BIO Exam 1

Properties of life

• Order (a highly ordered structure characterizes life)

• Evolutionary adaptation

• Regulation (example: regulation of blood flow maintains a constant body temperature)

• Response to the environment

• Energy processing (organisms need fuel to function)

• Growth and development

• Reproduction

Unifying themes of life

• Organization

• Information

• Energy and Matter

• Interactions

• Evolution

Alcohol

• Distinguished by the presence of the hydroxyl (-—OH) functional group

• Ethanol, propanol and methanol

Organization from space to the molecular level

• The biosphere

• Ecosystems

• Communities

• Populations

• Organisms

• Organs

• Tissues

• Cells

• Organelles

• Molecules

Biosphere

Consists of all life on Earth and the places where life exists

Ecosystems

Consists of all the living things in an area, along with all of the nonliving components such as soil, water, atmospheric gases and light

Communities

• The array of organisms inhabiting a particular ecosystem

• The set of populations that inhabit a particular area

• Each organism belongs to a particular species

Species

A group whose members can only reproduce with other members of the group

Population

• Consists of all the individuals of a species living within an area

• There may be a population of lupines and a population of deer in the same area

What are the major organs of plants?

Leaves, stems and roots

Organ

A body part made up of multiple tissues with specific functions

Tissue

A group of cells that work together to perform a special function

Chloroplasts

• An organelle

• Responsible for photosynthesis

• Found only in eukaryotic cells

Organelles

Functional components present in cells

Molecule

A chemical structure consists of 2 or more atoms

Chlorophyll

A molecule that makes leaves green and absorbs light during photosynthesis

Reductionism

Reducing complex systems to simpler components that are easier to study

Emergent properties

• New properties emerge at each level that are absent from the preceding one (starting at the molecular level)

• Due to the arrangement and interactions of parts as complexity increases

Systems biology

Exploring a biological system by analyzing the interactions among its parts (a single leaf cell can be considered a system, as can a frog, an ant colony, or a desert ecosystem)

Cell Theory

States that all living organisms are made of cells, which are the basic unit of life that can perform all activities required for life

Prokaryotic cells

• Lacks a nucleus and organelles

Found in 2 groups of single-celled microorganisms:

• Bacteria

• Archaea

Eukaryotic cell

• Found in plants and animals

• Larger than prokaryotic cells

• Contain membrane-enclosed organelles

Types of data that document evolution

• Direct observations

• Homology

• The fossil record

• Biogeography

Homology

Similarity resulting from common ancestry

Homologous structures

• Share common ancestry, not similar function

• Represent variations on a structural theme that was present in their common ancestor

• Example: the forelimbs of all mammals show the same arrangement of bones

Vestigial structures

Remnants of features that served a function in the organism’s ancestors.

Convergent evolution

The independent evolution of similar features in different lineages (example: Marsupials and Eutherians)

Analogous structures

• Share similar function, but not common ancestry

• Species share features because of convergent evolution

Biogeography

the scientific study of the geographic distributions of species

Continental drift

• The slow movement of Earth’s continents over time

• These movements united all of Earth’s landmasses into a single large continent called Pangaea

Adaptations

inherited characteristics of organisms that enhance their survival and reproduction in specific environments

Natural selection

• A process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than do other individuals because of those traits

• Over time, natural selection can increase the frequency of adaptations that are favorable in a given environment

• If an environment changes, or if individuals move to a new environment, natural selection may result in adaptation to these new conditions, sometimes giving rise to new species.

Evolution

• Descent with modification

• The process by which species accumulate differences from their ancestors as they adapt to different environments over time

• Can also be defined as a change in the genetic composition of a population from generation to generation

• Organisms share many characteristics (unity). Darwin attributed the unity of life to the descent of all organisms from an ancestor that lived in the remote past.

• He also thought that as the descendants of that ancestral organism lived in various habitats, they gradually accumulated diverse modifications, or adaptations, that fit them to specific ways of life.

• Darwin thought of evolution as a process in which both descent (shared ancestry, resulting in shared characteristics) and modification (the accumulation of differences) can be observed

• Individuals do not evolve. Rather, it is the population that evolves over time

Artificial selection

• Humans modify other species generations by selecting and breeding individuals that possess desired traits

• Crops, livestock animals, and pets often bear little resemblance to their wild ancestors

Darwin observations and inferences

• Observation #1: Members of a population often vary in their inherited traits

• Observation #2: All species can produce more offspring than their environment can support, and many of these offspring fail to survive and reproduce

• Inference #1: Individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more offspring than do other individuals

• Inference #2: This unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations.

Aristotle

• Viewed species as fixed (unchanging)

• Through his observations of nature, Aristotle recognized certain “affinities” among organisms

• He concluded that life-forms could be arranged on a ladder, or scale, of increasing complexity, later called the scala naturae (“scale of nature”). Each form of life, perfect and permanent, had its allotted rung on this ladder

Old Testament account of creation

• Holds that species were individually designed by God and therefore perfect

• Scientists interpreted the remarkable ways in which organisms are suited for life in their environment as evidence that the Creator had designed each species for a particular purpose

Carolus Linnaeus

• In the 1750s, Linnaeus developed the two-part, or binomial, format for naming species (such as Homo sapiens for humans) that is still used today.

• Used a nested classification system, grouping similar species into increasingly inclusive categories

• Linnaeus did not ascribe the resemblances among species to evolutionary kinship, instead he believed in the Old Testament account of creation

Formation of fossils

• Many fossils are found in sedimentary rocks formed from the sand and mud that settle to the bottom of seas, lakes, and swamps

• New layers of sediment cover older ones and compress them into superimposed layers of rock called strata

• The fossils in a particular stratum provide a glimpse of some of the organisms that populated Earth at the time that layer formed

Paleontology

The study of fossils

Georges Cuvier

• Developed the field of paleontology

• Inferred that extinctions must have been a common occurrence, but opposed the idea of evolution

• Speculated that each boundary between strata represented a sudden catastrophic event, such as a flood, that had destroyed many of the species living in that area

James Hutton

Proposed that Earth’s geologic features could be explained by gradual mechanisms, such as valleys being formed by rivers

Charles Lyell

• The leading geologist of Darwin’s time

• Incorporated Hutton’s thinking into his proposal that the same geologic processes are operating today as in the past, and at the same rate

Lamarck

He explained his findings using two principles that were widely accepted at the time:

• The first was use and disuse, the idea that parts of the body that are used extensively become larger and stronger, while those that are not used deteriorate. Among many examples, he cited a giraffe stretching its neck to reach leaves on high branches

• The second principle, inheritance of acquired characteristics, stated that an organism could pass these modifications to its offspring

• Lamarck also thought that evolution happens because organisms have an innate drive to become more complex.

DNA

• It’s structure was discovered by Watson and Crick

• Within cells, structures called chromosomes contain genetic material in the form of DNA (deoxyribonucleic acid)

• A DNA molecule is made up of two long chains, called strands, arranged in a double helix

• Each chain is made up of four kinds of chemical building blocks called nucleotides, abbreviated A, T, C, and G

• Specific sequences of these four nucleotides encode the information in genes

Genes

• Each chromosome contains one very long DNA molecule with hundreds or thousands of genes, each a section of the DNA of the chromosome

• Transmitted from parents to offspring, genes are the units of inheritance

• Encode the information necessary to build all of the molecules synthesized within a cell, which in turn establish that cell’s identity and function

Gene expression

• The process by which the information in a gene directs the manufacture of a cellular product

• Protein-encoding genes control protein production indirectly, using a related molecule called RNA as an intermediary

• The sequence of nucleotides along a gene is transcribed into mRNA

• The cell translates mRNA into a linked series of amino acids (protein building blocks)

• Once completed, the amino acid chain forms a specific protein with a unique shape and function

Genome

The entire “library” of genetic instructions that an organism inherits

Genomics

An approach where researchers study whole sets of genes in species rather than studying a single gene at a time

Proteomics

the study of sets of proteins and their properties

Proteome

The entire set of proteins expressed by a given cell, tissue, or organism

Bioinformatics

the use of computational tools to store, organize, and analyze the huge volume of data that results from high-throughput methods

Energy flow and chemical cycling

• Energy flows through an ecosystem in one direction, usually entering as light and exiting as heat

• In contrast, chemicals cycle within an ecosystem, where they are used and then recycled

Feedback regulation

The output or product of a process regulates that very process.

Negative feedback

• A loop in which the response reduces the initial stimulus

• After a meal the level of the sugar glucose in your blood rises, which stimulates cells of the pancreas to secrete insulin

• Insulin causes body cells to take up glucose and liver cells to store it, decreasing the blood glucose level. This eliminates the stimulus for insulin secretion, shutting off the pathway. Thus, the output of the process (insulin) negatively regulates that process

Positive feedback

• A loop in which an end product speeds up its own production.

• The clotting of your blood in response to injury is an example. When a blood vessel is damaged, platelets begin to aggregate at the site. Positive feedback occurs as chemicals released by the platelets attract more platelets. The platelet pileup then initiates a complex process that seals the wound with a clot

Global warming

• Humans have greatly increased the burning of fossil fuels (coal, oil, and gas).

• This practice releases large amounts of carbon dioxide CO2 and other gases into the atmosphere, causing heat to be trapped close to Earth’s surface

• CO2 added to the atmosphere has increased the average temperature of the planet

Climate change

A directional change to the global climate that lasts for three decades or more

Inquiry

the search for information and explanations of natural phenomena

Qualitative data

Often in the form of recorded descriptions rather than numerical measurements

Quantitative data

Expressed as numerical measurements and often organized into tables and graphs

Inductive reasoning

• Reasoning from a set of specific observations to reach a general conclusion (specific to general)

• “The sun always rises in the east” “All organisms are made of cells”

Hypothesis

• An explanation, based on observations and assumptions, that leads to a testable prediction

• Must be testable; there must be some observation or experiment that could reveal if such an idea is likely to be true or false

Deductive reasoning

• General to specific

• From general premises, we extrapolate to the specific results we should expect if the premises are true

• This deductive testing takes the form of “If . . . then” logic

Model organism

• A species that is easy to grow in the lab and lends itself particularly well to the questions being investigated.

• Because all species are evolutionarily related, such an organism may be viewed as a model for understanding the biology of other species and their diseases

Independent variable

The factor being manipulated by researchers

Dependent variable

• The factor being measured that is predicted to be affected by the independent variable

• Depends on the independent variable

Theory

• Explain a great diversity of observations

• General enough to spin off many new hypotheses

• Compared to a hypothesis, it is much broader and is supported by a greater body of evidence

Matter

• Anything that takes up space and has mass (rocks, metals, oils, gases and living organisms)

• All matter is made up of elements

Element

• A substance that can’t be broken down to other substances

• Consist of a certain type of atom

Compound

A substance consisting of 2 or more different elements combined in a fixed ratio

Essential elements

• Oxygen, carbon, hydrogen and nitrogen make up 96% of matter

• Calcium, phosphorus, potassium and sulfur make up 4%

Trace elements

• Required by an organism in only minute quantities

• Iron is a trace element needed by all life forms; iodine is essential only in vertebrates (animals with backbones)

Atom

• The smallest unit of matter that still retains the properties of an element

• Composed of subatomic particles

Nucleus

• Positive charge

• Contains protons and neutrons

Dalton

• Unit of measurement for atoms

• The same as atomic mass unit (amu)

Atomic number

• The number of protons

• Written as a subscript to the lower left of the symbol

• Tells us the number of electrons in a neutral atom

Mass number

• Total number of protons and neutrons

• Written as a subscript to the upper left of the symbol

How to find the number of neutrons

Number of neutrons = mass number - atomic number

Isotopes

• Atoms that have more neutrons than other atoms of the same element and therefore have greater mass

• Although the isotopes of an element have slightly different masses, they behave identically in chemical reactions

Stable isotope

Nuclei does not have a tendency to decay, the process of losing subatomic particles

Radioactive isotope

• Unstable

• The nucleus decays spontaneously, giving off particles and energy

• When the radioactive decay leads to a change in the number of protons, it transforms the atom to an atom of a different element

Half-life

The time it takes for 50% of the parent isotope to decay into its daughter isotope

Radiometric dating

A process in which scientists measure the ratio of different isotopes and calculate how many half-lives have passed since an organism was fossilized

Energy

The capacity to cause change- for instance, by doing work

Potential energy

• Energy that matter possess because of its location or structure

• Matter has a natural tendency to move toward the lowest possible state of potential energy

Electron shells

• The first shell is closest to the nucleus, and electrons have the lowest possible energy

• Electrons in shells that are farther out have more energy

• When an electron absorbs energy, it moves to higher energy level

• When an electron loses energy, it moves back to a shell closes to the nucleus, and the energy is typically lost to the environment as light

Valence shell

• Outermost electron shell with valence electrons

• The chemical behavior of an atom depends mostly on the number of electrons in this shell

• Atoms with the same number of electrons in their valence shells exhibit similar chemical behavior

Which elements are chemically unreactive?

Helium, neon and argon because they have full valence shells

Orbital

• The three-dimensional space where an electron is found 90% of the time

• No more than 2 electrons can occupy a single orbital

Electron orbitals

• The first electron shell has only one s orbital (called 1s) that can accommodate up to 2 electrons

• The second shell has four orbitals: one large s orbital (called 2s) and three dumbbell-shaped p orbitals (called 2p orbitals)

• The second shell can hold up to 8 electrons, with 2 in each orbital

Covalent bond

• The sharing of a pair of valence electrons by 2 nonmetal atoms

Molecule

Consists of 2 or more atoms held together by covalent bond

Different ways to represent molecules

• Molecular formula (H₂)

• Lewis dot structure (H:H)

• Structural formula (H—H)

• Space-filling model (comes closest to representing the actual shape of the molecule)

Valence

• Refers to the number of covalent bonds the atom can form

• Equals the number of electrons required to complete the valence shell

• The valence of hydrogen is 1; oxygen 2; nitrogen 3; carbon 4

Electronegativity

• The attraction of a particular atom for the electrons of a covalent bond

• The more electronegative an atom is, the more strongly it pulls shared electrons toward itself

Nonpolar covalent bond

In a covalent bond between two atoms of the same element, the electrons are shared equally because the two atoms have the same electronegativity—the tug-of-war is at a standoff

Polar covalent bond

When an atom is bonded to a more electronegative atom, the electrons of the bond are not shared equally

Example of polar covalent bond

• Bonds between oxygen and hydrogen atoms of a water molecule

• Electrons have a negative charge and are pulled toward oxygen in a water molecule, so the oxygen has partial negative charges (δ−, or “delta minus”), while the hydrogen atoms have partial positive charges (δ+, or “delta plus”)