Biology Module 4

What gives a gene its meaning?

- A gene's meaning to the cell is encoded in its specific sequence of the four DNA bases. o For example, the sequence 59-AGGTAACTT-39 means one thing, whereas the sequence 59-CGCTTTAAC-39 has a different meaning. o (Entire genes, of course, are much longer.) o The linear order of bases in a gene specifies the amino acid sequence—the primary structure—of a protein, which in turn specifies that protein's three-dimensional structure and its function in the cell.

What does DNA polymerase III do in synthesizing a complementary strand?

- Along one template strand, DNA polymerase III can synthesize a complementary strand continuously by elongating the new DNA in the mandatory 5′ → 3′ direction. - DNA pol III remains in the replication fork on that template strand and continuously adds nucleotides to the new complementary strand as the fork progresses. - To elongate the other new strand of DNA in the mandatory 5′ → 3′ direction, DNA pol III must work along the other template strand in the direction away from the replication fork. - The DNA strand made by this mechanism is called the leading strand. o Only one primer is required for DNA pol III to synthesize the entire leading strand - The DNA strand elongating in this direction is called the lagging strand

What is Telomerase?

- An enzyme called telomerase catalyzes the lengthening of telomeres in eukaryotic germ cells, thus restoring their original length and compensating for the shortening that occurs during DNA replication - This enzyme contains its own RNA molecule that it uses as a template to artificially "extend" the leading strand, allowing the lagging strand to maintain a given length. o This means that offspring don't receive shortened telomeres from their parents § It would only be a matter a time, if this wasn't the case, that telomeres were gone and DNA would be affected - However, telomerase is not active in most human somatic cells, only germ cells

What is antiparallel elongation?

- As we have noted previously, the two ends of a DNA strand are different, giving each strand directionality, like a one-way street o 3' and 5' end and they were flipped in the alpha helix so that they align together - In addition, the two strands of DNA in a double helix are antiparallel, meaning that they are oriented in opposite directions to each other, like the two sides of a divided street - When we look at a replication fork, only one of the two strands is able to be produced continuously o Because of their structure, DNA polymerases can add nucleotides only to the free 3′ end of a primer or growing DNA strand, never to the 5′ end - Thus, a new DNA strand can elongate only in the 5′ → 3′ direction.

What did Chargaff analyze?

- Chargaff analyzed the base composition of DNA from a number of different organisms. - In 1950, he reported that the base composition of DNA varies from one species to another. o For example, he found that 32.8% of sea urchin DNA nucleotides have the base A, whereas only 30.4% of human DNA nucleotides have the base A and only 24.7% of the DNA nucleotides from the bacterium E. coli have the base A - Chargaff's evidence of molecular diversity among species made DNA a more credible candidate for the genetic material. DNA within species is more similar than between species

Where do humans get their DNA?

- Chemically speaking, your genetic endowment is the DNA you inherited from your parents. - Of all nature's molecules, nucleic acids are unique in their ability to direct their own replication from monomers. o Indeed, the resemblance of offspring to their parents has its basis in the accurate replication of DNA and its transmission from one generation to the next. - Hereditary information in DNA directs the development of your biochemical, anatomical, physiological, and, to some extent, behavioural traits. - This information is important to examine species, genetic disorders, testing for COVID, evidence at crime scenes, etc.

How is DNA packed together? What about in bacteria?

- DNA is packaged into chromosomes, the structures that carry genetic information. o But chromosomes aren't just DNA, they are packed with proteins - For bacteria, DNA is in a double-stranded molecule stored in a circular chromosome - In eukaryotes, there is a specific packing structure for DNA

What is DNA?

- DNA is the genetic material that organisms inherit from their parents. - Each chromosome contains one long DNA molecule, usually carrying several hundred or more genes. - When a cell reproduces itself by dividing, its DNA molecules are copied and passed along from one generation of cells to the next

What are the structures of DNA and RNA molecules?

- DNA molecules have two polynucleotides, or "strands," that wind around an imaginary axis, forming a double helix - The two sugar-phosphate backbones run in opposite 5' → 3' directions from each other o this arrangement is referred to as antiparallel, somewhat like a divided highway - The sugar-phosphate backbones are on the outside of the helix, and the nitrogenous bases are paired in the interior of the helix. - The two strands are held together by hydrogen bonds between the paired bases - Most DNA molecules are very long, with thousands or even millions of base pairs o The one long DNA double helix in a eukaryotic chromosome includes many genes, each one a particular segment of the molecule.

What does DNA polymerase use in catalyzing the synthesis of DNA?

- DNA polymerases catalyze the synthesis of new DNA by adding nucleotides to the 3′ end of a preexisting chain. - In E. coli, there are several DNA polymerases, but two appear to play the major roles in DNA replication: o DNA polymerase I. o DNA polymerase III - DNA polymerase drives the dehydration reaction that occurs for two nucleotide monomers to join together

What was the contribution of Erwin Chargaff?

- DNA was known to be a polymer of nucleotides, each having three components: o a nitrogenous (nitrogen-containing) base o a pentose sugar called deoxyribose o a phosphate group - The base can be the four nucleic acids that make up DNA - adenine (A), thymine (T), guanine (G), or cytosine (C).

What is mRNA?

- Each gene along a DNA molecule directs synthesis of a type of RNA called messenger RNA (mRNA). - The mRNA molecule interacts with the cell's protein-synthesizing machinery to direct production of a polypeptide, which folds into all or part of a protein - We can summarize the flow of genetic information as DNA → RNA → protein

What is encoded in the structure of DNA?

- Encoded in the structure of DNA is the information that programs all the cell's activities. - The DNA, however, is not directly involved in running the operations of the cell o The process goes from DNA -> RNA -> proteins - Proteins are required to implement genetic programs - The molecular hardware of the cell consists mostly of proteins. o For example, the oxygen carrier in red blood cells is the protein hemoglobin, not the DNA that specifies its structure.

What happens with linear DNA?

- For linear DNA, such as the DNA of eukaryotic chromosomes, the usual replication machinery cannot complete the 5′ ends of daughter DNA strands. o (This is another consequence of the fact that a DNA polymerase can add nucleotides only to the 3′ end of a preexisting polynucleotide.) - In the diagram, the replication fork is at the top with the okazaki fragments o Then there are the RNA primers that are removed with Polymerase I § The problem is that once that primer is removed, it cannot be replaced with DNA because there is no 3′ end available for nucleotide addition o As a result, repeated rounds of replication produce shorter and shorter DNA molecules with uneven ("staggered") ends.

What is the dispersive model?

- In the dispersive model, all four strands of DNA following replication have a mixture of old and new DNA - These models remained possibilities until they could be ruled out. - in the late 1950s, Matthew Meselson and Franklin Stahl devised a clever experiment that distinguished between the three models which supported the semiconservative model of DNA replication

What are helicases?

- Helicases are enzymes that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands. - After the parental strands separate, single-strand binding proteins bind to the unpaired DNA strands, keeping them from re-pairing. - The untwisting of the double helix causes tighter twisting and strain ahead of the replication fork. o Topoisomerase is an enzyme that helps relieve this strain by breaking, swivelling, and rejoining DNA strands.

How did Hershey and Chase determine if it was protein or DNA?

- Hershey and Chase answered this question by devising an experiment showing that only one of the two components of T2 actually enters the E. coli cell during infection - In the experiment, separate samples of nonradioactive E. coli cells were tagged one on the protein and the other on DNA - The researchers then tested the two samples with bacteria shortly after the onset of infection to see which type of molecule—protein or DNA—had entered the bacterial cells and would therefore be capable of reprogramming them. - They then spun this in a spiral fuge - a fast moving machine - The found that the phage DNA entered the host cells but the phage protein did not. o When these bacteria were returned to a culture medium and the infection ran its course, the E. coli released phages that contained some radioactive phosphorus. o This result further showed that the DNA inside the cell played an ongoing role during the infection process.

What did Frederick Griffith discover?

- In 1928, a British medical officer named Frederick Griffith was trying to develop a vaccine against pneumonia. - He was studying Streptococcus pneumoniae, a bacterium that causes pneumonia in mammals. - Griffith had two strains (varieties) of the bacterium o one pathogenic (disease-causing) and one nonpathogenic (harmless). - He was surprised to find that when he killed the pathogenic bacteria with heat and then mixed the cell remains with living bacteria of the nonpathogenic strain, some of the living cells became pathogenic o Furthermore, this newly acquired trait of pathogenicity was inherited by all the descendants of the transformed bacteria. o This means that a chemical component of the dead pathogenetic cells caused this heritable change - Griffith called the phenomenon transformation o It was then defined as a change in genotype and phenotype due to the assimilation of external DNA by a cell.

What is another difference between DNA and RNA?

- In DNA the sugar is deoxyribose; in RNA it is ribose - The only difference between these two sugars is that deoxyribose lacks an oxygen atom on the second carbon in the ring - hence the name deoxyribose. o But oxygen is present in the ribosugar in RNA - a nucleoside (nitrogenous base plus sugar). - To complete the construction of a nucleotide, we attach a phosphate group to the 5′ carbon of the sugar o This completes the nucleotide polymer - The molecule is now a nucleoside monophosphate, more often called a nucleotide.

What is a polynucleotide?

- In a polynucleotide, each monomer has only one phosphate group. o The portion of a nucleotide without any phosphate groups is called a nucleoside. - Each nitrogenous base has one or two rings that include nitrogen atoms. o (They are called nitrogenous bases because the nitrogen atoms tend to take up H+ from solution, thus acting as bases.)

What is base pairing?

- In base pairing, only certain bases in the double helix are compatible with each other. o Adenine (A) in one strand always pairs with thymine (T) o in the other, guanine (G) always pairs with cytosine (C). - There is one exception to the rule, however o Note that in RNA, adenine (A) pairs with uracil (U) thymine (T) is not present in RNA.

When is the lagging strand synthesized?

- In contrast to the leading strand, which elongates continuously, the lagging strand is synthesized discontinuously - as a series of segments. - This synthesis of the lagging strand begins with primase joining the primer to the template DNA strand - DNA pol III adds nucleotides in the 5' to 3' direction o These segments of the lagging strand are called Okazaki fragments - Whereas only one primer is required on the leading strand, each Okazaki fragment on the lagging strand must be primed separately

What do eukaryotic chromosomes have with replication origins?

- In contrast, a eukaryotic chromosome may have hundreds or even a few thousand replication origins. o Multiple sites where the double strands uncoil and DNA replication occurs in both direction, like in bacteria. - At each end of a replication bubble is a DNA replication fork, a Y-shaped region where the parental strands of DNA are being unwound. o Several kinds of proteins participate in the unwinding of the strands for DNA replication

What are telomeres?

- It turns out that eukaryotic chromosomal DNA molecules have special nucleotide sequences called telomeres at their ends - Telomeres do not contain genes; instead, the DNA typically consists of multiple repetitions of one short nucleotide sequence. o In each human telomere, for example, the six-nucleotide sequence TTAGGG is repeated between 100 and 1000 times. o When DNA is replicated and it gets shorter, the telomeres are removed, not the genetic information in the gene - Telomeres have two protective functions.

What does the functional shape of RNA strands result in?

- Its functional shape results from base pairing between nucleotides where complementary stretches of the molecule can run antiparallel to each other o Ex: delivering amino acids to the ribosomes o Communicating for protein synthesis - Another difference between RNA and DNA is that DNA almost always exists as a double helix, whereas RNA molecules are more variable in shape. o RNAs are very versatile molecules, and many biologists believe RNA may have preceded DNA as the carrier of genetic information in early forms of life

What did Watson and Crick do?

- James Watson and Francis Crick shook the scientific world in April 1953 with their DNA model o double-helical structure of deoxyribonucleic acid, or DNA - Gregor Mendel's heritable factors and Thomas Hunt Morgan's genes on chromosomes are, in fact, composed of DNA.

What does one strand provide in DNA?

- Notice that if you cover one of the two DNA strands you can still determine its linear sequence of nucleotides by referring to the uncovered strand and applying the base-pairing rules. o The two strands are complementary; each stores the information necessary to reconstruct the other. - When a cell copies a DNA molecule, each strand serves as a template for ordering nucleotides into a new, complementary strand

What is nuclease?

- Nuclease is one enzymes that can help this process - In many cases, a segment of the strand containing the damage is cut out (excised) by a DNA-cutting enzyme—a nuclease—and the resulting gap is then filled by DNA polymerase and ligase as needed to restore the DNA o One such DNA repair system is called nucleotide excision repair - If mistakes in DNA are not caught, they stay in the daughter strand and result in mutations o perpetuated through successive replications. o Most mutations have no effect or are harmful § Occasionally they are beneficial

What are the components of nucleic acids?

- Nucleic acids are macromolecules that exist as polymers called polynucleotides o each polynucleotide consists of monomers called nucleotides. - A nucleotide, in general, is composed of three parts: o a nitrogen-containing (nitrogenous) base, o a five-carbon sugar (a pentose), o one or more phosphate groups

What are nucleic acids? what is a gene?

- Nucleic acids store, transmit, and help express hereditary information - Nucleic acids are polymers made of monomers called nucleotides. - The amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance known as a gene. - Genes consist of DNA, which belongs to the class of compounds called nucleic acids.

What do nucleotides do on the template?

- Nucleotides line up along the template strand according to the base-pairing rules and are linked to form the new strands. - Where there was one double-stranded DNA molecule at the beginning of the process, there are soon two, each an exact replica of the "parental" molecule. o The copying mechanism is analogous to using a photographic negative to make a positive image, which can in turn be used to make another negative, and so on.

What do RNA strands exist as?

- RNA molecules, by contrast, exist as single strands. - Complementary base pairing can occur, however, between regions of two RNA molecules or even between two stretches of nucleotides in the same RNA molecule. - In fact, base pairing within an RNA molecule allows it to take on the particular three-dimensional shape necessary for its function. - Consider, for example, the type of RNA called transfer RNA (tRNA), which brings amino acids to the ribosome during the synthesis of a polypeptide. - A tRNA molecule is about 80 nucleotides in length and is more versatile and carries out more tasks

What does one sequence of bases tell us?

- Reading the sequence of bases along one strand of the double helix would tell us the sequence of bases along the other strand. o If a stretch of one strand has the base sequence 5'-AGGTCCG-3', then the base-pairing rules tell us that the same stretch of the other strand must have the sequence 3'-TCCAGGC-5'. § The two strands of the double helix are complementary, each the predictable counterpart of the other. § It is this feature of DNA that makes it possible to generate two identical copies of each DNA molecule in a cell that is preparing to divide.

What do Histones do?

- The histones bind to the DNA and to each other to form nucleosomes o These two things together are called chromatin o They look like beads on a string - basic unit of DNA packing - Nucleosomes interact with each other and the DNA in between them to cause tis complex to coil and fold o Then this structure forms loops - called loops domains § These looped domains make up chromosomes

What is a Phosphodiester Linkage?

- The linkage of nucleotides into a polynucleotide involves a dehydration reaction. - In the polynucleotide, adjacent nucleotides are joined by a phosphodiester linkage, which consists of a phosphate group that links the sugars of two nucleotides. - This repeats to form the nucleic acid polymer o This bonding results in a repeating pattern of sugar-phosphate units called the sugar-phosphate backbone - The two free ends of the polymer are distinctly different from each other. o One end has a phosphate attached to a 5′ carbon, and the other end has a hydroxyl group on a 3′ carbon; o we refer to these as the 5′ end and the 3′ end, respectively.

What is the origin of replication?

- The replication of chromosomal DNA begins at particular sites called origins of replication, short stretches of DNA that have a specific sequence of nucleotides. - In prokaryotes, like E. coli, DNA is often stored in circular chromosomes o They have only one site of replication for each chromosomes o Proteins that initiate DNA replication recognize this sequence and attach to the DNA, separating the two strands and opening up a replication "bubble" - Replication of DNA then proceeds in both directions until the entire molecule is copied.

What are the sites of protein synthesis?

- The sites of protein synthesis are cellular structures called ribosomes. - In a eukaryotic cell, ribosomes are in the region between the nucleus and the plasma membrane (the cytoplasm), but DNA resides in the nucleus - Messenger RNA conveys genetic instructions for building proteins from the nucleus to the cytoplasm. o Prokaryotic cells lack nuclei but still use mRNA to convey a message from the DNA to ribosomes and other cellular equipment that translate the coded information into amino acid sequences

How do pyrimidines and purines differ?

- The specific pyrimidines and purines differ in the chemical groups attached to the rings.

What do unwound sections of parental DNA serve as?

- The unwound sections of parental DNA strands are now available to serve as templates for the synthesis of new complementary DNA strands. o However, the enzymes that synthesize DNA cannot initiate the synthesis of a polynucleotide; they can only add DNA nucleotides to the end of an already existing chain that is base-paired with the template strand. - The initial nucleotide chain that is produced during DNA synthesis is actually a short stretch of RNA, not DNA.

What happens after DNA polymerase III adds nucleotides?

- Then the next fragment is primed and DNA polymerase III binds again, adding nucleotides until it hits fragment one primer. o Then it releases again - Next, RNA polymerase I goes along the strand and removes the RNA primers and replaces them with DNA o Then there is a continuous strand of DNA o Ligase is needed in this process § It removes the primers and puts in nucleotides where the primers were o Ligase bonds the new strands of DNA with the rest of the newly synthesized fragment - This completes the process - All of the okazaki fragments of the lagging strand are connected and the full strand is complete

What are the two families of nitrogen bases?

- There are five nitrogenous bases that are divided into two families: o pyrimidines and purines. - A pyrimidine has one six-membered ring of carbon and nitrogen atoms. o The members of the pyrimidine family are: § cytosine (C) § thymine (T) § uracil (U). - Purines are larger with two rings - with a six-membered ring fused to a five-membered ring. - The purines are: o adenine (A) and guanine (G).

What are the two types of nucleic acids? What is their role? What is gene expression?

- There are two types of nucleic acids: o deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) - They enable living organisms to reproduce their complex components from one generation to the next - DNA provides directions for its own replication. o this entire process is called gene expression - DNA also directs RNA synthesis and, through RNA, controls protein synthesis

What are Chargaff's rules?

- These two findings became known as Chargaff's rules: o (1) DNA base composition varies between species o (2) for each species, the percentages of A and T bases are roughly equal, as are those of G and C bases § These rules reinforced base pairing § Whatever the percentage of A was, T matched · This makes sense because we know that they pair in DNA

What was the conclusion of the Hershey and Chase experiment?

- They concluded that the DNA injected by the phage must be the molecule carrying the genetic information that makes the cells produce new viral DNA and proteins. - When the cells were permitted to grow again they were found to produce T2 phage just like what happens during infection - The Hershey-Chase experiment was a landmark study because it provided powerful evidence that DNA, rather than proteins, are the hereditary material, at least for certain viruses.

What is the RNA chain called?

- This RNA chain is called a primer and is synthesized by the enzyme primase - Primase starts a complementary RNA chain with a single RNA nucleotide, and adds RNA nucleotides one at a time, using the parental DNA strand as a template. o The completed primer, generally 5-10 nucleotides long, is thus base-paired to the template strand. o This is called a primer because it primes for DNA synthesis § It is RNA and must take place before the synthesis of DNA can occur - The DNA will always synthesize from the 3′ end of the RNA primer.

What is the evidence that viral DNA can program cells?

- Viruses are much simpler than cells. - A virus is little more than DNA (or sometimes RNA) enclosed by a protective coat, which is often simply protein. o To produce more viruses, a virus must infect a cell and take over the cell's metabolic machinery. - Viruses are different for living cells because don't have organelles and cannot replicate on their own o They are not living even though they have DNA - They reproduce by injecting their DNA into a host which then hijacks the living cells metabolic machinery to make more viruses o Viral DNA blueprints override those of a host cell one ejects

What are the viruses that attack bacteria? what is T2?

- Viruses that attack bacteria are called phages - In 1952, Alfred Hershey and Martha Chase performed experiments showing that DNA is the genetic material of a phage known as T2. - biologists already knew that T2 was composed almost entirely of DNA and protein and that the T2 phage could quickly turn an E. coli cell into a T2-producing factory that released many copies of new phages when the cell ruptured. o Somehow, T2 could reprogram its host cell to produce viruses. - They wanted to figure out if it was protein or DNA causing this

What did Watson and Crick's model predict?

- Watson and Crick's model predicts that when a double helix replicates, each of the two daughter molecules will have one old strand, from the parental molecule, and one newly made strand. o This semiconservative model can be distinguished from a conservative model of replication, in which the two parental strands somehow come back together after the process § One parent strand is conserved from the previous generation and only one new daughter strand is formed

What does a polynucleotide have in its tructure?

- We can say that a polynucleotide has a built-in directionality along its sugar-phosphate backbone, from 5′ to 3′, somewhat like a one-way street. o The bases are attached all along the sugar-phosphate backbone. - The sequence of bases along a DNA (or mRNA) polymer is unique for each gene and provides very specific information to the cell. - Because genes are hundreds to thousands of nucleotides long, the number of possible base sequences is effectively limitless.

What happens when the cell divides?

- When the cell divides, the copies are distributed to the daughter cells, making them genetically identical to the parent cell. o Thus, the structure of DNA accounts for its function of transmitting genetic information whenever a cell reproduces.

What is proofreading?

-errors in the completed DNA molecule do occur o 1 in 100,000 nucleotides has errors - Many DNA polymerases proofread each nucleotide against its template as soon as it is covalently bonded to the growing strand. o Upon finding an incorrectly paired nucleotide, the polymerase removes the nucleotide and then resumes synthesis o This makes the error rate much lower - 1 in 1010 (10,000,000,000) - The process of synthesizing a new strand is fast o 500 nucleotides per second are added to a single strand of bacteria and 50 for humans

what characteristic of a DNA determines its structure/function?

The relationship between structure and function is manifest in the double helix

What happens if a mismatched nucleotide makes it through proofreading?

o Other enzymes can also play a role in mismatch repair - In fact, maintenance of the genetic information encoded in DNA requires frequent repair of various kinds of damage to existing DNA. o DNA molecules are constantly subjected to potentially harmful chemical and physical agents, such as cigarette smoke, ultraviolet rays and X-rays

What are the two protective functions of Telomeres?

o prevent the staggered ends of the daughter molecule from activating the cell's systems for monitoring DNA damage. § (Staggered ends of a DNA molecule, which often result from double-strand breaks, can trigger signal transduction pathways leading to cell cycle arrest or cell death.) o acts as a kind of buffer zone that provides some protection against the organism's genes shortening, somewhat like how the plastic-wrapped ends of a shoelace slow down its unravelling. § Telomeres do not prevent the erosion of genes near the ends of chromosomes; they merely postpone it. - Telomeres become shorter during every round of replication. - It has been proposed that shortening of telomeres is somehow connected to the aging process of certain tissues and even to aging of the organism as a whole.