Ch 6: (6.1, 6.2, 6.3, 6.4, 6.5)

Pyrimidines

(cytosine, thymine, and uracil) have a single six-membered ring Each individual carbon or nitrogen atom in the central ring structure of a nitrogenous base is assigned a number: 1-6 for pyrimidines. *notice how one purine and one pyrimidine form a base pair NOT purines with purines or pyrimidines with pyrimidines*

Transformation

(genetics) modification of a cell or bacterium by the uptake and incorporation of exogenous DNA process in which one strain of bacteria is changed by a gene or genes from another strain of bacteria

Transcription

(genetics) the organic process whereby the DNA sequence in a gene is copied into mRNA synthesis of an RNA molecule from a DNA template

Bacteria

(microbiology) single-celled or noncellular spherical or spiral or rod-shaped organisms lacking chlorophyll that reproduce by fission Bacteria: -carry their genetic material in a single circular chromosome that lies within the cell without being enclosed in a nuclear membrane. -do not undergo meiosis to produce germ cells, and they do not apportion their replicated chromosomes to daughter cells by mitosis; rather, they divide by a process known as binary fission

major and minor grooves of DNA

- The distances between the strand backbones - Major groove: when backbones are far apart from each other - Minor groove: the backbones are closer together - Certain proteins are going to bind to DNA to alter its structure (for transcription and replication). DNA binding proteins interact with the bases. Some proteins can recognize and bind to specific base pair sequences in double-stranded DNA (Fig. 6.15). This information emerges mainly from differences between the four bases that appear in the major and minor grooves. Proteins can access this information to sense the base sequence in a stretch of DNA without disassembling the double helix.

Hydrogen bonds in DNA

-DNA bases are held together by weak hydrogen bonds -bases are codes arranged in a sequence 2 bonds between A and T 3 bonds between C and G

B-form DNA

-the most common form of DNA in which molecular configuration *spirals to the right* Watson-Crick model DNA.

DNA strand separation

1) Specialized proteins known as *helicases* force DNA strands apart --> Creates two replication forks at the origin (bi-directional) 2) Single-stranded DNA-binding (SSB) proteins bind cooperatively --> Keep DNA single strands apart and protect them from nucleases 3) DNA topoisomerase work *AHEAD* of the replication fork (E.g bacterial DNA gyrase) relieve the tension, by removing *POSITIVE* supercoils

Questions to think about when reviewing DNA

1. How does the molecule carry information? 2. How is that information copied for transmission to future generations? 3. What mechanisms allow the information to change? 4. How does DNA-encoded information govern the expression of phenotype?

Models of DNA Replication

3 Models of DNA Replication: Semi-Conservative, Conservative, & Dispersive models of DNA replication. DNA follow the semi-conservative model, the others are just hypothesis of how DNA replication occured conservative replication: one of the two daughter double helixes would consist entirely of original DNA strands, while the other helix would consist of two newly synthesized strands. dispersive replication: both daughter double helixes would carry blocks of original DNA interspersed with blocks of newly synthesized material. *These alternatives are less satisfactory because they do not immediately suggest a mechanism for copying the information in the sequence of bases.*

possible combinations of amino acids

= 20^n where n is the number of amino acids present within the protein example for 4 amino acids in a chain, the possible cominations are: 20^4 which is 160,000

binary fission

A form of asexual reproduction in single-celled organisms by which one cell divides into two cells of the same size

polymer

A long molecule consisting of many similar or identical monomers linked together. DNA is a polymer of nucleotides joined by phosphodiester bonds. Nucleotides are made of deoxyribose, phosphate, and one of four nitrogenous bases.

Virus

A tiny, nonliving particle that invades and then reproduces inside a living cell. These phage particles can reproduce themselves only after infecting a bacterial cell. Thirty minutes after infection, the cell bursts and hundreds of newly made phages spill out In some viruses, the genetic material consists of relatively small, single-stranded DNA molecules. Once inside a cell, the single strand serves as a template (pattern) for making a second strand, and the resulting double-stranded DNA then governs the production of more virus particles.

Purines

Adenine and Guanine Bases with a double-ring structure. Each individual carbon or nitrogen atom in the central ring structure of a nitrogenous base is assigned a number: 1-9 for purines *notice how one purine and one pyrimidine form a base pair NOT purines with purines or pyrimidines with pyrimidines*

Primase

An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template. synthesizes RNA primer

DNA helicase

An enzyme that unwinds the DNA double helix during DNA replication

base pairs

Any of the pairs formed between complimentary bases in the two nucleotide chains of DNA, such as A-T and C-G (DNA); A-U and C-G (RNA)

nucleotides

Basic units of DNA molecule, composed of a sugar, a phosphate, and one of 4 DNA bases Each nucleotide consists of a deoxyribose sugar, a phosphate, and one of four nitrogenous bases one phosphate group binds two sugars through the hydroxyl group on the carbon #3 of one sugar and the carbon #5 on another sugar

DNA protien misconception

Because proteins are built of 20 different amino acids, whereas DNA is made of only four different nucleotides, many researchers thought proteins had greater potential for diversity and were better suited to serve as the genetic material. These same scientists assumed that even though DNA was an important part of chromosome structure, it was too simple to contain the complexity of genes.

transcription factors

Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.

Replication

Copying process by which a cell duplicates its DNA

DNA vs RNA

DNA (H): deoxyribose sugar, thymine (CH3 vs just H), double strand RNA (HO): ribose sugar, uracil (H vs CH3), single strand, contain far fewer nucleotides than the very long DNA molecules found in nuclear chromosomes. SEE PIC

DNA synthesis

DNA synthesis can proceed only by adding nucleotides to the 3′ end of an existing polynucleotide.

DNA replication

DNA unzips into two parts and splits with the cell. In it's new home each side of the DNA strand attack to matching nucleotides to create 2 exact copies. It is important in puberty and other times of growth as it is the reproducing of your cells. occurs at a precise moment in the cell cycle, depends on a network of interacting regulatory elements, requires considerable input of energy, and involves a complex array of the cell's molecular machinery, including the key enzymes

Erwin Chargaff

Discovered that DNA composition varies, but the amount of adenine is always the same as thymine and the amount of cytosine is always the same as guanine therefore base-pairing exists (A=T and G=C)

Frederick Griffith

Discovered transformation in pneumonia-causing bacteria. Discovered transformation during an experiment that involved injecting mice with smooth S cells, rough R cells, heat-killed S cells, and heat-killed S cells with living R cells. R is a product of a mutation of S cells Neither the heat-killed S forms nor the live R forms produced infection when injected into laboratory mice, but a mixture of the two killed the animals. Furthermore, bacteria recovered from the blood of the dead animals were living S forms. The ability of a substance to change the genetic characteristics of an organism is known as transformation.

DNA polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule catalyzes the formation of a new phosophodiester bond three strict requirements for DNA polymerase action: (1) The four dNTPs. (2) A single-stranded template. Double-stranded DNA must be unwound, and DNA polymerase moves along the template strand in the 3′-to-5′ direction. (3) A primer with a free 3′ hydroxyl group. DNA polymerase adds nucleotides successively to the 3′ end of the growing DNA chain. (That is, DNA polymerase synthesizes DNA only in the 5′-to-3′ direction.) However, DNA polymerase cannot establish the first link in a new chain. Polymerization therefore must start with a primer, a short, single-stranded molecule of DNA or RNA a few nucleotides long that base pairs with part of the template strand. formation of phosphodiester bonds by DNA polymerase is just one component of the highly coordinated process

restriction enzymes

Enzyme that cuts DNA at a specific sequence of nucleotides an enzyme produced chiefly by certain bacteria, having the property of cleaving DNA molecules at or near a specific sequence of bases.

Proteins and DNA

Enzymes are proteins in DNA replication proteins are made up of 20 different subunits or amino acids in the form of chains proteins come in various shapes and sizes

Watson and Crick

Figured out structure of DNA was a double helix (B form DNA)

sugar-phosphate backbone

In a polynucleotide (DNA or RNA strand), the alternating chain of sugar and phosphate to which nitrogenous bases are attached. Because DNA's backbone of alternating sugar and phosphate is chemically identical for every nucleotide in a DNA chain, *the only difference between nucleotides is in the identity of the nitrogenous base. Thus, the genetic information in DNA must consist of variations in the sequence of the A, G, T, and C bases.*

Z-form DNA

Left-handed helical form of DNA and the backbone takes on a zigzag shape

semiconservative replication

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 1) DNA begins to split 2) The newly replicated strands form as complementary bases align opposite the exposed bases on the two parental strands 3)Once the appropriate base has aligned opposite to and formed hydrogen bonds with its complement, enzymes join the base's nucleotide to the preceding nucleotide by a phosphodiester bond, eventually linking a whole new line of nucleotides into a continuous strand. 4) yields two daughter double helixes that each contain one of the original DNA strands intact (this strand is conserved) and one completely new strand

RNA folding

Most RNA molecules are single-stranded but are sufficiently flexible so that some regions can fold back and form base pairs with other parts of the same molecule. Within a single-stranded RNA molecule, folding can bring together two oppositely oriented regions that carry complementary nucleotide sequences to form a short, base paired stretch within the molecule. Therefore many RNAs have a complicated structure of short double-stranded segments interspersed with single-stranded loops

Various DNA forms

Most eukaryotes have *double-stranded, linear DNA*, but prokaryotes, chloroplasts and mitochondria, and some viruses have *double-stranded circular DNA*. Certain other viruses contain a *single-stranded DNA that can be linear or circular*.

nucleoside vs nucleotide

Nucleoside: nitrogenous base + sugar Nucleotide: nitrogenous base + sugar + phosphate group Covalent attachment of a nitrogenous base to the 1′ carbon of deoxyribose forms a *nucleoside*. The addition of a phosphate group to the 5′ carbon forms a complete *nucleotide*.

How does DNA differ from person to person?

Only the sequence and number of bases separates all organisms. Human DNA differs only between humans of 0.1% only identical twins have the same DNA sequence The information content of DNA resides in the sequence of its bases. The four bases in each chain are like the letters of an alphabet; Each word has its own meaning, that is, its own effect on phenotype. Although DNA has only four different letters, or building blocks, the potential for different combinations and thus different sets of information in a long chain of nucleotides is staggering. *The base sequence of DNA can be read from a single, unwound strand during replication or transcription. In addition, specialized proteins can recognize and bind to short base sequences accessible in the grooves of double-stranded DNA.*

Polymerase 1, 2, and 3

Polymerase 1: replaces RNA primer with DNA Polymerase 2: transcribes mRNA Polymerase 3: Adds DNA nuceotides to RNA primer and elongates new DNA strand being synthesized DNA polymerase synthesizes DNA in the 5′-to-3′ direction by adding nucleotides successively onto the 3′ end of a growing DNA chain. DNA polymerase requires: (i) a supply of the four deoxyribonucleotide triphosphates, (ii) a single-stranded DNA template, and (iii) a primer of either DNA or (in cells) RNA with a free 3′ hydroxyl group. At the DNA replication fork, DNA polymerase synthesizes one new strand (the leading strand) continuously, while the other (lagging strand) is synthesized as multiple Okazaki fragments that are then joined by DNA ligase.

Retrovirus

RNA virus that contains RNA as its genetic information An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses.

how genetic information is preserved

Redundancy: Either strand of the double helix can specify the sequence of the other. This redundancy provides a basis for checking and repairing errors arising either from chemical alterations sustained during storage or from rare malfunctions of the replication machinery. The remarkable precision of the cellular replication machinery: Evolution has perfected the cellular machinery for DNA replication to the point where errors during copying are exceedingly rare. Enzymes that repair chemical damage to DNA: The cell has an array of enzymes devoted to the repair of nearly every imaginable type of chemical damage.

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

antiparallel strands

Strands parallel to each other going in opposite directions (3'-5' and 5'-3') antipolarity causes this Phosphodiester bonds always form a covalent link between the 3′ carbon of one nucleotide and the 5′ carbon of the following nucleotide. Antiparallel means that one strand is oriented in the 5′-to-3′ direction, while the other, complementary strand is oriented in the 3′-to-5′ direction.

transforming principle

Substance responsible for transformation. DNA is the transforming principle. from griffins study it was found that: Enzymes that degraded RNA, protein, or polysaccharide had no effect on the transforming principle, but an enzyme that degrades DNA completely destroyed its activity. The tentative published conclusion was that the transforming principle appeared to be DNA.

template strand

The DNA strand that provides the pattern, or template, for ordering, by complementary base pairing, the sequence of nucleotides in an RNA transcript. Each of the two separated strands of original DNA acts as a template, or molecular mold, for the synthesis of a new second strand

The DNA structures of prokaryotes and eukaryotes are different in several ways, but one way in which they are the same is that _____.

The nuclear chromosomes of all eukaryotic organisms are long, linear double helixes, but some smaller chromosomes are circular. These include the chromosomes of prokaryotic bacteria, the chromosomes of organelles such as the mitochondria and chloroplasts that are found inside eukaryotic cells, and the chromosomes of some viruses, including the papovaviruses that can cause cancers in animals and humans. Such circular chromosomes consist of covalently closed, double-stranded circular DNA molecules. Although neither strand of these circular double helixes has an end, the two strands are still antiparallel in polarity

Deoxiribose sugar

This is one part of the nucleotides in DNA found between the phosphate group and the nitrogen base. This is what DNA is named after. It also forms part of the backbone of DNA. A small, 5-carbon sugar molecule used in DNA construction The carbon atoms of the deoxyribose sugar are distinguished from atoms within the nucleotide base by the use of primed numbers from 1′ to 5′.

Matthew Meselson and Franklin Stahl

Used isotopes of nitrogen to demonstrate that DNA replication could not be conservative or dispersive; evidence that DNA replication is semi-conservative Meselson and Stahl's observations are consistent only with semiconservative replication. In the first generation after transfer from the 15N to the 14N medium, one of the two strands in every daughter DNA molecule carries the heavy isotope label; the other, newly synthesized strand carries the lighter 14N isotope.

Hershey and Chase

Used radioactive material to label DNA and protein; infected bacteria passed on DNA; helped prove that DNA is genetic material not proteins aka Waring Blender Experiment Because proteins incorporate sulfur but no phosphorus and DNA contains phosphorus but no sulfur, phages grown on 35S would have radioactively labeled protein while particles grown on 32P would have radioactive DNA. The radioactive tags would serve as markers for the location of each material when the phages infected fresh cultures of bacterial cells *This result confirmed that the extracellular ghosts were indeed mostly protein, while the injected viral material specifying production of more phages was mostly DNA.*

Rosalind Franklin

Woman who generated x-ray images of DNA, she provided Watson and Crick with key data about DNA showed that the molecule is spiral-shaped, or helical; the spacing between repeating units along the axis of the helix is 3.4 Å (3.4 × 10−10 meters); the helix undergoes one complete turn every 34 Å; and the diameter of the molecule is 20 Å. This diameter is roughly twice the width of a single nucleotide, suggesting that a DNA mo

replication fork

a Y-shaped point that results when the two strands of a DNA double helix separate so that the DNA molecule can be replicated

phosphodiester bond

a bond that is responsible for the polymerization of nucleic acids by linking sugars and phosphates of adjacent nucleotides Phosphodiester bonds always form a covalent link between the 3′ carbon of one nucleotide and the 5′ carbon of the following nucleotide. one phosphate group binds two sugars through the hydroxyl group on the carbon #3 of one sugar and the carbon #5 on another sugar

DNA primer

a short strand of DNA (or RNA) that serves as a starting point for DNA synthesis

DNA topoisomerase

an enzyme that alleviates DNA supercoiling during DNA replication An enzyme that unwinds and winds coils of DNA that form during replication and transcription. The activity of topoisomerases thus allows replication to proceed through the entire chromosome by preventing supercoils from accumulating in front of the replication fork.

DNA ligase

an enzyme that eventually joins the sugar-phosphate backbones of the Okazaki fragments

binding proteins

bind a specific substrate, either to sequester it in the body or hold its concentration at steady state stabilize separate strands

diffraction pattern

bright spots and dark areas on a photographic plate determined that DNA was 3 dimensional double helix

Energy required for Replication

comes from the high-energy phosphate bonds associated with the four deoxyribonucleotide triphosphates (dATP, dCTP, dGTP, and dTTP; or dNTP as a general term) that provide bases for incorporation into the growing DNA strand.

DNA

deoxyribonucleic acid, a self-replicating material present in nearly all living organisms as the main constituent of chromosomes. It is the carrier of genetic information. double stranded composed of a sugar-phosphate backbone and nitrogenous bases DNA is localized almost exclusively within chromosomes. The DNA molecule is a double helix composed of two antiparallel strands, in each of which nucleotides are joined by phosphodiester bonds. Hydrogen bonding between the complementary bases—A with T, and G with C—holds the two strands together.

Friedrich Miescher

discovered nucleic acids

semiconservative replication and the eukaryotic cell cycle

early interphase: each eukaryotic chromosome contains a single continuous linear double helix of DNA. S-phase (mid interphase): the cell replicates the double helix semiconservatively; after this semiconservative replication, each chromosome is composed of two sister chromatids joined at their centromeres. Each sister chromatid is a double helix of DNA, with one strand of parental DNA and one strand of newly synthesized DNA. (which is what we see in prophase) End of mitosis: each of the two daughter cells receives one sister chromatid from every chromosome in the cell. This process preserves chromosome number and identity during mitotic cell division because the two sister chromatids are identical in base sequence to each other and to the original parental chromosome. for meiosis things get a bit complicated because crossing over occurs and swaps DNA fragments

dNTPs

free deoxyribonucleotides needed for extension. a free molecule of dATP forms hydrogen bonds with a complementary thymine base on the template strand. DNA polymerase (yellow) cleaves dATP between the first and second phosphate groups. This cleavage releases the energy needed to form a covalent phosphodiester bond between the terminal 3′-OH group on the preceding nucleotide to the first phosphate of the dATP substrate. Pyrophosphate (PPi ) is released as a by-product.

DNA replication overview

has two stages: *initiation*, during which proteins open up the double helix and prepare it for complementary base pairing, and *elongation*, during which proteins connect the correct sequence of nucleotides on both newly formed DNA double helixes. -multiple replication bubbles -bidirectional -lagging strand forms DNA away from replication fork -short segments of lagging strand = okazaki fragments -leading strand forms DNA towards replication fork Remember that before a cell divides, DNA replicates during S Phase This method of replication is called Semi-Conservative Replication because: The strands of the double helix separate Each strand is used as a template to form new strands Each resulting daughter molecule is ½ old and ½ new: One original strand One newly synthesized strand

Unwinding of DNA

helicase *Most Genetic Information Is Read from Unwound DNA Chains* Enzyme unzips the 2 strands so that they separate- results in 2 single strands of DNA The unwinding of a DNA molecule exposes a single sequence of bases on each of two strands (Fig. 6.14). Proteins read the information in a single DNA strand by synthesizing a stretch of RNA (a process called transcription) or DNA (a process called replication) complementary to a specific sequence.

3' end

hydroxyl group (-OH) it is the 3′ carbon of the final nucleotide that is free. Along the chain between the two ends, this 5′-to-3′ polarity is conserved from nucleotide to nucleotide. By convention, a DNA chain is described in terms of its bases, written with the 5′-to-3′ direction going from left to right

nitrogenous base

is a carbon ring structure that contains one or more atoms of nitrogen. In DNA, Adenine, Thymine, Cytosine, Guanine. Each individual carbon or nitrogen atom in the central ring structure of a nitrogenous base is assigned a number: 1-9 for purines, and 1-6 for pyrimidines An organic base that contains nitrogen, such as a purine or pyrimidine; a subunit of a nucleotide in DNA and RNA different combinations of the four bases in very long sequences of nucleotides can encode the information for constructing an organism.

DNA anatomy

nucleotides in each strand are joined by covalent bonds, alternating sugar and phosphate molecules form a backbone for each strand, the 2 strands are held together by hydrogen bonds between nitrogenous bases, 2 strands in helix, contains: adenine, thymine, guanine, and cytosine in nitrogenous bases. Adenine bonds to Thymine and Guanine bonds to Cytosine.

5' end

phosphate group (usually) but depending on how the DNA is synthesized or isolated, the 5′ carbon of the nucleotide at the 5′ end may carry either a hydroxyl or a phosphate group At the 5′ end, the sugar of the terminal nucleotide has a free 5′ carbon atom, free in the sense that it is not linked to another nucleotide.

Supercoiling of DNA

requires the action of topoisomerase enzymes Winding of DNA strands, this can reduce the size of DNA by 10.000x

RNA

ribonucleic acid single-stranded nucleic acid that contains the sugar ribose RNA has the same ability as DNA to carry information in the sequence of its bases, but it is much less stable than DNA. RNA fulfills several vital functions in all cells. It participates in gene expression and protein synthesis, and DNA replication

Feulgen reaction

stains DNA lead to the discovery that DNA resides in chromosomes

teleomeres

structures that cap the ends of chromosomes. They stabilize it and allow for DNA replication at the chromosome end. noncoding, repetitive DNA sequence at the end of a chromosome specialized termination structures known as telomeres, which ensure the maintenance and accurate replication of the two ends of each linear chromosome.

Deoxiribose

the five-carbon sugar in DNA molecules it is found mainly in cell nuclei; and it is acidic

Nuclein

the original name given to DNA when it was discovered in the nucleus of cells by Friedrich Miescher in 1869

bidirectional replication

the process in which DNA replication proceeds outward from the origin in opposite directions

coding strand

the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine

phages (bacteriophages)

viruses that infect bacteria

Leading Strand vs. Lagging Strand

works toward replication fork / works away from replication fork; both always move in the 5' ➝ 3' direction The leading strand is synthesized continously while lagging strand Okazaki fragments are synthesized in segments. leading strand (3'-5') is built continuously without break leading strand replicates nucleotides one by one. daughter strand 3' end is directed toward the replication fork. one RNA primer at origin of replication is enough to synthesize continuous strand of DNA