation proteins - specific DNA sequences (consensus) - specific helicase
similarities between RNA + DNA
1. deoxy/nucleoside TP as precursors - DNA: n(dXTP) --> (dXMP)n + nPPi - RNA: n(XTP) --> (XMP)n + nPPi 2. nucleotides - phosphodiester bonds, 5' phosphate group of incoming nucleotide to 3' OH group of previous nucleotide 3. both DNA and RNA have a 5' end and a 3' end 4. both synthesized in 5' to 3' direction
after termination (eukaryote): 3' poly A tail
1. endonuclease - cleavage 2. poly A polymerase - adds poly A ** increase stability of the mRNA molecule **IN NUCLEUS
initiation
1. enzyme (RNA polymerase) 2. proteins called transcription factors - rate of transcription 3. specific DNA sequences of the gene - promoter sequences -core promoter and regulatory sequences
central dogman of genetics
1. gene (Chromosomal DNA + stores information in units called genes) -transcription: produces an RNA copy of the gene 2. messenger RNA -translation: produces a polypeptide using the information in mRNA 3. polypeptide - becomes a part of a functional protein that contributes to an organism's trait
Griffith's experiment steps
1. injecting living IIIS (virulent) to mouse = mouse dies 2. injected living IIIR (avirulent) to mouse = mouse lives 3. injected heat killed IIIS to mouse = mouse lives 4. injected living IIIR and heat killed IIIS to mouse = mouse dies
steps of translation initiation
1. mRNA binds to small subunit along with initiation factors 2. initiator tRNA fmet binds to mRNA codon in P site 3. large subunit binds to complex, tRNA, into A site
DNA polymerases process two unusual features
1. they synthesize DNA only in the 5'-3' direction 2. cannot initiate DNA synthesis - pose a problem at the 3' end of the linear chromosome = the end of the strand cannot be replicated
Hershey-Chase Experiment steps
1. when bacteriophage infect bacteria, they transfer their genetic material to the bacteria 2. bacteriophage are composed of protein and DNA - protein or DNA transferred? - genetic material?
How many bases are necessary to complete one complete twist (360 degrees) of a DNA helix? 1000 100 10 5
10
ribosomes/subunits
16s rRNA + proteins = 30S 23 rRNA + 5S rRNA + proteins = 50s 50s subunit + 30s subunit = 70S ribosomes
eukaryotes: ribosomal subunit
18s, 28s, 5.8s,(=40s) 5s ( = 60s) 40s+60s=80s ribosome
James Watson + Francis Crick
1953 - published description of the structure of DNA - testing predictions based on available data they used ball-and-stick method that incorporated all known experimental observations
A=T
2 hydrogen bonds
In humans, there are _______ autosomal linkage groups, plus an X and Y chromosome linkage group. 92 46 23 22
22
anthrax
Bacillus anthracis - ciproflaxacin - bioterrorist weapon --> created by bacteria
A map distance of 23.6 between two genes indicates which of the following? 23.6% of the offspring exhibit recombination between the two genes. There are 23.6 other genes between the two genes of interest. The genes are 23.6 millimeters apart. 23.6% of the offspring do not survive.
23.6% of the offspring exhibit recombination between the two genes. The map distance is defined as the number of recombinant offspring divided by the total number of offspring, multiplied by 100. One map unit is equivalent to a 1% frequency of recombination.
C=G
3 hydrogen bonds
basic DNA replication
3' - 5' coding 5'-3' template
DNA replication cannot replicated ends of linear chromosomes
3' ss overhang - single stranded overhang *DNA does not like SS --> will be degraded
How many base pairs would be expected within three turns of a molecule of DNA? 3.4 0.34 300 340 10 30
30 There are about 10.0 nucleotides in each strand of DNA per complete 360° turn of the helix. Thus in three complete turns there would be 3 x 10 base pairs = 30.
initiation
30S small ribosomal subunits - mRNA - initiator tRNA charged with formyl methionine
Wobble Hypothesis - 3rd base
3rd base in codon is irrelevant and cannot be explained by the hypothesis alone
The correct tRNA is matched to each codon in the mRNA based on 1. three amino acids in the middle of its rRNA sequence. 2. the entire tRNA sequence. 3. which amino acid it is carrying. 4. three nucleotides in the middle of its tRNA sequence
4. three nucleotides in the middle of its tRNA sequence
how many possible codons?
43=64 - 61 codons for 20 amino acids
What process is important for the initiation of translation? 5' capping RNA editing base modification alternative splicing 3' polyA tailing
5' capping
Which of the following correctly depicts the directionality of the DNA molecule? 3' to 5' All DNA molecules are different in their directionality. 5' to 3' top to bottom right to left
5' to 3'
Kozak sequence
5' untranslated sequence (5'-UTR) in the mRNA that binds to 18s rRNA
transcription is asymmetric
5'-3' = top strand, coding strand, sense strand 3'-5' = bottom strand, template strand, antisense strand
which contains the three posttranscriptional modifications often seen in the maturation of mRNA in eukaryotes?
5'-capping, 3' poly A tail addition, splicing
Determine the base sequence of mRNA that would be transcribed from the following segment of DNA. Assume transcription is occuring from left to right. The bases need to be aligned exactly with each other. 5' ACT GAG AAT ATG CCC ATA AAC ACT AAG TAA ATG CGC 3' 3' TGA CTC TTA TAC GGG TAT TTG TGA TTC ATT TAC GCG 5' 3'ACU GAG AAU AUG CCC AUA AAC ACU AAG UAA AUG CGC 5' 5'ACT GAG AAT ATG CCC ATA AAC ACT AAG TAA ATG CGC 3' 5'ACU GAG AAU AUG CCC AUA AAC ACU AAG UAA AUG CGC 3' 3'UGA CUC UUA UAC GGG UAU UUG UGA UUC AUU UAC GCG 5' 5'TGA CTC TTA TAC GGG TAT TTG TGA TTC ATT TAC GCG 3'
5'ACU GAG AAU AUG CCC AUA AAC ACU AAG UAA AUG CGC 3'
if a DNA molecule is 60bp long, what is the approximate length in Ang or nm?
60bp/10bp * 3.4nm = 20.4nm * 100 = 204 Ang
how many different gametes is genes are linked and every possible cross over occurs?
8 gametes but not in the same proportion as in separate chromosomes
eu RNA polymerase products
8s' and 5s
if a DNA has 20% A what % is G?
A+C=T+G 20+30=20+G G = 30 since A=T 20=20 and A+C+T+G = 100
parental chromosomes
ABC (large #) abc (large #)
if a triple heterozygote AaBbCc has 3 linked genes in couple (1 gene has all dominant, 1 has all recessive), what are the possible sequence of those genes on the parental chromosomes?
ABC, BCA, CAB
inversion
ABCDEFG --> ADCBEFG relocation of loci on the allele
former RNA/diribonucleotide
ATP + ATP = ATP - AMP + PPi
genetic coding: start
AUG - Met
double cross over (d/co)
AbC (smallest #), ABC (smallest #)
single cross over (s/co)
Abc (mid #), aBc (mid#), ABc (mid#), abC(mid #)
Griffith carried out the fractionation experiment. A. True B. False
B. False
Uridine is a ______ A. base B. ribonucleoside C. ribonucleotide D. amino -acid E. none of the above
B. ribonucleoside
general TFs
BASAL - low level transcription + guide RNA pol to core promoter sequences
Differences between DNA and RNA
DNA - 2-deoxyribose (pentose sugar) ACTG (bases) -MP, -DP, -TP (phosphates, H on 2' C, OH on 3' C RNA - ribose (pentose sugar), ACUG (bases), -MP, -DP, -TP (phosphates) OH on both 2' and 3' C
DNA topoisomerase
DNA gyrase (prokaryote specific) relieves torsional stress ahead of replication forks (target to kill bacteria)
DNA repolication in prokaryotes
DNA is naked (not wrapped in histones - not chromatin) - circular chromosome
bidirectional replication
DNA is replicated in a bidirecitonal mode/2 replication forks at replication bubble/replicon
prokaryote initiation: specific DNA binding proteins
DnaA DnaB and DnaC (helicase activity) - all bind in a sequential coordinated manner
chromosome mutation karyotype
FISH analysis - fluorescence in-situ hybridization
A ribozyme is a catalytic protein that assists in the processing of tRNA. True False
False
What features of DNA were suggested by Rosalind Franklin's X-ray diffraction data? It had a helical structure. The helix had more than one strand. The helix contained about 10 bases per turn. The helices were antiparallel.
It had a helical structure. The helices were antiparallel.
2018 Nobel Prize for Physiology or Medicine
James Allison + Tasuku Honjo
nonreciprocal translocation
Movement of a chromosome segment to a nonhomologous chromosome or region without any (or with unequal) reciprocal exchange of segments.
ATP a protein?
NO - it's a ribonucleotide (adenosine triphosphate)
lagging strands
Okazaki fragments
prokaryote polymerase properties: molecules of polymerase/cell
Pol I - 400 pol II - ? pol III - 15
prokaryote elongation: enzymes leading
RNA polymerase (primase), DNA Pol III
prokaryote elongation: enzymes lagging
RNA polymerase (primase), DNA pol III
RNA pol II promoters
TATA box -25 bp regulatory sequences -50 to -100bp
RNA pol II transcription factors
TF II binds to core promoter for basal transcription - TFII...A, B, D, E, F, H, J - guide RNA pol II to core sequences of the promoter - initiation: RNA pol II + general TFIIs bind to TATA box
telomeric repeat sequence: mammals - humans
TTAGGG
35 bp site
TTGACA
prokaryote termination: DNA sequence
Ter sequence -DNA binding protein Tus (termination utilization substance) binds to Ter to signal stop
(T/F) RNA transcripts can be modified in a variety of ways, which include processing, splicing, 5' capping, 3' poly A tailing, RNA editing, and base modification.
True
The 1962 Nobel Prize went to ___ for the discovery of the structure of DNA
Watson and Crick, Maurice (Franklin died before award)
Rosalind Franklin
X-ray diffraction = when a purified substance is subjected to x-rays, they produce a diffraction pattern that reveals the regular structure of the molecule - data suggested: + helical structure + too wide for a single-stranded helix + 10 base pairs per turn of the helix
abnormalities in sex chromosome #: Turner syndrome
XO (45) female --> infertile - monosomy for x chromosome is viable
abnormalities in sex chromosome #: Klinefelter syndrome
XXY (47) MALE
abnormalities in sex chromosome #: Jacob syndrome
XYY (47) male - trisomy for sex chromosomes is viable
3-pt test cross b+wx+cn x bwxcn+ among the test cross offspring were b+wx+cn+ and b wx cn (+ = wild type)
b-cn-wx
RNA polymerase holoenzyme
binds to core promoter sequence (3) upstream of transcription start site
proteins in E. coli DNA replication: SSBPs
binds to single-stranded DNA and prevents it from re-forming a double-stranded structure
trimming/processing tRNA and rRNA
are made as large precursors, have to be cleaved at both 5' and 3' ends to produce mature, functional tRNA (exo and endonuclease activity)
messenger RNA
a temporary copy of a gene that contains information to make a polypeptide
labeling
a way to track using radioactive sulfur - methionine, cystine DNA - nucleotides w/normal (31P)
chromosome mutations
abnormal chromosome # and structures
RNA - ribonucleoside
adenine --> adenosine cytosine --> cytidine guanine --> guanosine uracil --> uridine ** base is bonded to the Cl on the ribose
RNA - ribonucleotides
adenylic acid (AMP, ADP, ATP) cytidylic acid (CMP, CDP, CTP) guanylic acid (GMP, GDP, GTP) uridylic acid (UMP, UDP, UTP) **phosphates hang out at C' 5
proteins in E. coli DNA replication: DnaC protein
aids DnaA in the recruitment of DNA helicase to the origin
In transcription, the closed complex consists of RNA polymerase. transcription factors. double-stranded DNA. single-stranded DNA.
all of the above
Select the stages of transcription. initiation elongation termination translation replication
all of the above
prokaryote polymerase properties: 3'-5' exonuclease (remove DNA)
all three
prokaryote polymerase properties: 5'-3' polymerization
all three
prokaryotic elongation
all transcription facots including sigma bonds leave RNA pol and transcription proceeds in the 5'-3' direction along the 3'-5' template strand
alpha helixes binding to the major groove
amino acids within helices hydrogen bond with bases in the promoter sequence elements
charging of tRNA
aminoacyl-tRNA sythetase (enzyme - one for each AA) 2 step process 1. activate AA 2. transfer the AA to 3' tRNA
An organism with an alteration in the number of particular chromosomes, so the total number of chromosomes is not an exact multiple of a set is
aneuploid
Hershey-Chase Experiment
bacteriophages/viruses and bacteria, bateriophage infection conclusion: confirmed that genetic material is DNA through labeling
DNA composition
base + deoxyribose
thymine is a....while cytidine is a....
base/nucleoside
players in translation -tRNA
becomes charged with specific amino acids (rRNA + ribosomal proteins) = ribosomes mRNA - translated
eukaryotic elongation
bidirectional - same principles as pro - continuous leading strand (primase, polymerase) - discontinuous lagging strand (primase, polymerase) **different polymerases
in bacteria (E. coli), replication is
bidirectional from a single origin of replication
E. Coli is
bidrection, single origin
bacterial DNA replication - prokaryotes
binary fision NO MITOSIS OR MEIOSIS
prokaryotic regulatory sequences: enhancers
bind specific TF (acitvators) - increase rate of transcription
prokaryotic regulatory sequences: repressors
bind specific TF (repressors) - decrease rate of transcription
transcription factors are DNA...
binding proteins
promoter sequences - core promoter
binds general transcription factors + RNA pol (basal level of transcription)
proteins in E. coli DNA replication: DnaA protein
binds to DnaA boxes within origin to initiate DNA replication
proteins in E. coli DNA replication: Tus
binds to Ter sequence and prevents the advancement of the replication fork
telomerase - abnormal
cancer cells - target for cancer treatment - knockout telomerase - no effect on cancer ** marketed as an anti-aging product
if a single stranded DNA molecule is 80 bases long and has 20 adenines, how many thymines will it have?
cannot tell
specific TFs
change rate - activators = increase rate -bind to regulator sequences (enhancer/activator sequences) - inhibitors/repressors = decreases rate - bind to regulator sequences (repressor/operator sequences)
chromatin remodeling complexes
chromatin - regulation of chromatin remodeling -- DNA
polyploidy
chromosome number = a multiple of n which is not 1n=haploid (not 2n=diploid) ex: 3n - triploidy, 4n-tetraploid
DNA forms a three-dimensional structure, such as is found in...
chromosomes
structure of RNA: stem loop structure
cloverleaf structure of tRNA
structure of RNA: hairpin
complementary regions held together by hydrogen bonds, noncomplementary regions have bases projecting away from double-stranded regions
forming a diribonucleotide
dATP + dATP = dATP - dAMP + PPi
exonuclease
degrade polynucleic acids "free end"
chromosome mutation: abnormal structure
delection ,duplication, non-homologous translocation, inversion
chromosome abnormalities
deletions, duplications, translocations, inversions
discovery of DNA structure: Erwin Chargaff
described how bases paired with each other = A/T & C/G
differences in eukaryotic elongation
different DNA polymerase enzymse - DNA poly (alpha, beta, gamma) --> greek letters = only in EUKARYOTES
n organism with two sets of chromosomes (2n) is
diploid
after 3 generations, the DNA is subject to a CsCl gradient and one band appears. What type of replication?
dispersive
deletion in the allele
does not appear in the parallel strand
why bidirectional? - 2 replication forks
efficiency (both directions = faster)
mRNA
encodes the sequence of amino acids within a polypeptide
activator STFII bidns to
enhancer elements to increase transcription rate
Select the eukaryotic regulatory elements. enhancers silencers cis-acting elements Pribnow box
enhancers silencers cis-acting elements
prokaryote replication: DNA polymerase
enzymes to synthesize the DNA molecule
-25bp TATA box
eukaryotes
An organism that has a chromosome number that is an exact multiple of a chromosome set is
euploid
A functional protein is made up of the information contained within what region of DNA? exons introns enhancers promoters
exons
if one compares the base sequences of related genes from different species, one is likely to find that corresponding...are usually conserved, but the sequences of....are much less well conserved
exons, introns
isoaccepting DNA
expect 61 tRNA - 61 different anticodons = 61 codons (NO) = 30 tRNA - tRNAs with different anticodons but linked to same amino acids
Meselsohn and Stahl (1958)
experiment labeling experiment 15N (heavy nitrogen) and 14N (light nitrogen) - no conservative strand - Generation II: Light and intermediate - Generation III: cells replicate 3x and get light/light
Avery, McCarty, MacLeod
factionation experiment conclusion: a nucleic acid of the deoxyribose type is the fundamental unit of the transforming principle of pneumococcus type IIIS
A genetic linkage map indicates that precise distance between two genes of interest. True False
false
DNA polymerase III has the ability to begin synthesis of the new daughter strands immediately following the formation of the replication fork. True False
false
T/F A crossover is more likely to occur in an inverted region if the chromosome segment with the inversion is small.
false
T/F Inversion heterozygotes are often phenotypically normal and have a low probability of producing gametes that are abnormal in their total genetic content.
false
T/F Pre-mRNA introns are removed via self splicing.
false
T/F The spliceosome is a multicomponent structure that recognizes intron sequences and removes them from group I and group II introns.
false
The RNA polymerase forms a closed complex during the process of elongation during transcription. True False
false
telomerase extends the 5' ss overhang
false
Map distance is the number of recombinant offspring divided by the total number of nonrecombinant offspring. True False
false Map distance = (Number of recombinant offspring) / (Total number of offspring) x 100
Crossing over is more likely to occur between genes that are ______ on a chromosome. close together far apart not
far apart In diploid eukaryotic species, homologous chromosomes can exchange pieces with each other, a phenomenon called crossing over. See Figure 7.9 and page 142 for additional information.
formyl methionine (amino acids)
first amino acid --> prokaryotes only
post-translational modification of proteins involve removal of
fmet
DnaA binds with DNA sequence and hand chromosome
formation of bubble brings DnaB+C in to start the unwinding process
catenanes
formation of two intertwined circular chromosomes -must separate = topoisomerase cuts to separate
RNA pol I transcription factors
general transcription factors - TFI binds core element for basal transcription specific transcription factors - activator STF I binds the UCE element, increase transcription rate
accuracy --> genetic mutation
genetic disease (death)
molecular genetics
genotype to phenotype (DNA - RNA - protein - protein function)
human genome
haploid, 3*10^9 bp, 3 mill bp = 1m in length - nucleus = 5um (5*10^-6)
Two strands of DNA interact with each other to form a double...
helix
polyploidy is not viable in...viable in...
humans, fish/plants (potatoes - hexaploid)
products of replication
identical base sequences
TATA box - eukaryotes
important in determining the precise start point for transcription
Transcription in Eukaryotes - differences
initiation - chromatin (DNA + histones) occurs in nucleus 3 RNA polymerases
DNA replication occurs in three stages
initiation, elongation, termination
RNA editing
involves the change of the base sequence of an RNA after it has been transcribed
splicing
involves the cleavage and removal of introns and the subsequent joining of exons
what is a characteristic of pol III
it has a 3'-5' exonuclease activity
prokaryote polymerase properties: 5'-3' exonuclease activity
just pol I
single stranded binding proteins - SSBPs
keeps single strands apart
prokaryote elongation: DNA synthesis
leading 3'-5', lagging Okazaki fragments
Z-DNA
left hand double helix - 12 bp/turn - bases substantially tilted relative to central axis - sugar-phosphate backbone follows zigzag pattern
DNA Pol III (pro)
main synthesis enzyme, proof reading
stem cells
many (unlimited) mitotic cell cycles - mitotic cell cycles outnumber the telomeric repeats - could lead to premature death - not consistent with life
chromatin has...
many origins of replication = differences
Chargaff's Rule
measurements of base content from a wide variety of organisms (A=T, C=G) - suggested interaction between A + T, C+G
tRNA has ACGU
methyl guanine, 4-thiouridine
cri-du chat (46, 5p-)
missing tip on the p arm of the 5th chromosome: cognitive delay, physical development delay, distinctive cry
how many different gametes form in genes are linked (in coupling) and not crossing?
not Mendel's Principle, ABC vs abc = either too close or too far apart that they cross 2x)
trisomy for autosomes is viable, but monosomy for autosomes is
not viable (non-disjunction in Meiosis I or II)
DNA
nucleic acid
eu - RNA pol ii
nucleoplasm -transcribeds mRNA, miRNA, snRNA
eu - RNA pol iii
nucleoplasm -transcribes tRNA + small rRNA (5s rRNA)
The repeating structural unit of nucleic acids are
nucleotides
nucleic acid/polynucleotides are composed of:
nucleotides
sythesize DNA/RNA
nucleotides: sugar + base + phosphates nucleosides: sugar + base
docking of small ribosome on mRNA: Shine-Dalgarno sequence
on mRNA and 16s rRNA which is part of the 30s small ribosomal unit
pyrimidine
one ring = cytosine, uracil, thymine
telomerase
only found in cell where # of telomerase repeats not sufficinet for many mitotic cell divisions - normal expression in stem cells - abnormal (Cancer cells)
oriC
origin of chromosomal replication
replicon
origin of replication (bubble) - specific starting points on DNA - specific DNA sequences
rho-independent
other proteins - RNA pol leaves the DNA, RNA transcript is released and DNA reforms to duplex DNA
replication of DNA 1. parental DNA/parental duplex
parental strands/old template - replication
gene sequence (coupling/repulsion)
parental, gene in middle is important, compare parental and d/co
nucleotides
pentose (5C sugar) + base + phosphate/s
eukaryotic translation elongation
peptidyl-transferase activity
phosphodiester linkage
phosphate connected the 5' carbon of one nucleotide to the 3' carbon of another (directionality of RNA synthesis 5' - 3')
ribonucleotides are covalently linked together by a
phosphodiester linkage
calculation of interference: # observed d/co < # expected d/co
positive interference
proteins in E. coli DNA replication: topoisomerase
removes positive supercoiling ahead of the replication fork
rho-dependent
rho proteins binds to the rut (rho utilization site) sequence on the RNA, will move along RNA and when it reaches stem loop, causes the RNA pol (previously paused) to fall off, and the RNA transcript dissociates from the DNA
rRNA
ribosomal RNA is necessary for the translation of mRNA, ribosomes are composed of both rRNAs and protein subunits
molecular genetics major players
ribosome (proteins + rRNA) + tRNA + mRNA
RNA + ribosomal proteins =
ribosomes
thomas cech 1989 nobel prize in chemistry
ribozymes - RNA as a enzyme
multicellular eukaryotes
same genome, same DNA BUT different gene transcription/gene expression
prokaryotes: transcription and translation
same place same time - nucleoid --> cytoplasm
ligases
seals = makes phosphodiester bond
"s"
sedimentation
similarities in replication of pro and eukaryotes
semiconservative mode replicated from replicating origins - replicons bidirectional mode semidiscontinuous mode
DNA is replicated in a...
semidiscontinuous mode leading strand - continuous lagging strand - discontinuous = Okazaki fragments
proteins in E. coli DNA replication: DNA helicase (DnaB)
separates double-stranded DNA
basic termination
sequence at the end of the gene is transcribed into RNA that folds into a stem-loop structure = causes RNA pol to pause
if there was a mutation in Tus, what are possible consequences?
several cantenanes could form
homologous recombination
several hundred homologous base pairs
microRNA
short RNA molecules that are involved in gene regulation in eukaryotes
duplication in the allele
shows two copies of the loci in the allele one after the other: ABCBCDE...
repressor STFII binds to
silencer/repressor/operator to decrease transcription rate
structure of RNA
single stranded, 5'-3' end, phosphodiester bond, folds into many different shapes
Holliday Model (physical aspect of recombination)
sister chromatids cross with non-sister - alignment of homologous chromosomes single strand breaks - nicking
prokaryote replication: origin of replication
site of initiation and point of control for whole process
alternativ types of double helixes
the DNA double helix can form different types of secondary structure
telomerase RNA
the enzyme telomerase, which is involved in the replication of eukaryotic telomeres, is composed of an RNA molecule and protein subunits
