Chapter 10: Flow of Genetic Information

Frameshift mutaiton

- A change in the genetic material that involves the insertion or deletion of one or more nucleotides in a gene, resulting in a change in the triplet grouping of nucleotides - The red cat ate the big rat. Deleting the second letter shifts the triplet frame and produces an entirely nonsensical message: Ter edc ata tet heb igr at. Frameshift mutations will most likely produce a nonfunctional polypeptide and often have disastrous effects.

How do mutations relate to evolution?

- A mutation might enhance the success of the mutant organism (and therefore its descendants) - They provide rich diversity

What are the differences between pre-mRNA and mature mRNA?

- Pre-mRNA and mRNA differ in a surprising way. - Pre-mRNA is an exact copy of the gene, nucleotide by nucleotide. However, it undergoes a process called splicing and capping. This involves removing chunks of the pre-mRNA that are not actually used to produce a polypeptide. These chunks are called introns, and the useful chunks are called exons. The "mature" mRNA contains only exons; this is what actually determines the polypeptide's composition.

Describe the flow of information in a eukaryotic cell

- Shows how a gene does not build proteins directly, rather, it dispatches instructions in the form of RNA, which in turn programs protein synthesis. - The molecular "chain of command" is from DNA in the nucleus of the cell to RNA to protein synthesis in the cytoplasm. The two main stages are transcription, the synthesis of RNA under the direction of DNA, and translation, the synthesis of protein under the direction of RNA.

What is the relationship between codons and amino acids?

- The flow of information from gene to protein is based on a triplet code - The genetic instructions for the amino acid sequence of a polypeptide chain are written in DNA and RNA as a series of non-overlapping three-base "words" called codons - Three-base codons in the DNA are transcribed into complementary three-base codons in the RNA, and then the RNA codons are translated into amino acids that form a polypeptide.

Where does the variation of DNA sequences come from? That is, you and an emu and an elephant and a bacterium all possess DNA, but how is your DNA different?

-Genetic variation can be caused by mutation (which can create entirely new alleles in a population), random mating, random fertilization, and recombination between homologous chromosomes during meiosis (which reshuffles alleles within an organism's offspring). -DNA can differ because the sequences of bases in each strand vary in numerous ways, and each gene has a specific and unique order of nucleotides (base sequence)

What does transfer RNA or tRNA do?

-To convert the three-letter "words" of nucleic acids (codons) to the amino acid "words" of proteins - More specifically, The function of a tRNA is to transfer amino acids from the cytoplasmic pool to a growing polypeptide in a ribosome. To perform this task, tRNA molecules must carry out two functions: (1) picking up the appropriate amino acids and (2) recognizing the appropriate codons in the mRNA. The unique structure of tRNA molecules enables them to perform both tasks.

What did Watson and Crick do to solve the structure of DNA?

-Watson and Crick began trying to construct a wire model of a double helix that would conform both to Franklin's data and to what was then known about the chemistry of DNA. -They knew that Franklin had concluded that the sugar-phosphate backbones must be on the outside of the double helix, forcing the nitrogenous bases to swivel to the interior of the molecule. But how were the bases arranged in the interior of the double helix? -At first, Watson and Crick imagined that the bases paired like with like—for example, A with A and C with C. But that kind of pairing did not fit the X-ray data, which suggested that the DNA molecule has a uniform diameter. An A-A pair, with two double-ring bases, would be almost twice as wide as a C-C pair, made of two single-ring bases. It soon became apparent that a double-ringed base (purine) on one strand must always be paired with a single-ringed base (pyrimidine) on the opposite strand to produce a molecule of uniform thickness. After considerable trial and error, Watson and Crick realized that the chemical structures of the bases dictated the pairings even more specifically.

Which 3 scientists won the Nobel Prize for the discovery of the structure of DNA? Why didn't Rosalind Franklin win the prize?

-Watson, Crick, and Wilkins -She died of multiple cancers in 1958 and was ineligible for the prize

What is the relationship between a codon and an anti-codon?

.During translation, codons pair with anticodons so that the correct amino acids can be linked to a given codon.

How does translation begin?

1. - An mRNA molecule binds to a small ribosomal subunit. - A special initiator tRNA base-pairs with the specific codon, called the start codon, where translation is to begin on the mRNA molecule. - The initiator tRNA carries the amino acid methionine (Met); its anticodon, UAC, base-pairs with the start codon, AUG. 2. Next, a large ribosomal subunit binds to the small subunit, creating a functional ribosome. The initiator tRNA fits into a tRNA binding site on the ribosome. This site, called the P site, will hold the growing polypeptide. The other tRNA binding site, called the A site, is shown vacant and ready for the next amino-acid-bearing tRNA.

Transcription and translation of codons

1. The pink strand underneath the enlarged DNA segment represents the results of transcription: an RNA molecule. The process is called transcription because the nucleic acid language of DNA has been rewritten (transcribed) as a sequence of bases on RNA. 2. The purple chain at the bottom of the figure represents the results of translation, the conversion of the nucleic acid language to the polypeptide language. Like nucleic acids, polypeptides are polymers, but the monomers that compose them are the 20 different kinds of amino acids. Again, the language is written in a linear sequence, and the sequence of nucleotides of the RNA molecule dictates the sequence of amino acids of the polypeptide. The RNA acts as a messenger carrying genetic information from DNA.

How many amino acids are there?

20

If a DNA molecule was made of 20% A, what percent of the DNA would be T? How much would G and C be?

20% 30% The amount of adenine in the DNA of any one species was equal to the amount of thymine and that the amount of guanine was equal to that of cytosine. A C-G base pair has functional groups that form three hydrogen bonds, whereas an A-T base pair has functional groups that form two hydrogen bonds.

TTQ: What is the minimum number of nucleotides necessary to code for 100 amino acids?

300 because each amino acid contains at least 2 nucleotides

Missense mutation

A change in the nucleotide sequence of a gene that alters the amino acid sequence of the resulting polypeptide. A codon is changed from encoding one amino acid to encoding a different amino acid For example, if an mRNA codon changes from GGC to AGC, as in the second row of Figure 10.16B, the resulting protein will have a serine (Ser) instead of a glycine (Gly) at this position. Some missense mutations have little or no effect on the resulting protein, but others, as in the case of sickle-cell disease, prevent the protein from performing its normal function.

Nonsense mutation

A change in the nucleotide sequence of a gene that converts an amino-acid-encoding codon to a stop codon. A nonsense mutation results in a shortened polypeptide For example, if an AGA (Arg) codon is changed to a UGA (stop) codon, the result will be a prematurely terminated protein, which probably will not function properly.

Mutagen

A chemical or physical agent that interacts with DNA and causes a mutation.

Silent mutation

A mutation in a gene that changes a codon to one that codes for the same amino acid as the original codon. The amino acid sequence of the resulting polypeptide is thus unchanged E.g. substitution For example, if a mutation causes an mRNA codon to change from GAA to GAG, no change in the protein product would result because GAA and GAG both code for the same amino acid

Each nucleotide consists of three components, what are they?

A nitrogen base (in DNA: A,C,T or G), a sugar (blue), and a phosphate group (yellow).

polynucleotide

A polymer made up of many nucleotide monomers covalently bonded together.

What does a ribosome consist of ?

A ribosome consists of two subunits—a large subunit and a small subunit—each made up of proteins and a kind of RNA called ribosomal RNA (rRNA).

How could a single nucleotide substitution result in a shortened protein product?

A substitution that changed an amino acid codon into a stop codon would produce a prematurely terminated polypeptide. (nonsense)

Codons

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

What type of base is the smallest "words" of uniform length that can specify all the amino acids?

A triplet base --> 64 (4^3) Allows for more than one base to represent an amino acid

What is an allele?

A version of a gene (a different DNA sequence)

What is the Watson-Crick pairing rule?

Adenine (A) pairs with thymine (T) and cytosine (c) pairs with guanine (G)

Introns

An internal, noncoding region of a gene that does not become part of the final messenger RNA molecule is therefore not expressed

Translation of a genetic message carried in the mRNA into the amino acid language of proteins requires what ? Why?

An interpreter: A cell that is producing proteins keeps its cytoplasm stocked with all 20 kinds of amino acids. But amino acids themselves cannot recognize the codons in the mRNA.

Difference between phenotype and genotype?

An organism's genotype, its genetic makeup, is the heritable information contained in the sequence of nucleotide bases in DNA. The phenotype is the organism's physical traits.

Describe the model that shows DNA replication

As shown in Figure 10.4A, the two strands of parental DNA (blue) separate. Each strand becomes a template for the assembly of a complementary strand from a supply of free nucleotides (gray) available within the nucleus. The nucleotides line up one at a time along the template strand in accordance with the base-pairing rules. Enzymes link the nucleotides to form the new DNA strands. The completed new molecules, identical to the parental molecule, are known as daughter DNA

What enzyme links DNA polymers together? What is important to remember about what these enzymes do in terms of direction?

DNA polymerase These enzymes add nucleotides only to the 3' end of the strand, never to the 5' end. Thus, a daughter DNA strand can only grow in the 5′→3′5′→3′ direction.

Mutations can occur during ____________, before a cell divides. Define mutation.

DNA replication Mutation: Any change to the genetic information of a cell or virus - Mutations create new alleles in a population

How does translation end?

Elongation occurs until a process called termination. Termination happens when a stop codon in the mRNA (UAA, UAG, or UGA) enters the A site. - Stop codons are recognized by proteins called release factors, which fit neatly into the P site (though they aren't tRNAs). - Stop codons do not code for amino acids but instead act as signals to stop translation

Labeling a gene Where does the ribosome begin translation?

The first AUG it encounters on the mRNA

Exons

The part of a gene that becomes part of the final messenger RNA and is therefore expressed

What are the functions of transcription and translation?

Transcription is the transfer of information from DNA to RNA. Translation is the use of the information in RNA to make a polypeptide.

True or false: The different somatic cell types in your body such as your liver and muscle cells) contain the exact same DNA.

True

Ribosomes bring together what players in the process of translation?

Ribosomes coordinate the functioning of mRNA and tRNA and catalyze the synthesis of polypeptides - tRNA anticodons and mRNA codons fit together on ribosomes. A fully assembled ribosome has a binding site for mRNA on the small subunit and binding sites (referred to as the P site and the A site) for tRNA on the large subunit. - The subunits of the ribosome act like a vise, holding the tRNA and mRNA molecules close together, allowing the amino acids carried by the tRNA molecules to be connected into a polypeptide chain.

Who was Rosalind Franklin? What did she contribute to the discovery of DNA structure?

Rosalind Franklin was a British chemist best known for her role in the discovery of the structure of DNA, as well as her pioneering use of X-ray diffraction (X-ray image of DNA)

What is different about somatic cells in your body?

Which proteins are being expressed or not expressed

What is a nucleotide?

a compound consisting of a nucleoside linked to a phosphate group. Nucleotides form the basic structural unit of nucleic acids such as DNA.

Consequence of mutations arising in germ cell

could be a genetic disease passed down through generations (mistake in DNA replication before MEIOSIS)

Where does translation occur?

cytoplasm

Where does DNA replication occur in the cell?

in the nucleus of eukaryotic cells and in the cytoplasm of prokaryotic cells

Each type of DNA nucleotide has a different ___________

nitrogen-containing base: (A) adenine, (c) cytosine, (g) guanine, (T) thymine

Silent, missense, and nonsense mutations all change the __________ of a protein by changing one nucleotide in its sequence

primary structure

Because nucleotides can occur in a polynucleotide in any __________ and because polynucleotides can be very _______, the number of possible polynucleotides is __________.

sequence, long, enormous

What is elongation?

tRNA molecules carrying amino acids add to the growing polypeptide chain

What is the goal of translation?

translation, messenger RNA (mRNA) is decoded in the ribosome decoding center to produce a specific amino acid chain, or polypeptide. The polypeptide later folds into an active protein and performs its functions in the cell.

What are the two important sites that every tRNA have?

—the anticodon and the amino acid attachment site—give tRNA its ability to match a particular nucleic acid "word" (a codon in mRNA) with its corresponding protein "word" (an amino acid).

What kind of bonds hold a nucleotides together in a polynucleotide? Are they strong?

Covalent bonds, very strong

Simplest way to describe the information flow

DNA is transcribed into RNA, which is then translated into protein. DNA→RNA→protein

If each single nucleotide base were to specify one amino acid, what would that mean?

Only four of the 20 amino acids could be accounted for (4^1)

Step by step - Codons and building proteins

Codons and Building Proteins 1. DNA is the code used to produce proteins. 2. First, the DNA is replicated, so that there are two identical copies of the DNA. Then, the DNA is transcribed into RNA, which is then translated, or read, by tRNA to make the proteins. 3. This process of replication, transcription, and translation, is called the "central dogma". 4. Just like DNA, RNA is composed of a four-letter alphabet. However, the thymine (T) in DNA is replaced by a uracil (U) in RNA. 5. The message encoded in RNA is read in three-letter words called codons. 6. Codons code for specific amino acids, which are the building blocks of proteins. 7. Therefore, by knowing the sequence of bases in a gene, it is possible to predict the codons and, ultimately, the amino acid sequence of the protein the gene makes. 8. There are twenty possible amino acids. However, most amino acids can be coded for by more than one codon. 9. The beginning of a coding sequence is signaled by a start codon, a unique sequence for this purpose; the start codon also codes for a methionine. 10. There are three codons that indicate the end of the amino acid sequence. These are called stop codons.

Consequence of mutation in somatic cell

Could be cancer (mistake in DNA replication before mitosis)

__________________ result in the nucleotide sequence after the mutation to be completely changed

Frameshift mutatuons

What are some mutagens that can damage DNA?

High energy radiation

A typical gene consists of _________________ of nucleotides in a specific sequence.

Hundreds of thousands

What kind of bonds hold two polynucleotides together (what holds the double helix together)? Are they strong?

Hydrogen bonds - weak

What happens when people tan?

Melanin is packaged in melanosomes (vesicles) that get transported to other skin cells (keratinocytes). - E.G. tyrosine ---> tyrosinase ---> melanin - ** ①Sun affects hormone production in keratinocytes (neighboring skin cells) ②Melanocyte receives nearby hormone signal ③Hormone stimulates a pathway that leads to TYROSINASE transcription - More sun = greater tyrosinase transcription

In a few sentences that are your own, describe the process of transcription. Be sure to explain where it occurs in the eukaryotic cell, how it starts, what the enzyme does, and how it ends. Be sure to include these terms in your description: RNA polymerase, template strand, promoter, RNA nucleotides, terminator, and pre-RNA transcript.

Occurs in the nucleus!!! 1. After separation of the two DNA strands, one strand serves as a template for a new RNA molecule; the other DNA strand is unused. 2. The transcription enzyme RNA polymerase moves along the gene, forming a new RNA strand by following the base-pairing rules-but remember that in RNA, U replaces T. 3. A specific nucleotide sequence called a promoter acts as a binding site for RNA polymerase and determines where transcription starts. 4. RNA polymerase adds RNA nucleotides until it reaches a sequence of DNA bases called the terminator, which signals the end of the gene.

If each single nucleotide were to specify two amino acids (e.g. AG), what would that mean?

Only 16 of the 20 arrangements would be possible (4^2)

Genes provide the instructions for making _____________. But a gene does not build a _______ itself. The bridge between DNA and protein synthesis is _______________,.

Specific proteins; protein; the nucleic acid RNA

How is transcription different from DNA replication?

Template: DNA replication: Parent DNA strand Transcription: DNA strand Enzyme: DNA replication: DNA polymerase Transcription: RNA polymerase Nucleotides incorporated? : DNA replication: DNA base pairs Transcription: RNA base pairs End result? DNA replication: 2 identical DNA strands Transcription: 1 RNA strand

What is the connection between genotype and phenotype?

The answer is that the DNA inherited by an organism specifies traits by dictating the synthesis of proteins (or, in some cases, just RNAs). In other words, proteins are the links between genotype and phenotype. However, a gene does not build a protein directly. Rather, a gene dispatches instructions in the form of RNA, which in turn programs protein synthesis.

What is a nucleotide substitution?

The replacement of one nucleotide and its base-pairing partner with another pair of nucleotides.

Why is it significant that there are structural differences between prokaryotic and eukaryotic ribosomes?

The ribosomes of bacteria and eukaryotes are very similar in function, but those of eukaryotes are slightly larger and different in structure. The differences are medically significant. Certain antibiotic drugs can inactivate bacterial ribosomes while leaving eukaryotic ribosomes unaffected. These drugs, such as tetracycline and streptomycin, are used to combat bacterial infections.