Margins Study Assistant

Chapter 1

Introduction to Biology

Summary

Living things are highly organized following a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. A diagram called a phylogenetic tree can be used to show evolutionary relationships among organisms. Biology is the science that studies living organisms and their interactions with one another and their environments. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere.

Key terms

phylogenetic tree: a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both
science: knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method
evolution: the process of gradual change in a population that can also lead to new species arising from older species
ecosystem: all living things in a particular area together with the abiotic, nonliving parts of that environment
molecule: a chemical structure consisting of at least two atoms held together by a chemical bond
atom: a basic unit of matter that cannot be broken down by normal chemical reactions
organ: a structure formed of tissues operating together to perform a common function

Chapter 2

Chemistry of Life

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Summary

Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can be donated or shared between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions It is polar, allowing for the formation of hydrogen bonds, which allow ions and other polar molecules to dissolve in water. It is made up of atoms of different elements.

Key terms

electron: a negatively charged particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a charge of -1
element: one of 118 unique substances that cannot be broken down into smaller substances and retain the characteristic of that substance; each element has a specified number of protons…
van der Waals interaction: a weak attraction or interaction between molecules caused by slightly positively charged or slightly negatively charged atoms
hydrogen bond: a weak bond between partially positively charged hydrogen atoms and partially negatively charged elements or molecules
ion: an atom or compound that does not contain equal numbers of protons and electrons, and therefore has a net charge
proton: a positively charged particle that resides in the nucleus of an atom; has a mass of 1 and a charge of +1
neutron: a particle with no charge that resides in the nucleus of an atom; has a mass of 1
solvent: a substance capable of dissolving another substance

Chapter 3

Cell Structure and Function

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Summary

All prokaryotes have plasma membranes, cytoplasm, ribosomes, a cell wall, DNA, and lack membrane-bound organelles. Therefore, scientists must use microscopes to study cells. The unified cell theory states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells

Key terms

cell: the smallest unit of life
unified cell theory: the biological concept that states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells
cell wall: a rigid cell covering made of cellulose in plants, peptidoglycan in bacteria, non-peptidoglycan compounds in Archaea, and chitin in fungi that protects the cell, provides…
cytoplasm: the entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals
plasma membrane: a phospholipid bilayer with embedded (integral) or attached (peripheral) proteins that separates the internal contents of the cell from its surrounding environment
ribosome: a cellular structure that carries out protein synthesis
organelle: a membrane-bound compartment or sac within a cell
microscope: the instrument that magnifies an object

Chapter 4

How Cells Obtain Energy

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Summary

The physical laws that describe the transfer of energy are the laws of thermodynamics. A cell’s metabolism refers to the combination of chemical reactions that take place within it. Catabolic reactions break down complex chemicals into simpler ones and are associated with energy release. Anabolic processes build complex molecules out of simpler ones and require energy

Key terms

catabolic: describes the pathway in which complex molecules are broken down into simpler ones, yielding energy as an additional product of the reaction
metabolism: all the chemical reactions that take place inside cells, including those that use energy and those that release energy
anabolic: describes the pathway that requires a net energy input to synthesize complex molecules from simpler ones
thermodynamics: the science of the relationships between heat, energy, and work
transfer of energy: the laws of thermodynamics
acetyl CoA: the combination of an acetyl group derived from pyruvic acid and coenzyme A which is made from pantothenic acid (a B-group vitamin)
citric acid cycle: a series of enzyme-catalyzed chemical reactions of central importance in all living cells that harvests the energy in carbon-carbon bonds of sugar molecules to generate ATP; the…
competitive inhibition: a general mechanism of enzyme activity regulation in which a molecule other than the enzyme’s substrate is able to bind the active site and prevent the substrate itself from…

Chapter 5

Photosynthesis

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Summary

The most common and abundant pigment is chlorophyll a . Only certain organisms, called autotrophs, can perform photosynthesis; they require the presence of chlorophyll, a specialized pigment that can absorb light and convert light energy into chemical energy. Eukaryotic autotrophs, such as plants and algae, have organelles called chloroplasts in which photosynthesis takes place In the first part of photosynthesis, the light-dependent reaction, pigment molecules absorb energy from sunlight.

Key terms

light-dependent reaction: the first stage of photosynthesis where visible light is absorbed to form two energy-carrying molecules (ATP and NADPH)
pigment: a molecule that is capable of absorbing light energy
chlorophyll: the green pigment that captures the light energy that drives the reactions of photosynthesis
chlorophyll a: the form of chlorophyll that absorbs violet-blue and red light
chloroplast: the organelle where photosynthesis takes place
autotroph: an organism capable of producing its own food

Chapter 6

Reproduction at the Cellular Level

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Summary

An organism’s traits are determined in large part by the genes inherited from each parent, but also by the environment that they experience. Human somatic cells have 46 chromosomes consisting of two sets of 22 homologous chromosomes and a pair of nonhomologous sex chromosomes. Human gametes have 23 chromosomes or one complete set of chromosomes. Genes are segments of DNA that code for a specific protein or RNA molecule.

Key terms

homologous chromosomes: chromosomes of the same length with genes in the same location; diploid organisms have pairs of homologous chromosomes, and the members of each pair come from different parents
organism’s traits: determined in large part by the genes inherited from each parent, but also by the environment that they experience
gene: the physical and functional unit of heredity; a sequence of DNA that codes for a specific peptide or RNA molecule
cell cycle: the ordered sequence of events that a cell passes through between one cell division and the next
gamete: a haploid reproductive cell or sex cell (sperm or egg)
FtsZ: a tubulin-like protein component of the prokaryotic cytoskeleton that is important in prokaryotic cytokinesis (name origin: F ilamenting t emperature- s ensitive mutant Z )
mitosis: the period of the cell cycle at which the duplicated chromosomes are separated into identical nuclei; includes prophase, prometaphase, metaphase, anaphase, and telophase
mitotic phase: the period of the cell cycle when duplicated chromosomes are distributed into two nuclei and the cytoplasmic contents are divided; includes mitosis and cytokinesis

Chapter 7

The Cellular Basis of Inheritance

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Summary

There are three main categories of life cycles: diploid-dominant, demonstrated by most animals; haploid-dominant, demonstrated by all fungi and some algae; and alternation of generations, demonstrated by plants and… Meiosis and fertilization alternate in sexual life cycles. However, the ways in which reproductive cells are produced and the timing between meiosis and fertilization vary greatly. The variation introduced into the reproductive cells by meiosis appears to be one of the advantages of sexual reproduction that has made it so successful.

Key terms

diploid-dominant: a life-cycle type in which the multicellular diploid stage is prevalent
haploid-dominant: a life-cycle type in which the multicellular haploid stage is prevalent
life cycle: the sequence of events in the development of an organism and the production of cells that produce offspring
fertilization: the union of two haploid cells typically from two individual organisms
alternation of generations: a life-cycle type in which the diploid and haploid stages alternate
meiosis: a nuclear division process that results in four haploid cells
meiosis II: the second round of meiotic cell division following meiosis I; sister chromatids are separated from each other, and the result is four unique haploid cells

Chapter 8

Patterns of Inheritance

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Summary

If the traits are inherited as dominant and recessive, the F 1 offspring will all exhibit the same phenotype as the parent homozygous for the dominant trait. The traits that were visible in the F 1 generation are referred to as dominant, and traits that disappear in the F 1 generation are described as recessive. When the F 1 plants in Mendel’s experiment were self-crossed, the F 2 offspring exhibited the dominant trait or the recessive trait in a 3:1 ratio, confirming that the recessive trait had been transmitted faithfully… If these heterozygous offspring are self-crossed, the resulting F 2 offspring will be equally likely to inherit gametes carrying the dominant or recessive trait, giving rise to offspring of which one quarter are…

Key terms

dominant: describes a trait that masks the expression of another trait when both versions of the gene are present in an individual
recessive: describes a trait whose expression is masked by another trait when the alleles for both traits are present in an individual
F 2: the second filial generation produced when F 1 individuals are self-crossed or fertilized with each other
reciprocal cross: a paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross
traits: inherited as dominant and recessive, the F 1 offspring will all exhibit the same phenotype as the parent homozygous for the dominant trait
F 1: the first filial generation in a cross; the offspring of the parental generation
heterozygous: having two different alleles for a given gene on the homologous chromosomes
homozygous: having two identical alleles for a given gene on the homologous chromosomes

Chapter 9

Molecular Biology

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Summary

Each nucleotide is composed of a nitrogenous base, a five-carbon sugar (deoxyribose), and a phosphate group. Each strand is composed of nucleotides bonded together covalently between the phosphate group of one and the deoxyribose sugar of the next. The DNA molecule is a polymer of nucleotides. There are four nitrogenous bases in DNA, two purines (adenine and guanine) and two pyrimidines (cytosine and thymine).

Key terms

deoxyribose: a five-carbon sugar molecule with a hydrogen atom rather than a hydroxyl group in the 2' position; the sugar component of DNA nucleotides
nitrogenous base: a nitrogen-containing molecule that acts as a base; often referring to one of the purine or pyrimidine components of nucleic acids
phosphate group: a molecular group consisting of a central phosphorus atom bound to four oxygen atoms
DNA molecule: a polymer of nucleotides
alternative RNA splicing: a post-transcriptional gene regulation mechanism in eukaryotes in which multiple protein products are produced by a single gene through alternative splicing combinations of the…
lagging strand: during replication of the 3' to 5' strand, the strand that is replicated in short fragments and away from the replication fork
leading strand: the strand that is synthesized continuously in the 5' to 3' direction that is synthesized in the direction of the replication fork
mismatch repair: a form of DNA repair in which non-complementary nucleotides are recognized, excised, and replaced with correct nucleotides

Chapter 10

Biotechnology

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Summary

In molecular cloning with bacteria, a desired DNA fragment is inserted into a bacterial plasmid using restriction enzymes and the plasmid is taken up by a bacterium, which will then express the foreign DNA. Cloning may involve cloning small DNA fragments (molecular cloning), or cloning entire organisms (reproductive cloning). Fragmented or whole chromosomes can be separated on the basis of size by gel electrophoresis. DNA can be cut (and subsequently re-spliced together) using restriction enzymes.

Key terms

biotechnology: the use of artificial methods to modify the genetic material of living organisms or cells to produce novel compounds or to perform new functions
desired DNA fragment: inserted into a bacterial plasmid using restriction enzymes and the plasmid is taken up by a bacterium, which will then express the foreign DNA
gel electrophoresis: a technique used to separate molecules on the basis of their ability to migrate through a semisolid gel in response to an electric current
plasmid: a small circular molecule of DNA found in bacteria that replicates independently of the main bacterial chromosome; plasmids code for some important traits for bacteria and can be…
restriction enzyme: an enzyme that recognizes a specific nucleotide sequence in DNA and cuts the DNA double strand at that recognition site, often with a staggered cut leaving short single strands…
cloning: the production of an exact copy—specifically, an exact genetic copy—of a gene, cell, or organism
reproductive cloning: cloning of entire organisms
model organism: a species that is studied and used as a model to understand the biological processes in other species represented by the model organism

Chapter 11

Evolution and Its Processes

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Summary

Evolution by natural selection arises from three conditions: individuals within a species vary, some of those variations are heritable, and organisms have more offspring than resources can support. The consequence is that individuals with relatively advantageous variations will be more likely to survive and have higher reproductive rates than those individuals with different traits. The modern synthesis of evolutionary theory grew out of the reconciliation of Darwin’s, Wallace’s, and Mendel’s thoughts on evolution and heredity. Population genetics is a theoretical framework for describing evolutionary change in populations through the change in allele frequencies.

Key terms

modern synthesis: the overarching evolutionary paradigm that took shape by the 1940s and is generally accepted today
natural selection: the greater relative survival and reproduction of individuals in a population that have favorable heritable traits, leading to evolutionary change
consequence: that individuals with relatively advantageous variations will be more likely to survive and have higher reproductive rates than those individuals with different traits
population genetics: the study of how selective forces change the allele frequencies in a population over time
population; this: known as Hardy-Weinberg equilibrium principle
variation: the variety of alleles in a population
analogous structure: a structure that is similar because of evolution in response to similar selection pressures resulting in convergent evolution, not similar because of descent from a common ancestor
homologous structure: a structure that is similar because of descent from a common ancestor

Chapter 12

Diversity of Life

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Summary

However, today many scientists build phylogenetic trees to illustrate evolutionary relationships and the taxonomic classification system is expected to reflect evolutionary relationships Historically, organisms were organized into a taxonomic classification system. Each group of organisms went through its own evolutionary journey, called its phylogeny. To build phylogenetic trees, scientists must collect character information that allows them to make evolutionary connections between organisms.

Key terms

class: the category in the taxonomic classification system that falls within phylum and includes orders
phylogenetic tree: diagram used to reflect the evolutionary relationships between organisms or groups of organisms
phylogeny: evolutionary history and relationship of an organism or group of organisms
taxon: a single level in the taxonomic classification system
taxonomic classification system: expected to reflect evolutionary relationships
domain: the highest level category in the classification system and that includes all taxonomic classifications below it; it is the most inclusive taxon
shared derived character: a character on a phylogenetic tree that is shared only by a certain clade of organisms
shared ancestral character: a character on a phylogenetic branch that is shared by a particular clade

Chapter 13

Diversity of Microbes, Fungi, and Protists

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Summary

Microbial mats are thought to represent the earliest forms of life on Earth, and there is fossil evidence, called stromatolites, of their presence about 3.5 billion years ago. During the first 2 billion years, the atmosphere was anoxic and only anaerobic organisms were able to live. Cyanobacteria began the oxygenation of the atmosphere. Prokaryotes existed for billions of years before plants and animals appeared.

Key terms

cyanobacteria: bacteria that evolved from early phototrophs and oxygenated the atmosphere; also known as blue-green algae
stromatolite: a layered sedimentary structure formed by precipitation of minerals by prokaryotes in microbial mats
microbial mat: a multi-layered sheet of prokaryotes that may include bacteria and archaea
anaerobic: refers to organisms that grow without oxygen
Black Death: a devastating pandemic that is believed to have been an outbreak of bubonic plague caused by the bacterium Yersinia pestis
plastid: one of a group of related organelles in plant cells that are involved in the storage of starches, fats, proteins, and pigments
transformation: a mechanism of genetic change in prokaryotes in which DNA present in the environment is taken into the cell and incorporated into the genome

Chapter 14

Diversity of Plants

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Summary

All land plants share the following characteristics: alternation of generations, with the haploid plant called a gametophyte and the diploid plant called a sporophyte; formation of haploid spores in a sporangium; and… Land plants include nonvascular plants and vascular plants. Vascular plants, which include seedless plants and plants with seeds, have apical meristems, and embryos with nutritional stores.

Key terms

vascular plant: a plant in which there is a network of cells that conduct water and solutes through the organism
sporangium: (plural: sporangia) the organ within which spores are produced
nonvascular plant: a plant that lacks vascular tissue formed of specialized cells for the transport of water and nutrients
apical meristem: the growing point in a vascular plant at the tip of a shoot or root where cell division occurs
gametophyte: the haploid plant that produces gametes
sporophyte: the diploid plant that produces spores
anther: a sac-like structure at the tip of the stamen in which pollen grains are produced
diplontic: describes a life cycle in which the diploid stage is the dominant stage

Chapter 15

Diversity of Animals

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Summary

Animals with three germ layers, called triploblasts, are further characterized by the presence or absence of an internal body cavity called a coelom. Most animals reproduce sexually, leading to a developmental sequence that is relatively similar across the animal kingdom Animals are eukaryotic, multicellular, heterotrophic organisms that ingest their food and usually develop into motile creatures with a fixed body plan. Most members of the animal kingdom have differentiated tissues of four main classes—nervous, muscular, connective, and epithelial—that are specialized to perform different functions.

Key terms

bilateral symmetry: a type of symmetry in which there is only one plane of symmetry that creates two mirror-image sides
germ layer: a collection of cells formed during embryogenesis that will give rise to future body tissues
coelom: a lined body cavity derived from mesodermal embryonic tissue
animal kingdom: classified based on their body morphology and development
triploblast: an animal that develops from three germ layers
body plan: the shape and symmetry of an organism
notochord: a flexible, rod-shaped structure that is found in the embryonic stage of all chordates and in the adult stage of some chordates

Chapter 16

The Body’s Systems

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Summary

The blood vessels that transport blood into and out of the kidneys arise from and merge with the aorta and inferior vena cava, respectively. The urine leaves the kidney through the ureter and is stored in the urinary bladder. It is an equilibrium because body functions are kept within a normal range, with some fluctuations around a set point. The kidneys are the main osmoregulatory organs in mammalian systems; they function to filter blood and maintain the dissolved ion concentrations of body fluids.

Key terms

kidneys: the main osmoregulatory organs in mammalian systems; they function to filter blood and maintain the dissolved ion concentrations of body fluids
inferior vena cava: the major vein of the body returning blood from the lower parts of the body to the right atrium
aorta: the major artery that takes blood away from the heart to the systemic circulatory system
equilibrium because body functions: kept within a normal range, with some fluctuations around a set point
kidney: the organ that performs excretory and osmoregulatory functions
set point: the target value of a physiological state in homeostasis
urinary bladder: the structure that the ureters empty the urine into
ureter: the urine-bearing tubes coming out of the kidney

Chapter 17

The Immune System and Disease

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Summary

Viruses are acellular entities that can usually only be seen with an electron microscope. Their genomes contain either DNA or RNA, and they replicate using the replication proteins of a host cell. Viruses consist of a nucleic-acid core surrounded by a protein capsid with or without an outer lipid envelope A viral infection may be productive, resulting in new virions, or nonproductive, meaning the virus remains inside the cell without producing new virions

Key terms

virion: an individual virus particle outside a host cell
T cell: a lymphocyte that matures in the thymus gland
capsid: the protein coating of the viral core
innate immunity: an immunity that occurs naturally because of genetic factors or physiology, and is not caused by infection or vaccination
major histocompatibility complex (MHC) I: a group of proteins found on the surface of all nucleated cells that signals to immune cells whether the cell is normal or is infected or cancerous; it also provides the…
antibody: a protein that is produced by plasma cells after stimulation by an antigen; also known as an immunoglobulin

Chapter 18

Animal Reproduction and Development

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Summary

Asexual reproduction in animals occurs through fission, budding, fragmentation, and parthenogenesis. Reproduction may be asexual when one individual produces genetically identical offspring, or sexual when the genetic material from two individuals is combined to produce genetically diverse offspring. Sexual reproduction may involve fertilization inside the body or in the external environment. A species may have separate sexes or combined sexes; when the sexes are combined they may be expressed at different times in the life cycle.

Key terms

asexual reproduction: a mechanism that produces offspring that are genetically identical to the parent
budding: a form of asexual reproduction that results from the outgrowth of a part of an organism leading to a separation from the original animal into two individuals
fission: (also, binary fission) a form of asexual reproduction in which an organism splits into two separate organisms or two parts that regenerate the missing portions of the body
sexual reproduction: a form of reproduction in which cells containing genetic material from two individuals combines to produce genetically unique offspring
parthenogenesis: a form of asexual reproduction in which an egg develops into a complete individual without being fertilized
fragmentation: the breaking of an organism into parts and the growth of a separate individual from each part
sexes: combined they may be expressed at different times in the life cycle
genetic material from two individuals: combined to produce genetically diverse offspring

Chapter 19

Population and Community Ecology

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Summary

When resources become limiting, populations follow a logistic growth curve in which population size will level off at the carrying capacity Life tables are useful to calculate life expectancies of individual population members. Survivorship curves show the number of individuals surviving at each age interval plotted versus time Populations are individuals of a species that live in a particular habitat.

Key terms

ecology: the study of the relationships among living organisms and their environment
carrying capacity: the maximum number of individuals of a population that can be supported by the limited resources of a habitat
survivorship curve: a graph of the number of surviving population members versus the relative age of the member
life table: a table showing the life expectancy of a population member based on its age
logistic growth: the leveling off of exponential growth due to limiting resources
population size: the number of individuals in a population
climax community: the final stage of succession, where a stable community is formed by a characteristic assortment of plant and animal species
keystone species: a species whose presence is key to maintaining biodiversity in an ecosystem and to upholding an ecological community’s structure

Chapter 20

Ecosystems and the Biosphere

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Summary

Organisms in an ecosystem acquire energy in a variety of ways, which is transferred between trophic levels as the energy flows from the base to the top of the food web, with energy being lost at each transfer. There is energy lost at each trophic level, so the lengths of food chains are limited because there is a point where not enough energy remains to support a population of consumers. Ecosystems exist underground, on land, at sea, and in the air. Fat soluble compounds biomagnify up a food chain causing damage to top consumers.

Key terms

ecosystem: a community of living organisms and their interactions with their abiotic environment
lengths of food chains: limited because there is a point where not enough energy remains to support a population of consumers
food web: a web of trophic (feeding) relationships among producers, primary consumers, and higher level consumers in an ecosystem
food chain: a linear sequence of trophic (feeding) relationships of producers, primary consumers, and higher level consumers
trophic level: the position of a species or group of species in a food chain or a food web
arctic tundra: a biome characterized by low average temperatures, brief growing seasons, the presence of permafrost, and limited precipitation largely in the form of snow in which the dominant…
dead zone: an area in a lake and ocean near the mouths of rivers where large areas are depleted of their normal flora and fauna; these zones can be caused by eutrophication, oil spills…
detrital food web: a type of food web that is supported by dead or decaying organisms rather than by living autotrophs; these are often associated with grazing food webs within the same ecosystem

Chapter 21

Conservation and Biodiversity

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Summary

These include numbers of species, genetic diversity, chemical diversity, and ecosystem diversity. Biodiversity exists at multiple levels of organization, and is measured in different ways depending on the goals of those taking the measurements. The number of described species is estimated to be 1.5 million with about 17,000 new species being described each year. Biodiversity is negatively correlated with latitude for most taxa, meaning that biodiversity is higher in the tropics.

Key terms

biodiversity: the variety of a biological system, typically conceived as the number of species, but also applying to genes, biochemistry, and ecosystems
secondary plant compound: a compound produced as a byproduct of plant metabolic processes that is typically toxic, but is sequestered by the plant to defend against herbivores
genetic diversity: the variety of genes and alleles in a species or other taxonomic group or ecosystem; the term can refer to allelic diversity or genome-wide diversity
number of described species: estimated to be 1.5 million with about 17,000 new species being described each year
chemical diversity: the variety of metabolic compounds in an ecosystem
ecosystem diversity: the variety of ecosystems
extinction: the disappearance of a species from Earth; local extinction is the disappearance of a species from a region