General Genetics Exam 2

Ace your homework & exams now with Quizwiz!

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


Related study sets

NCLEX 10000 ENDOCRINE AND METABOLIC

View Set

Consolidated Financial Statements Subsequent to the Date of Acquisition

View Set

Tax final-Deductions: employee and self-employed related exp

View Set

HURST QBank Health Promotion & Maintenance

View Set