Chapter 1

The Study of Life

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Summary

The main goal of basic science is to expand knowledge without any expectation of short-term practical application of that knowledge. Biology is the science that studies living organisms and their interactions with one another and their environments. Science has many fields; those fields related to the physical world and its phenomena are considered natural sciences Inductive reasoning uses particular results to produce general scientific principles.

Key terms

natural science

field of science that is related to the physical world and its phenomena and processes

results

section of a scientific paper in which the author narrates the experimental findings and presents relevant figures, pictures, diagrams, graphs, and tables, without any further…

science

knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method

basic science

science that seeks to expand knowledge and understanding regardless of the short-term application of that knowledge

deductive reasoning

form of logical thinking that uses a general inclusive statement to predict specific results

inductive reasoning

form of logical thinking that uses related observations to arrive at a general conclusion

organ

collection of related tissues grouped together performing a common function

Chapter 2

The Chemical Foundation 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 transferred, shared, or cause charge disparities between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions It is a polar molecule, allowing for the formation of hydrogen bonds. Hydrogen bonds allow ions and other polar molecules to dissolve in water.

Key terms

ion

atom or chemical group that does not contain equal numbers of protons and electrons

van der Waals interaction

very weak interaction between molecules due to temporary charges attracting atoms that are very close together

electron

negatively charged subatomic particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a negative charge of -1 unit

element

one of 118 unique substances that cannot be broken down into smaller substances; each element has unique properties and a specified number of protons

hydrogen bond

weak bond between slightly positively charged hydrogen atoms and slightly negatively charged atoms in other molecules

proton

positively charged particle that resides in the nucleus of an atom; has a mass of one amu and a charge of +1

atom

the smallest unit of matter that retains all of the chemical properties of an element

neutron

uncharged particle that resides in the nucleus of an atom; has a mass of one amu

Chapter 3

Biological Macromolecules

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Summary

Proteins, carbohydrates, nucleic acids, and lipids are the four major classes of biological macromolecules—large molecules necessary for life that are built from smaller organic molecules. When polymers are broken down into smaller units (monomers), a molecule of water is used for each bond broken by these reactions; such reactions are known as hydrolysis reactions. Dehydration and hydrolysis reactions are similar for all macromolecules, but each monomer and polymer reaction is specific to its class. Macromolecules are made up of single units known as monomers that are joined by covalent bonds to form larger polymers.

Key terms

biological macromolecule

large molecule necessary for life that is built from smaller organic molecules

carbohydrate

biological macromolecule in which the ratio of carbon to hydrogen and to oxygen is 1:2:1; carbohydrates serve as energy sources and structural support in cells and form the a…

polymer

chain of monomer residues that is linked by covalent bonds; polymerization is the process of polymer formation from monomers by condensation

molecule of water

used for each bond broken by these reactions; such reactions are known as hydrolysis reactions

lipid

macromolecule that is nonpolar and insoluble in water

nucleic acid

biological macromolecule that carries the genetic blueprint of a cell and carries instructions for the functioning of the cell

hydrolysis

reaction that causes breakdown of larger molecules into smaller molecules with the utilization of water

protein

biological macromolecule composed of one or more chains of amino acids

Chapter 4

Cell Structure

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Summary

All prokaryotes have plasma membranes, cytoplasm, ribosomes, and DNA that is not membrane-bound. Electron microscopes provide higher magnification, higher resolution, and more detail than light microscopes. 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 Prokaryotes are single-celled organisms of the domains Bacteria and Archaea.

Key terms

cell

the smallest unit of life

unified cell theory

a 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

rigid cell covering made of various molecules that protects the cell, provides structural support, and gives shape to the cell

cytoplasm

entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals

electron microscope

an instrument that magnifies an object using a beam of electrons passed and bent through a lens system to visualize a specimen

light microscope

an instrument that magnifies an object using a beam visible light passed and bent through a lens system to visualize a specimen

plasma membrane

phospholipid bilayer with embedded (integral) or attached (peripheral) proteins, that separates the internal content of the cell from its surrounding environment

prokaryote

unicellular organism that lacks a nucleus or any other membrane-bound organelle

Chapter 5

Structure and Function of Plasma Membranes

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Summary

The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The passive forms of transport, diffusion and osmosis, move materials of small molecular weight across membranes. The landscape of the membrane is studded with proteins, some of which span the membrane.

Key terms

plasma membrane

composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other

fluid mosaic model

describes the structure of the plasma membrane as a mosaic of components including phospholipids, cholesterol, proteins, glycoproteins, and glycolipids (sugar chains attached to…

osmosis

transport of water through a semipermeable membrane according to the concentration gradient of water across the membrane that results from the presence of solute that cannot pass…

fluid nature of the membrane

due to temperature, the configuration of the fatty acid tails (some kinked by double bonds), the presence of cholesterol embedded in the membrane, and the mosaic nature o

diffusion

passive process of transport of low-molecular weight material according to its concentration gradient

hydrophobic

molecule that does not have the ability to bond with water; “water-hating”

landscape of the membrane

studded with proteins, some of which span the membrane

plasmolysis

detaching of the cell membrane from the cell wall and constriction of the cell membrane when a plant cell is in a hypertonic solution

Chapter 6

Metabolism

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Summary

Glucose synthesis and glucose breakdown are examples of anabolic and catabolic pathways, respectively A cell’s metabolism refers to the chemical reactions that take place within it. Objects in motion do physical work, and kinetic energy is the energy of objects in motion. Cells perform the functions of life through various chemical reactions.

Key terms

metabolism

all the chemical reactions that take place inside cells, including anabolism and catabolism

catabolic

(also, catabolism) pathways in which complex molecules are broken down into simpler ones

anabolic

(also, anabolism) pathways that require an input of energy to synthesize complex molecules from simpler ones

kinetic energy

type of energy associated with objects or particles in motion

coenzyme

small organic molecule, such as a vitamin or its derivative, which is required to enhance the activity of an enzyme

heat

energy transferred from one system to another that is not work (energy of the motion of molecules or particles)

energy coupling

process during which energy released by one reaction is used to drive another reaction

chemical energy

potential energy in chemical bonds that is released when those bonds are broken

Chapter 7

Cellular Respiration

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Summary

The two processes of ATP regeneration that are used in conjunction with glucose catabolism are substrate-level phosphorylation and oxidative phosphorylation through the process of chemiosmosis When ATP is used in a reaction, the third phosphate is temporarily attached to a substrate in a process called phosphorylation. The structure of ATP is that of an RNA nucleotide with three phosphates attached. As ATP is used for energy, a phosphate group or two are detached, and either ADP or AMP is produced.

Key terms

chemiosmosis

process in which there is a production of adenosine triphosphate (ATP) in cellular metabolism by the involvement of a proton gradient across a membrane

phosphate group or two

detached, and either ADP or AMP is produced

substrate-level phosphorylation

production of ATP from ADP using the excess energy from a chemical reaction and a phosphate group from a reactant

phosphorylation

addition of a high-energy phosphate to a compound, usually a metabolic intermediate, a protein, or ADP

glycolysis

process of breaking glucose into two three-carbon molecules with the production of ATP and NADH

third phosphate

temporarily attached to a substrate in a process called phosphorylation

oxidative phosphorylation

production of ATP using the process of chemiosmosis and oxygen

structure of ATP

that of an RNA nucleotide with three phosphates attached

Chapter 8

Photosynthesis

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Summary

Only certain organisms, called photoautotrophs, can perform photosynthesis; they require the presence of chlorophyll, a specialized pigment that absorbs certain portions of the visible spectrum and can capture energy… The pigments of the first part of photosynthesis, the light-dependent reactions, absorb energy from sunlight. The process of photosynthesis transformed life on Earth. Eukaryotic autotrophs, such as plants and algae, have organelles called chloroplasts in which photosynthesis takes place, and starch accumulates.

Key terms

light-dependent reaction

first stage of photosynthesis where certain wavelengths of the visible light are absorbed to form two energy-carrying molecules (ATP and NADPH)

pigment

molecule that is capable of absorbing certain wavelengths of light and reflecting others (which accounts for its color)

process

less localized and occurs within folded membranes, extensions of the plasma membrane, and in the cytoplasm

photoautotroph

organism capable of producing its own organic compounds from sunlight

chloroplast

organelle in which photosynthesis takes place

light-independent reaction

second stage of photosynthesis, though which carbon dioxide is used to build carbohydrate molecules using energy from ATP and NADPH

photosystem

group of proteins, chlorophyll, and other pigments that are used in the light-dependent reactions of photosynthesis to absorb light energy and convert it into chemical energy

photosystem II

integral protein and pigment complex in thylakoid membranes that transports electrons from water to the electron transport chain; oxygen is a product of PSII

Chapter 9

Cell Communication

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Summary

Signaling cells secrete ligands that bind to target cells and initiate a chain of events within the target cell. The four categories of signaling in multicellular organisms are paracrine signaling, endocrine signaling, autocrine signaling, and direct signaling across gap junctions. Endocrine signals are carried long distances through the bloodstream by hormones, and autocrine signals are received by the same cell that sent the signal or other nearby cells of the same kind. Internal receptors are found in the cell cytoplasm.

Key terms

endocrine signal

long-distance signal that is delivered by ligands (hormones) traveling through an organism's circulatory system from the signaling cell to the target cell

internal receptor

(also, intracellular receptor) receptor protein that is located in the cytosol of a cell and binds to ligands that pass through the plasma membrane

paracrine signal

signal between nearby cells that is delivered by ligands traveling in the liquid medium in the space between the cells

autocrine signal

signal that is sent and received by the same or similar nearby cells

ligand

molecule produced by a signaling cell that binds with a specific receptor, delivering a signal in the process

signaling cell

cell that releases signal molecules that allow communication with another cell

target cell

cell that has a receptor for a signal or ligand from a signaling cell

receptor

protein in or on a target cell that bind to ligands

Chapter 10

Cell Reproduction

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Summary

Human gametes have 23 chromosomes representing one complete set of chromosomes; a set of chromosomes is complete with either one of the sex chromosomes. An organism’s traits are determined by the genes inherited from each parent. Genes are segments of DNA that code for a specific protein. Duplicated chromosomes are composed of two sister chromatids.

Key terms

chromatid

single DNA molecule of two strands of duplicated DNA and associated proteins held together at the centromere

cell cycle

ordered series of events involving cell growth and cell division that produces two new daughter cells

gene

physical and functional unit of heredity, a sequence of DNA that codes for a protein

gamete

haploid reproductive cell or sex cell (sperm, pollen grain, or egg)

organism’s traits

determined by the genes inherited from each parent

set of chromosomes

complete with either one of the sex chromosomes

cyclin-dependent kinase

one of a group of protein kinases that helps to regulate the cell cycle when bound to cyclin; it functions to phosphorylate other proteins that are either activated or…

FtsZ

tubulin-like protein component of the prokaryotic cytoskeleton that is important in prokaryotic cytokinesis (name origin: F ilamenting t emperature- s ensitive mutant Z )

Chapter 11

Meiosis and Sexual Reproduction

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Summary

During meiosis, variation in the daughter nuclei is introduced because of crossover in prophase I and random alignment of tetrads at metaphase I. Sexual reproduction requires that diploid organisms produce haploid cells that can fuse during fertilization to form diploid offspring. Meiosis is a series of events that arrange and separate chromosomes and chromatids into daughter cells. The cells that are produced by meiosis are genetically unique

Key terms

meiosis

a nuclear division process that results in four haploid cells

meiosis I

first round of meiotic cell division; referred to as reduction division because the ploidy level is reduced from diploid to haploid

crossover

exchange of genetic material between non-sister chromatids resulting in chromosomes that incorporate genes from both parents of the organism

tetrad

two duplicated homologous chromosomes (four chromatids) bound together by chiasmata during prophase I

daughter nuclei

introduced because of crossover in prophase I and random alignment of tetrads at metaphase I

fertilization

union of two haploid cells from two individual organisms

meiosis II

second round of meiotic cell division following meiosis I; sister chromatids are separated into individual chromosomes, and the result is four unique haploid cells

Chapter 12

Mendel's Experiments and Heredity

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Summary

When the offspring 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… Observable traits are referred to as dominant, and non-expressed traits are described as recessive. Reciprocal crosses generated identical F 1 and F 2 offspring ratios. Working with garden pea plants, Mendel found that crosses between parents that differed by one trait produced F 1 offspring that all expressed the traits of one parent.

Key terms

recessive

trait that appears “latent” or non-expressed when the individual also carries a dominant trait for that same characteristic; when present as two identical copies, the recessive…

F 2

second filial generation produced when F 1 individuals are self-crossed or fertilized with each other

dominant

trait which confers the same physical appearance whether an individual has two copies of the trait or one copy of the dominant trait and one copy of the recessive trait

product rule

probability of two independent events occurring simultaneously can be calculated by multiplying the individual probabilities of each event occurring alone

reciprocal cross

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

F 1

first filial generation in a cross; the offspring of the parental generation

trait

variation in the physical appearance of a heritable characteristic

blending theory of inheritance

hypothetical inheritance pattern in which parental traits are blended together in the offspring to produce an intermediate physical appearance

Chapter 13

Modern Understandings of Inheritance

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Summary

Disorders in chromosome number, or aneuploidies, are typically lethal to the embryo, although a few trisomic genotypes are viable. The Chromosomal Theory of inheritance, proposed by Sutton and Boveri, states that chromosomes are the vehicles of genetic heredity. Sturtevant devised a method to assess recombination frequency and infer the relative positions and distances of linked genes on a chromosome on the basis of the average number of crossovers in the intervening region… Whereas linkage causes alleles on the same chromosome to be inherited together, homologous recombination biases alleles toward an inheritance pattern of independent assortment

Key terms

Chromosomal Theory of Inheritance

theory proposing that chromosomes are the vehicles of genes and that their behavior during meiosis is the physical basis of the inheritance patterns that Mendel observed

homologous recombination

process by which homologous chromosomes undergo reciprocal physical exchanges at their arms, also known as crossing over

recombination frequency

average number of crossovers between two alleles; observed as the number of nonparental types in a population of progeny

X inactivation

condensation of X chromosomes into Barr bodies during embryonic development in females to compensate for the double genetic dose

aneuploid

individual with an error in chromosome number; includes deletions and duplications of chromosome segments

euploid

individual with the appropriate number of chromosomes for their species

karyogram

photographic image of a karyotype

trisomy

otherwise diploid genotype in which one entire chromosome is duplicated

Chapter 14

DNA Structure and Function

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Summary

Avery, MacLeod, and McCarty proved that DNA is required for the transformation of bacteria. Some of the salient features are that the two strands that make up the double helix are complementary and anti-parallel in nature. Deoxyribose sugars and phosphates form the backbone of the structure, and the nitrogenous bases are stacked inside. DNA was first isolated from white blood cells by Friedrich Miescher, who called it nuclein because it was isolated from nuclei.

Key terms

salient features

that the two strands that make up the double helix are complementary and anti-parallel in nature

transformation

process in which external DNA is taken up by a cell

leading strand

strand that is synthesized continuously in the 5'-3' direction which is synthesized in the direction of the replication fork

primer

short stretch of nucleotides that is required to initiate replication; in the case of replication, the primer has RNA nucleotides

nucleotide excision repair

type of DNA repair mechanism in which the wrong base, along with a few nucleotides upstream or downstream, are removed

primase

enzyme that synthesizes the RNA primer; the primer is needed for DNA pol to start synthesis of a new DNA strand

lagging strand

during replication, the strand that is replicated in short fragments and away from the replication fork

Chapter 15

Genes and Proteins

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Summary

The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three nonsense codons. In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus sequences that recruit RNA polymerase. The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet (20 amino acids). The Central Dogma describes the flow of genetic information in the cell from genes to mRNA to proteins.

Key terms

consensus

DNA sequence that is used by many species to perform the same or similar functions

codon

three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation

core enzyme

prokaryotic RNA polymerase consisting of α , β , and β ' but missing σ ; this complex performs elongation

genetic code

degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three nonsense codons

Central Dogma

states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins

promoter

DNA sequence to which RNA polymerase and associated factors bind and initiate transcription

nonsense codon

one of the three mRNA codons that specifies termination of translation

process of transcription; mRNA

used to synthesize proteins by the process of translation

Chapter 16

Gene Regulation

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Summary

Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time.

Key terms

DNA

first transcribed into RNA, which is then translated into proteins

gene expression

processes that control the turning on or turning off of a gene

nucleus and

separate from the translation that occurs in the cytoplasm

type and amount of protein

regulated by controlling gene expression

5' cap

a methylated guanosine triphosphate (GTP) molecule that is attached to the 5' end of a messenger RNA to protect the end from degradation

catabolite activator protein (CAP)

protein that complexes with cAMP to bind to the promoter sequences of operons that control sugar processing when glucose is not available

enhancer

segment of DNA that is upstream, downstream, perhaps thousands of nucleotides away, or on another chromosome that influence the transcription of a specific gene

Chapter 17

Biotechnology and Genomics

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Summary

Genetic testing is performed to identify disease-causing genes, and gene therapy is used to cure an inheritable disease Fragmented or whole chromosomes can be separated on the basis of size by gel electrophoresis. The term “cloning” may refer to cloning small DNA fragments (molecular cloning), cloning cell populations (cellular cloning), or cloning entire organisms (reproductive cloning). Transgenic organisms possess DNA from a different species, usually generated by molecular cloning techniques.

Key terms

genomics

study of entire genomes including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species

biotechnology

use of biological agents for technological advancement

recombinant DNA

combination of DNA fragments generated by molecular cloning that does not exist in nature; also known as a chimeric molecule

gene therapy

technique used to cure inheritable diseases by replacing mutant genes with good genes

gel electrophoresis

technique used to separate molecules on the basis of size using electric charge

genetic testing

process of testing for the presence of disease-causing genes

cellular cloning

production of identical cell populations by binary fission

transgenic

organism that receives DNA from a different species

Chapter 18

Evolution and Origin of Species

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Summary

Evolution is the process of adaptation through mutation which allows more desirable characteristics to be passed to the next generation. For living organisms to adapt and change to environmental pressures, genetic variation must be present. With genetic variation, individuals have differences in form and function that allow some to survive certain conditions better than others. Evolution may be convergent with similar traits evolving in multiple species or divergent with diverse traits evolving in multiple species that came from a common ancestor.

Key terms

species

group of populations that interbreed and produce fertile offspring

vestigial structure

physical structure present in an organism but that has no apparent function and appears to be from a functional structure in a distant ancestor

adaptation

heritable trait or behavior in an organism that aids in its survival and reproduction in its present environment

variation

genetic differences among individuals in a population

habitat isolation

reproductive isolation resulting when populations of a species move or are moved to a new habitat, taking up residence in a place that no longer overlaps with the other…

reproductive isolation

situation that occurs when a species is reproductively independent from other species; this may be brought about by behavior, location, or reproductive barriers

behavioral isolation

type of reproductive isolation that occurs when a specific behavior or lack of one prevents reproduction from taking place

gametic barrier

prezygotic barrier occurring when closely related individuals of different species mate, but differences in their gamete cells (eggs and sperm) prevent fertilization from taking…

Chapter 19

The Evolution of Populations

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Summary

The modern synthesis of evolutionary theory grew out of the cohesion of Darwin’s, Wallace’s, and Mendel’s thoughts on evolution and heredity, along with the more modern study of population genetics. It describes the evolution of populations and species, from small-scale changes among individuals to large-scale changes over paleontological time periods. To understand how organisms evolve, scientists can track populations’ allele frequencies over time. If they differ from generation to generation, scientists can conclude that the population is not in Hardy-Weinberg equilibrium, and is thus evolving

Key terms

modern synthesis

overarching evolutionary paradigm that took shape by the 1940s and is generally accepted today

population genetics

study of how selective forces change the allele frequencies in a population over time

founder effect

event that initiates an allele frequency change in part of the population, which is not typical of the original population

frequency-dependent selection

selection that favors phenotypes that are either common (positive frequency-dependent selection) or rare (negative frequency-dependent selection)

genotype frequency

the proportion of a specific genotype in a population relative to all other genotypes for those genes that are present in the population

Hardy-Weinberg principle of equilibrium

a stable, non-evolving state of a population in which allelic frequencies are stable over time

geographical variation

differences in the phenotypic variation between populations that are separated geographically

Chapter 20

Phylogenies and the History of Life

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Summary

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

Key terms

taxonomic classification system

hierarchical system of classifying organisms, including the classification of domain, kingdom, phylum, class, order, family, genus, and species

phylogenetic tree

diagram used to reflect the evolutionary relationships among organisms or groups of organisms

phylogeny

evolutionary history and relationship of an organism or group of organisms

taxon

(plural: taxa) single level in the taxonomic classification system

class

division of phylum in the taxonomic classification system

analogy

(also, homoplasy) characteristic that is similar between organisms by convergent evolution, not due to the same evolutionary path

shared derived character

describes a characteristic on a phylogenetic tree that is shared only by a certain clade of organisms

shared ancestral character

describes a characteristic on a phylogenetic tree that is shared by all organisms on the tree

Chapter 21

Viruses

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Summary

Viruses consist of a nucleic acid core surrounded by a protein capsid with or without an outer lipid envelope. The capsid shape, presence of an envelope, and core composition dictate some elements of the classification of viruses. Viruses are tiny, acellular entities that can usually only be seen with an electron microscope. Their genomes contain either DNA or RNA—never both—and they replicate using the replication proteins of a host cell.

Key terms

envelope

lipid bilayer that envelopes some viruses

capsid

protein coating of the viral core

asymptomatic disease

disease where there are no symptoms and the individual is unaware of being infected unless lab tests are performed

lysogenic cycle

type of virus replication in which the viral genome is incorporated into the genome of the host cell

lytic cycle

type of virus replication in which virions are released through lysis, or bursting, of the cell

horizontal transmission

between members of an ecosystem that are not in a parent-progeny relationship

permissive

cell type that is able to support productive replication of a virus

Chapter 22

Prokaryotes: Bacteria and Archaea

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Summary

During the first 2 billion years, the atmosphere was anoxic and only anaerobic organisms were able to live. Cyanobacteria evolved from early phototrophs and began the oxygenation of the atmosphere. Fossilized microbial mats are called stromatolites and consist of laminated organo-sedimentary structures formed by precipitation of minerals by prokaryotes. Hot springs and hydrothermal vents may have been the environments in which life began.

Key terms

phototroph

organism that is able to make its own food by converting solar energy to chemical energy

cyanobacteria

bacteria that evolved from early phototrophs and oxygenated the atmosphere; also known as blue-green algae

stromatolite

layered sedimentary structure formed by precipitation of minerals by prokaryotes in microbial mats

microbial mat

multi-layered sheet of prokaryotes that may include bacteria and archaea

hydrothermal vent

fissure in Earth’s surface that releases geothermally heated water

anaerobic

refers to organisms that grow without oxygen

Black Death

devastating pandemic that is believed to have been an outbreak of bubonic plague caused by the bacterium Yersinia pestis

Chapter 23

Plant Form and Physiology

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Summary

A plant is composed of two main types of tissue: meristematic tissue and permanent tissue. A vascular plant consists of two organ systems: the shoot system and the root system. As growth occurs, meristematic tissue differentiates into permanent tissue, which is categorized as either simple or complex. The root system supports the plant and is usually underground.

Key terms

plant

composed of two main types of tissue: meristematic tissue and permanent tissue

permanent tissue

plant tissue composed of cells that are no longer actively dividing

shoot system

aboveground portion of the plant; consists of non-reproductive plant parts, such as leaves and stems, and reproductive parts, such as flowers and fruits

dermal tissue

protective plant tissue covering the outermost part of the plant; controls gas exchange

root system

belowground portion of the plant that supports the plant and absorbs water and minerals

ground tissue

plant tissue involved in photosynthesis; provides support, and stores water and sugars

meristematic tissue

tissue containing cells that constantly divide; contributes to plant growth

meristem

plant region of continuous growth

Chapter 24

The Animal Body: Basic Form and Function

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Summary

The four primary tissues are epithelia, connective tissues, muscle tissues, and nervous tissues The basic building blocks of complex animals are four primary tissues. Animal bodies come in a variety of sizes and shapes. Limits on animal size and shape include impacts to their movement.

Key terms

four primary tissues

epithelia, connective tissues, muscle tissues, and nervous tissues

connective tissue

type of tissue made of cells, ground substance matrix, and fibers

columnar epithelia

epithelia made of cells taller than they are wide, specialized in absorption

pseudostratified

layer of epithelia that appears multilayered, but is a simple covering

fusiform

animal body shape that is tubular and tapered at both ends

cartilage

type of connective tissue with a large amount of ground substance matrix, cells called chondrocytes, and some amount of fibers

ventral cavity

body cavity on the anterior or front portion of an animal that includes the thoracic cavities and the abdominopelvic cavities

dorsal cavity

body cavity on the posterior or back portion of an animal; includes the cranial and vertebral cavities

Chapter 25

Animal Nutrition and the Digestive System

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Summary

Ruminants that consume large amounts of plant material have a multi-chambered stomach that digests roughage. Humans and many other animals have monogastric digestive systems with a single-chambered stomach. Birds have evolved a digestive system that includes a gizzard where the food is crushed into smaller pieces. Pseudo-ruminants have similar digestive processes as ruminants but do not have the four-compartment stomach.

Key terms

roughage

component of food that is low in energy and high in fiber

digestion

mechanical and chemical break down of food into small organic fragments

monogastric

digestive system that consists of a single-chambered stomach

ruminant

animal with a stomach divided into four compartments

stomach

saclike organ containing acidic digestive juices

gizzard

muscular organ that grinds food

gizzard where the food

crushed into smaller pieces

Chapter 26

The Nervous System

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Summary

The nervous system is made up of neurons and glia. Most neurons contain dendrites, which receive these signals, and axons that send signals to other neurons or tissues. Glia are non-neuronal cells in the nervous system that support neuronal development and signaling. Neurons are specialized cells that are capable of sending electrical as well as chemical signals.

Key terms

nervous system

made up of neurons and glia

axon

tube-like structure that propagates a signal from a neuron’s cell body to axon terminals

dendrite

structure that extends away from the cell body to receive messages from other neurons

neuron

specialized cell that can receive and transmit electrical and chemical signals

glia

(also, glial cells) cells that provide support functions for neurons

basal ganglia

interconnected collections of cells in the brain that are involved in movement and motivation; also known as basal nuclei

refractory period

period after an action potential when it is more difficult or impossible for an action potential to be fired; caused by inactivation of sodium channels and activation of…

temporal lobe

part of the cerebral cortex that processes auditory input; parts of the temporal lobe are involved in speech, memory, and emotion processing

Chapter 27

Sensory Systems

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Summary

A sensory activation occurs when a physical or chemical stimulus is processed into a neural signal (sensory transduction) by a sensory receptor. Humans have special senses: olfaction, gustation, equilibrium, and hearing, plus the general senses of somatosensation Each sensory receptor is responsive to stimuli within a specific region in space, which is known as that receptor’s receptive field. Perception is an individual interpretation of a sensation and is a brain function.

Key terms

sensory receptor

specialized neuron or other cells associated with a neuron that is modified to receive specific sensory input

sensory transduction

conversion of a sensory stimulus into electrical energy in the nervous system by a change in the membrane potential

physical or chemical stimulus

processed into a neural signal (sensory transduction) by a sensory receptor

receptive field

region in space in which a stimulus can activate a given sensory receptor

perception

individual interpretation of a sensation; a brain function

cone

weakly photosensitive, chromatic, cone-shaped neuron in the fovea of the retina that detects bright light and is used in daytime color vision

Chapter 28

The Endocrine System

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Summary

Hormones can affect cells directly through intracellular hormone receptors or indirectly through plasma membrane hormone receptors Amino acid-derived hormones are relatively small molecules and include the adrenal hormones epinephrine and norepinephrine. Peptide hormones are polypeptide chains or proteins and include the pituitary hormones, antidiuretic hormone (vasopressin), and oxytocin Lipid-derived hormones are structurally similar to cholesterol and include steroid hormones such as estradiol and testosterone.

Key terms

oxytocin

hormone released by the posterior pituitary to stimulate uterine contractions during childbirth and milk let-down in the mammary glands

norepinephrine

hormone released by the adrenal medulla in response to a short-term stress hormone production by the gonads

epinephrine

hormone released by the adrenal medulla in response to a short term stress

plasma membrane hormone receptor

a hormone receptor on the surface of the plasma membrane of a cell

intracellular hormone receptor

a hormone receptor in the cytoplasm or nucleus of a cell

hormone receptor

the cellular protein that binds to a hormone

lipid-derived hormone

hormone derived mostly from cholesterol

peptide hormone

hormone composed of a polypeptide chain

Chapter 29

The Musculoskeletal System

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Summary

The axial skeleton is composed of the bones of the skull, ossicles of the ear, hyoid bone, vertebral column, and ribcage. The human skeleton is an endoskeleton that is composed of the axial and appendicular skeleton. The skull consists of eight cranial bones and 14 facial bones. The three types of skeleton designs are hydrostatic skeletons, exoskeletons, and endoskeletons.

Key terms

human skeleton

an endoskeleton that is composed of the axial and appendicular skeleton

appendicular skeleton

composed of the bones of the upper limbs, which function to grasp and manipulate objects, and the lower limbs, which permit locomotion

axial skeleton

forms the central axis of the body and includes the bones of the skull, the ossicles of the middle ear, the hyoid bone of the throat, the vertebral column, and the thoracic cage…

cranial bone

one of eight bones that form the cranial cavity that encloses the brain and serves as an attachment site for the muscles of the head and neck

facial bone

one of the 14 bones that form the face; provides cavities for the sense organs (eyes, mouth, and nose) and attachment points for facial muscles

rib

one of 12 pairs of long, curved bones that attach to the thoracic vertebrae and curve toward the front of the body to form the ribcage

vertebral column

(also, spine) surrounds and protects the spinal cord, supports the head, and acts as an attachment point for ribs and muscles of the back and neck

exoskeleton

a secreted cellular product external skeleton that consists of a hard encasement on the surface of an organism

Chapter 30

The Respiratory System

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Summary

The respiratory bronchioles open into the alveolar ducts, alveolar sacs, and alveoli. Air then travels down the pharynx, through the trachea, and into the lungs. In the lungs, air passes through the branching bronchi, reaching the respiratory bronchioles, which house the first site of gas exchange. These include the hair and mucus in the nasal cavity that trap dust, dirt, and other particulate matter before they can enter the system.

Key terms

respiratory bronchiole

terminal portion of the bronchiole tree that is attached to the terminal bronchioles and alveoli ducts, alveolar sacs, and alveoli

particulate matter

small particle such as dust, dirt, viral particles, and bacteria that are in the air

pharynx

throat; a tube that starts in the internal nares and runs partway down the neck, where it opens into the esophagus and the larynx

mucus

sticky protein-containing fluid secretion in the lung that traps particulate matter to be expelled from the body

trachea

cartilaginous tube that transports air from the larynx to the primary bronchi

alveolar sac

structure consisting of two or more alveoli that share a common opening

bronchiole

airway that extends from the main tertiary bronchi to the alveolar sac

alveolar duct

duct that extends from the terminal bronchiole to the alveolar sac

Chapter 31

The Circulatory System

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Summary

Circulatory systems may be open (mixed with the interstitial fluid) or closed (separated from the interstitial fluid). Closed circulatory systems are a characteristic of vertebrates; however, there are significant differences in the structure of the heart and the circulation of blood between the different vertebrate groups due to… In most animals, the circulatory system is used to transport blood through the body. However, complex organisms use the circulatory system to carry gases, nutrients, and waste through the body.

Key terms

circulatory system

used to transport blood through the body

closed circulatory system

system in which the blood is separated from the bodily interstitial fluid and contained in blood vessels

double circulation

flow of blood in two circuits: the pulmonary circuit through the lungs and the systemic circuit through the organs and body

unidirectional circulation

flow of blood in a single circuit; occurs in fish where the blood flows through the gills, then past the organs and the rest of the body, before returning to the heart

gill circulation

circulatory system that is specific to animals with gills for gas exchange; the blood flows through the gills for oxygenation

lymph node

specialized organ that contains a large number of macrophages that clean the lymph before the fluid is returned to the heart

red blood cell

small (7-8 μm) biconcave cell without mitochondria (and in mammals without nuclei) that is packed with hemoglobin, giving the cell its red color; transports oxygen through the body

Chapter 32

Osmotic Regulation and Excretion

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Summary

It is the number of solute molecules and not the molecular size that is important in osmosis. Osmoregulation and osmotic balance are important bodily functions, resulting in water and salt balance. Osmosis occurs to equalize the number of solute molecules across a semi-permeable membrane by the movement of water to the side of higher solute concentration. Osmolarity is measured in units of milliequivalents or milliosmoles, both of which take into consideration the number of solute particles and the charge on them.

Key terms

osmoregulation

mechanism by which water and solute concentrations are maintained at desired levels

osmotic balance

balance of the amount of water and salt input and output to and from a biological system without disturbing the desired osmotic pressure and solute concentration in every…

semi-permeable membrane

membrane that allows only certain solutes to pass through

mole

gram equivalent of the molecular weight of a substance

molarity

number of moles of solute per liter of solution

countercurrent multiplier

osmotic gradient in the renal medulla that is responsible for concentration of urine

distal convoluted tubule (DCT)

part of the renal tubule that is the most distant from the glomerulus

Chapter 33

The Immune System

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Summary

Using a combination of cellular and molecular attacks, the innate immune system identifies the nature of a pathogen and responds with inflammation, phagocytosis, cytokine release, destruction by NK cells, and/or a… T H cells stimulate B cells that have engulfed and presented pathogen-derived antigens. APCs display antigens via MHC molecules to complementary naïve T cells. The innate immune system serves as a first responder to pathogenic threats that bypass natural physical and chemical barriers of the body.

Key terms

cytokine

chemical messenger that regulates cell differentiation, proliferation, gene expression, and cell trafficking to effect immune responses

inflammation

localized redness, swelling, heat, and pain that results from the movement of leukocytes and fluid through opened capillaries to a site of infection

T cell

lymphocyte that matures in the thymus gland; one of the main cells involved in the adaptive immune system

B cell

lymphocyte that matures in the bone marrow and differentiates into antibody-secreting plasma cells

pathogen

an agent, usually a microorganism, that causes disease in the organisms that they invade

antigen

foreign or “non-self” protein that triggers the immune response

complement system

array of approximately 20 soluble proteins of the innate immune system that enhance phagocytosis, bore holes in pathogens, and recruit lymphocytes; enhances the adaptive response…

Chapter 34

Animal Reproduction and Development

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Summary

Asexual reproduction occurs through fission, budding, and fragmentation. 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 mean the joining of sperm and eggs within animals’ bodies or it may mean the release of sperm and eggs into the environment. Sexual reproduction starts with the combination of a sperm and an egg in a process called fertilization.

Key terms

asexual reproduction

form of reproduction that produces offspring that are genetically identical to the parent

budding

form of asexual reproduction that results from the outgrowth of a part of a cell leading to a separation from the original animal into two individuals

fission

(also, binary fission) method by which multicellular organisms increase in size or asexual reproduction in which a unicellular organism splits into two separate organisms by…

fragmentation

cutting or fragmenting of the original animal into parts and the growth of a separate animal from each part

sexual reproduction

mixing of genetic material from two individuals to produce genetically unique offspring

genetic material from two individuals

combined to produce genetically diverse offspring

estradiol

most potent form of estrogen that is responsible for the development of female secondary female characteristics, maintenance of female reproductive organs, and preparation for…

oviparity

process by which fertilized eggs are laid outside the female’s body and develop there, receiving nourishment from the yolk that is a part of the egg

Chapter 35

Ecology and the Biosphere

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Summary

Biogeography is the study of the geographic distribution of living things and the abiotic factors that affect their distribution. Ecologists studying an ecosystem examine the living species (the biotic components) of the ecosystem as well as the nonliving portions (the abiotic components), such as air, water, and soil, of the environment Ecology is the study of the interactions of living things with their environment. Endemic species are species that are naturally found only in a specific geographic area.

Key terms

ecology

study of interaction between living things and their environment

distribution of living things

influenced by several environmental factors that are, in part, controlled by the latitude or elevation at which an organism is found

endemic

species found only in a specific geographic area that is usually restricted in size

biogeography

study of the geographic distribution of living things and the abiotic factors that affect their distribution

abiotic

nonliving components of the environment

biotic

living components of the environment

biome

ecological community of plants, animals, and other organisms that is adapted to a characteristic set of environmental conditions

emergent vegetation

wetland plants that are rooted in the soil but have portions of leaves, stems, and flowers extending above the water’s surface

Chapter 36

Population and Community Ecology

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Summary

Ecologists measure characteristics of populations: size, density, dispersion pattern, age structure, and sex ratio. 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 All species have evolved a pattern of living, called a life history strategy, in which they partition energy for growth, maintenance, and reproduction.

Key terms

ecology

the study of the relationships among living organisms and their environment

life history

inherited pattern of resource allocation under the influence of natural selection and other evolutionary forces

survivorship curve

graph of the number of surviving population members versus the relative age of the member

life table

table showing the life expectancy of a population member based on its age

age structure

proportion of population members at specific age ranges

fecundity

potential reproductive capacity of an individual

climax community

final stage of succession, where a stable community is formed by a characteristic assortment of plant and animal species

commensalism

relationship between species wherein one species benefits from the close, prolonged interaction, while the other species neither benefits nor is harmed

Chapter 37

Ecosystems

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Summary

Analytical models are used to describe linear food chains, and simulation models work best with holistic food webs Organisms in an ecosystem acquire energy in a variety of ways, which is transferred between trophic levels as the energy flows from the bottom to the top of the food web, with energy being lost at each transfer. Modeling of ecosystem energy is best done with ecological pyramids of energy, although other ecological pyramids provide other vital information about ecosystem structure Ecosystems exist on land, at sea, in the air, and underground.

Key terms

ecosystem

community of living organisms and their interactions with their abiotic environment

analytical model

ecosystem model that is created with mathematical formulas to predict the effects of environmental disturbances on ecosystem structure and dynamics

simulation model

ecosystem model that is created with computer programs to holistically model ecosystems and to predict the effects of environmental disturbances on ecosystem structure and dynamics

conceptual model

(also, compartment models) ecosystem model that consists of flow charts that show the interactions of different compartments of the living and non-living components of the…

ecological pyramid

(also, Eltonian pyramid) graphical representation of different trophic levels in an ecosystem based of organism numbers, biomass, or energy content

food chain

linear representation of a chain of primary producers, primary consumers, and higher-level consumers used to describe ecosystem structure and dynamics

food web

graphic representation of a holistic, non-linear web of primary producers, primary consumers, and higher-level consumers used to describe ecosystem structure and dynamics

efficiency of these transfers

important for understanding the different behaviors and eating habits of warm-blooded versus cold-blooded animals

Chapter 38

Conservation Biology and Biodiversity

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Summary

These measurements include numbers of species, genetic diversity, chemical diversity, and ecosystem diversity. Biodiversity recovery times after mass extinctions vary, but have been up to 30 million years. 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.

Key terms

biodiversity

variety of a biological system, typically conceived as the number of species, but also applying to genes, biochemistry, and ecosystems

extinction

disappearance of a species from Earth; local extinction is the disappearance of a species from a region

genetic diversity

variety of genes 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

variety of metabolic compounds in an ecosystem

secondary plant compound

compound produced as byproducts of plant metabolic processes that is usually toxic, but is sequestered by the plant to defend against herbivores