Biology Chapter 10

process of replication (start of transcription)

-a parental molecule at its origin of replication site (here there are short stretches of DNA with a specific sequence of nucleotides where proteins attach to the DNA and separate the strands). -replication occurs in both directions, creating multiple replication bubbles which speed the process -parental DNA strand serve as templates for the daughter strands -bubbles are portions of the parental DNA molecule that have opened as daughter strands elongate on both sides, providing a site for two replication forks, Y-shaped regions where the parental strands of DNA are being unwound -enzyme helicase is responsible for untwisting the double helix at the replication forks, separating the two parental strands -at each replication fork, DNA polymerases, enzymes that link DNA nucleotides to a growing daughter strand, add nucleotides only to the 3' end of the strand -so, the daughter DNA strand can only grow in the 5' to 3' direction -5' to 3' strand that is being continuously made is called the leading strand; it's synthesized in one continuous piece by a DNA polymerase working toward the forking point of the parental DNA -but the DNA polymerase can't start the synthesis of a polynucleotide -first nucleotide chain that's produced during DNA synthesis is actually a short stretch of RNA called a primer and is synthesized by the enzyme primase -primase adds RNA nucleotides one at a time, using the parental DNA strand as a template -new DNA strand will start from the 3' end of the RNA primer -other daughter strand, the 5' to 3' strand that moves in pieces, called Okazaki fragments, is called the lagging strand -in order to make this strand, polymerases must work outward from the forking point and the new strand is synthesized in Okazaki fragments as the fork opens up -DNA ligase forms the final bond between Okazaki fragments on the lagging strand, synthesizing the strand -result: two daughter DNA molecules which will then serve as templates for transcription.

purine

Adenine and Guanine; double ring structure

retrovirus

An RNA virus that reproduces by means of a DNA molecule. It reverse transcribes its RNA into DNA, inserts the DNA into a cellular chromosome, and then transcribes more copies of RNA from the viral DNA. HIV and a number of cancer causing viruses are retroviruses.

promoter

a specific nucleotide sequence in DNA, located near the start of a gene, where the RNA polymerase attaches and initiates transcription

RNA primer

a strand of short nucleic acid sequences (generally about 10 base pairs) that serves as a starting point for DNA synthesis. It is required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA.

codon

a three-nucleotide sequence in mRNA that specifies a particular amino acid or polypeptide termination signal; the basic unit of genetic code.

replication bubble

portions of the parental DNA molecule that have opened as daughter strands elongate on both sides

"transforming factor"

in Griffith's experiment, a chemical substance responsible for transforming a living R strain to a pathogenic S strain

stop codon

in mRNA, a sequence of three nucleotides that signals translation to stop (UAG, UAA, UGA)

anticodon

on a tRNA molecule, a specific sequence of three nucleotides that is complementary to a codon triplet sequence on mRNA

start codon

on mRNA, a specific three nucleotide sequence (AUG) to which an initial tRNA molecule binds; codes for start of translation and the amino acid MET

S (smooth) strain

pathogenic and have an outer capsule that protects them from an animal's immune system

significance of transcription and translation

They are the main processes whereby genes control the structures and activities of cells or the way the genotype produces the phenotype.

compare replication in prokaryotes and eukaryotes

prokaryotic (bacteria)- has single origin of replication, forming one replication bubble. Replication proceeds in both directions until entire molecule is copied eukaryotic- has hundreds or thousands of replication origins. multiple replication bubbles form and eventually fuse, speeding up copying of DNA molecules. also proceeds in both directions from origin

coding strand

the DNA strand which has the same base sequence as the RNA transcript produced (although with thymine replaced by uracil). This strand is used in transcription to transcribe mRNA. It is this strand which contains codons, while the non-coding strand contains anti-codons.

Okazaki fragments

short pieces on the lagging strand bonded together by DNA ligase

primase

synthesizes RNA primer by adding RNA nucleotides one at a time, using the parental DNA strand as a template

ligase

the enzyme that forms the final bond b/w Okazaki fragments

polymerase

the enzyme that link DNA nucleotides to a growing daughter strand, adding nucleotides only to the 3' and never to the 5' end. So, can only move from 3'->5'

helicase

the enzyme that unwinds a DNA molecule; separating the 2 strands at the replication fork

nucleotide

the monomer of nucleic acids, consisting of a five carbon sugar covalently bonded to a nitrogenous base and one or more phosphate groups

how nucleotide sequence is related to the concept of genotype

the nucleotide sequence determines the genes, therefore determining the genotype

replication

the process where a double-stranded DNA molecule is copied to form 2 identical daughter DNA molecules

capsid

the protein shell that encloses a viral genome

telomere

the repetitive DNA at the end of a eukaryotic chromosome; are not used in protein synthesis/don't code for anything

leading strand

the strand being synthesized continuously by polymerase

lagging strand

the strand being synthesized in Okazaki fragments

double helix

the structure of a DNA molecule, two strands and twisted in a spiral

transcription

the synthesis of RNA on a DNA template

translation

the synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change in "language" from nucleotides to amino acids.

how transcription is related to replication

-DNA double helix is untwisted by breaking hydrogen bonds b/w bases -there's a point where replication and transcription starts (origin of replication or promoter region) -both processes occur in nucleus -both involve enzyme polymerase (DNA polymerase for replication and RNA polymerase in transcription -both involve collection and arrangement of free nucleotides complementary to the template strand

role of tRNA

-cell's "molecular interpreter" -matches amino acids to the appropriate codons to form the new polypeptide -to do this, must: 1. pick up appropriate amino acids 2. recognize the appropriate codons in the mRNA -tRNA molecules contain a strand of RNA including an anticodon that matches with a codon on mRNA, and a corresponding amino acid to that specific anticodon sequence (which binds by a specific enzyme and ATP) -tRNA is used in ribosomes and attaches to the corresponding codons in the mRNA to add the next amino acid to the polypeptide chain.

function/process of transcription

-function: to make mRNA that hold codons that tRNA will translate into amino acids, and eventually a polypeptide -transfer of genetic info. from DNA to RNA -occurs in nucleus 1. initiation- attachment of RNA polymerase to promoter and start of RNA synthesis 2. elongation- RNA strand grows longer. As RNA synthesis continues, the RNA strand peels away from its DNA template, allowing the 2 DNA strands to be brought back together in the region that is already transcribed 3. termination- RNA polymerase reaches a sequence of bases in DNA template called the terminator. This sequence marks the end of the gene. The RNA polymerase detaches from the RNA molecule and the gene

function/process of translation

-function: to transfer genetic information from RNA to protein -occurs in cytoplasm 1. amino acid attachment- each amino acid attaches to its proper tRNA with the help of a specific enzyme and ATP 2. initiation of polypeptide synthesis- the mRNA, the first tRNA, and the ribosomal subunits come together -FIRST mRNA molecule binds to small ribosomal subunit -special initiator tRNA binds to specific codon called start codon where translation is to begin on mRNA molecule -initiator tRNA carries the amino acid MET; its anticodon binds to start codon -SECOND a large ribosomal subunit binds to the small one, creating a functional ribosome -initiator tRNA fits into one of the two tRNA binding sites on the ribosome -this site, called P site, will hold growing polypeptide chain while the A site is vacant and ready from the next amino-acid bearing tRNA 3. elongation- a succession of tRNAs add their amino acids to the polypeptide chain as the mRNA is moved through the ribosome, one codon at a time -CODON RECOGNITION: anticodon of an incoming tRNA molecule, carrying its amino acid, pairs with mRNA codon in A site of ribosome -PEPTIDE BOND FORMATION: polypeptide separates from tRNA in the P site and attaches by a new peptide bond to the amino acid carried by the tRNA in the A site -ribosome catalyzes formation of the peptide bond, adding one more amino acid to the growing polypeptide chain -TRANSLOCATION: P site tRNA leaves ribosome and ribosome translocates (moves) the remaining tRNA in the A site, with the growing polypeptide, to the P side -codon and anticodon remain hydrogen-bonded and mRNA and tRNA move as a unit -this movement brings into the A site the next mRNA codon to be translated and the process can start again with step 1 4. termination- The ribosome recognizes a stop codon. Polypeptide is terminated and released. 5. 2 ribosomal subunits come apart. tRNA and mRNA are released.

types of mutations (and mutagens that cause them)

-mutation: any change in the nucleotide sequence of DNA -divided into 2 general categories: 1. nucleotide substitutions: replacement of one nucleotide and its base pairing partner with another pair of nucleotides -silent mutation: a type of substitution, when no change in protein product would result (substitution mutations have no effect at all) -missense mutations: change amino acid coding; some have little/no effect on shape of function of resulting protein while others prevent protein from performing normal function (i.e. sickle cell disease) -nonsense mutations: change an amino acid codon into a stop codon; resulting in a prematurely terminated protein which probably won't function properly 2. nucleotide deletions or insertions: adding or subtracting of nucleotides may alter the reading frame (triplet grouping) of message; often have disastrous effects -mutagenesis, production of mutations, can occur many diff. ways: 1. spontaneous mutations are due to errors that occur during DNA replication or recombination 2. mutagens, physical or chemical agents, cause mutations. -physical mutagen: high-energy radiation (X-rays of ultraviolet light0 -chemical mutagen: chemicals similar to normal DNA bases but pair incorrectly or are otherwise disruptive when incorporated into DNA

phosphate group

A functional group comprised of phosphorus attached to four oxygen, and with a net negative charge, thus represented as PO4-

why telomeres exist and link b/w them and aging

B/c eukaryotes have linear chromosomes, telomeres exist at the end of chromosomes to prevent the DNA at the end of the chromosomes from shortening and degrading with each replication. Telomeres lengthen and shorten, as our cells and us age and grow older. As DNA is replicated, less of the strand is copied, causing less info to be copied from there forward

biology of transformation and Griffith's experiment

DNA from outside, meaning the bacterium environment, changed bacteria from non deadly to deadly. Transformation is a change in genotype and phenotype due to assimilation (bringing in) of foreign DNA. For instance, the rough bacterium gets attacked by a white blood cell b/c it has a capsule while the smooth bacterium doesn't b/c it didn't have glycoproteins on the outside so white blood cells don't recognize it; its foreign.

anti-parallel

DNA is assembled with two complementary strands that go in opposite directions; one goes 3' to 5', and the other goes 5' to 3'.

why ligase is necessary in replication of DNA

DNA ligase is responsible for forming a final bond b/w Okazaki fragments on the lagging strand. It synthesizes the strands in these short pieces as the fork opens up. It removes the RNA primers from the lagging strand of new DNA and replaces it with DNA nucleotides to complete the strand of DNA

how DNA nucleotide sequences represents a specific polypeptide structure

DNA's language is written as a linear sequence of nucleotide bases on a polynucleotide. Specific sequences of bases, each with a beginning and end, make up the genes on a DNA strand. The nucleic acid language of DNA is rewritten as a sequence of bases on RNA (transcription). The language is still that of nucleic acids, although the nucleotide bases on the RNA molecule are complementary to those on the DNA strand. This is b/c RNA was synthesized using the DNA as a template. Then is the conversion of nucleic acid language to the polypeptide language (translation). Language is written in linear sequence and sequence of nucleotides of RNA molecule dictates the sequence of amino acids of the polypeptide.

how alternative RNA splicing allows one gene to code for more than one polypeptide

Each kind of polypeptide is encoded by an mRNA molecule containing a different combination of exons.

one gene, one polypeptide hypothesis

Gene is a segment of DNA that codes for a protein. A protein is a polypeptide b/c it's made of a bunch of amino acids linked by polypeptide bonds. This is false b/c of alternative RNA splicing

experiment of Griffith

Griffith used mice in his experiment to help prove that DNA is the genetic material.He was working with bacteria that causes pneumonia and found there were two strains, the S strain, called that b/c it looked "smooth" underneath a microscope. When he injected the S strain into the mouse, it died. He found a different strain called the R strain, called b/c it looks rough. When he injected it into the mouse, it lived. He wanted to figure out how he could make the dead mouse living so he killed the S strain bacteria by heating, which denatured the protein and lysed the cell. He injected that into the mouse and the mouse was healthy. Then, he took the rough bacteria and the heat-killed smooth bacteria (neither of which caused the mouse to die) and mixed them. He injected that mixture into the mouse and the mouse died. Hypothesis: There's a chemical substance, a transforming factor, that isn't alive that takes rough bacteria and transforms them into smooth bacteria. Conclusion: The living R bacteria had been transformed into pathogenic S bacteria by a transforming factor (chemical substance) from the dead S cells that allowed the R cells to make capsules.

nitrogen base

One of the nitrogen-containing purines (adenine or guanine) or pyrimidines (cytosine, thymine, or uracil) found in the nucleic acids DNA and RNA. The bases may be attached to a sugar (deoxyribose in DNA, ribose in RNA) to form nucleosides.

function of RNA polymerase

RNA polymerase is the enzyme that builds mRNA on the template of DNA. The enzyme initially begins where there is a promoter sequence in the DNA. Transcription factors mediate the binding of RNA polymerase and the initiation of transcription. RNA polymerase opens up the DNA and synthesizes a strand of RNA on the template of the DNA by complementary base pairs. In prokaryotes, ribosomes attach to the mRNA strand while the mRNA is being transcript so that translation can happen simultaneously. In eukaryotes, the mRNA is made by the RNA polymerase, and then stays in the nucleus for processing before it can exit into the cytoplasm and to the ribosomes.

how RNA in spliceosomes utilizes base pairing to allow for precise splicing of mRNA in nucleus

Spliceosomes are large protein complexes made up of snRNP's (small nuclear ribonucleic proteins) and proteins. This is where RNA splicing occurs and introns are cut out. One kind of snurp binds to the 5' end of an intron by forming base pairs with the complementary sequences on the intron. Another kind of snurp binds to the 3' end of the intron. Additional introns interact, forming a loop and bringing the ends of the introns together. A complex of snRNP's is formed and it excises the introns, joining the exons together. The snRNP's are then released.

evolutionary significance of RNA primer

The first nucleotide chain that's produced during DNA synthesis is actually a short stretch of RNA called a primer and is synthesized by the enzyme primase

RNA primase

The job of RNA primase is to make, or synthesize, a primer for replication to start. First it waits for DNA helicase to open a replication fork. Then it swings in behind helicase to lay down a primer.

pyrimidine

Thymine and Cytosine; single ring structure

replication fork

Y-shaped regions where the parental strands of DNA are being unwound

ribosome

a cell structure consisting of protein and RNA organized into two sub units and functioning as the site of protein synthesis in the cytoplasm

mutation

a change in the nucleotide sequence of an organism's DNA

RNA polymerase

a large molecular complex that links together the growing chain of RNA nucleotides during transcription, using a DNA strand as a template.

spliceosome

a large protein complex made up of proteins and snurps, small nuclear ribonuclear proteins, that excise introns from a transcribed pre-mature RNA

template

a molecule (as of DNA) that serves as a pattern for the synthesis of another macromolecule (as messenger RNA)

base pair

a pair of complementary bases in a double-stranded nucleic acid molecule, consisting of a purine in one strand linked by hydrogen bonds to a pyrimidine in the other. Cytosine always pairs with guanine, and adenine with thymine (in DNA) or uracil (in RNA).

intron

a piece of mRNA that gets cut out of the mRNA strand during processing

exon

a piece of mRNA that will be expressed; is not taken out when mRNA is processed

polypeptide

a polymer of amino acids linked by peptide bonds

plasmid

a small, circular DNA molecule separate from the bacterial chromosome

tRNA

a type of ribonucleic acid that functions as an interpreter in translation; it has an amino acid attachment site where a specific amino acid binds with the help of ATP and a specific enzyme; also has an anticodon which binds to the complementary codon in the mRNA

reverse transcription

an enzyme used by retroviruses that catalyzes the synthesis of DNA on a RNA template

role of rRNA

associates with a set of proteins to form ribosomes. These complex structures, which physically move along an mRNA molecule, catalyze the assembly of amino acids into protein chains. They also bind tRNAs and various accessory molecules necessary for protein synthesis. Ribosomes are composed of a large and small subunit, each of which contains its own rRNA molecule or molecules.

5' DNA strand

at the end of strand, the sugar's 5' carbon atom is attached to a phosphate group; antiparallel to 3' strand

3' DNA strand

at the end of the strand, the sugar's 3' carbon atom is attached to an -OH group; antiparallel to 5' strand

hydrogen bonds

bonds that connect base pairs in DNA, a weak type of chemical bond where the partially positive hydrogen atom in a polar covalent bond in one molecule is attracted to a partially negative atom in a polar covalent bond of another molecule

role of mRNA

carries the genetic information copied from DNA in the form of a series of three-base code "words," each of which specifies a particular amino acid.

DNA

deoxyribonucleic acid: a double stranded helical nucleic acid molecule consisting of nucleotide monomers with deoxyribose sugar, phosphate, and the nitrogenous bases Adenine, Thymine, Guanine, and Cytosine; capable or replicating, DNA is an organisms genetic material

antiparallel nature of DNA

each strand of DNA has a 5' end and a 3' end. At the end of the 3' strand, there's a -OH group attached and at the end of the 5' end there's a phosphate group. The strands run in opposite orientations. The 5' end of a strand is antiparallel to the other 5' end of the other strand. Instead, it's parallel to the 3' end of a strand. This antiparallel nature is important in DNA replication

complementary strand

either of the two chains that make up a double helix of DNA, with corresponding positions on the two chains being composed of a pair of complementary bases.

composition of DNA

made up of the sugar deoxyribose and phosphate groups, creating sugar-phosphate backbone; and nitrogen bases C,T, (pyrimidine bases) and A, G (purine bases)

mRNA

messenger RNA; synthesized from a DNA template during transcription, that mediates the transfer of genetic information from the cell nucleus to ribosomes in the cytoplasm, where it serves as a template for protein synthesis.

R (rough) strain

non-pathogenic and lack a capsule

how retroviruses function

reproduces by means of a DNA molecule. It reverse transcribes its RNA into DNA, inserts the DNA into a cellular chromosome, and then transcribes more copies of RNA from the viral DNA. HIV and a number of cancer causing viruses are retroviruses.

experiment of Hershey and Chase

showed DNA to be genetic material of T2 (virus that infects bacteria E. coli) -when phage infect bacteria, they attach to surface of bacteria and inject DNA into cell -the protein coat remains outside of the cell -first part of experiment, phage were contained in sulfur radioactively labeled amino acids -this resulted with radioactively labeled proteins but no radioactively labeled DNA -phage attached to bacterial cell and injected their DNA but radioactively labeled protein coat remained outside the cell -phage produced in these cells contained no radioactivity -vigorous shaking caused empty protein coats to be removed -production of phages within cell -second part of experiment, phage were contained in radioactive phosphorus solution (basically used different radioactive isotopes to label DNA and protein in T2) -resulted in radioactively labeled DNA but not radioactively labeled protein -phage attaches to bacterial cell and injects DNA -DNA causes bacterial cells to produce new phage proteins and DNA molecules which cause cell to lyse, releasing newly produced phages

bacteriophage

virus that exclusively infect bacteria

an understanding of the triplet code

what the flow of info. from gene to protein is based on. It is a sequence of three bases (ex. AGT) along a single strand of DNA. The three bases are called codons. They're genetic instructions written in DNA and RNA as a series of non-overlapping three-base words called codons. First, a triplet code is transcribed into a complementary triplet code in RNA and then a triplet code is translated into amino acids that will form a polypeptide.

how and why mRNA must be processed before translation

why? -b/c mRNA must exit the nucleus via nuclear pores before entering the cytoplasm, where mechanisms for protein synthesis are how? 1. mRNA processing -addition of a short cap (a single G nucleotide) on one end and a long tail (50-250 A nucleotides) on the other end -they facilitate the export of mRNA from the nucleus -they prevent mRNA from being attacked by cellular enzymes and help ribosomes bind to the mRNA 2. RNA splicing -mRNA is made up of introns (noncoding sequences that interrupt coding regions) and exons (coding regions & part of a gene that are expressed) -introns are cut out -exons are joined together to form a continuous coding sequence of mRNA -catalyzed by splicesomes or by the RNA transcript itself