Cellular Respiration, Photosynthesis, Cell Division & Reproduction, Genetics, DNA & Protein Synthesis, DNA Technology, and Evolution

Cellular Respiration

• A process where $O<em>2$ is consumed during the breakdown of organic molecules to $CO</em>2$ and $H_2O$, releasing energy.
• Occurs in three main stages.
• Not all cells need oxygen to produce energy, but all cells require a mechanism for producing ATP.

ATP (Adenosine Triphosphate)

• All cells require a mechanism for producing ATP.
• Cellular respiration banks energy in ATP molecules.
• Most of the ATP produced by cellular respiration is generated by oxidative phosphorylation.

Aerobic Conditions

• Cellular respiration explores how cells produce ATP in the presence of oxygen.
• Prokaryotic cells that use aerobic respiration have steps that occur in the cytosol, and the electron transport chain is built into the plasma membrane.

Anaerobic Conditions

• Cells can produce energy under anaerobic conditions, which is the absence of $O_2$.

Glucose

• Glycolysis begins cellular respiration by breaking glucose.
• Glucose is spoken of as the fuel for cellular respiration.
• The breakdown of glucose to pyruvate releases energy.

Kilocalories (kcal)

• Energy units used to measure the energy required for voluntary activities.
• The "Calories" listed on food packages are actually kilocalories.

Basal Metabolic Rate (BMR)

• The energy requirement for basic life-sustaining activities, which may range from 1,300 to 1,800 kcal a day.

Electron Transfer and Energy Release

• Understanding these is necessary to explore cellular respiration.

Oxygen ($O_2$)

• Required for cellular respiration and is supplied by breathing.
• Its characteristic is its extreme electronegativity, which is very powerful in pulling electrons down the electron transfer chain.
• Electrons are finally passed to oxygen, which becomes reduced to $H_2O$.

Stages of Cellular Respiration

• There are three main stages:
  • Stage 1: Glycolysis
    • Occurs in the cytosol of the cell.
    • Begins cellular respiration by breaking glucose into two molecules of pyruvate.
    • Glycolysis harvests chemical energy by oxidizing glucose to pyruvate.
    • During glycolysis, glucose is oxidized, and $NAD^+$ is reduced to NADH.
    • It produces a net gain of two molecules of ATP.
    • Glycolysis is considered an ancient metabolic pathway because it occurs universally, does not require oxygen, and does not occur in a membrane-enclosed organelle.
  • Stage 2: Pyruvate oxidation and the citric acid cycle
    • Take place within the mitochondria.
    • Together, they complete the breakdown of glucose to carbon dioxide.
    • Most of the $CO_2$ from cellular respiration is released during the citric acid cycle.
    • In this stage, pyruvate is further oxidized, producing additional NADH to be used in stage 3.
  • Stage 3: Oxidative phosphorylation
    • Occurs in the inner mitochondrial membrane.
    • Most of the ATP produced by cellular respiration is generated by oxidative phosphorylation.
    • It uses energy released by redox reactions in the electron transport chain to make ATP.
    • Oxidative phosphorylation involves the flow of both electrons and $H^+$.

Electron Transport Chain

• Electrons from NADH must pass down an electron transport chain located in the inner mitochondrial membrane.
• Energy is released as electrons fall down an energy staircase from NADH through an electron transport chain to $O_2$.
• The electron transport chain pumps hydrogen ions ($H^+$) across the inner mitochondrial membrane into the intermembrane space.

Chemiosmosis

• The potential energy of the $H^+$ concentration gradient across the inner mitochondrial membrane is used to make ATP.
• This couples the electron transport chain to ATP synthesis.

NAD+ / NADH

• In glycolysis, $NAD^+$ is reduced to NADH.
• The energy in NADH can be used when its electrons pass down an electron transport chain.
• Your body makes $NAD^+$ from niacin, a B vitamin.

FAD

• Your body makes FAD from riboflavin, a B vitamin.

Pyruvate

• Glucose is broken into two molecules of pyruvate during glycolysis.
• Pyruvate still possesses about 90% of the energy available from glucose.

Carbon Dioxide ($CO_2$)

• The $CO_2$ you exhale is generated in the mitochondria during the second stage of respiration.
• Breathing removes $CO_2$.

Water ($H_2O$)

• Oxygen becomes reduced to $H_2O$ in oxidative phosphorylation.

Organic Molecules as Fuel

• Cells use many kinds of organic molecules, besides glucose, as fuel, including carbohydrates (sucrose, starch, glycogen), fats, and proteins.
• These can be funneled into glycolysis.

Metabolic Pathways

• There are connections between energy-harvesting pathways (cellular respiration) and biosynthetic pathways used to construct organic molecules.
• Excess carbohydrates can be converted to fats using metabolic pathways.

Glyceraldehyde 3-Phosphate (G3P)

• Intermediate molecule used to make fat.

Acetyl CoA

• Intermediate molecule used to make fat.

Photosynthesis

• Uses solar energy to produce organic molecules and $O<em>2$ from $CO</em>2$ and $H_2O$.
• It is not a single process, but two linked processes.
• The word means "light" (photo) and "putting together" (synthesis).
• Photosynthesis occurs in chloroplasts in plant cells.
• Photosynthesis provides food and $O_2$ for almost all living organisms.
• It taps into the energy of the sun.

Chloroplasts

• The actual site of photosynthesis in plant cells.
• They are concentrated in the mesophyll tissue of the leaf.
• Chloroplasts have an envelope of two membranes enclosing an inner compartment called the stroma.
• Suspended in the stroma is a system of interconnected membranous sacs called thylakoids.

Mesophyll

• The green tissue in the interior of the leaf where chloroplasts are concentrated.

Stomata (singular: stoma)

• Tiny pores on leaves through which $CO<em>2$ enters and $O</em>2$ exits.

Veins

• Deliver water absorbed by roots to the leaves and export manufactured sugar to other parts of the plant.

Chlorophyll

• A light-absorbing pigment in chloroplasts that plays a central role in converting solar energy to chemical energy.
• Built into the thylakoid membranes, pigments absorb some wavelengths of light and reflect others.

Thylakoids

• Interconnected membranous sacs suspended in the stroma of a chloroplast.
• They enclose an internal compartment called the thylakoid space.
• Thylakoids are concentrated in stacks called grana.
• Chlorophyll molecules are built into the thylakoid membranes.
• The light reactions occur in the thylakoid membranes.

Grana (singular: granum)

• Stacks of thylakoids.

Stroma

• A thick fluid filling the inner compartment of a chloroplast.
• The Calvin cycle occurs in the stroma.

Electromagnetic Energy/Radiation

• Sunlight is a type of energy called electromagnetic energy.

Wavelength

• The distance between the crests of electromagnetic waves.

Electromagnetic Spectrum

• The full range of electromagnetic wavelengths.

Visible Light

• A small fraction of the electromagnetic spectrum, consisting of wavelengths from about 380 nm to about 750 nm.

Photons

• Discrete packets of energy that light also behaves as.
• A photon has a fixed quantity of energy; shorter wavelengths have greater energy photons.

Pigments

• Light-absorbing molecules built into the thylakoid membranes.
• They absorb some wavelengths and reflect or transmit others.

Two Stages of Photosynthesis

• Linked by ATP and NADPH.
  • Light Reactions
    • Referred to by the "Photo" part of photosynthesis.
    • They occur in the thylakoid membranes.
    • Light energy is converted to chemical energy.
    • They capture solar energy, energizing electrons in chlorophyll.
    • Water is split, $O_2$ is released, and electrons are funneled to photosystem II.
    • Photoexcited electrons are transferred through an electron transport chain, where energy is harvested to make ATP by chemiosmosis and reduce $NADP^+$ to NADPH.
    • They produce ATP and NADPH.
  • Calvin Cycle
    • Referred to by the "Synthesis" part of photosynthesis.
    • It occurs in the stroma of the chloroplast.
    • It is a cyclic series of reactions that assembles sugar molecules using $CO_2$ and the energy-rich products from the light reactions (ATP and NADPH).
    • The Calvin cycle reduces $CO_2$ to sugar.
    • ATP is used as an energy source, and NADPH provides high-energy electrons for reducing $CO_2$ to sugar.
    • The output is an energy-rich, three-carbon sugar, glyceraldehyde 3-phosphate (G3P).

ATP and NADPH

• Both are generated by the light reactions.
• They link the two stages of photosynthesis.
• They power sugar synthesis in the Calvin cycle.

Glyceraldehyde 3-Phosphate (G3P)

• The output of the Calvin cycle.
• A plant cell uses G3P to make glucose, sucrose, and other organic molecules.

Chemiosmosis

• Energy is harvested to make ATP by this process in the light reactions.
• As electrons are transferred down the electron transport chain, energy is released and used to pump $H^+$ across the thylakoid membrane into the thylakoid space.
• The concentration gradient of $H^+$ drives $H^+$ through ATP synthase to produce ATP.

Autotrophs

• Organisms that make their own food.
• Photoautotrophs are producers of food consumed by virtually all heterotrophic organisms.

Heterotrophs

• Organisms that cannot make their own food and are dependent on organic matter made by photosynthesizers.
• Humans and other animals are heterotrophs.

Starch

• Plants store excess sugar as starch.

Cellulose

• Glucose molecules are linked together to make cellulose, the main component of cell walls.

Carbon Sequestration

• Expanding forests can help mitigate climate change by sucking $CO_2$ out of the atmosphere and storing it in biomass.

Greenhouse Effect

• Warming of the Earth's surface, where Earth radiates heat to the atmosphere, and $CO_2$ and other gases absorb and reradiate some heat back to Earth.

Cell Division & Reproduction

• Cell division is necessary to all forms of life.
• It plays many important roles in the lives of organisms.
• Cell division is at the heart of the reproduction of cells and organisms.
• It allows for growth, replacement of damaged cells, development, and the formation of eggs and sperm in multicellular organisms.
• Cells originate only from preexisting cells.

Reproduction

• The ability to transmit genetic information is necessary for reproduction.
• Cell division results in reproduction.

Genetic Information

• Each species carries and transmits its own specific genetic information at the cellular level.
• DNA is the form of genetic information in chromosomes.

Chromosomes

• Structures that contain most of the cell's genetic information in the form of DNA.
• Eukaryotic chromosomes consist of one long DNA molecule bearing genes and protein molecules.
• Before cell division, a cell duplicates its chromosomes.
• Individual eukaryotic chromosomes are visible only when the cell is dividing; otherwise, they are thin, loosely packed chromatin fibers.

Asexual Reproduction

• One simple principle of inheritance: the lone parent and each of its offspring have identical genes.
• Offspring are genetic copies of the parent and identical to each other (clones).

Sexual Reproduction

• Requires the fusion of gametes (egg and sperm).
• The production of gametes involves a particular type of cell division that occurs only in reproductive organs.
• Gametes have half as many chromosomes as the parent cell and contain unique combinations of genes.
• It creates a variety of offspring.

Gametes

• Egg and sperm cells produced during sexual reproduction.

Mitosis

• A type of cell division mentioned as occurring in eukaryotic cells.
• Mitosis is unique to eukaryotes and allocates an identical copy of the whole set of chromosomes to two daughter cells.
• Mitotic cell division ensures that all body cells receive copies of the original set of chromosomes.
• It is part of the mitotic phase of the cell cycle.
• The stages of mitosis can be guided by visible changes in chromosomes.

Meiosis

• A type of cell division involved in the production of gametes.
• Meiosis is preceded by interphase, during which chromosomes duplicate.
• Meiosis I involves the separation of homologous chromosomes.

Daughter Cells

• The two cells that result from cell division.
• They are genetically identical to each other and the parent cell after asexual reproduction.

Parent Cell

• The original cell that splits into two daughter cells.

DNA (Deoxyribonucleic Acid)

• Contains the cell's genetic information.
• The DNA molecule of each chromosome is replicated before the cell divides.

Proteins

• Protein molecules are attached to DNA in chromosomes, helping maintain structure and control gene activity.

Chromatin

• The entire complex consisting of roughly equal amounts of DNA and protein in eukaryotic chromosomes.
• Most of the time, it exists as a diffuse mass of long, thin fibers.
• As a cell prepares to divide, chromatin coils up, forming distinct chromosomes.

Sister Chromatids

• Duplicated chromosomes consist of two copies called sister chromatids, joined copies of the original chromosome.
• They are attached along their lengths by proteins.
• In meiosis I, sister chromatids remain attached.

Centromere

• A region where the two sister chromatids are most closely attached.

Cell Cycle

• An ordered sequence of events from the formation of a cell from a parent cell to its own division.
• It consists of interphase and the mitotic phase.

Interphase

• The growing stage of the cell cycle, lasting at least 90% of the total time.
• The cell's metabolic activity is high, it performs normal functions, grows, and duplicates its chromosomes.
• Meiosis is preceded by an interphase where chromosomes duplicate.

Mitotic Phase (M phase)

• The actual cell division stage.
• It includes mitosis and cytokinesis.

Cytokinesis

• Division of the cytoplasm, part of the mitotic phase.

Homologous Chromosomes

• Pairs of chromosomes in a diploid cell.
• Meiosis I separates homologous chromosomes.

Genetic Variability

• Results from sexual reproduction.

Crossing Over

• Exchange of chromosome segments between nonsister chromatids during prophase I of meiosis.
• This shuffles genes and contributes to genetic variability.

Karyotype

• An arrangement of chromosomes from a single diploid cell, typically used to detect chromosomal abnormalities.
• To prepare one, cells are treated to stimulate and then arrest mitosis at metaphase.

Diploid Cell

• A cell with 46 chromosomes in humans.
• Karyotypes arrange chromosomes from a single diploid cell in homologous pairs.

Autosomes

• Homologous pairs of chromosomes numbered from 1 to 22 in a human karyotype.
• Unusual numbers of autosomes seem to upset the genetic balance more than unusual numbers of sex chromosomes.

Sex Chromosomes

• The pair of chromosomes (X and Y in males) that determine sex.
• Unusual numbers of sex chromosomes may result from multiple nondisjunctions.

Trisomy 21

• A chromosomal abnormality, the basis of Down syndrome, detectable by karyotyping.
• It involves having an extra copy of chromosome 21.
• Extra copies of other chromosomes are probably fatal, which is why Trisomy 21 individuals are more numerous than those with extra copies of other chromosomes like 3 or 16.

Down Syndrome

• A condition resulting from trisomy 21.

Klinefelter Syndrome

• Caused by an extra X chromosome in a male (XXY), leading to abnormally small testes, sterility, subnormal intelligence, and potentially female body characteristics.

Nondisjunction

• An error in cell division that can lead to unusual numbers of sex chromosomes or polyploid organisms (with extra sets of chromosomes).

Alterations of Chromosome Structure

• Chromosome breakage can lead to rearrangements:
  • Deletion: A segment of a chromosome is removed.
  • Duplication: A segment of a chromosome is copied and inserted into the homologous chromosome.
  • Inversion: A segment of a chromosome is removed and then reinserted opposite to its original orientation.
  • Reciprocal translocation: Segments of two nonhomologous chromosomes swap locations. An example is associated with chronic myelogenous leukemia.

Binary Fission

• How prokaryotic cells reproduce asexually.
• As the single chromosome replicates, copies move apart, and the growing membrane divides the cell.

Cancer

• Occurs when control of cell division is lost.
• Cancerous cells are not subject to anchorage dependence and density-dependent inhibition.
• Chromosome rearrangements in somatic cells can cause cancer.

Genetics

• Inherited traits: Traits passed from parents to offspring.
• Genes: Located on chromosomes. Genes control phenotypic traits through the expression of proteins. A gene dispatches instructions in the form of RNA, which programs protein synthesis. A gene is a region of DNA that can be expressed to produce a functional product that is either a polypeptide or an RNA molecule.
• Alleles: Different versions of a gene. An organism inherits two alleles of a gene, one from each parent.
• Homozygous: An organism with two identical alleles for a gene.
• Heterozygous: An organism with two different alleles for a gene.
• Dominant allele: If two alleles differ, the dominant one determines the organism's appearance. Represented by uppercase italic letters. A single copy of a dominant allele will produce its trait.
• Recessive allele: If two alleles differ, the recessive one has no noticeable effect on appearance. Represented by lowercase italic letters. Two copies of a recessive allele are required to produce its trait.
• Genotype: An organism's genetic makeup; the heritable information contained in the sequence of nucleotide bases in DNA.
• Phenotype: The organism's physical traits. Proteins are the links between genotype and phenotype.
• P, F1, F2 generations: Terminology used in genetic crosses.

Genetic Testing / Screening

• Technologies available for detecting genetic conditions.
• Can inform decisions about family planning.

Amniocentesis

• A procedure typically performed between weeks 14 and 16 of pregnancy to collect amniotic fluid containing fetal cells for karyotyping and biochemical tests.
• It carries a risk of miscarriage.

Chorionic Villus Sampling (CVS)

• A procedure to extract a tiny sample of chorionic villus tissue from the placenta.
• Results can be available within 24 hours and it can be performed earlier than amniocentesis (weeks 10-12, or as early as 8).
• The primary benefit is that it allows genetic screening to be performed earlier.
• The primary risk is that it carries a risk of miscarriage.

Newborn Screening

• Simple tests routinely performed at birth to detect some genetic disorders, such as phenylketonuria (PKU).

Phenylketonuria (PKU)

• A recessively inherited disorder where individuals cannot properly break down phenylalanine, which can lead to developmental disabilities if untreated.
• A special diet low in phenylalanine can usually prevent symptoms.
• Newborns are routinely screened for PKU.

Ethical Considerations in Genetic Testing

• Issues include confidentiality, potential stigmatization of carriers, access to information by employers or insurance companies, government genetic files, obligation to warn relatives, and the possibility of people avoiding or being compelled to be tested.
• Counseling is stressed for patients seeking genetic testing.

DNA and Protein Synthesis

• Nucleic acid: DNA and RNA are nucleic acids and serve as the molecule of heredity.

DNA (Deoxyribonucleic Acid)

• The molecule of heredity.
• It is a polymer of nucleotides.
• DNA is located in the nuclei of eukaryotic cells.
• The genetic information in a chromosome is encoded in the nucleotide sequence of DNA.
• DNA serves as a template for transcription.

RNA (Ribonucleic Acid)

• A nucleic acid.
• It is a polymer of nucleotides.
• RNA is the bridge between DNA and protein synthesis.
• RNA is transcribed from DNA.

Nucleotides

• The monomers that make up DNA and RNA.
• Each nucleotide contains a phosphate group, a sugar, and a nitrogenous base.

Phosphate Group

• A component of a nucleotide, with a phosphorus atom and four oxygen atoms.
• Gives DNA and RNA their acidic nature.
• Forms the sugar-phosphate backbone.

Sugar

• A component of a nucleotide. It has five carbon atoms.

Deoxyribose

• The sugar in DNA. It is missing an oxygen atom compared to ribose.

Ribose

• The sugar in RNA.

Nitrogenous Base

• A component of a nucleotide.
• DNA contains Adenine (A), Guanine (G), Cytosine (C), and Thymine (T).
• RNA contains Adenine (A), Guanine (G), Cytosine (C), and Uracil (U) instead of Thymine.
• The chemical groups of the bases are responsible for specific base pairing.

Pyrimidines

• Single-ring nitrogenous bases: Thymine (T), Cytosine (C), and Uracil (U).

Purines

• Larger, double-ring nitrogenous bases: Adenine (A) and Guanine (G).

Polynucleotide

• A polymer of nucleotides.
• DNA is typically a double-stranded polynucleotide.
• An RNA molecule is typically a single-stranded polynucleotide chain.

Double Helix

• The structure of DNA, consisting of two polynucleotide strands.
• The two strands are held together by hydrogen bonds between the bases.

Sugar-Phosphate Backbone

• Formed by covalent bonds joining the nucleotides in a polynucleotide chain.
• The two sugar-phosphate backbones in a DNA double helix run in opposite directions.

Antiparallel Strands

• The two strands of a DNA double helix run in opposite directions, with one strand oriented 5' to 3' and the other 3' to 5'.

3' End and 5' End

• Refer to the carbon atoms of the nucleotide sugars.
• At one end of a DNA strand, the sugar's 3' carbon is attached to an -OH group; at the other end, the sugar's 5' carbon is attached to a phosphate group.

DNA Replication

• The process by which the DNA molecule is replicated.
• Proceeds in two directions at many sites simultaneously.

DNA Polymerases

• Enzymes that link DNA nucleotides to a growing daughter strand during DNA replication.
• They are also involved in repairing damaged DNA.

DNA Ligase

• An enzyme that connects the short pieces of the lagging strand during DNA replication.
• Also involved in repairing damaged DNA.

Gene Expression

• The process by which the information in a gene is used to produce a functional product (protein or RNA).
• Genes control phenotypic traits through gene expression.

Central Dogma

• The molecular "chain of command" from DNA to RNA to protein synthesis.
• Information flows as DNA -> RNA -> protein.

Transcription

• The synthesis of RNA under the direction of DNA.
• It is the transfer of information from DNA to RNA.
• Occurs in the nucleus in eukaryotic cells and the cytoplasm in prokaryotes.
• Uses RNA polymerase.

Translation

• The synthesis of protein under the direction of RNA.
• It is the use of information in RNA to produce a polypeptide.
• Occurs in the cytoplasm.
• Requires mRNA, tRNA, amino acids, enzymes, ATP, and ribosomes.
• It can be divided into initiation, elongation, and termination phases.

RNA Polymerase

• An enzyme that joins RNA nucleotides along one strand of the DNA template during transcription.
• It binds to a promoter sequence on DNA.

Promoter

• The binding site for RNA polymerase on DNA, marking the start of a gene.

Terminator

• A sequence of bases on DNA that marks the end of a gene.

Codons

• Nonoverlapping three-base "words" that make up the genetic instructions for amino acid sequence.
• Codons are found in DNA and RNA.
• Codons in RNA are translated into amino acids.
• 61 of 64 triplets code for amino acids.

Triplet Code

• The flow of information from gene to protein is based on a triplet code.

Start Codon

• A specific codon (AUG) on mRNA that signals where translation is to begin.
• It also codes for methionine.

Stop Codons

• Three codons (UAA, UGA, UAG) that do not designate amino acids but mark the end of translation.

Genetic Code

• The set of rules that dictates how codons are translated into amino acids.
• It is nearly universal among organisms.
• There is redundancy (more than one codon for an amino acid) but no ambiguity (no codon represents more than one amino acid).

mRNA (Messenger RNA)

• Produced by transcription from a DNA template.
• It carries the genetic message from DNA to the ribosomes.
• Eukaryotic mRNA is processed before leaving the nucleus.

RNA Processing

• In eukaryotes, RNA transcribed from genes is processed before leaving the nucleus.

Introns

• Noncoding segments of RNA that are spliced out during RNA processing in eukaryotes.
• Eukaryotic genes are longer than the mRNA that leaves the nucleus because they contain introns.

Exons

• The parts of eukaryotic RNA that are spliced together to form the final mRNA.

Cap and Tail

• Added to the ends of eukaryotic mRNA during processing.

tRNA (Transfer RNA)

• Molecules that serve as interpreters during translation.
• They transfer amino acids from the cytoplasm to a growing polypeptide in a ribosome.
• A tRNA molecule is made from a single strand of RNA.
• Each tRNA carries a specific amino acid.

Anticodon

• A special triplet of bases at one end of a tRNA molecule.
• It is complementary to a codon triplet on mRNA and recognizes the appropriate codon by base-pairing rules during translation.
• It couples the tRNA to the complementary codon in the mRNA.

Amino Acids

• The monomers that compose polypeptides.
• There are 20 different kinds.
• Each amino acid is joined to the correct tRNA by a specific enzyme and ATP.

Polypeptide

• A polymer of amino acids.
• Ribosomes build polypeptides.
• Proteins are formed from polypeptides.
• The sequence of codons in DNA, via mRNA, spells out the primary structure of a polypeptide.

Ribosomes

• Structures in the cytoplasm that coordinate mRNA and tRNA function and catalyze polypeptide synthesis.
• They consist of a large and small subunit, each made of proteins and rRNA.
• Ribosomes have binding sites for mRNA and tRNA (P site and A site).
• They hold tRNA and mRNA together, allowing amino acids to be connected into a polypeptide chain.

rRNA (Ribosomal RNA)

• A kind of RNA that makes up ribosomal subunits along with proteins.

P Site

• A tRNA binding site on the ribosome that holds the growing polypeptide.

A Site

• A tRNA binding site on the ribosome where the next tRNA arrives with its amino acid.

Initiation (of translation)

• Brings together the mRNA, the first tRNA (carrying methionine), and the ribosomal subunits.
• Establishes where translation begins.

Elongation (of translation)

• Successive tRNAs add their amino acids to the polypeptide chain as mRNA moves through the ribosome.

Termination (of translation)

• The ribosome recognizes a stop codon, the polypeptide is terminated and released.

Mutations

• Changes in the genetic information of a cell or virus.
• Caused by errors in DNA replication or recombination, or by mutagens.
• Can affect genes.
  • Substitutions, Insertions, Deletions: Types of mutations that alter a gene with varying effects. Substitution of one nucleotide can result in no effect on the polypeptide encoded by a gene.

Viruses

• Nonliving entities that infect cells.
• Can reprogram host cells to produce more viruses by injecting their DNA.
• Some viruses have RNA genomes.

Phages (Bacteriophages)

• Bacterial viruses.
• Phage T2 infects E. coli.
• Phages inject their DNA into the bacterium.

Retrovirus

• A virus that makes DNA on an RNA template.
• HIV is a retrovirus.

Reverse Transcriptase

• An enzyme carried by retroviruses like HIV that uses its RNA genome as a template for making DNA.
• This enzyme is critical to producing cDNAs from mRNA.

Prions

• Infectious proteins that can cause brain diseases in animals.
• Not destroyed by normal cooking temperatures.

DNA Technology

• Methods for studying and manipulating genetic material.
• Can save lives.

Gene Cloning

• A method to produce multiple copies of a gene of interest.

Recombinant DNA

• DNA from different sources combined together.

Restriction Enzymes

• Enzymes used to "cut" DNA at specific nucleotide sequences.
• They cut both strands of the DNA double helix.

Vectors

• Carriers used to insert genes into other organisms.
• Bacterial plasmids can serve as carriers for gene transfer.

Plasmids

• Small, circular DNA molecules separate from the bacterial chromosome.
• Used in gene cloning.

E. coli

• A bacterium often used in gene cloning and engineering to produce proteins like human insulin or human growth hormone.
• Plasmid isolated from E. coli can be a vector.

cDNA (Complementary DNA)

• A DNA strand synthesized from eukaryotic mRNA using reverse transcriptase.
• cDNA is useful for studying genes responsible for specialized functions of a particular cell type.
• Production requires a viral enzyme, reverse transcriptase, because most cells lack such an enzyme to produce DNA from RNA.

PCR (Polymerase Chain Reaction)

• A technique used to amplify (make many copies of) a specific target segment of DNA.
• Only miniscule amounts of DNA are needed, and it can be partially degraded.
• PCR is highly sensitive due to the use of primers that bind only to the target sequences.
• It is widely used in research and biotechnology.

DNA Profiling

• Analysis of genetic markers to determine whether two samples of DNA come from the same individual.

DNA Sequencing

• Determining the nucleotide sequence of DNA.
• Next-generation and third-generation sequencing machines can determine the sequence of stretches of DNA.

Genomics

• The scientific study of whole genomes.
• Genomics researchers have sequenced many prokaryotic and eukaryotic genomes.

Human Genome Project

• Determined the nucleotide sequences of human genes and identified many encoded proteins.
• Revealed that most of the human genome does not consist of genes but includes a large amount of noncoding and repetitive DNA.

Genetically Modified Organisms (GMOs)

• Organisms that have had genes inserted into them.
• Use raises questions and concerns about risks to human and environmental health.
• A transgenic organism is one that has been genetically engineered to contain genes from another species.

Gene Therapy

• Changing a defective gene to a normal one in a living human.
• Shows promise but actual successes are rare.
• Potential future option for treating inherited disorders.
• Raises serious ethical issues.

Evolution

• Understanding evolution informs all of biology.
• The origin of species is the source of biological diversity.

Descent with Modification

• Darwin's theory that explains that all life is connected by common ancestry and that descendants have accumulated adaptations to changing environments over vast spans of time.

Natural Selection

• The mechanism for evolution that Darwin proposed.
• Occurs through interactions between individual organisms and the environment.
• It can amplify or diminish only heritable traits.
• It is sometimes described as "survival of the fittest," but fitness is best measured by how many fertile offspring an organism produces.
• It leads to adaptive evolution.

Fossil Record

• Provides strong evidence for evolution.
• Reveals the historical sequence in which organisms have evolved.
• Many fossils are found in sedimentary rocks.

Sedimentary Rocks

• Formed from layers of sand or mud that settle and are compressed.

Strata (singular: stratum)

• Layers of sedimentary rock.
• Younger strata are on top of older ones, allowing relative ages of fossils to be determined by the layer they are found in.

Transitional Forms

• Fossils of transitional forms support Darwin's theory.
• Speciation in a small, isolated population or in a relatively short time may make them difficult to find in the fossil record.

Homologies

• Similarities that provide strong evidence for evolution.
• They indicate patterns of descent.
  • Structural homologies: Similarities in body structures, such as the forelimbs of humans and whales. Comparing early stages of development in different species can reveal homologies not