BCP II: MCAT Midterm Review Subject: Biological Sciences Instructor: Michael Ullo, BS

I.

Foundations

The main things that goes on inside the cell, are chemical reactions. Catalyst helps reactions happen faster. Enzymes are organic catalyst that catalyzed biological reactions. They help get reactants together and therefore, make the reactions happen more quickly. The word substrate is used to refer to reactants in an enzyme-catalyzed reaction. The place at which the substrate attached to the enzyme molecule is called the active site. Enzymes specificity refers to the fact that one enzyme is usually designed to fit the reactants for only one particular reaction. When the substrate is attached to the enzyme they caused a slight change in the shape of the enzyme, which is called an induced fit. When the reaction is over, the enzyme resumes its usual shape. Remember that an enzyme is not a reactant and that all enzymes are made of protein. A living cell is similar to a bag full of chemicals. Many of the chemicals have the potential to react with many other of the chemicals. Enzymes determine which chemicals will react with which chemicals. Therefore, it is the availability of enzymes that determines what reactions will take place in a cell and what reactions will not. An enzyme would not work just anywhere and it would not work under any and every condition either. One of the very important things to remember about enzymes is that everyone has an optimum pH, which is the pH at which it works best. When pH differs even a little bit from an enzymes optimum pH, the enzyme works very poorly. Enzymes also work better at high temperatures. As temperature increases enzymes work better. For every enzyme there some temperature that is too high. When temperature is raised high enough, any enzyme denatures. When an enzyme denatures, it does not work anymore. Once the amount of substrate added matches the amount of enzyme at work, the reaction rate levels off and adding substrate will not increased the reaction rate. Many enzymes would not work alone, but need to perform in the presence of inorganic substance called cofactor or an organic molecule called coenzyme. The activity of enzymes is also affected by feedback inhibition. Feedback inhibition means that a function of an enzyme is inhibited by the product of the reaction it catalyzes. This way you do not end up with too much of any one product in the cell because an excess of the product will turn off the enzyme. Every cell uses energy and they get their energy from ATP. ATP is the energy currency. ATP is made of an adenosine molecule which is the nitrogenous base adenine with the rival sugar tacked on and three phosphate molecules attached to it. In almost all living cells, ATP is the lowest recognizable chemical form in which energy is found before it is taken to perform work. Cells store energy in the form of glucose. Glucose is a six carbon molecule and it has energy in it. The energy is in the chemical bonds between carbon atoms and in the chemical bonds between carbon and hydrogen atoms. ATP is made by putting together an ADP molecule and a phosphate molecule using the energy from glucose. When cells need to get some glucose out of storage to form some ATP, they start with the process called glycolysis. In the process of glycolysis the cell starts with the molecule of glucose. Glucose uses two ATPs to start the process. The cell ends up with two molecules of pyruvic acid and four ATPs. Therefore, when a glucose molecule goes through the process of glycolysis, it ends up with the net production of two ATP molecules. References: ExamKrackers 7th Edition Biological Sciences, Guyton & Hall Textbook of Medical Physiology, www.freemcatprep.com

Remember that the glycolysis is anaerobic process. It occurs without oxygen. After glycolysis is complete the cell has form some ATP and is left with tow molecules of pyruvic acid. Each molecule of pyruvic acid is then converted to a molecule of acetyl CoA, which is a two-carbon molecule by oxidative decarboxylation. The cell now has two molecules of acetyl CoA. With its two molecules of acetyl CoA, the cell next undergoes the Krebs cycle which is also called the citric acid cycle. When the cell undergoes the Krebs cycle, acetyl CoA combines with the four-carbon molecule to form a six-carbon molecule. Within the Krebs cycle each molecule of acetyl CoA produces one molecule of GTP. The GTP molecule is then readily converted to an ATP molecule. The cell starts out with two molecules of acetyl CoA, which means that it undergoes the Krebs cycle twice. So, for each molecule of glucose that cell starts out with, the Krebs cycle yields two molecules of ATP, four molecules of CO2, six molecules NADH, and two molecules of FADH2. The Krebs cycle is the final common pathway in the oxidation of fatty acids into amino acids. The Krebs cycle requires oxygen that means the process is available to aerobic organisms but it is not available to anaerobic organisms. Anaerobic bacteria can conduct glycolysis because that does not require oxygen but they cannot conduct the Krebs cycle because that requires oxygen. The Krebs cycle occurs inside a cells mitochondrion. A mitochondrion has an outer membrane and inner membrane a space between the two membranes and a matrix. After the Kreb cycle there are two more processes that occur, the electron transport via the electron transport chain and oxidative phosphorylation. After the Krebs cycle is complete the cell is left with lots of NADH and FADH2. Each FADH2 gives up H2, then the H2 molecule divides to form 2 hydrogen atoms and each hydrogen atom gives up an electron. NADH gives up an H atom and then H atom gives up one electron. Each electron is transferred to the electron transport chain. The electron transport chain involves a lot of carrier molecules that contain iron. Once, the electrons are transferred over to the electron transport system. The system hands each electron down from one carrier to the next. With each hand down of an electron, energy is released. The cell takes the energy and uses it to pump hydrogen ions from the inside of the mitochondrial matrix to the space between the two mitochondrial membranes. That means the cell ends up with more hydrogen ions outside the matrix than inside. That produces an electro chemical gradient. Once an electron has been handed down through all of the carriers in a series of redox reactions, it gets together with another electron that has come down the carrier system and the two electrons are passed finally to an atom of oxygen. That forms a negatively charged oxygen. Each negatively charged oxygen ion then gets together with two charged hydrogen ions and forms a molecule of water. Since the electron transport system ultimately passes each electron to an oxygen molecule, it requires oxygen and its anaerobic process. Because of the electrochemical gradient that is produced during electron transport, hydrogen ions start right away via passive diffusion to diffuse inward back into the mitochondrial matrix. Now, as the hydrogen ions diffuse back across the inner mitochondrial membrane ADP and phosphate that are sitting right on the membrane, get together and form ATP. So when the hydrogen ion crosses the inner membrane, it causes the production of ATP from ADP and phosphate. The hydrogen ion crosses the inner mitochondrial membrane by passing through channels made of a substance called ATP synthase which is also sitting on the inner membrane. Even though there are separate processes, electron transport an oxidative phosphorylation happen at the same time. As the electron transport chain starts to pump hydrogen ions out across the inner mitochondrial membrane, the hydrogen ion start right away to cross back into the matrix. So the hydrogen ion gradient is not allowed to progress very far. In anaerobic organism the cell conducts fermentation. References: ExamKrackers 7th Edition Biological Sciences, Guyton & Hall Textbook of Medical Physiology, www.freemcatprep.com

This means that the two molecules are pyruvic acid left from glycolysis are transformed to either ethanol or lactic acid. Fermentation produces only two ATPs. When a rapidly exercising human muscle cant get all of the oxygen it needs to conduct aerobic respiration, it conducts fermentation and produces lactic acid. II. Bacteria A bacterium is a single-celled organism and it usually has a cell wall. A bacterium is a prokaryotic cell. A typical bacterium has one ring-shaped chromosome made of DNA. At some point in its life, the bacterium replicates the whole chromosome. The bacterium then develops a cell wall across its transverse length and divides into two daughter bacteria, each of which has one chromosome. The whole process is asexual and it is called binary fission. Bacteria, however, have ways of mixing their chromosomes with chromosomes from other bacteria. In that way, they achieve genetic recombination. There are three words that signify the ways in which bacteria achieve genetic recombination; conjugation, transformation and transduction. Conjugation is when two bacteria can get together and one can transfer some DNA to another through structures called pili. One bacterium is called the donor and it has a plasmid called the F-factor that participates in the transfer of DNA. The other bacterium is called the recipient. Transformation is when one bacterium receives pieces of DNA from a second bacterium. The two bacteria do not actually get together as they do in conjugation. Instead, pieces of chromosome from the second bacterium have gotten loose and are floating around on their own, the first bacterium incorporates those pieces into its own chromosome. Transduction is when a virus takes some DNA from bacterium and carries it to another. Some bacteria are round; they are called cocci, singular is coccus. Some bacteria are spiral, they are called spirilla, singular is spirillum. Some bacteria look like straight rods, they are bacilli, singular is bacillus. Remember, the following types of organisms and their method of obtaining nutrition. Autotrophs are organisms that can produce their own nutrition via photosynthesis. Heterotrophs are organisms that cannot perform photosynthesis and must derive their nutrition from an outside source. Parasites are organisms that have no digestive system and absorb nutrients from the living body of a host organism at the expense of the host. Saprophytes are organisms that have no digestive system and absorb nutrients from the dead bodies of other organisms. Carnivores are organisms that have digestive systems and eat animals. Herbivores are organisms that have digestive systems and eat plants. Now remember, the following types of bacteria and their need for oxygen. Obligate anaerobes derive energy via fermentation only. They cannot survive in the presence of oxygen. Facultative anaerobes derive energy via aerobic respiration or fermentation and can survive with or without oxygen. Aerobes derive energy via aerobic respiration only and cannot survive without oxygen. Some bacteria are called nitrogen-fixing bacteria, which mean that they have the ability to take nitrogen from the air and often provided to the plants. Virus A virus does not have a plasma membrane. It does not have a nucleus and it does not have any of the organelles we have talked about. A virus has a coat which is called a capsid. This coat is made of References: ExamKrackers 7th Edition Biological Sciences, Guyton & Hall Textbook of Medical Physiology, www.freemcatprep.com Basics of Microbiology

protein. Inside the virus protein coat, there is nucleic acid. There are two kinds of nucleic acids, DNA and RNA. Some viruses have DNA, and are called DNA viruses. Some have RNA, and are called RNA viruses. A virus cannot reproduce without the help of some other cell. So when a virus wants to reproduce, here is what it does. First, it latches on to some other cell. It might latch on to a bacterial cell, fungal cell, plant cell or animal cell. The other cell is called the host. Second, once the virus has latched on to his host, it injects its nucleic acid into the host. Third, the virus nucleic acid somehow uses the host cells equipment to reproduce itself many times. While inside the host cell, the virus nucleic acid replicates itself repeated and each copy of the viral nucleic acid somehow causes a new protein coat to form around the nucleic acid. Fourth, the new viral particles now burst out of the host cell and emerge. Bursting is called host cell lysis. The sequence of events in a lysogenic infection is a little different. The virus latches on the cells, as usual, and injects its nucleic acid. Then, the viral nucleic acid integrates into the hosts nucleic acid. When the host cell replicates itself, the viral nucleic acid, which is now called prophage, also replicates. Certain conditions can cause the prophage to become lytic and follow the lytic phase. There is something about a virus protein coat that decides what kind of host cell it will attack. A virus cannot settle on a host cell unless the host cell has some kind of receptor for the virus protein coat on its surface. There is a type of virus called bateriophage. A bateriophage is a virus that uses bacteria as its host. The bateriophage, like all other viruses, has a protein coat and nucleic acid inside it. The nucleic acid inside a bateriophage is DNA. A bateriophage also has a tail. A bateriophage reproduces just like other viruses, except that when it latches on to its host, it uses its tail. Fungi It is hard to decide whether fungi are plants or animals. It is also hard to decide whether a fungus is a single-celled organism or a multi-celled organism. A fungus is like many cells all joined together in one and that is why it sometimes called a multi-nucleated cell. A fungus is like a plant and that it has one big cell wall around it. It is also a eukaryotic cell and that it has many, many copies of the usual organelles and many nuclei. Fungi are usually haploid. Some of them reproduce asexually and some reproduce sexually. Some, however, can reproduce asexually or sexually. Budding is when a piece of a fungus breaks off and becomes a brand new fungus. Spores are tiny cells that a fungus expels usually from long structures called hyphae. These spores germinate is some suitable environment, and a new fungus grows. The new fungus is an identical twin to the original because its chromosomes are exactly the same as the original. Fungi reproduce by each contributing a piece of itself by conjugation. Each piece has a haploid number of chromosomes and when they get together to form a zygote, the zygote has the deployed number of chromosomes. The zygote hangs around in a dormant state for a few months and does not do much. This dormant state is the only part of the fungus life cycle that is diploid. After the zygote is through dormancy, it undergoes mitosis and forms spores, each one having the haploid number of chromosomes. The spores germinate somewhere and we get new fungi, each having the haploid number of chromosomes, so spores can be produce sexually and asexually. III. Genes & Genetics

We will now, talk a little about chromosomes. Chromosomes are made of deoxyribonucleic acid, which is called DNA. Chromosomes are found in the nucleus of every cell through out the entire body. Human References: ExamKrackers 7th Edition Biological Sciences, Guyton & Hall Textbook of Medical Physiology, www.freemcatprep.com

beings have a total of 46 chromosomes but these chromosomes exist in pairs. So, sometimes we say that human beings have 23 pairs of chromosomes. Think for a second about one pair of chromosomes the two members of any recognized pair of chromosomes are similar but not exactly alike. The two members of a recognized pair of chromosomes are called homologous chromosomes. If we took the 23 pairs of chromosomes from a human cell and then from each cell we removed one number of the pair will be left altogether with 23 different chromosomes and this cell would be called haploid. When we say haploid, we mean a cell for which the chromosomes are not paired. A normal human cell that has 23 pairs of chromosomes is said to have a diploid number of chromosomes and the cell is therefore called a diploid cell. Now let us talk a little about DNA. DNA is made of little subunits called nucleotides. A nucleotides is made up of pentose sugar attach to a phosphate and to a nitrogenous base. A nucleotide can have as its base anyone of the following four possible bases; adenine, guanine, cytosine, and thymine. One strand of DNA is formed when many nucleotides bond together in one base order or another and form a chain. A chromosome can be thought of as two strands of DNA put together side by side. Each stand is said to be the compliment of the other. A chromosome looks like a ladder the sides of the ladder are made up of the phosphate sugar components of all of the nucleotides. Each wrung of the ladder is made from a pair of bases. One base comes from a nucleotide on one strand of DNA and the other base comes from nucleotide on the other strand of DNA. By convention, when we list the sequence of nucleotides in a nucleotide strand we read from the five prime to the three prime end. When two strands of DNA get together to form a chromosome, the wrungs are formed by the bonding of two bases. But it turns out that each base is only willing to get together with one of the other bases. You must remember that adenine bonds with thymine and guanine bonds with cytosine. There are two hydrogen bonds between adenine and thymine and three hydrogen bonds between guanine and cytosine. If you know the base sequence of one strand you can figure out the base sequence of its compliment. Suppose we tell you that in one area of a DNA molecule, one of the strands has the base sequence adenine, cytosine, thymine and guanine by knowing the base pairing rules you can figure out the base sequence of the complimentary strands, which is thymine, guanine, adenine, and cytosine. One other thing you should know is that two of these bases are called Purines and two are called Pyrimadines. It is easy to remember which are which. Remember out alphabetized list of nucleotides bases adenine is a purine, cytosine is pyrimadine, guanine is a purine and thymine is a pyrimadine. Notice that the first one is a purine and that the terms pyrimadine and purine alternate along the rest of the list. You will also notice that each purine bonds with one of the pyrimadines and likewise each pyrimadine bonds with one of the purines. Purines do not bond with purines and pyrimadine do not bond with pyrimadines. When the double stranded DNA molecule is fully formed it is twisted. The twisted ladder shape is called a double helix. Watson and Crick are the scientist who figured out the shape of DNA. And that is why the doublehelix shape is sometimes called the Watson Crick model of DNA or the Watson Crick double helix. It is easy to see how DNA reproduces its self. The first thing that happens is that using DNA helices enzymes the double helix unwinds and unzipped so that the two strands of DNA can separate. Remember DNA synthesis always proceeds in a five prime to three prime direction. DNA synthesis begins at a particular site called the origin of replication. An RNA primer is used to add subunits to the three prime end of the DNA strand. The next thing that happens is that with help of the enzymes DNA polymerase the nucleotides line up References: ExamKrackers 7th Edition Biological Sciences, Guyton & Hall Textbook of Medical Physiology, www.freemcatprep.com

according to the rules of base pairing. Cytosines line up next to guanines and guanines line up next to cytosines, adenines line up next to thymines and thymines line up to next to adenines. Along side of each separated strand nucleotides lines up and form a new second strand both strand are replicated at the same time. One strand continuously called the leading strand and the other strand discontinuously called the lagging strand. Bonds formed between the base pairs and among the sugar phosphate components of the nucleotides. An organisms chromosomes contain all of its genetic information. In terms of what you are born with chromosomes make you who you are. They do that basically by determining what proteins your cell will manufacture. Since proteins often serves as enzymes chromosomes determine what enzymes your cells manufacture. Enzymes determine what chemical reactions will and will not occur in your cells and thats what makes you more or less who you are. DNA directs protein synthesis through RNA. RNA looks like very much like DNA but there are three important differences between them. RNA is single stranded. The nucleotides that form RNA have ribose instead of deoxyribose as their sugar. In fact, RNA stands for ribonucleic acid and DNA stands for deoxyribonucleic acid. RNA nucleotides never contain thymine as a base instead they contained a base called uracil. So the four bases found in RNA nucleotides are adenine, cytosine, guanine, and uracil. RNA is formed under the direction of DNA. Sometimes a DNA molecule will unzipped when it is not planning to replicate and one of the strands will serve as template for the formation of an RNA molecule. The RNA molecule is formed using the enzyme RNA polymerase, usually one strand is transcribed. The process can be induced or suppressed depending on the needs of the cell. In RNA molecule is formed just like a DNA molecule except that you think of uracil instead of thymine. If a DNA strand has the sequence guanine, thymine, adenine and cytosine the RNA molecule that it forms will have the sequence cytosine, adenine, uracil, and guanine. The order of nucleotides and the RNA molecule is determined by the order of nucleotides on the DNA strand that produces it. If a different DNA strand had served as template, a different RNA molecule would have resulted. The process of making RNA molecules from DNA is called transcription. Since RNA is formed from chromosomes, it is formed in the nucleus. However, after it is formed it moves out into the cytoplasm. RNAs are important because they are involved in protein synthesis. There are three types of RNAs. First there is mRNA which id formed in the nucleus from a DNA template. This is the RNA that goes out into the cytoplasm to locate itself on ribosomes it called messenger-RNA because it carries a message from the nucleus to the cytoplasm, second is tRNA. TRNA stands for transfer-RNA. The tRNA reads the mRNA codon and brings the appropriate amino acid into line. The third RNA is called rRNA. RRNA stands for ribosomal-RNA. Ribosomal-RNA is made in the nucleolus and it makes a part of the ribosome. Every three RNA nucleotides bases are called a codon. Each codons specifies an amino acid, each codons are like a message from the chromosomes directing the ribosomes to produce a certain proteins. The three base sequence on the tRNA molecule is called an anti-codon. The anti-codon can recognize a codon on the mRNA by complimentary base pairing. Translation is the process in which the amino acids line up in accordance with the codons that appears on a molecule of RNA. The ribosome has subunits a large one and a small one. The ribosome also has two special tRNA binding sites called the A site and P site. A special tRNA called methanol tRNA is the initiator of protein synthesis. It attaches at one end to methionine and to a sequence of three nucleotide bases at the other References: ExamKrackers 7th Edition Biological Sciences, Guyton & Hall Textbook of Medical Physiology, www.freemcatprep.com

end. This initiator binds to the ribosome at the P site. The P stands for peptidyl tRNA binding site. Once initiation is complete the amino acids are ready to added one by one to the initial amino acid which is methionine. The next amino acid is carried by a TRNA a peptide bond is formed between the two amino acids after the peptide bond is formed methionine is now attach to the tRNA at the A site. The tRNA is released from the P site. The tRNA at the A site carries the growing polypeptide. Next the tRNA in the A site jumps to the P site. This is called translocation. This process allows for the next tRNA to come in and attach to the next amino acid. This translocation process requires energy which is provided by the hydrolysis of GTP. The mRNA moves through the ribosome in the five prime to three prime direction. Chromosomes are the template from which mRNA is formed. That means that the base sequence in an mRNA molecule is a reflection of the base sequence of the DNA molecule that served as its template. The mRNA goes out into the cytoplasm and there each of its three base sequences or codons attracts the molecule of tRNA with a complimentary three-base sequence or anti codon. The tRNA molecule is attached to a particular amino acid for which it is specific. The amino acids thus line up in an order dictated by the order of the codons on the mRNA molecule. Now remember this, chromosomes are DNA molecules. These DNA molecules give rise to complimentary mRNA molecules. A molecule dictates the order in which amino acids get together to form proteins. Proteins serves as enzymes and enzymes determine what chemical reaction occur in our bodies. Chromosomes make us who we are because they carry all of the genetic information that governs your biochemical activity. The genetic information is found in the DNA. The DNA has nucleotide basis of either A, T, C or G. We know that the particular sequence of a segment of DNA is very important. A specifically ordered string of nucleotide basis determines that a particular enzyme is made. When a particular enzyme is made, its biochemical effect will produce some trait that we will exhibit. A particular sequence of nucleotides and DNA that codes for a specific enzyme is called a gene. A gene produces an enzyme and an enzyme produces a trait. A gene is inherited by an organisms offspring, and because the gene is inherited, the trait that the gene produces is inherited. Genes are located along the length of a chromosome and the exact location of a gene on a chromosome is called its locus. The locus of a gene actually pinpoints the genes physical place on its assigned chromosome. In homologous chromosomes, the locus for one gene is lined up right next to the locus for the same gene on its chromosome partner. In homologous chromosomes, those two genes sitting next to each other code for one particular trait. Allele is the name given to each gene of the set that code for the same trait. Alleles for a particular trait are genes that can exist in slightly different forms. The two alleles that make up the genes for a trait are called the genotype for that trait. When a persons alleles are different, and that they code for different expressions of a trait, the person is said to be heterozygous for that trait. For an organism that is heterozygous for a trait, both alleles can be thought of as competing for expression of that trait. The allele which wins is called the dominant allele. The dominant allele will appear as the characteristic trait of the organism. We symbolize a dominant allele for a trait with a capital letter. The alternative allele of the pair remains as part of the genotype for that trait, but you cant detect it in the appearance of the organism. This allele is called the recessive allele. We symbolize a recessive allele for a trait with a small letter. You should know a little about Mendels laws. Mendels law of segregation says that for any given trait in the diploid parent cell, one allele for the trait goes to one gamete and the other allele for the trait goes to another gamete. Mendels law of independent assortment says that for any group of traits in an References: ExamKrackers 7th Edition Biological Sciences, Guyton & Hall Textbook of Medical Physiology, www.freemcatprep.com

organism, each trait will segregate independently of the other traits during meiosis. Its important to know that crossing over leads to genetic recombination. The chromatids of each homologous pair do not have the same arrangement of genes after crossing over as they did before crossing over. The chromatids have a new combination of genes as a result of crossing over. Remember, the Hardy-Weinberg law which states that even with all of the shuffling of genes that go on, individual alleles for traits still prevail overtime. They dont get lost in the shuffle. The more prevalent gene doesnt become even more prevalent, and the less prevalent gene doesnt disappear. However, the Hardy-Weinberg law applies only to ideal populations, Meaning, it is subject to these five conditions: very high numbers of individuals in a population, no mutations, no immigration or emigration, random mating and any one gene has the same chance of reproducing as any other. If these five conditions are met, you can be pretty sure that there is equilibrium in the gene pool of a given population. Remember this Hardy-Weinberg equation, P2 + 2PQ + Q2 = 1 or P +Q = 1. Theres a thing called genetic drift which says that when a population is small, some genes get lost overtime, and some genes become more frequent overtime. The 23rd chromosome pair is the sex chromosome. When the sex chromosomes are XX, they determine that a person will be female. When the sex chromosomes are XY, they determine that a person will be male. Because it is only the male who carries the Y chromosome, the Y chromosome of the male offspring can only be inherited from a father. Since each parent contributes one-half of the sex chromosome pair, then the X chromosome of the male offspring must come from the mother. On the other hand, since the female has sex chromosomes that are XX, and each parent contributes one-half of the chromosomes, then one X chromosome of the female offspring must come from the mother, and one X chromosome come from the father. When traits get carried on the pair of sex chromosomes, these traits are called sex-linked traits and are usually carried only on the X chromosome and not on the Y chromosome. If a female carries a recessive abnormal trait on only one X chromosome, she will still appear normal for that trait because the accompanying X chromosome overrides the recessive trait. The male has no spare X once the Y chromosome directs that the offspring is to be male. It has little else to do with inherited traits. That X chromosome that a male receives from his mother determines his faith with regard to a sex-linked trait. If the X chromosome carries the trait, then the male will show that trait even though that trait can be recessive.

References: ExamKrackers 7th Edition Biological Sciences, Guyton & Hall Textbook of Medical Physiology, www.freemcatprep.com