The Molecular Basis of Inheritance Flashcards
Griffith
● Performed experiements with several different strains of the bacterium Diplococcus pneumoniae in 1927
● Some strains are virulent and cause pneumonia in human and mice, and some strains are harmless
● He discovered bacterial transformation
Bacterial transformation
● bacteria have hte ability to transform harmless cells into virulent ones by transferring some genetic factor from one bacteria cell to another
Avery, Macleod, and McCarty
● Published their classic findings that Griffith’s transformation factor is DNA in 1944
● It proved that DNA was the agnet htat carried the genetic characteristics from the virulent dead bacteria tot he living nonvirulent bacteria
● Provided direct experimental evidence that DNA, not protein, was hte genetic material
Hershey and Chase
● Carried out experiments that lent strong support to the theory that DNA is the genetic material in 1952
● Proved that DNA from the viral nucleus, not protein from the viral coat, was infecting bacteria and producing thousands of progeny
Rosalind Franklin
● Carried out the X-ray crystallography analysis of DNA that showed DNA to be a helix in 1950-1953
Watson and Crick
● Proposed the couble helix structure of DNA in a one-page paper in the British journal Nature in 1953
● Two major pieces of informaiton they used were hte biochemical analysis of DNA and the X-ray diffraction analysis of DNA
Meselson and Stahl
● Proved that DNA replicates in a semiconservative fashion
Double helix
● Structure of DNA molecule
● Shaped like a twisted ladder, consisting of two strands unning in opposite directions–antiparallel
Nucleotides
● Consists of a 5-carbon sugar–doxyribose, a phosphate, and a nitrogen base
Nitrogenous bases
● Adenine (A) – purines
● Thymine (T) – pyrimidines
● Cytosine (C) – purines
● Guanine (G) – pyrimidines
Histones
● A large amount of proteins that combine with eukaryotic DNA
● Only separates briefly during replication
Chromatin
Comples of DNA plus histones
Nucleosomes
● THe double helix of DNA wraps twice around a core of histones forms nucleosomes
● Looks like beads on a string
Deoxyribonucleic aci
● DNA
● Double helix
● Made up of nucleotides
Ribonucleic acid
● RNA
● SIngle-strandd helix
● Four bases: Adenine, Cytosine, Guanine, and Uracil (U) that replaces thymine
● Has 5-carbon sugar called ribose
DNA replication
● The making of an exact replica of the DNA molecule by semiconservative replication
● THe DNA double helix unzips, and each strand serves as a template for the formation of a new strand composed of complementary nucleotides: A with T, C with G
● THe two new molecules each consist of one old strand and one new strand
Replication fork
● A Y-shaped region where the new strands of DNA are elongating
● At each end of the replication bubble
Replication bubbles
● Site of DNA replication
● Eventually all replication bubbles fuse
DNA polymerase
● Enzyme that catalyzes the antiparallel elongation of the new DNA strands
● Builds a new strand from the 5’ to the 3’ direction by moving along the template strand and pushing the replication fork ahead of it
● In humans, the rate of elongation is about 50 nucleotides persecond
● Cannot initiate synthesis
RNA primer
● produced by primase
● First binds to the template, allowing DNA polymerase to add nucleotides to to 3’ end of it
Primase
● Produce RNA primer
Leading strand
● Unbroken, linear fashing that is built in one of the strand
● Formed toward the replication fork
Lagging stand
● Formed away from the replication fork
● Form Okazaki fragments
Okazaki fragments
● Fragments in the lagging strand
● about 100-200 nucleotides long and will joined into one continuous strand by theenzyme DNA ligase
Helicases
● enzymes that untwist the double helix at the replication fork
● Separate the two parental strands, making these strands available as templates
Single-stranded binding proteins
● Act as scaffolding, holding the two DNA strands apart
Topoisomerases
● Lessen the tension on the ithgtly wound helix by breaking, swiveling, and rejoining the DNA strands
Mismatch repair
● proofreading that corrected errors
● Carries out by DNA polymerase
Telomeres
● Nonsesne nucleotide sequences at the ends of hte chromomes in eukaryotes
● Each time the DNA replicates, some nucleotides from the ends of the chromosomes are lost
● THye are created and maintained by the enzyme telomerase
● Normal body cells contain little telomerase–when it gets shorter overtime, this may serve as a clock that counts cell divisions and causes the cell to stop dividing as the cell ages
Transcription
● Process by which the information in a DNA sequence is copied (transcribed) into a complementary RNA sequence
Messenger RNA
● When a sequence of DNA is expressed, one of two starands of DNA is copied into mRNA according to the base-pairing rules
Ribosomal RNA
● Structural
● Along with proteins, it makes up the ribosome, which consists of two subunits, one large and one small
● THe ribosome has one mRNA binding site, and three tRNA binding sites, known as A, P, E sites
● Ribosome is a protein synthesis factory
Transcription RNA
● tRNA is shaped like a coverleaf and has a binding site for an amino acid at one end and another binding site foran anticodon sequence that binds to mRNA at the other
Initiation (trascription)
● RNA polymerase recognizes and binds to DNA at hte promoter region
● Once RNA polymerase is attached to the promoter, DNA transcription of the DNA template begins
Promoter
● Tells RNA polymerase where to begin transcription and which of the two strands to transcribe
● Transcription factors recognize the TATA box, and mediate hte binding of RNA polymerase to the DNA
TATA box
● a key area within the promoter, the TATA box, and mediate hte binding of RNA polymerase to the DNA
Transcription initiation complex
● THe completed assembly of transcription factors and RNA polymerase bound ot the promoter
Elongation (transcription)
● Contieus as RNA polymerase adds nucleotides to the 3’ end of a growing chain
RNA polymerase
● Binds to DNA at the promoter region
● Adds nucleotides to the 3’ end of a growing chain
● Pries the two strands of DNA apart and attaches RNA nucleotides according to the base pairing rules
● Has mechanisms for proofreading during transcription
Transcription unit
● The stretch of DNA that is transcribed into an mRNA molecule
● Each unit consists of codons
Codon
● Triplets of bases in mRNA
● Code for specific amino acids
Termination (Transcription)
● Final stage in transcription
● Elongation continues for a short distance after the RNA polymerase transcribes the termination sequence (AAUAAA)
● At this point, mRNA is cut free from the DNA template
RNA processing
● Before the newly formed pre-RNA strand is shipped out of the nucleus to the ribosome in the cytoplasm, it is altered or processed by a series of enzymes
● 5’ cap
● Poly A tail
● Splicing
5’ cap
● Consisting of a modified guanine nucleotide is added to the 5’ end
● This cap helps the RNA strand bind to the ribosome in the cytoplasm during translation
Poly A tail
● Consisting of a tring of adenine nucleotides
● Added to the 3’ end
● THis tail protects the RNA strand from degradation by hydrolytic enzymes, and facilitates the release of mRNA from the nucleus into the cytoplasm
Splicing
● Introns are removed by snRNPs, small nuclear ribonucleoproteins, and splicesomes
● This removal allows only exons to leave the nucleus
● mRNA that leaves the nucleus is a great deal shorter than the original transcription unit
Introns
● Noncoding regions of the mRNA
● AKA intervening sequences
Exons
● Expressed sequences
Alternative splicing
● Different RNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns
● Regulatory proteins specific to a cell type control intron-exon choices by binding to regulatory sequences within the primary transcript
Translation
● The process by which the codons of an mRNA sequence are changed into an amino acid sequence
● Include three steps: initiation, elongation, termination
Anticodon
● Nucleotid triplet on one end of the tRNA molecule specific to an amino acid
● Complementary to codons
Aminoacyl-tRNA synthetase
A specific enzyme that joins each amino acid to the correct tRNA
Start codon
● Codon AUG
- also codes for methionine
Stop codon
● UAA, UGA, UAG
● Terminate all sequences
Wobble effect
● The pairing rules for the third base of a codon are not as strict as they are for the fist two bases
● Ex) UCU, UCC, UCA, UCG all code for the amino acid serine
Initiation (Translation)
● Begins when mRNA becomes attached to a subunit of the ribosome
● First codon is always AUG
- It must be positioned correctly in order for transcription of an amino acid sequence to begin
Elongation (Translation)
● Continues as tRNA brings amino acids to the ribosome and polypeptide chain is formed
● One mRNA molecule is generally translated simultaneously polyribosomes
Polyribosomes
Several ribosomes in clusters
Termination (Translation)
● Complete when a ribosome reaches one of three termination or stop codons
● The polypeptide chain of amino acid is freed by the release factor from the ribosome and mRNA is broken down
Release factor
● Breaks the bond between the tRNA and the last amino acid of hte polypeptide chain
Mutations
● Permanent changes in genetic material
● Occur spontaneously and randomly
● Can be caused by mutagenic agents, including toxic chemicals and radiation
● In somatic cells disrupts normal cell functions
● Are the raw material for natural selection
● In gametes are transmitted to offspring and can change the gene pool of a population
Point mutation
● Base-pair substitution
● Responsible for sicke cell anemia–abnormal hemoglobin that can cause red blood cells to sickle when oxygen tension is low
- A variety of tissues may be deprived of oxygen and suffer severe, permanent damage
● Could result in a beneficial change or no change (wobble)
Base-pair substitution
A chemical change in just one base pair in a single gene
Insertion/deletion
Addition or loss of one letter into the DNA sentence
Frameshift
● Insertion and deletion are a type of this kind
● The entire reading frame is altered
Missense mutation
When point mutations or frameshifts change a codon within a gene into a stop codon, translation will be altered into a missense mutation (different meaning)
Nonsense mutation
When point mutations or frameshifts change a codon within a gene into a stop codon, translation will be altered into a nonsense mutation (produce a stop codon)
Virus
● Parasite htat can live only inside another cell
● Commandeers the host cell machinery to transcribe and translate all the proteins it needs to fashion new viruses
Capsid
A protein coat enclosing DNA or RNA in a virus
Virual envelope
● Derived from membranes of host cells
● Cloaks the capside
● Aids the virus in infecting the host
Host range
The range of organisms that a virus can attack
Bacteriophages
● The most complex and best understood virus
● Infects bacteria
● Can reproduce in different ways
Lytic cycle
● The phage enters a host cell, takes control of the cell achinery, replicates itself, and then causes hte cell to burst, releasing a new generation of infectious phage viruses
● These new viruses infect and kill thousands of cell sin the same manner
Lysogenic cycle
● Viruses replicate without destroying the host cell
● The phage virus become sincorporated into a specific site in the host’s DNA
● It remains dormant within the host genome and is called a prophage
● As the host cell divides, the phage is replicated along with it and a single infeced cell gives rise to a population of infected cells
● At some point an environmental trigger causes the prophasge to switch to the lytic phase
Temperate viruses
Viruses capable of both modes of reproducing, ltic and lysogenic, within a baceterium
Virulent phage
A phage that replicates only by a lytic cycle
Retroviruses
● Viruses that contain RNA instead of DNA and replicate in an unusual way
● Following infection of the host cell, the retrovirus RNA serves as a template for the synthesis of complementary DNA
● They reverse the usual flow of information from DNA to RNA
● Usually inserts itself into the host genome, becomes a permanent resident, called a prophage, and is capable of making multiple copies of hte viral genome for years
Reverse transcriptase
An enzyme that direct the reverse transcription process taken by retroviruses
Transduction
● Phage viruses acquire bits of bacterial DNA as they infect one cell after naother
- This process, which leads to genetic combination, is called transduction
Generalized transuction
● Moves random pieces of bacterial DNA as the phage lyses one cell and infects another during the lytic cycle
Restricted/Specialized transduction
● Involves the transfer of specific pieces of DNA
● During the lysogenic cycle, a phage integrates into the host cell at a specific site
● At a later time, when the phage ruptures out of the host DNA, it sometimes carries a piece of adjacent host DNA with it and inserts this host DNA into the next host it infects
Bacterial chromosome
● Ciruclar, double-stranded DNA molecule
● Tightly condensed into a structure called a nucleoid–no nuclear membrane
● Replicate in both directions from a single point of origin
Conjugation
● Primitive sexual reproduction by bacteria
● Bacterias exchange DNA
Binary fission
● The main mode of reproduction of bacteria
● Asexual
● Results in a population with all identical genes, but mutations do occur spontaneously
Bacterial transformation
● Either a natural or an artificial process tha tprovides a mechanism for the recombination fo genetic information in some bacteria
● Small pieces of extracellular DNA are taken up by a living bacterium, ultimately leading to a stable genetic change in the recipient cell
Plasmid
● Foreign, small, circular, self-replicating DNA molecule that inhabits a bacterium
● A bacterium can harbor many plasmids and will express the genes carried by the plasmid
F plasmid
● First plasmid discovered
● F stands for fertility
● Bacteria that contain the F plasmid are called F+; others are called F-
● Contains genes fro the production of pili
Pili
● Cytoplasmic bridges that connect to an adjacent cell
● Allows DNA to move from one cell to another in a form of primitive sexual reproduction called conjugation
R plasmid
● Makes the cell in which it is carried resistant to specific antibiotics, such as ampicillin or tetracycline
● Can be transferred to other bacteria by conjugation
● Bacteria that carry this have a distinct evolutionary advantage
Operon
● Disvoered in the bacterium E. coli
● Important model of gene regulation
● A set of genes and the switches that control the expression of those genes
Inducible/lac operon
● Three enzymes, B-galactosidase, permease, and transacetylase, must be synthesized to break down lactose into glucose and galactose
● In order for these three genes to be transcribed, the repressor must be prevented from binding tot he operator and RNA polymerase must bind to the promoter region
● Allolactose is the inducer that facilitates this process by binding to the active repressor and inactivating it
Repressible/tryptophan operon
● Consists of a promoter and five adjacent structural genes (A,B,C,D,E) that code for five separate enzymes necessary to synthesize the amino acid trypotophan
● As long as RNA polymerase binds to the promoter, one long strand of mRNA containing start and stop codons is transcribed
● If adequate tryptophan is present, tryptophan itself acts as a corepressor activating the repressor
● The activated repressor binds to the operator, preventing RNA polymerase from binding to the promoter
● Transcription ceases
CAP and cAMP
● Catabolite activator protein and cyclic AMP
● Allosteric regulatory protein that switches the energy source to lactose when glucose is in short supply
● The attachment of CAP to the promoter directly stimualtes gene expression
Positive gene regulation
● Directly stimulates gene expression
● Ex) Attachment of CAP
RNA polymerase
Enzyme that transcribes a new RNA chain by linking ribonucleotides to nucleotids on a DNA template
Operator
● Sequence of nucleotides near the start of an operon to which the active repressor can attach
● The binding of the repressor prevents RNA polymerase from attaching tot he promoter and transcribing the operon’s genes
Promoter
● Nucleotide sequence in the DNA of a gene that is hte binding site of RNA polymerase, positioning the RNA polymerase to begin to transcribe RNA at hte appropriate position
Repressor
● Protein that inhibits gene transciption
● In the operon of prokaryotes, repressors bind tot he operator
Regulator gene
● Gene that codes for a repressor
● It is located some distance from its operon and has its own promoter
Prions
● Misfoolded versions of a protein normally foudn in the brain
● They cause all the normal versions of hte protein to misfold in the same way
● Infectious and cause several brain diseases
- Scrapie in sheep
- Mad cow disease in cattle
- Creutzfeldt-Jakob disease in human
Tandem repeats
Back-to-back repetitive sequences
Telomeres
● made up of tandem repeats
● At the end of DNA strands to protect the DNA from information loss
Polymorphic regions
● Certain noncoding regions of DNA
● Are highly variable from one region to the next
Histones
● Eukarotic DNA is packaged with proteins called histones in an elaborate complex knwon as chromatin, the basic unit of which is the nucleosome
● Changes to the histone structure alter chromatin configuration, binding it more tightly or more loosely, thus making DNA less or more accessible for transcription and expression
Acetylation of histone tails
● Adding of acetyle groups (-COCH3) to the histone tails
● Promotes the loosening of that chromatin structure and permits transcription
● Removal of acetyl groups block transcription
Methylation of certain bases
● Adding methyl groups–CH3 to DNA
● Silences the DNA temporarily or for long periods of time
● Removal of methyl groups can turn genes on
● Probably responsible for the long-term X-chromosome deactivation in females and genes necessary fro normal cell differentiation in embryonic development
Epigenetic inheritance
● Alterations to the genome that do not directly invovle the nucleotide sequence
● THese chagnes are reversible
● Environmental factors like diet, stress, and prenatal nutrition can alter the expression of genes
Degradation of mRNA
● Bacterial mRNA molecules are degraded within minutes of their synthesis
● THis rapid degradation of mRNA may be the reason that bacteria change their patterns of protein synthesis and are so adpatable to changes in the environemnt
● human mRNA may continually translate protein for hours or weeks
● molecules of mRNA in developing red blood cells are stable and may translate hemoglobin molecules repeatedly for an exteended time
Noncoding RNA
● ncRNA
● Bind to and are assisted by specialized binding proteins called Argonaute proteins
● They regulate much of our DNA
MicroRNA
● miRNA
● Single-stranded RNA about 22 nucleotides long, forms a complex with proteins
● Targets specific mRNA molecules to either dgrade them or block their translation
Small interfering RNA
● siRNA
● Similar to miRNA in size and function
● The blocking of gene expression by siRNA is called RNA interference (RNAi)
Piwi-associated RNA
● piRNA
● Recently discovered
● Large class of ncRNAs that guide PIWI proteins to complementary RNAs which are derived from transposable elements
● Similar to RNAi, they protect germ line cells from attack by transposons
Recombinant DNA
● Tkaing DNA from two or more sources and combining them into one molecule
● occurs in nvature during viral transcution, bacterial transformation, and conjugation and when transposons jump around the genome
● Scientists can also manipulate the gnes–biotechnology or genetic engineering
Vector
A cell that will carry the plasmid, such as a bacterium
Restriction enzymes
● Extracted from bacteria
● Cut DNA at specific recognition sequences or sites, such as GAATTC
- OFten these cuts are staggered, leaving single-stranded sticky ends to form a temporary union with other sticky ends
Restriction fragments
The fragments that result from the cuts made by restriction enzymes
Gel electrophoresis
● Separates large molecules of DNA on the basis of their rate of movement through an agarose gel in an electric field
● The smaller the molecule, the faster it runs
● The concnetration of the gel can be altered to provide a greater impediment to the DNA, allowing for finer separation
DNA probe
● Identify the location of a specific sequence within the DNA
● Radioactively labeled single strand of nucleic acid molecule
● Bonds to the complementary sequence wherever it occurs, and hte radioactivity enables scientists to detect its location
Polymerase Chain Reaction (PCR)
● Cell-free, automated technique by which a piece of DNA can be rapidly copied or amplified
● The DNA piece htat is to be amplified is placed into a test tube with Taq polymerase along with a supply of nucleotides and primers necessary for DNA synthesis
Restriction fragment length polymorphism (RFLPs)
● The differences of the restriction fragment pattern in every individual
● A RFLP analysis of someone’s DNA gives a human DNA fingerprint that looks like a bar code
● Used in paternity suits to determine if a particular man is hte father of a particular child
● Routinely used to identify the perpetrator in rape and murder cases
Complementary DNA (cDNA)
● DNA produced by retroviruses–without introns
● Extract fully processed mRNA from cells and then use the enzye reverse transcriptase to make DNA transcripts of this RNA
● The resulting DNA molecule carries the complete coding sequence of interest but without introns
Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)
● Genetic engineering tool made of RNA that can be guided to modify a stretch of DNA
● THe targets a particular sequence and permanently disrupts it or can add small pieces of corrective DNA to the same location
DNA chips
● DNA probes are being coupled with the technology of the semiconductor industry to produce DNA chips that are about 1/2 inch square and can hold personal information about someone’s genetic makeup
● The chips scan a person for mutations, including mutations in the immune system or the breast cancer genes and for a predisposition to tother cancers or heart attacks
What’s the paring pattern in nitrogenous bases?
● Adenine nucleotide bonds by a double hydrogen bond to the thymine nucleotide
● Cytosine nucleotide bonds by a triple hydrogen bond to the guanine nucleotide
Where and how does DNA replication begin?
● Speical sites called origins of replication, where hte two strands of DNA separate to form replication bubbles
● Thousands of these bubbles can be seen along the DNA molecule by using the giant DNA molecule that consists of 6 billion nucleotids
● A replication bubble expands as replication proceeds in both directions at once
What are the enzymes used in DNA replication (in order)?
- Helicase
- Single-stranded binding protein
- Topoisomerase
- Primase
- DNA polymerase I
- Nuclease
- DNA polymerae III
8 Ligase
Give a sumaary of how DNA makes protein.
● THe triplet code in DNA is transcribed into a codon seuence in messenger-RNA inside the nucleus
● This newly formed strand of RNA, knwon as pre-RNA, is processed or modified in the nucleus
● THe codon sequence leaves the nucleus and is translated into an amino acid sequence (a polypeptide) in the cytoplasm at the ribosome
What are the kinds of RNA invovled in protein synthesis?
● Messenger RNA is invovled in transcription
● Ribosomal RNA is invovled in translation
● Transcription RNA carries amino acids from the cytoplasmic pool of amino acids to mRNA at the ribosome
What does the tRNA do in translation?
● Brings amino acids present in the cytoplasm to the codons of hte mRNA strand at hte ribosome according to the base pairing rules
● Can be used repeatedly
What energy provide for translation?
● Guanosine triphosphate (GTP)
● A molecule closely related to ATP
Why do some tRNA molecules have anticodons that can recognize two or more different codons?
Wobble effect
What does “there are redundancies in the code, but htere is no ambiguity” mean?
● Many codons can cod for the same amino acid–redundancy
● One codon only codes for one particular amino acid–no ambiguity
Why are some regions of DNA more vulnerable to mutations than others?
● Regions of As and Ts are subject to more breakages than regions of Cs and Gs
● A and T are connected by a double hydrogen bond whereas Cs and Gs are connected by a triple hydrogen bond
Why can each type of virus only infect one specific cell type?
Because it gains entrance into a cell by binding to specific receptors on the cell surface
What are the two wyas a bacteriophage can reproduce itself?
● Lytic cycle
● Lysogenic cycle
Why do bacteria with R plasmid have an evolutionary adtage over bacteria that are not resistant to antibiotics?
Resistant bacteria will be selected for (survive) and their populations will increase while nonresistant bacteria die out
When glucose and lactose are both present in the intestine, what does E. coli preferentially metabolize?
Glucose
What are the potential uses of recombinant DNA or gene cloning?
● To produce a protein product, such as human insulin, in large quantities as an inexpensive pharmaceutical
● To replace a nonfunctioning gene in a person’s cells with a functioning gene by gene therapy
- Sometimes the human subjects become ill from the viral vector used to carry the gene
- Other times, the gene is inserted successfully and begins to produce hte necessary protein but stops working in a short time
● To prepare multiple copies of a gene itself for analysis
● To engineer bacteira to clean up the environment
- One modified species can even eat toxic waste
What are the steps of gene cloning
● Isolate a gene of interest
● Insert hte gene into a plasmid
● Insert the plasmid into a vector
- A bacterium must be made competant, which means be able to take up a plasmid
● Clone the gene
- As the bacteria reproduce themsleves by fission, the plasmid and the selected gene are also being cloned
● Identify the bacteria that contain the selected gene and harvest in from the culture
How can the gel electrophoresis be used?
● To separate protein and amino acids
● DNA must be cut up by restriction enzymes into pieces amll enough to migrate through a gel
● The DNA can be analyzed in many ways once separated
- The DNA strands can be sequenced to determine the sequence of bases A,C,T,G
- The gel can also be used in a comparison with other DNA samples
What are the limitations of the PCR technique?
● Some information about the nucleotide sequence of the target DNA must be known in advance in order to make the necessary primers
● The size of the piece htat can be amplified must be very short
● Contamination is a major problem
- A few skin cells from the technician working with the sample could make obtainin accurate results difficult or impossible
Why can’t scientist clone a human gene in a bacterium without treating it?
● The human genes have introns but the bacterias don’t
● The bacterium have no way to edit the introns out after transcription
What are some safety concerns of genetic enginnering?
● Individuals are concerned that the genes that have been inserted into the vegetables may be dangerous to those who eat them
What are some privacy concerns of genetic engineering?
● The possibiity that the personal iinformation on a DNA chip might not remain private has caused much controversy
● Health insurance company might charge you a higher premium
