Biology Exam 1

mRNA Processing

After transcription, the removal of introns and splicing of exons occur before mature mRNA leaves the nucleus and passes into the cytoplasm. Alternative mRNA processing is a mechanism by which the same primary-mRNA can produce different protein products according to which exons are spliced together to form mature mRNAs.

The Watson and Crick Model

Based on the available data, they knew the following: DNA is a polymer of four types of nucleotides with the bases adenine (A), guanine (G), cytosine (C), and thymine (T). Based on Chargaff's rules, the amount of A = T and the amount of G = C. Based on Franklin's X-ray diffraction photograph, DNA is a double helix with a repeating pattern. The model showed that the deoxyribose sugar-phosphate molecules are bonded to one another to make up the sides of a twisted ladder. The nitrogenous bases make up the rungs of the ladder—they project into the middle and hydrogen bond with bases on the other strand. Indeed, the pairing of A with T and G with C—now called complementary base pairing—results in rungs of a consistent width, as elucidated by the X-ray diffraction data.

Structure of DNA

Before Erwin Chargaff began his work, it was known that DNA contains four different types of nucleotides based on their nitrogen-containing bases. The bases adenine (A) and guanine (G) are purines with a double ring, and the bases thymine (T) and cytosine (C) are pyrimidines with a single ring

From DNA to RNA to Protein

Consider that, in eukaryotes, DNA resides in the nucleus but RNA is found both in the nucleus and in the cytoplasm where protein synthesis occurs. This means that DNA must pass its genetic information to mRNA, which then actively participates in protein synthesis. The central dogma of molecular biology states that genetic information flows from DNA to RNA to protein.

Replication of DNA

DNA replication refers to the process of making an identical copy of a DNA molecule. DNA replication occurs during the S phase of the cell cycle. During DNA replication, the two DNA strands, which are held together by hydrogen bonds, are separated and each old strand of the parent molecule serves as a template for a new strand in a daughter molecule. This process is referred to as semiconservative, since one of the two old strands is conserved, or present, in each daughter molecule.

Transcription

During transcription of DNA, a strand of RNA forms that is complementary to a portion of DNA. While all three classes of RNA are formed by transcription, we will focus on transcription to create mRNA.

Transfer RNA Takes Amino Acids to the Ribosomes

Each tRNA is a single-stranded nucleic acid that doubles back on itself such that complementary base pairing results in the cloverleaf-like shape. There is at least one tRNA molecule for each of the 20 amino acids found in proteins. The amino acid binds to one end of the molecule. The opposite end of the molecule contains an anticodon, a group of three bases that is complementary to a specific codon of mRNA. During translation, the order of codons in mRNA determines the order in which tRNAs bind at the ribosomes. When a tRNA-amino acid complex comes to the ribosome, its anticodon pairs with an mRNA codon. After translation is complete, a protein contains the sequence of amino acids originally specified by DNA. This is the genetic information that DNA stores and passes on to each cell during the cell cycle, then to the next generation of individuals. DNA's sequence of bases determines the proteins in a cell, and the proteins determine the function of each cell.

Chromatin Condensation

Eukaryotes utilize chromatin condensation as a way to keep genes turned on or off. The more tightly chromatin is compacted, the less often genes within it are expressed. Darkly staining portions of chromatin, called heterochromatin, represent tightly compacted, inactive chromatin. When heterochromatin undergoes unpacking, it becomes euchromatin, a more loosely packed form of chromatin that contains active genes. You learned in Chapter 8 that, in eukaryotes, a nucleosome is a portion of DNA wrapped around a group of histone molecules. When DNA is transcribed, a chromatin remodeling complex pushes aside the histone portions of nucleosomes, so that transcription can begin (Fig. 11.22). In other words, even euchromatin needs further modification before transcription can begin.

DNA

Finding the structure of DNA was the first step toward understanding how DNA is able to do the following: Be variable in order to account for species differences Replicate so that every cell gets a copy during cell division Store information needed to control the cell Undergo mutations, accounting for evolution of new species

Franklin's X-Ray Diffraction Data

First, Franklin made a concentrated, viscous solution of DNA and then saw that it could be separated into fibers. Under the right conditions, the fibers were enough like a crystal that, when they were X-rayed, a diffraction pattern resulted. The X-ray diffraction pattern of DNA shows that DNA is a double helix.

Gene Expression in Eukaryotes

In bacteria, a single promoter serves several genes that make up a transcription unit, while in eukaryotes, each gene has its own promoter where RNA polymerase binds. Bacteria rely mostly on transcriptional control, but eukaryotes employ a variety of mechanisms to regulate gene expression. These mechanisms affect whether the gene is expressed, the speed with which it is expressed, and how long it is expressed. Some mechanisms of gene expression occur in the nucleus; others occur in the cytoplasm. In the nucleus, chromatin condensation, DNA transcription, and mRNA processing all play a role in determining which genes are expressed in a particular cell type.

transcription factors

In eukaryotes, transcription factors are DNA-binding proteins that help RNA polymerase bind to a promoter. Several transcription factors are needed in each case; if one is missing, transcription cannot take place. All the transcription factors form a complex that also helps pull double-stranded DNA apart and even acts to position RNA polymerase so that transcription can begin. The same transcription factors, in different combinations, are used over again at other promoters, so it is easy to imagine that, if one malfunctions, the result could be disastrous to the cell. In eukaryotes, transcription activators are DNA-binding proteins that speed transcription dramatically. They bind to a DNA region, called an enhancer, that can be quite a distance from the promoter. A hairpin loop in the DNA can bring the transcription activators attached to enhancers into contact with the transcription factor complex.

Transcription and Translation

In eukaryotes, transcription takes place in the nucleus, and translation takes place in the cytoplasm. During transcription, a portion of DNA serves as a template for mRNA formation. During translation, the sequence of mRNA bases (which are complementary to those in template DNA) determines the sequence of amino acids in a polypeptide.

Ribosomal RNA

In eukaryotic cells, ribosomal RNA (rRNA) is produced in the nucleolus of a nucleus, where a portion of DNA serves as a template for its formation. Ribosomal RNA joins with proteins made in the cytoplasm to form the subunits of ribosomes, one large and one small. Each subunit has its own mix of proteins and rRNA. The subunits leave the nucleus and come together in the cytoplasm when protein synthesis is about to begin.

Signaling Between Cells in Eukaryotes

In multicellular organisms, cells are constantly sending out chemical signals that influence the behavior of other cells. During animal development, these signals determine the specialized role a cell will play in the organism. Later, the signals help coordinate growth and day-to-day functions. Plant cells also signal each other, so that their responses to environmental stimuli, such as direct sunlight, are coordinated.

Translation Has Three Phases

Initiation- This is the step that brings all of the translation components together: The small ribosomal subunit attaches to the mRNA in the vicinity of the start codon (AUG). The anticodon of the initiator tRNA-methionine complex pairs with this codon. The large ribosomal subunit joins to the small subunit. Elongation Cycle During this step the polypeptide chain increases in length one amino acid at a time: The tRNA at the P site contains the growing peptide chain. This tRNA passes its peptide to tRNA-amino acid at the A site. The tRNA at the P site enter the E site. During translocation, the tRNA-peptide moves to the P site, the empty tRNA in the E site exits the ribosome, and the codon at the A site is ready for the next tRNA-amino acid. Termination occurs when a stop codon appears in the A site. Then, the polypeptide and the assembled components that carried out protein synthesis are separated from one another. A protein called a release factor binds to the stop codon and cleaves the polypeptide from the last tRNA. The mRNA, ribosomes, and tRNA molecules can then be used for another round of translation.

Messenger RNA

Messenger RNA (mRNA) is produced in the nucleus of eukaryotes, as well as in the nucleoid of prokaryotes. DNA serves as a template for the formation of mRNA during a process called transcription. Which DNA genes are transcribed into mRNA is highly regulated in each type of cell and accounts for the specific functions of all cell types. Once formed, mRNA carries genetic information from DNA in the nucleus to the ribosomes in the cytoplasm, where protein synthesis occurs through a process called translation.

RNA Structure and Function

Ribonucleic acid (RNA) is made up of nucleotides containing the sugar ribose, thus accounting for its name. The four nucleotides that make up an RNA molecule have the following bases: adenine (A), uracil (U), cytosine (C), and guanine (G). Notice that, in RNA, uracil replaces the thymine in DNA. RNA, unlike DNA, is single-stranded, but the single RNA strand sometimes doubles back on itself, allowing complementary base pairing to occur. There are three major types of RNA, each with a specific function in protein synthesis.

Epigenetics

Scientists are beginning to recognize that some changes in gene regulation may be inherited from one generation to the next, especially at the cellular level. Epigenetic inheritance, or the inheritance of changes in gene expression that are not the result of changes in the sequence of nucleotides on the chromosome. Epigenetic inheritance explains other physiological processes as well, such as genomic imprinting, in which the sex of the individual determines which alleles are to be expressed in the cell by suppressing genes on chromosomes inherited from the opposite sex.

Protein Activity

Some proteins are not active immediately after synthesis. Many proteins are short-lived in cells because they are degraded or destroyed.

Chargaff's rules

The amount of A, T, G, and C in DNA varies from species to species. In each species, the amount of A = T and the amount of G = C. Chargaff's data suggest that DNA has a means to be stable, in that A can pair only with T and G can pair only with C. His data also show that DNA can be variable as required for the genetic material. Today, we know that the paired bases may occur in any order and the amount of variability in their sequences is overwhelming.

mRNA Translation

The cytoplasm contains proteins that can control whether translation of mRNA takes place.

The Genetic Code

The information contained in DNA and RNA is written in a chemical language different from that in the protein specified by the DNA and RNA. The cell needs a way to translate one language into the other, and it uses the genetic code. Each three-letter (nucleotide) unit of an mRNA molecule is called a codon, which codes for a single amino acid. Sixty-one triplets correspond to a particular amino acid; the remaining three are stop codons that signal the end of a polypeptide. The codon that stands for the amino acid methionine is also used as a start codon that signals the initiation of translation. Most amino acids have more than one codon, which offers some protection against possibly harmful mutations that might change the sequence of the amino acids in a protein.

mRNA Is Processed

The newly synthesized primary-mRNA must be processed in order for it to be used properly. Processing occurs in the nucleus of eukaryotic cells. Three steps are required: capping, the addition of a poly-A tail, and splicing. After processing, the mRNA is called a mature mRNA molecule.

Replication of DNA cont.

To begin replication, the DNA double helix must separate and unwind. This is accomplished by breaking the hydrogen bonds between the nucleotides, then unwinding the helix structure using an enzyme called helicase. At this point, new nucleotides are added to the parental template strand. Nucleotides, ever present in the nucleus, will complementary base pair onto the now single-stranded parental strand. The addition of the new strand is completed using an enzyme complex called DNA polymerase. The daughter strand is synthesized by DNA polymerase in a 5′-3′ direction. Any breaks in the sugar-phosphate backbone are sealed by the enzyme DNA ligase.

mRNA Is Formed

Transcription begins when the enzyme RNA polymerase binds tightly to a promoter, a region of DNA with a special nucleotide sequence that marks the beginning of a gene. RNA polymerase opens up the DNA helix just in front of it, so that complementary base pairing can occur. Then the enzyme adds new RNA nucleotides that are complementary to the template DNA strand, and an mRNA molecule results. The resulting mRNA transcript is a complementary copy of the sequence of bases in the template DNA strand. Once transcription is completed, the mRNA is ready to be processed before it leaves the nucleus for the cytoplasm.

DNA Transcription

Transcription in eukaryotes follows the same principles as in bacteria, except that many more regulatory proteins per gene are involved. The occurrence of so many regulatory proteins allows for not only greater control but also a greater chance of malfunction.

Transfer RNA

Transfer RNA (tRNA) is also produced in the nucleus of eukaryotes. Appropriate to its name, tRNA transfers amino acids present in the cytoplasm to the ribosomes. There are twenty different amino acids, and each has its own tRNA molecule. At the ribosome a process called translation joins the amino acids to form a polypeptide chain.

Translation

Translation is the second step by which gene expression leads to protein (polypeptide) synthesis. Translation requires several enzymes, mRNA, and the other two types of RNA: transfer RNA and ribosomal RNA.

Levels of Gene Expression Control

gene expression is controlled in a cell, and this control accounts for its specialization

cell-signaling

occurs because a chemical signal binds to a receptor protein in a target cell's plasma membrane. The signal causes the receptor protein to initiate a series of reactions within a signal transduction pathway. The end product of the pathway (not the signal) directly affects the metabolism of the cell.

Gene Expression

one gene directs the synthesis of one enzyme. Today we know that genes are also responsible for specifying any type of protein in a cell, not just enzymes, so their finding has been modified to "one gene-one polypeptide. Gene expression has occurred when a gene's product—the protein it specifies—is functioning in a cell. Specifically, gene expression requires two processes, called transcription and translation.

Gene Expression in Prokaryotes

promoter: In an operon, a sequence of DNA in which RNA polymerase binds prior to transcription. operon: Group of structural and regulating genes that function as a single unit. Jacob and Monod proposed that a regulatory gene (In an operon, a gene that codes for a protein that regulates the expression of other genes) located outside the operon codes for a repressor (In an operon, a protein molecule that binds to an operator, preventing transcription of structural genes)—a protein that, in the lac operon, normally binds to the operator, which lies next to the promoter. When the repressor is attached to the operator, transcription of the lactose-metabolizing genes does not take place because RNA polymerase is unable to bind to the promoter. The lac operon is normally turned off in this way because lactose is usually absent.