Chapter 4- Learning Outcomes

Describe how DNA is replicated.

- The double helix unwinds from the histones. -Like a zipper, the enzyme DNA helicase opens up one short segment of the helix at a time, exposing its nitrogenous bases. The point where the DNA is opened up is called the replication fork. -Molecules of the enzyme DNA polymerase. move along each strand; read the exposed bases; and arrange "marriages" with complementary free nucleotides. The two separated strands of DNA are copied by separate polymerase molecules, proceeding in opposite directions. On one strand the DNA polymerase moves towards the replication fork and makes a long, continuous new strand of DNA to complement the old one. On the other strand, the DNA polymerase moves away from the replication fork and copies only a short segment of DNA at a time. The segments are then joined together by another enzyme called DNA ligase. Ultimately from the old parental DNA molecule, two new daughter DNA molecules are made. Each new daughter DNA consists of one new helix synthesized from free nucleotides and one old helix conserved from the parent DNA. This process is called semiconservative replication. -While DNA is synthesized in the nucleus, new histones are synthesized in the cytoplasm. Millions of histones are transported into the nucleus within a few minutes after DNA replication and each new DNA helix wraps around them to make new nucleosomes. -Thousands of polymerase molecules work simultaneously on each DNA molecule and all 46 chromosomes are replicated within 6-8 hours.

Describe ways a gene can be turned on or off.

-Cells can turn some genes permanently off: Example: liver cells turn off hemoglobin genes -Cells can turn genes on only when needed: The level of gene expression can vary from day to day or hour to hour. This can be controlled by chemical messengers such as hormones. Example: mammary gland cells turn on gene for casein protein only when breast milk is produced.

Discuss the consequences of replication errors.

-Changes in DNA structure, called mutations, can be a result from replication errors or from environmental factors such as radiation, chemicals and viruses. -Uncorrected mutations can be passed on to the descendants of that cell -Some mutations cause no ill effects, others kill the cell, turn it cancerous or cause genetic defects in future generations.

Explain how DNA and proteins are organized to form the chromosomes.

-DNA does not exist as a naked double helix in the nucleus of a cell, but is complexed with proteins to form a fine filamentous material called chromatin. In most cells chromatin occurs as 46 long filaments called chromosomes. - In nondividing cells, under an ESM, chromatin appears granular like beads on a string. Each "bead" is a disc-shaped cluster of eight proteins called histones. A DNA molecule winds around the cluster, for a little over one and a half turns, and then continues on its way until it reaches the next histone cluster and winds around that one. The average chromatin thread repeats this pattern almost 800,000 times and thus appears divided into segments, called nucleosomes. Each nucleosome consists of a core particle and a short segment of linker DNA leading to the next core particle. The nucleosome is arranged in a zigzag pattern, folding the chromatin like an accordion. Then the strand is thrown into complex, irregular loops and coils to make it thicker and much shorter than the DNA molecule. Finally each chromosome is packed into its own spheroidal region of the nucleus called a chromosome territory. The territory is permeated with channels that allow regulatory chemicals to have access to the genes. This is not a static structure, but changes from moment to moment according to the genetic activity of the cell as individual genes are turned on and off. Whole chromosomes then migrate to new territories as a cell develops, allowing genes on different chromosomes to partner with each other in bringing about developmental changes in the cell. -When a cell is preparing to divide, it makes an exact copy of all its nuclear DNA, increasing its allotment to about 4 m of DNA. Each chromosome then consists of two parallel filaments called sister chromatids. The sister chromatids are joined together at a pinched spot in the middle called the centromere. On each side of the centromere, there is a protein plaque called a kinetochore which plays a role in cell division.

Explain what the human genome is and its relationship to health sciences.

-Human Genome is all the DNA in one 23-chromosome set. There are 3.1 billion nucleotide pairs in the human genome. -46 human chromosomes come in two sets of 23 chromosomes. One set of 23 chromosomes comes from each parent. -Because of genomics we have been able to discover the chromosomal locations of more than 1,400 disease-producing mutations and has opened the door for medical diagnosis and therapy called genomic medicine.

Define genetic code and describe how DNA codes for protein structure.

-The body can make millions of different proteins (the proteome) from just 20 amino acids and encoded by genes made of just four nucleotides (A,T,C,G) -The genetic code is a system that enables these four nucleotides to code for the amino acid sequences of all proteins. -The minimum code to symbolize 20 amino acids is 3 nucleotides per amino acid, and indeed, this is the case in DNA. A sequence of 3 DNA nucleotides that stands for 1 amino acid is called a base triplet. -When messenger RNA is produced, it carries a coded message based on these DNA triplets. A 3 base sequence in mRNA is called a codon. The genetic code is expressed in terms of codons. -There are 64 possible codons available to represent the 20 amino acids. 61 code for amino acids and 3 are stop codons. Start codon- AUG codes for methionine and begins the amino acid sequence of the protein. Stop codons- UAG, UGA and UAA signal the "end of message," like the period at the end of a sentence.

Describe the assembly of amino acids into a protein.

-When a gene is activated, a mRNA is made, a mirror image of the gene, then migrates from the nucleus to the cytoplasm where it serves as a code for assembling amino acids in the right order to make a particular protein. -Think of the process as: DNA--->mRNA--->protein The step between DNA--->mRNA is called transcription. This is where DNA codes for mRNA within the nucleus. The step between mRNA--->protein is called translation. This is where mRNA codes for the protein within the cytoplasm. -During transcription, which is the process of copying genetic instructions from DNA to mRNA, an enzyme called RNA polymerase binds to the DNA and assembles the mRNA. Certain base sequences (often TATATA or TATAAA) inform the polymerase where to begin. -The polymerase then opens up the DNA helix about 17 base pairs as a time. It reads the bases from one strand of DNA and makes a corresponding mRNA. Where it finds a C on the DNA it adds a G on the mRNA, where it finds a G on the DNA it adds a C on the mRNA and where it finds a T on the DNA it adds an A to the mRNA. However, where it finds an A on the DNA it adds a U on the mRNA (replacing the thymine with the uracil.) The enzyme then rewinds the DNA helix behind it. Another RNA polymerase may follow closely behind the first one; thus a gene may be transcribed by several polymerase molecules at once and numerous copies of the same RNA are made. At the end of the gene is a base sequence that serves as a terminator, which tells the polymerase to stop. -The RNA produced by transcription is an immature form called pre-mRNA. This molecule contains segments called exons that will be translated into a protein and segments called introns that must be removed before translation. Enzymes will cut out the introns and then splice the exons together into a functional mRNA molecule. This is when it will leave the nucleus. Introns are not useless but are most likely used in control of protein synthesis. -Alternative splicing: variations in the way exons are spliced allow for a variety of proteins to be produced from one gene. One gene can code for more than one protein and exons can be spliced together into a variety of different mRNA's. -Translation: process that converts the language of nucleotides into the language of amino acids. There are three main participants in translation: 1. Messenger RNA (mRNA) carries code from nucleus to cytoplasm -Has protein cap that is recognition site for ribosome. 2. Transfer RNA (tRNA) delivers a single amino acid to the ribosome for it to be added to growing protein chain. -One end contains an anticodon (series of 3 nucleotides that are complementary to codon of mRNA.) -Other end has binding site specific for one amino acid -tRNA picks up free amino acid in cytosol -Cost of binding an amino acid to the tRNA is one ATP 3. Ribosomes—organelles that read the message -Found free in cytosol, on rough ER, and on nuclear envelope -Consist of large and small subunits, where each subunit is made of several enzymes and ribosomal RNA (rRNA) molecules -mRNA molecule begins with leader sequence -Acts as binding site for small ribosomal subunit -Large subunit attaches to small subunit -Ribosome pulls mRNA molecule through it like a ribbon, reading the bases as it goes -When start codon (AUG) is reached, protein synthesis begins -All proteins begin with methionine when first synthesized

Define allele and discuss how alleles affect the traits of an individual.

Alleles—different forms of gene at same locus on two homologous chromosomes •Dominant allele (represented by capital letter)-If present, corresponding trait is usually seen in the individual -Masks effect of recessive allele -Often produces protein responsible for visible trait •Recessive allele (represented by lowercase letter) -Corresponding trait only seen when recessive allele present on both homologous chromosomes -Often codes for a nonfunctional variant of the protein Genotype—alleles an individual possesses for a particular trait -Homozygous individuals—two identical alleles for the trait -Heterozygous individuals—different alleles for that gene •Phenotype—an observable trait -An allele is expressed if it shows in the phenotype of an individual •Punnet square—diagram showing possible genotype and phenotype outcomes from parents of known genotype Gene pool—genetic makeup of whole population •Multiple alleles—more than two allelic forms of gene -Example: three alleles for ABO blood types •IA, IB, i alleles for ABO blood types •Codominance—both alleles equally dominant -Both are phenotypically expressed -Example: IAIB=typeABblood •Incomplete dominance -Heterozygous individual shows phenotype intermediate between traits each allele would have produced alone -Example: familial hypercholesterolemia

Give a working definition of a gene.

An information-containing segment of DNA that codes for the production of a molecule of RNA that plays a role in synthesizing one or more proteins.

Describe the life history of a cell, including the events of mitosis.

Cell cycle—cell's life from one division to the next -Includes interphase and mitotic phase -Interphase includes three subphases: G1, S, G2 Mitotic phase includes multiple subphases: Prophase, Metaphase, Anaphase, Telophase Mitosis is cell division resulting in two genetically identical daughter cells. Functions of mitosis: -Development of the individual from one fertilized egg to roughly 50 trillion cells -Growth of all tissues and organs after birth -Replacement of cells that die -Repair of damaged tissues Four phases of mitosis-prophase, metaphase, anaphase, telophase Prophase -Genetic material condenses into compact chromosomes as it is easier to distribute to daughter cells than chromatin -46 chromosomes •Two chromatids per chromosome -Nuclear envelope disintegrates -Centrioles sprout spindle fibers (long microtubules) •Spindle fibers push centriole pairs apart •Some spindle fibers attach to kinetochores of centromeres of chromosomes Metaphase -Chromosomes are aligned on cell equator -Spindle fibers complete mitotic spindle (lemon-shaped) -Shorter microtubules from centrioles complete an aster which anchors itself to inside of cell membrane Anaphase -Enzyme cleaves two sister chromatids apart at centromere -Single-stranded daughter chromosomes migrate to each pole of the cell as motor proteins in kinetochores crawl along spindle fibers• Telophase -Chromosomes cluster on each side of the cell -Rough ER makes new nuclear envelope around each cluster -Chromosomes uncoil to chromatin -Mitotic spindle disintegrates -Each nucleus forms nucleoli Cytokinesis—division of cytoplasm into two cells -Telophase is the end of nuclear division but overlaps cytokinesis •Achieved by myosin protein pulling on actin in the terminal web of cytoskeleton •Creates cleavage furrow around the equator of cell •Cell eventually pinches in two Cells divide when: •They have enough cytoplasm for two daughter cells •They have replicated their DNA •They have adequate supply of nutrients •They are stimulated by growth factors (chemical signals) •Neighboring cells die, opening up space Cells stop dividing when: •They snugly contact neighboring cells •Nutrients or growth factors are withdrawn •They undergo contact inhibition—the cessation of cell division in response to contact with other cells

Explain how DNA indirectly regulates the synthesis of nonprotein molecules.

Cells synthesize glycogen, fat, steroids, phospholipids, pigments, and other compounds -No genes for these products, but their synthesis is under indirect genetic control -They are produced by enzymatic reactions, and enzymes are proteins encoded by genes. Example: production of testosterone (a steroid) -A cell of the testes takes in cholesterol -Enzymatically converts it to testosterone -Only occurs when genes for enzyme are active

Describe the structure of DNA and relate this to its function.

DNA: (DeoxyriboNucleic Acid) is an acidic, phosphorus-rich substance that is the repository for our genes. -It is a long threadlike molecule with a uniform diameter of 2 nm, although its length varies greatly from the smallest to the largest chromosomes. -46 DNA molecules (chromosomes) in nucleus of most human cells. Average human DNA molecule is about 2 in. long. -DNA and other nucleic acids are polymers of nucleotides. Nucleotides consist of sugar, phosphate group and nitrogenous base. **one sugar- deoxyribose **one phosphate group **one nitrogenous base --->Pyrimidines (single ring) are Cytosine (C) and Thymine (T) --->Purines (double ring) are Adenine (A) and Guanine (G) --->In RNA, Thymine (T) is replaced with Uracil (U) ---> DNA bases are then A, T, C, G -DNA's double helix shape resembles a spiral staircase. Each side piece is a backbone of phosphate groups alternating with deoxyribose. The step-like connections between the backbones are pairs of nitrogen bases. -Nitrogenous bases are united by hydrogen bonds: --->a purine on one strand is always bound to a pyrimidine on the other. --->A-T has two hydrogen bonds. --->C-G has three hydrogen bonds. --->DNA base pairings are then A-T and C-G. --->Law of complementary base pairing says that one strand determines base sequence of the other. **The essential function of DNA is to carry instructions, called genes, for the synthesis of proteins. Humans are estimated to have about 20,000 genes but these only constitute about 2% of DNA. The other 98% does not code for proteins but plays various roles in chromosome structure and regulation of gene activity.

Three steps to Translation: Initiation, Elongation, Termination

Initiation -Leader sequence in mRNA binds to small ribosomal subunit -Initiator tRNA (bearing methionine) pairs with start codon -Large ribosomal subunit joins the complex and the now fully formed ribosome begins reading bases Elongation -Next tRNA(with its amino acid) binds to ribosome while its anticodon pairs with next codon of mRNA -Peptide bond forms between methionine and second amino acid -Ribosome slides to read next codon and releases initiator tRNA(empty) -Next tRNA with appropriate anticodon brings its amino acid to ribosome -Another peptide bond forms (between 2nd and 3rd amino acids) -Process continually repeats, extending peptide to a protein Termination -When ribosome reaches stop codon a release factor binds to it -Finished protein breaks away from ribosome -Ribosome dissociates into two subunits.

Describe the paired arrangement of chromosomes in the human karyotype.

Karyotype—chart of 46 chromosomes laid out in order by size •23 pairs—the two members of each pair are called homologous chromosomes -1 chromosome from each pair inherited from each parent •22 pairs called autosomes-Look alike and carry the same genes •1 pair of sex chromosomes (X and Y)-Female has homologous pair of X chromosomes-Male has one X and one much smaller Y chromosome

Explain what happens to a protein after its amino acid sequence has been synthesized.

Protein synthesis is not finished when the amino acid sequence (primary structure) has been assembled. -To work, protein must fold into precise secondary and tertiary structures. -Chaperone proteins guide their folding into the proper shapes -Proteins to be used in the cytosol are made on free ribosomes in the cytosol -Proteins destined for packaging into lysosomes or secretion from the cell are assembled on rough ER and sent to Golgi complex for packaging. -Entire polyribosome migrated to the rough ER and docks on its surface -Assembled amino acid chain completed on rough ER -Sent to Golgi for final modification ER modifies protein by posttranslational modification -Removing some amino acid segments; folding the protein; stabilizing protein with disulfide bridges; adding carbohydrates -When rough ER is finished with protein: -Pinches off bubble-like transport vesicle coated with clathrin -Clathrin helps select the proteins to be transported in vesicles and helps mold forming vesicle -Vesicles detach from ER and carry protein to the nearest cisternae of Golgi complex Vesicles fuse and unload proteins into Golgi cisterna -Golgi complex further modifies the protein --Often adds carbohydrate chains and assembles glycoproteins --Golgi cisterna farthest from ER buds off new coated Golgi vesicles containing finished protein -Some Golgi vesicles become lysosomes -Other Golgi vesicles become secretory vesicles and migrate to plasma membrane, fuse to it, and release their cell product by exocytosis.

Describe the types of RNA, their structural and functional differences and how they compare with DNA.

RNA: (Ribonucleic Acid) are the smaller molecules that resemble DNA. They can have less than 100 or just over 10,000 bases per molecule where DNA averages more than 100 million base pairs long. -Where DNA is a double helix, RNA consists of only one nucleotide chain, not held together by complementary base pairs except in certain short regions where the molecule folds folds back on itself. -Where the sugar in DNA is deoxyribose, RNA consists of ribose. -Where DNA contains the four nitrogenous bases adenine, cytosine, guanine and thymine, in RNA the thymine is replaced with Uracil. -RNA is a disposable molecule that works mainly in the cytoplasm, where DNA is irreplaceable and remains safely behind the nucleus giving the orders. There are three types of RNA: -Messenger RNA (mRNA) is a mirror image of a gene. It will carry the genetic code from the nucleus to the cytoplasm. -Ribosomal RNA (rRNA) is part of the protein-synthesizing organelle known as a ribosome and that is exported to the cytoplasm to help translate the information in messenger RNA (mRNA) into protein. -Transfer RNA (tRNA) is a relatively small RNA whose job is to bind a free amino acid in the cytosol and deliver it to the ribosome to be added to a growing protein chain. -The essential function of the three principal RNA's is to interpret the code in DNA and use those instructions to synthesize proteins.