biol 1001

midterm

What is an organism ?

is a life-form—a living entity made up of one or more cells.

The five fundamental characteristics organisms share

cells
replication
evolution
information
energy

what is a gene

hereditary, or genetic, information encoded in units

To stay alive and reproduce, organisms have to acquire and use

energy

what is a theory

an explanation for a very general class of phenomena or observations that is supported by a wide body of evidence.

what is a hypothesis

testable statement to explain a phenomenon or a set of observations.


Biologists usually use the word "theory" to refer to proposed explanations for broad patterns in nature and prefer "hypoth esis" to refer to explanations for more tightly focused questions. A theory serves as a framework for developing new hypotheses.

cell theory

All organisms are made of cells, and all cells come from preexisting cells.

hypothesis vs theory

Biologists usually use the word "theory" to refer to proposed explanations for broad patterns in nature and prefer "hypoth- esis" to refer to explanations for more tightly focused questions.
(A theory serves as a framework for developing new hypotheses.)

experiment

allow researchers to test the effect of a single, well-defined fac- tor on a particular phenomenon.(testing a hypothesis)

An experimental prediction describes a measurable or observable result that must be correct if a hypothesis is valid.

describes a measurable or observable result that must be correct if a hypothesis is valid.

Darwin and wallence theory claims

1. Species are related by common ancestry

2.The characteristics of species can be modified from genera- tion to generation.

Evolution is

Evolution is a change in the characteristics of a population over time.

population is

group of individuals of the same species living in the same area at the same time.

natural selection explains how

evolution occurs

The two conditions for natural selection to happen are :-

1. Individuals within a population vary in characteristics that are heritable

2. certain versions of these heritable traits help individuals survive better or reproduce more than other versions.

heritable traits that lead to success in production

become more common over time (evolution)

evolution occurs when

heritable variation leads to differential success in reproduction.

natural selection

occur in individuals

evolutionary change occur

in populations

what is speciation

natural selection has caused populations of one species to diverge and form new species.

t/f All species come from preexisting species, and all species, past and present, trace their ancestry back to a single common ancestor.

true

Fitness( survival of the fittest)

an individual's ability to produce viable offspring (not the srtongest or the biggest, the more an organism produce the more they are fit

Adaptation

a trait that increases the fitness of an individual in a particular environment.

what happens during natural selection

adaption + survival of the fittest

chromosome theory of inheritance

hereditary or genetic information is encoded in genes, the units located on chromosomes.

DNA, genes and chromosomes

a chromosome consists of a molecule of DNA.

Genes consists of segments of DNA that code for products in the cell.

the four building blocks

a-t, g-c

T/F DNA is double helix

true

DNA can be copied, and the information encoded in the DNA is faithfully preserved.

central dogma

the flow of information in cell ( DNA codes for RNA, which codes for proteins)

Molecular machinery in cells makes a copy of a particular gene's information in the form of a closely related molecule called

rna

molecular machinery reads a messenger RNA molecule to determine what building blocks are required to make a

protein

Organisms have two fundamental nutritional needs:-

1. ATP (or adenosine triphosphate)

2. obtaining molecules that can be used as building blocks for the synthesis of DNA, RNA, pro- teins, the cell membrane, and other large, complex compounds required by the cell.

tree of life

a tree of organisms

Phylogeny

The evolutionary history of a species or group of related species "tribe source" (genealogical relationship)

rRNA

These are an essential part of ribosomes, which are cellular machinery that all cells use to grow and reproduce.

rRNA bases

a-u, g,c

analyzing genetic variation by

1. comparing ribonucleotide sequence in rRNA
then seeing the differences and similarities

phylogenetic tree

A diagram that shows evolutionary history in t

family tree vs phylogentic tree

family tree shows relationships among individuals, a phylogenetic tree shows relationships among species.

Researchers who study the origin of life propose that the tree's root extends even further back to the

"last universal common ancestor" of cells, or LUCA.

fundamental groups in tree of life

(1) the Bacteria, (2) the Archaea, and (3) the Eukarya.

Eukaryotes vs Prokaryotes

have nucleus, does not have a nucleus

Taxonomy

The scientific study of how living things are classified

Domain

A taxonomic category above the kingdom level. The three domains are Archaea, Bacteria, and Eukarya.

Phylum

Group of closely related classes with(inside a domain) remember photo

T/F the tree of life is so new, though, naming systems are still being worked out.

T

Genus

A genus is made up of a closely related group of species.

species

The second term in the two-part name identifies the organism's species

scientific name

The name given to each species, consisting of its genus and its species label (genus then species) genus capitalized ex Homo sapiens.

how To if something fits into scientific methods

1. it should deal with our natural world (doesn't deal with supernatural)
2.can be observed: you must be able to identify the process
3. should be testable : can produce a prediction
4.can be self correcting and can be changed to match the results

Examine the following DNA sequences and determine which two species would be closest on a phylogenetic tree:
Species A: A A C T A G C G C G A T

Species B: A A C T A G C G C C A T

Species C: T T C T A G C G G T A T

A and b

Scientific names and terms are

often based on Latin or Greek word roots that are descriptive

artificial selection

when humans select certain individuals to produce the most offspring.

null hypothesis

a statement or idea that can be falsified, or proved wrong (what should be observed when the hypothesis being tested isn't correct.)

prediction specifies

what we should observe if a hypothesis is correct. Good scientific hypotheses make testable predictions—predictions that can be supported or rejected by collecting and analyzing data.

why is is important to add a control in a experiment ?

A control checks for factors, other than the one being tested, that might influence the experiment's outcome.(one factor is changed)

A good hypothesis is:

one that is simple, consistent with the available facts, and can be tested.

Hypotheses are proposed explanations that

make testable predictions.

Predictions describe observable outcomes of particular conditions.

Well-designed experiments alter just one condition—a condition relevant to the hypothesis being tested.

Explain why researchers formulate a null hypothesis in addition to a hypothesis when designing an experimental study.

because it helps researchers see what is observed when the hypothesis tested is being wrong

scientific theory have two components

The pattern component is a statement that summarizes a series of observations about the natural world. The pattern component is about facts—about how things are in nature.


The process component is a mechanism that produces that pattern or set of observations.

Scientific Revolution

overturns an existing idea about how nature works and replaces it with another,

Plato

Plato claimed that every organism was an example of a perfect essence, or type, created by God, and that these types were unchanging

Aristotle

proposed that species were fixed types organized into a sequence based on increased size and complexity. The scale started with minerals, rising through "lower" and "higher" plants, then "lower" and "higher" animals, with humans at the top.

Lamarck and the idea of evolution as change through time

the pattern component of Lamarck's theory was initially based on the scale of nature.

Lamarck claimed that simple organisms originate at the base of the scale by spontaneous generation and then evolve by moving up the scale over time

Thus, Lamarckian evolution is progressive, in the sense of always producing larger and more complex, or "better," species.

Darwin and Wallace's theory of evolution by natural selection was revolutionary because it \_____.

emphasized that the process responsible for change through time—evolution—occurs because traits vary among the individuals in a population,

population

consists of individuals of the same species that are living in the same area at the same time.

typological vs population thinking

typological: Plato and his followers emphasized the existence of fixed types. population thinking: evolution by natural selection is all about change and diversity.

reasons why theory of evolution is revolutionary

It overturned the idea that species are static and unchanging. Instead, it suggested that species change through time and are related by common ancestry


It replaced typological thinking with population thinking.


It was scientific. It proposed a mechanism that could account for change through time and made predictions that could be tested through observation and experimentation

descent with modification

principle that each living species has descended, with changes, from other species over time

the pattern component of the theory of evolution

Species change through time.

Species are related by common ancestry.

Fossil

A Fossil Is Any Trace of an Organism That Lived in the Past.

fosil record

made up of all the fossils ever discovered on Earth

sedimentary rock

A type of rock that forms when particles from other rocks or the remains of plants and animals are pressed and cemented together

geologic time scale

scale used by paleontologists to represent evolutionary time

Darwin ideas are influenced by

(dont memorize names )Buffon (1707-1788) - organismal differences related to environments inhabited


Lamarck (1744-1829) - proposal of how evolution occurred
•species changed through time; changes passed to kids

Both:• Suggested populations are changing• Stressed the importance of variation in natural populations.

Hutton (1726-1797) - gradualism

Lyell (1797-1875) - uniformitarianism

the concept of gradualism and uniformitarianism

'The present is the key to the past.'

Gradualism - slow processes over long geologic time periods
•Accumulation of small changes over long periods of time can add up to big changes

•Uniformitarianism - present is key to past & vice-versa•Current geological processes occurred in past at same rate as today.

Evidence for evolution - fossil record

Less complex (simple) body plans evolved before complex ones•
• Transitional fossils• Diversification of groups

Most recent fossils most similar to living spp

transitional fossils

ossil spp with traits intermediate b/w those of older & younger spp(evidence of evolution)

Radiometric dating is based on three pieces of information:

Observed decay rates of parent-to-daughter atoms.


The ratio of parent-to-daughter atoms present in newly formed rocks—such as the amount of uranium atoms versus lead atoms when uranium-containing molten rock first cools. (Uranium decays to form lead.)

The ratio of parent-to-daughter atoms present in a particular rock sample.

How old is the Earth?

4.6 billion years old

extinction of species

A type of species that no longer lives anywhere on the Earth.

Darwin mentioned that species are

are not static, immutable entities, unchanged since the moment of special creation. His reasoning was that if species have gone extinct, then the array of species living on Earth has changed through time.

law of succession

extinct species in the fossil record were succeeded in the same region by similar species

transitional feature

a trait in a fossil species that is intermediate between those of ancestral and derived species

vestigial traits

a reduced or incompletely developed structure that has no function or reduced function but is clearly similar to functioning organs or structures in closely related species.

Homology

Similarity in characteristics resulting from a shared ancestry.

Homology levels

1. Genetic: occurs in DNA nucleotide sequences, RNA nucleotide sequences, or amino acid sequences

2. Developmental:
recognized in embryos.


3. Structural: similarity in adult morphology, or form.

internal consistency

when the facts presented within a single source do not clash with each other

application of phylogenetic trees

in medicine, to understand the spread of disease, such as AIDS and Ebola;

in forensics, to identify a body, such as the species of bird that got caught up in a jet engine, causing an airplane to crash;

in taxonomy, to define species
in conservation, to identify the origin of illegally traded mate-
rials, such as elephant ivory and rhino horn;

also in conservation, to identify species that are a priority for preservation (see Chapter 54);
in agriculture, to identify wild species for breeding to improve disease resistance in crops;


in anthropology, to study the history of languages and other aspects of culture;

in food science, to track the identity of foods in the marketplace.

Parts of a phylogenetic tree

Branch a line representing a population through time


Root The most ancestral branch in the tree


Tip (terminal node)
Endpoint of a branch; represents a living or extinct group of genes, species, families, phyla, or other taxa


Outgroup a taxon that diverged prior to the taxa that are the focus of the study; helps to root the tree


Node (fork) a point within
the tree where a branch splits into two or more branches;
the node represents the most recent common ancestor of the descendant groups


Polytomy a node that depicts an ancestral branch dividing into three or more (rather than two) descendant branches; usually indicates that insufficient data were available to resolve which taxa are more closely related

Homology vs. Homoplasy

Homology when traits are similar due to shared ancestry;

homoplasy: when traits are similar for reasons other than common ancestry.

convergent evolution

Process by which unrelated organisms independently evolve similarities when adapting to similar environments

homology vs. convergent evolution

trait inherited from a common ancestor vs. evolved to have coincidentally similar traits probably for similar uses (imilar traits in organisms facing similar challenges)

types of evidence for homology

phylogenetic, structural, genetic

Consilience

different branches of evidence support, or are consistent with, other branches

Fossilization

Dead plants and animals that fossilize. when the remains of an organism are buried in sediments, where decay is slow.

palaeontologist

A scientist who studies fossils

Limitation of Fossil Record

habitat bias: Because burial in sediments is so crucial to fossilization, there is a strong habitat bias in the database.


taxonomic: Slow decay is almost always essential to fossilization, so organisms with hard parts such as bones or shells are most likely to leave fossil evidence


temporal bias: Recent fossils are much more common than ancient fossils. This causes a temporal bias in the fossil record.

abundance bias: Organisms that are abundant, widespread, and present on Earth for long periods of time leave evidence much more often than species that are rare, local, or ephemeral.