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Bio- Test #1 (Chapters 16&17)
Terms in this set (49)
Explain why researchers originally thought protein was the genetic material.
-Proteins are macro-molecules w/ great heterogeneity and functional specificity
-little was known about nucleic acids
-the physical and chemical properties of DNA seemed too uniform to account for the multitude of inherited traits
Explain how Watson and Crick deduced the structure of DNA and describe the evidence they used. Explain the significance of research of Rosalind Franklin .
-They built models of a double helix to conform to the x-rays and chemistry of DNA
-Franklin's x-ray crystallographic images of DNA enabled Watson to deduce that DNA was helical and the width suggested DNA was made of two strands (double helix)
-Franklin concluded there were two anti-parallel sugar phosphate backbones w/ the nitrogenous bases paired in the molecules interior
studied Streptococcus pneumoniae bacterium. R cell was harmless, the other S cell was pathogenic. He mixed heat killed S cell with the live R cell & injected into a mouse & mouse died. Concluded that the living R bacteria had been
transformed into pathogenic S bacteria by a heritable substance. He called this transformation.
Hersey and Chase
used radioactive sulfur and phosphorus to trace the fates of protein and DNA. Proteins labeled (batch 1), radioactivity remained outside the cells; but DNA labeled (batch 2), radioactivity was found inside the cells. concluded that DNA, not protein, functions as the genetic material of phage T2
noted that the ratio of nitrogenous bases in the DNA from various organisms was species specific. Also determined that the number of adenines and thymine & guanines and cytosines was approximately equal.
Describe the structure of DNA. Explain the base-pairing rule and describe its significance.
-Double helix made of two strands w/ attachments of sugar-phosphate backbones on the outside & bases paired inside the molecules
-made up of nucleotides comprised of a 5-carbon sugar, a nitrogenous base and a phosphate group
-Chargaff's rule: amount of A = T & amount of G = C
-Two hydrogen bonds for A&T while G&C have three hydrogen bonds
subunits run in opposite directions
Describe the process of DNA replication, including the role of origins of replication and the replication forks.
1.) Begins at sites called origin of replication
2.) Proteins that initiate replication separate the two strands, which open a replication bubble. At the end of the bubble there is a replication fork --DNA strands elongating
3.) Helicase untwists the double helix at replication forks
4.) Once separated, single stranded binding proteins bind to the unpaired DNA bases allowing stabilization
5.)Topoisomerase relieves the strain by breaking, swiveling, and rejoining DNA strands.
6.) Primer is formed by primase starts an RNA chain from a single RNA nucleotide and adds more RNA nucleotides
7.) DNA poly III adds a DNA nucleotide to the RNA primer and continues adding until it reaches the RNA primer to the right where a Okazaki fragment is formed
8.) DNA poly I comes in and replaces the RNA nucleotides with DNA nucleotides
9.) DNA ligase comes in and joins the sugar-phosphate backbones of all Okazaki fragments into a continuous strand
Describe the semi-conservative model of replication, and significance of Matthew Meselson & Franklin Stahl.
method of DNA replication in which parental strands separate, act as templates, and produce molecules of DNA with one parental DNA strand and one new DNA strand.
Meselson&Stahl's experiment showed in the second replication produced both light and hybrid DNA, a result that refuted the dispersive model and supported the semiconservative model.
Explain role of DNA polymerase in replication.
enzymes that catalyze DNA synthesis by adding new nucleotides, remove RNA primer and replaces it with DNA nucleotides.
-can only copy in the free 3'-5' direction and add to a free 3' end
Explain what energy source drives the polymerization of DNA.
When a nucleotide is being added to a growing DNA strand, two of the phosphates are removed and the energy produced creates a phosphodiester bond that attaches the remaining phosphate to the growing chain
Distinguish between the leading strand and the lagging strand.
-Leading strand: in the 5'-3' direction, is continuously synthesized (DNA polymerase synthesizes the copied strand continuously by moving in the complementary 5'-3' direction)
-Lagging strand: in the 3'-5' direction and is discontinuously synthesized
Explain how the lagging strand is synthesized even though DNA polymerase can add nucleotides only to the 3' end. Describe the significance of Okazaki fragments.
-the lagging strand is synthesized as a series of segments called Okazaki fragments joined by DNA ligase--catalyzes the formation of a covalent bond between the 3' end of each fragment to the 5' end of the chain
-Each fragment requires a primer
-Okazaki fragments needed for replication of DNA from lagging strand
Explain the roles of DNA ligase, primer, primase, helicase, topoisomerase, and single-strand binding proteins.
-DNA ligase: binds together Okazaki fragments
-Primer: starts reading
-Primase: enzyme that allows the primer to attach
-Helicase: unzips the DNA
-Topoisomerase: helps relieve this
strain by breaking, swiveling, and rejoining DNA strands
-Single-strand binding proteins: binds to and stabilizes single-stranded DNA until it can be used as a template
Define "anti-parallel" and explain why continuous synthesis of both DNA strands is not possible.
-The two DNA strands run in different directions; one 5'-3'and the other 3'-5', DNA replication can only occur from the 5'-3' direction so the strand running 3'-5' must be done in pieces running from 5'-3' in fragments called Okazaki fragments
Explain the roles of DNA polymerase, mismatch repair enzymes, and nuclease in DNA proofreading and repair.
a.) DNA polymerase: proofreads each nucleotide against it's template as soon as it is added to the growing strand
b.) mismatch repair: cells use special enzymes to fix incorrectly paired nucleotides
c.) Nuclease: DNA cutting enzyme used to cut out damaged segments
Describe the structure and function of telomeres.
-Telomeres is a region at the ends of DNA molecules that consist of multiple repetitions of one short nucleotide sequence. They postpone the erosion of genes near the ends of DNA molecules
-shortening of telomeres connected to aging
Explain the possible significance of telomerase in germ cells and cancerous cells.
germ cells:catalyzes the lengthening of telomeres in eukaryotic germ cells, thus restoring their original length and compensating for shortening that occurs during DNA replication
in cancer cells: stabilizes telomere length and allows cancer cells to persist (continue)
Compare a bacterial chromosome and a eukaryotic chromosome.
-Bacterial: a double-stranded, circular DNA have smaller chromasomal DNA in the form of plasmids. Prokaryotic DNA does not have the non-coding regions or introns. Bacteria do not have histones
-Eukaryotic: linear DNA molecules interspersed w/ non-coding regions that may control gene regulation. Within a gene sequence, there are exons (coding regions) and introns (non-coding regions that will be removed from the mRNA). Prokaryotic chromosomes are tightly wrapped around proteins called histones. Eukaryotic chromosomes are contained in a nucleus.
Describe how the packing of chromatin changes during the course of the cell cycle.
-In interphase the chromatin is highly extended
-As a cell prepares for mitosis, its chromatin coils and folds up (condenses), eventually forming a characteristic number of short thick metaphase chromosomes that are distinguishable
Explain the reasoning that led Archibald Garrod to first suggest that genes dictate phenotypes through enzymes.
the symptoms of an inherited disease reflect a person's inability to synthesize a particular enzyme. "inborn errors of metabolism."
Urine turns black; contains alkapton
Hypothesized a missing enzyme for brealing down alkapton
Describe Beadle and Tatum's experiments with Neurospora and explain the contribution they made to our understanding of how genes control metabolism.
identified mutants that could not survive on minimal medium, because they were unable to synthesize certain essential molecules from the minimal ingredients. deduced that each class of mutant was unable to carry out one step in the pathway for synthesizing arginine, presumably because it lacked the necessary enzyme.
Distinguish between the "one gene-one enzyme" hypothesis and the "one gene-one polypeptide" hypothesis and explain why the original hypothesis was changed.
One gene-one enzyme
Each gene makes an enzyme
But some proteins are not enzymes
Counter examples: insulin, keratin, hemoglobin
One gene-one polypeptide
Counter examples: RNA genes, regulatory sequences
Explain how RNA differs from DNA.
RNA: found in the nucleus, ribose sugar, A-U-G-C, single-stranded, expresses traits
DNA: outside of the nucleus, deoxyribose (one more -OH group), A-T-G-C, double-stranded, stores & transmits traits
Briefly explain how information flows from gene to protein. Is the central dogma ever violated?
-In DNA the order of the bases = information copied by base-pairing rule into mRNA by transcription.
-Ribosome clamps onto mRNA, moving along three bases at a time.
-Each mRNA codon matches an anti-codon on a specific tRNA.
-The tRNA carries a specific anti-codon at one end, the amino acid matching that anti-codon at the other end
-Ribosomes align proper tRNA's and form peptide bonds
Distinguish between transcription and translation.
-Transcription: (nucleus) produces mRNA, process of coding mRNA from DNA code. After the double helix is forked in half, mRNA builds 5' to 3' from a start to stop codon. After going through the membrane and being sliced, translation begins.
-Translation: synthesis of a protein (5'-3') off of the mRNA backbone with ribosomes and tRNA
Compare where transcription and translation occur in bacteria and eukaryotes.
-Bacteria: (no nucleus) transcription & translation occur in the cytoplasm
-Eukaryotes: transcription occurs in the nucleus (pre-mRNA processed to mRNA) and translation occurs in the cytoplasm
Define "codon" and explain the relationship between the linear sequence of codons on mRNA and the linear sequence of amino acids in a polypeptide.
-Codon: a sequence of three nucleotides that codes for an amino acid. Located on the mRNA.
-The linear codon and linear amino acid sequence both have a 3-nucleotide to 1-amino acid correspondence. Meaning that for every codon (or set of 3 nucleotides) there will be one amino acid on the polypeptide --excluding the stop codon--
Explain the early techniques used to identify what amino acids are specified by the triplets UUU, AAA, GGG, and CCC.
-In 1961, Marshal Nirenburg synthesized an artificial mRNA consisting of only uracil. Therefore this means mRNA could give rise to only one possible codon: UUU. Upon adding this poly(U) chain to a mixture of amino acids, ribosomes and other components resulted in a long polypeptide chain of only phenylalanine (Phe). This same procedure was used to determine the amino acids specified by AAA, GGG and CCC.
Explain why polypeptides begin with methionine when they are synthesized.
MET is one of the start codons
Explain what it means to say the genetic code is redundant and unambiguous.
-Redundant: more than one codon signify one amino acid; ex: UUA & UUG both are Leucine
-Unambiguous: each codon is always translated into the same one single amino acid; ex: UUA is the code for Leucine no matter what
Explain the significance of the reading frame during translation.
The reading frame is important because it define the codons of the mRNA. The reading frame ensures that codons start and stop at the proper bases.
Explain the evolutionary significance of a nearly universal genetic code.
-All organisms use the same genetic code meaning that there is a single common ancestor of all living things.
Explain how RNA polymerase recognizes where transcription should begin. Describe the role of the promoter, the terminator, and the transcription unit.
RNA polymerase binds to the DNA sequence called the "promoter" where transcription starts.
In bacteria, the sequence signaling the end of transcription is called the "terminator".
A "transcription unit" is a sequence of nucleotides in DNA that codes for an RNA molecule. This includes the promoter and terminator.
Explain the general process of transcription, including the three major steps of initiation, elongation, and termination.
Initiation- the first step of transcription, RNA polyermase binds to the promoter in DNA , which is the starting point for the process.
Elongation- RNA polymerase moves along the template strand of the DNA and attaches complementary RNA nucleotide bases, creating an RNA strand.
Termination- RNA strands breaks off of the DNA molecule and moves on to other cell processes.
Explain how RNA is modified after transcription on eukaryotic cells.
-Both ends of the primary transcript are usually altered.
-One end, the 5' end is capped off with a modified form of a guanine nucleotide.
-At the 3' end an enzyme makes a poly(A) tail consisting of 50-250 adenine nucleotides.
-The most prominent stage of RNA processing is when a large portion of RNA is removed called RNA splicing.
-This makes the coding sequence of DNA non-continuous.
Describe the functional and evolutionary significance of introns.
Functional: may control gene activity/alternate splicing--the # of different proteins an organism can produce is much greater that it's # of genes
Evolutionary: Exons code for functional domains of proteins, exon shuffling may result in the evolution of the new proteins
Describe the structure and function of tRNA.
-translates an mRNA message into a protein
-molecules of tRNA are not identical; carries specific amino acid sequence (3') on one end and an anti-codon on the other end
-consists of single RNA strand- about 80 nucleotides long
-flattened in one plane to reveal it's base pairing ---> cloverleaf, L-shaped
-because of hydrogen bonds to mRNA codon, tRNA can twist & fold into three-dimensional molecule
Explain the significance of wobble.
Wobble: flexible pairing at third base of a codon
-allows some tRNA's to bind to more than one codon
Explain how tRNA is joined to appropriate amino acid.
1.) A correct match between a tRNA and an amino acid, done by enzyme aminoacyl-tRNA synthase
2.) A correct match between the tRNA anti-codon and an mRNA codon
Describe the structure and functions of ribosomes.
-facilitate specific coupling of tRNA anticodons w/ mRNA codons in protein synthesis
-two ribosomal subunits: proteins & RNA <-- made in nucleus
-P-site: holds tRNA that carries growing polypeptide chain
-A-site: holds tRNA that carries the next amino acid to be added to the chain
-E-site: exit; discharged tRNA leaves the ribosome
Describe the process of translation (including initiation, elongation and termination) and explain which enzymes, protein factors, and energy sources are needed for each stage.
Initiation: when mRNA, tRNA and the first amino acid come together with the ribosome; protein initiation factors bring everything together to begin
Elongation: amino acids are added one by one, helped by protein elongation factors;
1. Codon recognition--mRNA codon makes a hydrogen bond with the tRNA anticodon
2. Peptide bond formation--a ribozyme catalyzes the peptide bond creating a polypeptide which then separates from it's tRNA
3. Translocation--tRNA moves to another part of the ribosome and the next codon to be translocated steps up ... finally tRNA leaves
Termination: elongation continues until there is a stop codon; a protein release factor binds and adds a water to finish the polypeptide
Describe the significance of polyribosomes,
Enables a cell to make many copies of a polypeptide very quickly
Explain what determines the primary structure of a protein and describe how a polypeptide must be modified before it becomes fully functional.
Primary structure = amino acid order dictated by mRNA, DNA determines it
During and after its synthesis, a polypeptide chain begins to coil and fold spontaneously, forming a functional protein of a specific conformation; a three-dimensional molecule with secondary and tertiary structure.
A gene determines primary structure which in turn determines conformation.
Additional steps called post translocational modification make a polypeptide fully functional. Sugars lipids or phosphates may be added, amino acids may be removed and more than one chain may be bound together.
Describe what determines whether a ribosome will be free in the cytosol or attached to the rough endoplasmic reticulum.
Free--suspended in cytosol and mostly synthesize proteins that dissolve in the cytosol and function there
Bound--attached to the cytosol side of the ER and makes proteins, which are secreted from the cell
-occurs if the growing polypeptide itself cues the ribosomes to attach to the ER--marked by a signal peptide, which targets the protein to the ER
Define "point mutations". Distinguish between base-pair substitutions. Give an example of each and note the significance of such changes.
Point mutations are chemical changes in just one base pair of a gene.
-Base-pair substitution: replaces one nucleotide and it partners with another pair of nucleotides, can be either silent; does not change the phenotype, /or missense or nonsense
-Base-pair insertion: additions of nucleotide pairs in gene, creates a frameshift mutation which reads the nucelotides incorrectly.
Distinguish between missense and a nonsense mutation.
Missense: a substitution that changes one amino acid into a different one
Nonsense: causes a change in an amino acid codon and turns it into a stop codon
Why is an insertion or deletion more likely to be deleterious than a substitution?
An insertion/deletion is worse than a substitution because it reads the whole genetic message and not just one amino acid, causing a whole different protein
Define the term 'mutation'. Give an example of a physical and chemical agent of mutation.
Mutations are changes in the genetic material of a cell or virus
-mutagen are physical or chemical agents that can cause mutations
ex: sunlight, radiation, and smoking --physical
ex: errors during DNA replication --chemical
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