Biology – Study Guide

Cellular Chemistry

-Atoms, Elements, and Compounds

• An atom is the smallest basic unit of matter. Every physical hing is made up of atoms.
• An atom consists of protons, neutrons, and electrons. Protons and neutrons are found in the nucleus whereas electrons are found outside of the nucleus. Protons have a positive charge and electrons have a negative charge. Neutrons have no charge and are neutral.
• An element is a particular type of atom. An element cannot be broken into smaller pieces. Familiar elements are hydrogen and oxygen. Two different elements such as hydrogen and oxygen have atoms that contain different numbers of protons. Hydrogen atoms have one proton and oxygen atoms have eight protons.
• Electrons determine the properties of an element. Electrons are contained in different energy levels around the nucleus. Each energy level holds a different number of electrons. The first energy level holds two electrons and then second energy level holds eight electrons.
• A compound is a substance made from many elements that are bonded together. A common example of a compound is water, which is made from the elements hydrogen and oxygen that are bonded together.

-Bonding

• An atom that has gained or lost one or more electrons is known as an ion. Atoms gain or lose electrons to fill their outermost energy level in order to become more stable. This gain or loss of an electron will cause the ion to be charged. A general rule is if an atom has few electrons in its outer energy level it tends to lose electrons and become positively
  charged whereas if the atom has many electrons in its outer energy level it tends to gain electrons and become negatively charged. For example. Chlorine will gain an electron and become negatively charged.
• Ions form when atoms transfer electrons back and forth. This forms an ionic bond which is an electrical force between oppositely charged ions. For example, sodium chloride is bonded by ionic bonds between the positively charged sodium and the negatively charged chloride.
• A covalent bond forms when atoms share electrons rather than transfer them. Atoms can share electrons with many other atoms. For example, carbon dioxide shares electrons so that each atom has stable outer energy levels.
• A molecule is formed when two or more atoms are held together by covalent bonds.
• Hydrogen bonds are the attractive interaction between partially positive charged hydrogen and partially negative charged atoms such as nitrogen, oxygen, or fluorine. Water is a polar molecule with partially positive hydrogen and a partially negative oxygen. Polar molecules have an unequal sharing of electrons.
• The ability of water to hydrogen bond gives it unique characteristics. Water has a high specific heat and resists changes in temperature. It takes much more heat to increase the temperature of water than it does other compounds. Water exhibits cohesion and adhesion. Cohesion is the attractive force between molecules of the same substance. This means that water molecules stick together because of hydrogen bonding. This is why surface tension is produced. Adhesion is the attractive force between molecules of different substances. This means that water molecules stick to other things.

–Solutions

• A solution is a mixture of substances and contains two parts, the solute and the solvent. The solute is the substance that dissolves in the solvent. The solvent dissolves in another substance and is present in greater amounts in the solution. For example, when salt dissolves in water the salt is the solute and the water is the solvent.
• Polar molecules dissolve in water because they are both polar and the interaction between the water and the solute molecules is greater than the interaction between the solute molecules themselves. Ionic compounds also dissolve in water because the charges of water are attracted to the charges of the ionic compound. Nonpolar molecules do not dissolve in water because they do not have a charge and are not attracted to the polar nature of water.

-Acids and Bases

• An acid is a compound that releases a proton when dissolved in water.
• A base is a compound that absorbs a proton when dissolved in water.
• The pH scale is a measure of a solution’s proton concentration and determines how acidic the solution is. This scale is between 0-14. Solutions with a pH less than 7 are considered acidic, solutions with a pH of 7 are considered neutral, and solutions with a pH greater than 7 are considered basic. Acidic solutions contain a high concentration of
  protons whereas basic solutions contain a low concentration of protons.

-Biological Molecules

• Carbohydrates are composed of carbon, hydrogen, and oxygen and are broken down to provide chemical energy for cells. The basic unit of a carbohydrate is a simple sugar known as a monosaccharide. A well-known simple sugar is glucose which provides energy for many processes in cells.
• Lipids are composed of carbon, oxygen, and hydrogen made into fats, oils and cholesterol. They are nonpolar molecules. Fatty acids are acids with long carbon chains attached. There are two types of fatty acids, saturated fatty acids and unsaturated fatty acids. Saturated fatty acids contain only carbon-carbon single bonds and pack tightly.
  They are usually solid at room temperature such as butter. Unsaturated fatty acids contain at least one carbon-carbon double bond and are unable to pack tightly. They are usually liquid at room temperature such as oil.
• Proteins are made from amino acids linked together by peptide bonds. Peptide bonds are covalent bonds between amino acids.
• Nucleic acids are made from nucleotides. Nucleotides are composed of a sugar, a phosphate group, and a nitrogen-containing base. DNA and RNA are examples of nucleic acids.

-Chemical Reactions

• Reactants are the substances that are changed during a reaction. Reactants are on the left side of a chemical reaction.
• Products are the substances produced during a reaction. Products are on the right side of a chemical reaction.
• In order for a reaction to occur, energy is needed to break bonds so that new bonds can then be formed. This energy is known as bond energy. When bonds form energy is released. The bond energy required to break bonds equals the energy that is released when bonds form for a reaction.
• A chemical reaction can reach equilibrium when the reactants are being used up at the same rate that products are forming.
• To start a chemical reaction some energy must be absorbed by the reactants. This energy is known as the activation energy.
• Some reactions release energy while other reactions absorb energy. A reaction that absorbs more energy than it releases is known as an endothermic reaction. A reaction that releases more energy than it absorbs is known as an exothermic reaction.

-Enzymes

• Enzymes lower the activation energy need to start a chemical reaction. The reactants that enzymes act on are known as substrates.

Cellular Structure

-Cell Theory

• Hooke, Leeuwenhoek, Schleiden, Schwann, and Virchow contributed to the formation of cell theory.
• Major principles:
  • All organisms are made of cells
  • All cells come from other cells
  • The cell is the basic unit of life

-Prokaryotes vs. Eukaryotes

• Prokaryotic cells do not contain a nucleus and have no membrane bound organelles. Prokaryotes are only one celled. An example of a prokaryote is bacteria.
• Eukaryotic cells have a nucleus and have membrane bound organelles. Eukaryotes can be one celled or multicellular. An example of a eukaryote is animals.

-Cytoskeleton

• The cytoskeleton is the cellular scaffolding made from proteins inside a cell.
• The three main fibers that make up the cytoskeleton are microtubules, intermediate filaments, and microfilaments.

-Nucleus

• The nucleus is where genetic information, DNA, is stored in the cell. It provides protection and easily accessibility of the DNA.
• The nucleus has a double membrane around it called the nuclear membrane. This membrane has holes in it to allow for large molecules to pass between the nucleus and the cytoplasm.
• A special region of the nucleus called the nucleolus is where ribosomes are assembled.

-Endoplasmic reticulum

• The endoplasmic reticulum is a large network of folded membranes where synthesis of proteins and lipids occurs.
• Protein synthesis occurs in the rough endoplasmic reticulum because it is studded with ribosomes. Ribosomes are organelles that synthesize proteins.
• Lipid synthesis and drug detoxification occur in the smooth endoplasmic reticulum.

-Golgi Apparatus

• The Golgi apparatus is where proteins are processed, packaged, and delivered. Some proteins stay within the cell while others are secreted outside the cell.
• Proteins are transported around the cell in membrane-bound sacs known as vesicles.

-Mitochondria

• The mitochondria are the powerhouse of the cell and supply energy.
• Mitochondria contain both an inner and outer membrane.
• Mitochondria convert things we eat like glucose into usable energy for cells.
• Mitochondria have their own ribosomes and DNA that are different from that cell that it is contained in.

-Vacuole

• Vacuoles are used for storage of materials by a cell. Things like water, food, and enzymes can be stored.
• Animals only have small vacuoles but plants have a large central vacuole. This central vacuole takes up most of the space in a plant cell and provides strength and support for a plant. Plants wilt because they don’t have enough fluid in the central vacuoles to provide support.

-Lysosomes

• A lysosome is a membrane-bound organelle that contains enzymes. They digest and recycle foreign material such as bacteria as well as damaged or old cell parts.

-Centrosome and Centrioles

• The centrosome is the region in the cell that produces microtubules.
• The centrioles are organelles made from microtubules that are contained in the centrosome. They help the DNA divide during cell division.

-Cell Walls

• The cell membrane around plant cells is known as the cell wall. The cell wall provides rigid structure, support, and protection of the cell walls.

-Chloroplasts

•  Plants have organelles that carry out photosynthesis known as chloroplasts. Chloroplasts allow the plant to convert light energy into usable energy for the cells in the plant.
• Chloroplasts have their own DNA and ribosomes that are different from the cell they are contained in.
• Plants have both mitochondria and chloroplasts.

-Cell Membrane

• The cell membrane is what separates the inside of the cell from the outside environment and also controls what goes in and out of the cells.
• The membrane is made up of a lipid bilayer which is made from many phospholipids in a double layer. Phospholipids have a charge phosphate group and glycerol head with two fatty acid chains that form the tail. The head is charged so it is polar and the tail is nonpolar. The polarity of the head makes it hydrophilic (meaning water loving) and the tails are hydrophobic (meaning water-fearing). The heads are exposed to the outside environment and the cytoplasm whereas the tails aggregate together on the inside of the membrane.

• The membrane also has other molecules in it. Protein channels assist materials in crossing the membrane. Cholesterol provides strength to the membrane. Carbohydrates are attached and serve as identification tags.
• The fluid mosaic model is used to describe the cell membrane. The membrane is fluid because it is flexible and the phospholipids can move around. The proteins embedded in the membrane do not flip vertically. The membrane is also a mosaic because it contains many different molecules.
• The cell membrane is selectively permeable which means some materials are able to cross the membrane while others can’t.

-Receptors

• A receptor is a protein that binds to its signal molecule and then performs an action in response to the binding. The signal molecule the receptor binds to is known as a ligand.
• Intracellular receptors are receptors that are within the cell and bind to molecules that have crossed the membrane and are in the cell. These molecules are usually nonpolar and relatively small because they can easily cross the membrane. For example, aldosterone (an important hormone) binds to an intracellular receptor that then interacts with DNA and turns on certain genes.
• Membrane receptors are embedded in the membrane and bind to molecules outside the cell and then send a signal to the cell interior. When the molecule binds, a complex chain of events is triggered inside the cell.

-Transport of Materials

• Passive transport is when molecules move across the membrane without using energy.
• Diffusion is a type of passive transport that occurs when a fluid or gas moves along a concentration gradient. A concentration gradient occurs when the concentration of a substance changes in two different areas. When a molecule moves along a concentration gradient it goes from an area of high concentration to an area of low concentration.
• Osmosis is another form of passive transport that occurs when water moves from an area of higher water concentration to and area of lower water concentration.
• Facilitated diffusion also is a passive transport mechanism where molecules diffuse across the membrane with the help of a transport protein. The molecules still use a concentration gradient.
• Active transport requires energy and it occurs when a molecule travels against the concentration gradient and crosses the membrane from a region of low concentration to a region of high concentration. Chemical energy, such as ATP, must be used to transport the molecule.
• Endocytosis occurs when the cell intakes large molecules or liquids by engulfing them in a membrane. The substance is surrounded by a membrane that then pinches off inside the cell to form a vesicle around the substance.
• Phagocytosis, a type of endocytosis, occurs when the cell intakes large particles by engulfing them in a membrane.
• Exocytosis occurs when the cell releases substances outside of the cell by putting them into a vesicle that fuses with the membrane. This is the opposite of endocytosis.

Matter Cycles and Energy Transfer

-Cellular Respiration

• Adenosine triphosphate (ATP) is the molecule that transfers energy within a cell.
• Adenosine triphosphate (ADP) is a lower energy molecule that can be converted to ATP by adding a phosphate group.
• Cellular respiration is when chemical energy from sugars is released to make ATP. It is an aerobic process which means it needs oxygen to occur. This process occurs in the mitochondria.
• There are two parts to cellular respiration: the Krebs cycle and the electron transport chain. Glycolysis occurs before cellular respiration can occur.
• Glycolysis is an anaerobic process and doesn’t need oxygen to occur. Glucose splits into two three-carbon molecules known as pyruvate using up 2 ATP to do so. 4 ATP molecules are made (a net of 2 ATP) and NADH is produced.
• The Krebs cycle is the first step of cellular respiration. The pyruvate formed in glycolysis is broken down and bonded to coenzyme A. This intermediate is what enters the Krebs cycle. Citric acid is formed and then broken down into a five-carbon molecule. This five-carbon molecule is broken down into a four-carbon molecule. For one pyruvate during this process 3 molecules of carbon dioxide are given off, one molecule of ATP is made, 4 NADH molecules are made, and 1 molecule of FADH2 are made. There are 2 pyruvate molecules formed during glycolysis so double the products are made so 2 ATP molecule are produced.
• The electron transport chain takes place in the inner membrane of the mitochondria. Oxygen is the final electron acceptor in the chain. Electrons from NADH and FADH2 are stripped and transported down the chain. As the electrons travel down the chain hydrogen ions are transported across the inner membrane. The hydrogen ions then flow through the ATP synthase causing ADP to be changed into ATP. When the oxygen picks up electrons and the hydrogen ions water is formed. Up to 34 ATP molecules are produced from using the electron transport chain.
• A total of 38 ATP molecules are produced from the three processes: 2 ATP from glycolysis, 2 ATP from the Krebs cycle, and 34 ATP from the electron transport chain.

-Fermentation

• Fermentation is an anaerobic process (no oxygen is present) and allows glycolysis to continue. When oxygen is not present cellular respiration can’t occur so the products of glycolysis must be used elsewhere. Pyruvate and NADH are used to convert pyruvate into lactic acid. The NADH is converted into NAD+. The NAD+ are recycled and used in the glycolysis. This conversion from NADH to NAD+ is what allows glycolysis to continue to occur.

-Photosynthesis

• Photosynthesis is the process where energy from sunlight is harvested to make sugars that store chemical energy.
• Chloroplasts are membrane-bound organelles where photosynthesis occurs. They contain chlorophyll that absorbs energy in visible light.
• Photosynthesis has two separate reactions that occur. Light-dependent reactions capture energy from sunlight. Water and sunlight are needed for this reaction to occur. Light-independent reactions use the energy captured from the light-dependent reaction to make sugars. Carbon dioxide is need for this reaction.
• In the light-dependent reaction the energy from sunlight is captured by two groups of photosystems known as photosystem I and photosystem II. This reaction begins when the chlorophyll in photosystem II absorbs energy from sunlight and this energy is
  transferred in the form of electrons. The electrons enter the electron transport chain. As electrons are passed down the chain water molecules are split causing oxygen and hydrogen ions to accumulate. The oxygen is a waste product and the concentration of hydrogen ions builds and they are transported inside the thylakoid. The electrons that
  pass through the electron transport chain of photosystem II continue to photosystem I. Photosystem I also absorbs sunlight via its chlorophyll. The electrons produced are added to NADP+ to produce NADPH. The hydrogen ions that have built up in the thylakoid membrane flow through the ATP synthase and produce ATP.
• In the light dependent reaction there is the Calvin cycle. This cycle cannot occur without the ATP produced in the light-dependent reaction. At the start of the cycle carbon dioxide molecules enter the cycle and are added to a five-carbon molecule to form a six-carbon
  molecule. Energy in the form of ATP and NADPH which were produced in the lightdependent reaction are used to split the six- carbon molecule into two three-carbon molecules. Some of the three-carbon molecules leave the cycle and are bonded together to build a six-carbon sugar such as glucose. The three-carbon molecules that stay in the cycle are then converted to five-carbon molecules. These five-carbon molecules stay in the cycle and are added to new carbon dioxide molecules that enter the cycle.

Cellular Reproduction

-The Cell Cycle

• The cell cycle is the process of cell growth, DNA replication, and cell division. The four stages are: gap 1, synthesis, gap 2, and mitosis.
• Interphase is the phases of gap 1, synthesis, and gap 2.
• Gap 1 is the phase when the cell prepares for synthesis. The cells increase in size and the organelles increase in number. After this phase the cells move to synthesis but they must pass through a critical checkpoint.
• Synthesis is the phase when the cell copies its DNA. Now the cell contains two complete sets of DNA.
• Gap 2 is the stage when the cell continues to grow. After this stage there is a critical checkpoint before entering mitosis.
• Mitosis is the stage when the cell divides. For the nucleus to divide the nuclear membrane dissolves and the duplicated DNA splits so that two new nuclei can form. The cytoplasm divides in a process called cytokinesis. After mitosis there are two daughter cells that are genetically identical.
• Cells divide at different rates.
• Some cells stop dividing and enter a stage called G0.

-Mitosis

• Chromosomes are long threads of DNA. The human body cells have 46 chromosomes.
• When DNA is loose it is known as chromatin.
• When chromosomes are duplicated, one half of the chromosome is called a chromatid. These chromatids are held together by a centromere.
• The ends of the DNA are called telomeres and have repeating nucleotides that do not form genes.
• There are 4 phases of mitosis: prophase, metaphase, anaphase, and telophase.
• Prophase occurs when chromatin condenses into tightly coiled chromosomes. The nuclear envelope breaks down and the centrosomes and centrioles begin to migrate to opposite sides of the cell.
• Metaphase occurs when the spindle fibers attached to the centromere and align the chromosomes along the cell equator.
• Anaphase occurs when sister chromatids separate. This occurs when spindle fibers begin to shorten and pull the sister chromatids to opposite sides of the cell.
• Telophase occurs when the chromosomes are completely separated and the nuclear membrane begins to form. Also the spindle fibers fall apart and the chromosomes uncoil.
• Cytokinesis is the last stage of the cell cycle and occurs when the cytoplasm divides into two.

-Regulation of the Cell Cycle

• Growth factors are proteins that stimulate cell division. They do this by binding to receptors that trigger cell growth.
• Hormones can also stimulate cell growth.
• Kinases and cyclins also trigger cell growth.
• Apoptosis is programmed cell death.

-Asexual Reproduction

• Asexual reproduction is a mode of reproduction where the offspring arise from a single parent. The offspring are genetically identical to the parent.
• Binary Fission is a type of asexual reproduction where an organism divides into two equal parts. Binary fission produces daughter cells that are genetically identical to the parent cell.

-Development

• A group of cells that work together are known as tissues. A group of tissues that work together are known as organs. Organs that work together are known as organ systems.
• The process by which unspecialized cells become specialized and perform a specific
  function is known as cell differentiation.
• A cell is differentiated based on its location in the embryo. For example, a cell in the
  outer cell layer would differentiate into skin cells while a cell in the inner layer would
  differentiate into a digestive lining cell.
• Stem cells are cells that remain undifferentiated. When a stem cell divides it can divide
  into 2 stem cells or 1 stem cell and 1 specialized cell.

-Cells and Chromosomes

• Somatic cells are body cells. For example, cells that make up your liver, stomach lining,
  and skin are somatic cells.
• Gametes are sex cells. For example, eggs and sperm cells are gametes.
• Each person receives 23 chromosomes from their mother and 23 chromosomes from their
  father. A set of these chromosomes, one from the mom and one from the dad, that have
  the same general appearance is a homologous chromosome. Each person has 46
  chromosomes in 23 pairs.
• 22 pairs of these chromosomes do not directly relate to the sex of the organism and are
  autosomes.
• The one pair that controls the sex of the organism is the sex chromosome. A female’s
  sex chromosome is XX and a male’s sex chromosome is XY.
• Diploid cells contain two copies of each chromosome whereas haploid cells only contain
  one copy of each chromosome.

-Meiosis

• Meiosis is the cell division used in sexual reproduction that causes diploid cells to divide into haploid cells.
• There are two parts to meiosis, meiosis I and meiosis II. They both have 4 phases.
• Meiosis I:
  • Prophase I: The nuclear membrane breaks down and the spindle fibers start to form. The centrioles and centrosomes begin to move to opposite sides of the cell. The homologous chromosomes pair up after the duplicated chromosomes condense.
  • Metaphase I: The homologous chromosomes line up along the middle of the cell with help from the spindle fibers. The way the chromosomes line up is random which contribute to genetic diversity.
  • Anaphase I: The spindle fibers shorten and pull the paired homologous chromosomes to opposite ends. The sister chromatids stay attached.
  • Telophase I: The cell divides in half by cytokinesis.
  • Result: Two cells with with 23 duplicated chromosomes.
• Meiosis II:
  • Prophase II: The nuclear membrane breaks down and the spindle fibers start to form. The centrioles and centromeres begin to move to opposite sides of the cell.
  • Metaphase II: The 23 chromosomes line up along the middle of the cell with the help from the spindle fibers.
  • Anaphase II: The spindle fibers shorten and pull the sister chromatids to opposite ends.
  • Telophase II: The cell divides in half by cytokinesis.
  • Result: Four haploid cells

-Mitosis vs. Meiosis

• Mitosis produces cells that are all genetically the same while meiosis produces
  genetically different cells.
• Mitosis produces diploid cells while meiosis produces haploid cells.
• Mitosis occurs constantly in the body while meiosis occurs during certain times.
• Mitosis only has one cell division while meiosis has two cell divisions.

Traits, Genes, and Alleles

-Mendel

• Traits are distinguishing characteristics of an organism. This would be things like your
  hair color or eye color.
• Genetics is the study of inheritance and genes in organisms.
• Mendel used pea plants to conduct experiments to learn about genetics. He would cross,
  or mate, two plants and observe the outcome
• Mendel developed the law of segregation. This law states that organisms only donate
  one copy of each gene so the two copies of the genes segregate during meiosis.
• He also developed the law of independent assortment. This law states that allele pairs
  separate independently during meiosis.

-Definitions

• Genes are pieces of DNA that contain the instructions for the cell to make proteins.
• Alleles are the forms of the gene that can occur on a single locus.
• Homozygous means the alleles are the same on the same locus.
• Heterozygous means the alleles are different on the same locus.
• A genome is all of the genetic material contained in an organism.
• When an allele is expressed when two different alleles are present it is a dominant allele.
• When an allele is expressed when two of the same allele are present it is a recessive
  allele.
• Alleles are represented by a single letter. Uppercase letters are used for dominant alleles
  and lowercase letters are used for recessive alleles. For example, for a given trait the
  dominant allele would be AA or Aa and the recessive allele would be aa.
• The genotype refers to the genetic component of a gene. For example, for a given trait
  the genotype would be AA, Aa, or aa.
• The phenotype refers to the physical component of a gene. For example, for the trait of
  flower color the genotype would be AA, Aa, or aa but we would say that the phenotypes
  are red or white. The red color would be the dominant allele and would have the
  genotype AA or Aa. The white color would be the recessive allele and would have the
  genotype aa. The phenotype does not always directly reflect the genotype.

-Punnett Squares

• Punnett squares are used to help predict the possible genotypes when two organisms are
  crossed.
• A Punnett square has 4 boxes and each box represents a possible genotype of the
  offspring from the cross. The parents’ genotypes are written on the axes of the grid.

• A monohybrid cross only examines one trait while a dihybrid cross examines two
  traits.
• A monohybrid cross between two homozygous parents (AA x AA) will result all
  offspring having the genotype Aa.
• A monohybrid cross between two heterozygous parents (Aa x Aa) will result in a 1:2:1
  genotypic ratio (AA:Aa:aa) and a 3:1 genotypic ration (dominant:recessive).
• A monohybrid cross between a heterozygous parent and a homozygous parent (Aa x aa)
  will result in a 1:1 genotypic ratio (Aa:aa) and a 1:1 phenotypic ratio
  (dominant:recessive).
• A dihybrid cross between two heterozygous parents will result in a 9:3:3:1 phenotypic
  ration.

Genetic Inheritance

-Genetic Diversity

•  Genetic diversity is created by independent assortment but it can also be created by
  crossing over during meiosis. Crossing over is the exchange of small pieces of the
  chromosomes during prophase I. This occurs between the homologous pairs.
• Genes that are located close together on a chromosome have genetic linkage and tend to
  be inherited together. This means that during crossing over the two genes are not
  separated. If gene A and B are genetically linked then during crossing over if gene A is
  exchanged from one chromatid to the other then gene B will also be exchanged.

-Genetic Disorders

• Disorders caused by recessive alleles which means two copies of the recessive allele must
  be present for the person to have the disorder. Usually the parents are heterozygotes, or
  carriers, for the allele. This means they have one “good” allele and one “bad” allele and
  the good allele masks the effects of the bad allele.
• Disorders causes by dominant alleles occur when the disease is caused by the dominant
  allele.

-Sex-Linked Genes

• Sex-linked genes are genes located on the sex chromosome.
• In humans the female has two X chromosomes and the male has one X and one Y.
  Therefore women can only pass on an X chromosome to their offspring but men can pass
  on a X or a Y to their offspring.
• The Y chromosome is smaller than the X chromosome and has less genes.
• For a disease that is sex-linked on the X chromosome the male will express the disease if
  he inherits a bad X chromosome because there is no other X chromosome to mask the
  effect like in the case of a female.
• In women each individual cell only uses one of the X chromosomes and the other is
  turned off by X chromosome inactivation. In a calico female cat the mix of white, black,
  and orange fur occurs because of inactivation. Along the same lines this is why the male
  cat is only one color.

-Complex Patterns of Inheritance

• Sometimes one allele is not completely dominant over the other and inheritance can be by
  incomplete dominance. This causes the heterozygote to not phenotypically match the dominant homozygote. In complete dominance a dominant red flower crossed with a recessive white flower will have the genotypic ratio 1:2:1 (RR:Rr:rr) and the phenotypic ratio is 3:1 (red: white). In incomplete dominance a dominant red flower crossed with a recessive white flower the genotypic ratio remains the same but the phenotypic ratio changes to 1:2:1 (red:pink:white).
• In the case of codominance neither allele is dominant or recessive and both are expressed. The most common example is blood types. The three alleles are iA, iB, and i. The possible blood types are iAi, iBi, ii, and iAiB. Both A and B can be expressed at the same time.
• Some traits are not determined by one gene but are determined by multiple genes. These
  kinds of traits are called polygenic traits. An example of this is skin color.

DNA and Proteins

-Structure of DNA

• Nucleotides are the smallest unit of DNA. Each nucleotide consists of a phosphate group, a sugar, and a nitrogen containing base.
• The four bases of DNA are adenine (A), guanine (G), cytosine (C), and thymine (T). A and G are double-ring structures whereas C and T are single-ring structures.
• DNA forms a double helix structure where two strands of complementary DNA fit together. A pairs with T and C pairs with G. The complementary strand of ACGT would be TGCA.

-DNA Repliction

• DNA is copied by replication.
• An enzyme unzips the double helix. DNA polymerase adds nucleotides to the original two strands of DNA forming two new double helices. Each helix has one strand from the original helix and one new strand.

-Transcription

• Transcription is the process by which the DNA message is converted into RNA.
•  First the RNA polymerase recognizes the start of a gene and forms a complex with other proteins and begins to unwind a segment of the DNA. RNA polymerase then creates a complementary strand of RNA to the DNA it is reading except RNA uses uracil (U) instead of thymine (T). The DNA helix comes back together after being read. When the
  DNA strand is complete the RNA polymerase terminates transcription and the complex falls apart.
•  The RNA produced for making proteins is messenger RNA or mRNA.

-Translation

• Translation is the process by which the mRNA is converted into a polypeptide.
•  mRNA is translated into a polypeptide by reading the codons. A codon is a sequence of three nucleotides that codes for an amino acid. There are 20 amino acids that are coded for.
• Each codon attracts the complementary tRNA that contains the anticodon which is a set of three nucleotides that is complementary to the mRNA codon. For example a codon CGC would have the anticodon GCG.
• The start codon is always methionine (Met). There are three stop codons that signal for the termination of translation.
•  Translation occurs only when a ribosome is bound to the mRNA. The ribosomes job is to help form a peptide bond between the amino acids.

-Gene Expression and Regulation

• Transcription is controlled by promoters and operators.
•  Promoters are DNA segments that allow a gene to be transcribed. Operators are DNA segments that turn the gene on or off.
•  A promoter, operator, and structural genes together are known as an operon.
•  After mRNA is transcribed certain modifications occur. A cap is added to the start to help the mRNA strand bind to a ribosome. A tail of A nucleotides is added to help the mRNA exit the nucleus. Segments of the mRNA are sliced out. The exons are the portions that remain in the mRNA and the introns are the portions that are sliced out.

-Mutations

• A change in the DNA is a mutation.
• There are many different types of mutations.
• A mutation where one nucleotide is substituted for another is a point mutation. For example, ACGG with a point mutation would become ACGC. The G nucleotide at the end has been substituted with a C nucleotide.
• A mutation where a nucleotide is inserted or deleted is a frameshift mutation. For example, ACGG with a frameshift mutation would become ACG. The G nucleotide at the end has been deleted.
• Chromosomal mutations can occur during crossing over with homologous chromosomes during meiosis. If the chromosomes do not align with each other gene duplication can occur. This results in one chromosome having two copies of a gene. Translocation occurs when segments of a chromosome move to a nonhomologous chromosome.
• Agents that can change DNA are called mutagens.

Evolution

-Scientists Involved

• Evolution is the process of biological change that causes decedents to be different from their ancestors.
• Carolus Linnaeus developed a classification for organisms. The system grouped organisms by their similarities. He believed that organisms are not fixed and change over time.
• Georges Louis Leclerc de Buffon believed species shared ancestors instead of independently arising. He also believed the Earth was older than 6000 years old.
• Erasmus Darwin believed that all living things came from a common ancestor.
• Jean-Baptiste Lamarck believed that organisms evolved towards perfection as well as complexity. He believed that species do not become extinct but evolve to something else. Lamarck believed that organisms pass on beneficial traits to their offspring.

-Principles of Evolution

• An adaptation is a feature that allows an organism to better survive.
• A species is a group of organisms that can reproduce and produce fertile offspring.
• A population is a group of individuals of a species that live in an area.
• Artificial selection is the process by which humans change a species by breeding for a certain trait. Humans select the organisms with the best traits and breed them together.
• The ability of a trait to be passed down from one generation to the next generation is heritability.
• Natural selection is the process by which organisms with beneficial traits pass these traits to more offspring on average than other organisms.
• Natural selection only acts on the physical traits and not the genetic material itself. Mutation as well as recombination cause changes in the genetic material. Natural selection only acts on traits that already exist.
• Natural selection can exhibit a normal distribution where the phenotypes in the middle range are most likely to survive and reproduce and the phenotypes at the extremes are less likely to reproduce. Depending on the external pressures this normal distribution can be changed. Directional selection occurs when one extreme of the phenotypic range is favored. Stabilizing selection occurs when the middle range phenotypes are more common. Disruptive/diversifying selection occurs when both extreme phenotypes are favored.

• One common driving force in natural selection is changes in the environment. As the environment changes the beneficial traits change and only the best suited organisms will survive. For example, suppose a change in environment caused the large seeds to be scarce but the amount of soft small seeds to increase. The large-beaked birds would be most prevalent before the change because they have the beaks needed to crack open the large seeds. Now that the environment has changed there will be an increase in small-beaked birds because they have the beak needed to eat the small soft seeds.
• An organism’s fitness is its ability to survive and reproduce more offspring in comparison to other organisms in the population.
• Gene flow is the movement of alleles from one population to another. For example, when animals move between populations they cause gene flow.
• Genetic drift is the change in allele frequencies due to chance. Examples of genetic drift are the bottleneck effect and the founder effect. The bottleneck effect is when an event reduces the size of a population. For example, a large hurricane that wipes out a majority of a population of fish. The fish that are left do not represent the original alleles in the population. The founder effect occurs when a small number of individuals colonize a new area. The small population that moved does not have the same gene pool as the original population.
• Genetic drift limits the genetic variation of the population.
• Sexual selection occurs when the trait increases mating success.
• Genetic drift, gene flow, mutation, sexual selection, and natural selection can lead to evolution.

-Isolation

• Many types of isolation prevent populations from reproducing together.
• Reproductive isolation occurs when members of a population can no longer mate with each other.
• Behavioral isolation occurs when there are differences in mating or courtship behaviors between two organisms.
• Geographic isolation occurs when there are physical barriers that divide the population into two or more groups.
• Temporal isolation occurs when timing prevents reproduction between populations.

-Evidence foe Evolution

• Fossil evidence supports the claims made regarding evolution. The fossil record is incomplete but no fossil found has ever contradicted the theories of evolution.
• Analysis of DNA sequence is used to determine how similar two organisms are. The more similar the DNA the more related the two organisms are.
• Pseudogenes are pieces of DNA that are no longer function but are still passed from generation to generation. They provide a way to figure out evolutionary relationships.
• Homeobox genes are genes that control the development of specific structures. The sequences of genes can help relate organisms.
• Comparing the proteins found in different organisms can also help determine similarities among organisms.

-Origin of Life

• The solar system was formed by a condensing nebula. 4.6 billion years ago the Sun was formed from a nebula and over the next millions of years collisions of space debris formed the planets.
• Hypothesis of how life-supporting molecules appeared on Earth
  • Miller-Urey experiment: It was hypothesized that the formation of organic molecules from inorganic molecules present in the Earth’s atmosphere occurred from the input of energy from lightening. Miller and Urey tested this hypothesis by building a model system and passing an electric current through a mixture of methane, ammonia, hydrogen, and water vapor gas. Organic compounds such as amino acids were able to be formed.
  • Meteorite hypothesis: A meteorite found in 1969 in Murchison, Australia contained more than 90 amino acids. This suggested that amino acids could have been present when the Earth formed or from a meteorite impact on Earth.
• Hypothesis of how the first cells formed
  • Iron-sulfide bubbles hypothesis: Martin and Russell in the 1990s observed that hot iron sulfide rising from the ocean floor forms chimney structures with many compartments when combined with cool ocean water. This process was mimicked in a laboratory. It is proposed that 4 billion years ago biological molecules combined with the chimney compartments and acted as the first cell membranes.
  • Lipid membrane hypothesis: Lipid molecules make membrane-enclosed spheres called liposomes, spontaneously. It is proposed that at some point the liposome formed a bilayer membrane. The liposomes formed around organic compounds and formed a membrane like in cells today.
• Hypothesis of genetic material: This hypothesis is known as the RNA world hypothesis. It is proposed that the first genetic material in living things was RNA and not DNA. RNA molecules can catalyze specific reactions and their own replication and synthesis by using ribozymes. Eventually DNA replaced RNA because it is more stable and can store genetic information better.

-Evolution of Life

• Organisms on Earth started as single-celled organisms.
• The first prokaryotes were anaerobic and didn’t use oxygen.
• High levels of oxygen in the atmosphere allowed for aerobic prokaryotes to evolve.
• Eukaryotic evolution occurred by endosymbiosis where an early mitochondria was taken up by a larger prokaryote and was not digested because it helped the larger cell gain energy.
• The evolution of multicellular organisms occurred because the size of a single-cell is limited so in order for an organism to increase in size it must become multicellular. Large groups of cells began to depend on their neighbor cells and function as a colony.
• These multicellular organisms first appeared in the Paleozoic era (542 million years ago 251 million years ago).
• The Cambrian explosion occurred early in the Paleozoic era. During this time there was a large number of new animal species that evolved.
• During the Paleozoic era life moved from the ocean onto land.
• The Mesozoic era (251 million years ago-65 million years ago) was dominated by reptiles, birds, and flowering plants. This is the era in which the dinosaurs roamed the Earth.
• The Cenozoic era (65 million years ago- present) is when mammals evolved and diversified.
• The common ancestor of primates arose 65 million years ago. Primates are split into two main subgroups, prosimians and anthropoids. Prosimians are the older living primates. Anthropoids are humanlike primates and are divided into Old World monkeys, New World monkeys, and hominoids. Hominoids are divided into the lesser apes, the great apes, and the hominids. Hominids walk upright, have opposable thumbs, and relatively large brains. This group includes humans.

-Taxonomic Classification

• The science of naming and classifying animals is called taxonomy.
• The naming system used to today was created by Linnaeus.
• The classification system has many different levels: Kingdom, phylum, class, order, family, genus, and species.
• An organism is named using binomial nomenclature. Its name has to parts. It gives the genus and then species.

Ecology

-Definitions

• Ecology is the study of interactions of living things.
• The level of organization of nature is: organism, population, community, ecosystem, and biome.
• A community is a group of different species that live together in one area.
• An ecosystem is the community and the nonliving things in one area.
•  A biome is a regional community.
•  A biotic factor is any living thing in an ecosystem.
•  An abiotic factor is any nonliving thing in an ecosystem.
•  Biodiversity is the variety of living things in an ecosystem.
•  A species with a large effect on the ecosystem in which it lives is a keystone species.

-Energy in Ecosystems

• Organisms obtain their energy from many sources such as sunlight, plants, or other organisms.
•  Organisms that make their own food are known as producers or autotrophs.
•  Organisms that obtain their energy by eating living or once-living resources are known as consumers or heterotrophs.
•  The ecosystem depends on producers because they provide the energy for the ecosystem. Most producers use sunlight to make food by means of photosynthesis.
• Energy flow is tracked through an ecosystem by using a food chain. This chain shows the feeding relationship. For example, a chain might show energy flowing from grass to a rabbit to a hawk. The rabbit eats the grass and the hawk eats the rabbit.
•  Multiple feeding relationships shown together is a food web. This will show the feeding relationships in an ecosystem.
•  During each step of the food chain there is a loss of energy. When the rabbit eats grass it uses some of the energy to grow or for other things. This means when the hawk eats the rabbit there is less energy to obtain. The longer the chain the less energy there is for the
  final consumer to obtain.

-Matter in an Ecosystem

• The hydrologic cycle, or water cycle, is the movement of water through an ecosystem. Water in the atmosphere is transferred to the ground in the form of precipitation. Water is returned to the atmosphere by evaporation.
• A biogeochemical cycle is the movement of a chemical through an ecosystem.
• Oxygen is cycled through an ecosystem because plants release oxygen during photosynthesis and then organisms use this oxygen.
• The carbon cycle is the movement of carbon through an ecosystem. Carbon can be found as a solid, liquid, or gas. Plants use carbon dioxide for photosynthesis. The carbon is now incorporated into the plant. When an organism eats the plant it now contains the carbon. The carbon will now be passed from organism to organism as they eat one another. Carbon dioxide is returned back to the environment by respiration or by decomposition of dead organisms. Burning fossil fuels also releases carbon dioxide.
• The nitrogen cycle is the movement of nitrogen through an ecosystem. A majority of the nitrogen cycle occurs underground. Nitrogen fixation occurs when bacteria convert nitrogen as a gas into ammonia. Bacteria can then change this ammonia into ammonium and then into nitrate. Plants take up nitrates and convert them into organic compounds. Nitrogen will continue through the cycle as organisms eat plants and each other. Ammonification occurs when nitrogen is turned to ammonium in soil when decomposers break down animal excretions or dead animals.
• The phosphorus cycle is the movement of phosphorus through an ecosystem. There is no phosphorous in the atmosphere. Weathering rock can release phosphorous that is then taken up by plants. The phosphorous continues through the food web. Phosphorous is released from dead organisms through decomposers.

-Factors that Affect the Biosphere

• The biosphere is the region where life exists on Earth.
• Climate affects the biosphere through temperature, sunlight, water, and wind changes.
• The amount of direct sunlight determines the climate. The regions around the equator receive the most direct sunlight and have a warm tropical climate. The tilt of the Earth’s axis is what causes the seasons.
• The sunlight heats the water and the air causing movement. Warm air is less dense and rises. This air will then cool and condense and be released as precipitation. This is why the warm tropical areas receive lots of rain. The movement of air leads to the movement of water causing currents.
• Organisms must adapt to the climate where they live in order to survive.
• Humans have a large impact on the biosphere.
• Air pollution from the burning of fossil fuels can hurt an ecosystem. Burning fossil fuels can also lead to acid rain. Acid rain is precipitation with a lower pH than normal. Acid rain can pollute water supplies.
• Water pollution can also occur when toxic chemicals and debris is introduced into water sources.
• Introducing a species that is not native to the area can have a large impact on an ecosystem. This new species can interrupt the food web and the stability of the ecosystem.