Biology - Quiz 2

Chapter 25.1/3.1-3.4/7.1-7.3/44.1,44.3/slideshow/readings/films/

Phylogeny

The evolutionary history of a group of organisms.

Phylogenetic tree

A branching diagram that depicts the evolutionary relationships among species or other taxa.

Systematics

The subdiscipline of biology that characterizes and classifies the relationship among all organisms on Earth.

Tree of life

The phylogenetic tree that includes all organisms.

Taxonomy

The branch of biology concerned with describing, naming, and classifying groups of organisms.

Taxon (taxa)

Any named group of organisms at any level of a classification system

Polytomy

A node in a phylogenetic tree that depicts an ancestral branch dividing into three or more descendant branches; usually indicated that insufficient data were available to tesolve which taxa are more closely related.

Branch

A line representing a species or othe taxon through time
1. Apart of phylogenetic tree that represents population through time
2. A lateral extention of a plant's shoot system.

Root

The most ancestral branch in the tree.

Tip

Endpoint of a branch; represents a living or extinct species or other taxon

Outgroup

A taxon that diverged before the taxa that are the focus of the study; helps to 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

Sister groups

Two lineages that are each other's closest relatives, represented by two branches emerging from a node in a phylogenetic tree.

Character/trait

Any heritable genetic, morphological, physiological, developmental, or behaviora; characteristic of an organism to be studied. Also called a trait

Ancestral trait

A trait found in the ancestors of a particular group.

Derived trait

A trait that is a modified form of an ancestral trait, found in a descendant.

Synapomorphy

A shared, derived trait found in two or more taxa is present in their most recent common ancestor but is missing in more distant ancestors. Useful for inferring evolutionary relationships.

Monophyletic group (Clade or lineage)

An evolutionary units that includes an ancestral population and all of its descendants but no others. Also called clade or lineage. Compare with paraphyletic group and polyphyletic group.

Homology (homologous)

Similarity among organisms or different species due to share ancestry. Features that exhibit such similarity (e.g., DNA sequences, proteins, body parts) are said to be homologous. compare with homoplasy

Homoplasy

Similarity among organisms of different species due to reasons other than common ancestry, such as convergent evolution. Compare with homology.

Parsimony

The principle that the most likely explanation of a phenomenon is the most economical or simplest. When applied to comparison of alternative phylogenetic trees, it suggests that the one requiring the fewest character changes is most likely.

Evolutionary distance

Unlike parsimony analysis, distance methods acknowledge that more rapid evolutionary change may occur is some branches than others. Evolutionary distance methods begin by quantifing the average frequency of character changes between individuals pairs of taxa, then they search for the tree that best aligns with the total data set.

Maximum likelihood and Bayesian analysis

These mathematical models are more complex than the other methods because they required more information than is provided in the data matrix, such as the probability that in a DNA sequence, a G would be substitued by an A ratherthan a C or T. These methods are popular with molecular data sets because they can produce relatively precise estimates of evolutionary history with more statistical power than the other methods.

Convergent evolution

The independent evolution of similar traits in different species due to adaptation to similar environmental conditions and a similar way of life.

Phylogenetic evidence

A molecular phylogeny of plants shows that water lilies and roses fall into a monophyletic group, called angiosperms. Note that all the other lineages in this group also have flowers. This result suggest that water lilies and wild roses have flowers because they inherited these structures from a common ancestor that also had flowers.

Structural evidence

Although flowers are diverse, most are build on the same general template: four concentric whorls of cells that form sepals, petals, stamen, and carpels.

Genetic and developmental evidence

The genetic toolkit and development patterns responsible for the development of floral structures are similar in different plants, including the involvement of MADS-box genes.

Amino acids

A small organic molecule with a central carbon atom bonded to an amino group (-NH3), a carboxyl group (-COOH), a hydrogen atom, and a side chain. When amino acids are linked together to form proteins, they are referred to as residues.

Amino acid structure

1. H - a hydrogen atom
2. NH2 - an amino functional group
3. COOH - a carboxyl functional group
4. R-group (side chain)

R-group (side chain)

Part of an amino acid'd core structure that varies from a single hydrogen atom to large structure that varies from a single hydrogen atom to large structures containing carbon rings. R-group variability is responsible for the variability in amino acid structure and function. Also called side chains.

Hydrophilic

Interacting readily with water. Hydrophilic compounds are typically polar compounds containing or fully charged atoms. Compare with hydrophobic.

Hydrophobic

Not interacting readily with water. Hydrophobic compounds are typically nonpolar molecules. Compare with hydrophilic.

R group with a negative charge

Its an acidic and has lost a proton

R group with a positive charge

Its a basic and has picked up a proton

Uncharged R Group with Oxygen

Then the highly electronegative oxygen will form a polar covalent bond in the R-group, thus making it uncharged polar like serine.

How do amino acids link to form proteins?

Peptide bond

The convalent bond fromed by a condensation reaction between two amino acids.

R group orientation

The side chains of each residue extend out from the backbone, making it possible for them to interact with each other and with water.

Directionality

There is an amino group (-NH3+) on one end of the backbone and a carboxyl group (-Coo-) on the other. The end ofthe residue sequence that has the free amino group is called the N-terminus, or amino terminus, and the end with the free carboxyl group is called the C-terminus, or carboxy terminus. By convention, biologists always write amino acid residue sequences from the N-terminus to the C-terminus, because the N-terminus is the start of the chain when proteins are synthesized in cells.

Flexibility

Although the peptide bond itself cannot rotate because of its double-bond nature, the single bonds on either side of the peptide bond can rotate. As a result, the structure as a whole is flexible.

Oligopeptides or peptide

A chain composed of fewer than 50 amino acid residues linked together by peptide bonds. Often referred to simple as peptide.

Polypeptides

A chain typically consisting of 50 or more amino acids linked together by peptide bonds. Compare with oligopeptide and protein.

Protein

Amacromolecule consisting of one or more polypeptide chains. Each polypeptide has a unique sequence of amino acids and each protein generally possesses a characteristic three-dimensional shape.

Can amino acids spontaneously assemble into proteins?

The current consensus is that several mechanisms could have led to self-polymerization of amino acids under early earth conditions.

What do proteins look like?

The structure give them there function

DNA

RNA

Primary structure of protein

The sequence of amino acid residues in a protein polymer; also the sequence of nucleotides in a single nucleic acid strand. Compare with secondary, tertiary, and quaternary structure.

Secondary structure of protein

In proteins, localized folding of a polypeptide chain into regular structures (i.e.,alpha-helices and beta-pleated sheets) stabilized by hydrogen bonding between atoms peptide backbone. In nucleic acids, elements ofstructure (e.g., helices and hairpins) stabilized by hydrogen bonding between complementary bases and hydrophobic interactions with the aqueous environment. Compare with primary, tertiary, and quaternary structures.

Alpha-helix

A secondary structure in proteins formed when the polypeptide backbone coils into a spiral shape stabilized by hydrogen bonding.

Beta-pleated sheet

Asecondary structure in proteins, formed when the polypeptide backbone folds into a sheetlike shape stabilized by hydrogen bonding.

tertiary structure of protein

The overall three-dimensional shape of a single polypeptide chain, resulting from multiple interactions among the amino acid side chains and the peptide backbone. In nucleic acids, three-dimensional shape is formed by hydrogen bonding between complementary bases and other interactions. Compare with primary, secondary, and quaternary structure.

Hydrogen bonding

A weak interaction between two molecules or different of the same molecule resulting from the attraction between a hydrogen atom with a partial positive charge and another atom (usually O or N) partial negative charge. Compare with covalent bond and ionic bond.

Hydrophobic interactions

Very weak interactions between nonpolar molecules, or nonpolar regions of the molecule, when exposed to an aqueous solvent. The surrounding water molecules support these interactions by interacting with one another and encapsulating the nonpolar molecules.

Van der Walls interactions

A weak electrical attraction between two non poloar moleculs or parts of a molecule that have been brought together, often through hydrophobic interactions. In proteins, it contributes to tertiary and quaternary structures.

Covalent bonding

Ab type of chemical bond in which two atoms share one or more pairs of electrons. Compare with Hydrogen bond and ionic bond.

Disulfide bonds

A covalent bond between two sulfur atoms, typically in the side chains of certain amino acids (e.g., cysteine). Often contributes to tertiary and quaternary levels of protein structure.

Ionic bonding

Achemical isformedwhenan electron is completely transferred from one atom to another. Resulting ions remain associated due to their opposite electric charges. Compare with covalent bond and hydrogen bond.

Quaternary structure of a protein

In proteins, the over all three-dimensional shape formed combination of two or more polypeptide chains (subunits); determined by the number, relative positions, and interactions ofthe subunits. In nucleic acids, two or more distinct single strands will form this level of structure through hydrogen bonding between bases and hydrophobic interactions aqueous environment. Compare with primary, secondary, and tertiary structures.

Macromolecular machines

A group of proteins, and possibly other nonprotein macromolecules, that assemble to carry out a particuler function.

Protein folding

Is derected by the sequence of amino acids present in the primary structure.

Denatured (denaturation)(denature)

For a macromolecule, loss ofits three-dimensional structure due to breakage of covalent and/or noncovalent chemical bonds, usually caused by exposure to heat, certain chemicals, or extreme pH conditions.

Molecular chaperones

A protein that facilitates the folding or refolding of a protein in to its correct three-dimensional shape.

Prions

An infectious particle that consists entirely of protein. Prion proteins adopt two differently folded shapes: a normally folded shape and an infectious, often disease-causing shape. The infectious version can bind normally folded prion proteins and cause them to adopt the infectious shape. Also called proteinaceous infectious particles.

Catalysis (catalyst

Acceleration of the rate of a chemical reaction due to a decrease in the free energy of the transition state, called the activation energy.

Catalyze of protein

Many proteins are specialized to catalyze, or speed up, chemical reactions. A protein that functions as a catalyst is called an enzyme. The carbonic anhydrase molecules in red blood cells are enzymes. So is the salivary amylase protein in your mouth. Salivary amylase begins the digestion of starch into simple sugars. Most chemical reactions that make life possible depend on enzymes.

Enzyme

A protein catalyst used by living organisms to increase the rate of biological reactions.

Structure of protein

Structural proteins make up body components such as fingernails and hair, and form the internal "skeleton" fo individual cells. .Structural proteins keep red blood cells flexible and in their normal disc-like shape.

Movement of protein

Motor proteins and contractile proteins are responsible for moving the cell itself, or for moving large molecules and other types of cargo inside the cell. As you turn this page, for example, specialized proteins called actin and myosin will slide past one another to flex or extend muscle cells in your fingers and arm.

Signaling of protein

Proteins are involved in carrying and receiving signals from cell to cell inside the body. Many ofthem reside on the cell's membrane to interact with neighboring cells. If sugar levels in your blood are low, a small peptide called glucagon will bind to receptor proteins on your liver cells, triggering enzymes inside to release sugar into your bloodstream.

Transport of protein

Proteins allow particular molecules to enter and exit cells or carry them throughout the body. Hemoglobin is a particularly well-studied transport protein, but virtually every cell is studded with membrane proteins that control the passage of specific molecules and ions.

Defense of protein

Proteins called antibodies attack and destroy viruses and bacteria that cause disease don't occur fast enough to support life unless a catalyst is present. Enzymes are the most effective catalysts on Earth.

Why are enzymes good catalysts?

Substrates

1. Areactantthatinteractswithacatalyst, such as an enzyme or ribozyme, in a chemical reaction.
2. A surface on which a cell or organism sits.

Active site

The location in anenzy memolecule where substrates (reactant molecules) bind and react.

Morphology

The overall shape and appearance of an organism and its component parts.

Phylogeny

The evolutionary history of a group of organisms.

Transmission Electron Microscope (TEM)

A microscope that produces images by passing a focused beam ofelectrons through extremely thin sections of a specimen stained with heavy metals. Compare with scanning electron microscope.

Cytoplasm

All the contents of a cell bounded by the plasma membrane, excluding the nucleus (if present).

Chromosome

Gene-carrying structure consisting of a single long molecule of double-stranded DNA and associated proteins (e.g., histones) . Most prokaryotic cells contain a single circular chromosome; eukaryotic cells contain multiple noncircular (linear) chromosomes located in the nucleus.

Genes

1. In a molecular context, a section of DNA (or RNA, for some viruses) that contains the regulatory sequences and coding in for mation for the transcription of one or more related functional RNA molecules, some of which encode polypeptides.
2. In Mendelian genetics, the hereditary determinant ofa trait, such as flower color or seed shape in pea plants.

Nucleoid

In prokaryotic cells, a dense, centrally located region that contains DNA but is not surrounded by a membrane.

Plasmid

A small, usually circular, supercoiled DNA molecule that exists independently ofthe cell's main chromosome(s) in prokaryotes and some eukaryotes.

Ribosomes

A large macromolecular machine that synthesizes protenins by using the genetic information encoding in messenger RNA. Consists of two subunits, each composed of ribosomal RNA and proteins.

Cytoskeleton

In eukaryotic cells, a network of protein fibers in the cytoplasm that are involved in cell shap, support, locimotion, and transport of materials within the cell. Prokaryotic cells have a similer but much less extensive network of fibers.

Organelles

Anydiscrete,oftenmembrane-bound compartment within a cell (e.g., mitochondrion) that has a characteristic structure and function.

Cell wall

A fibrous layer found plasma membrane of most bacteria and archaea and many eukaryotes.

Flagellum (flagella)

A long, cellular projection that undulated (in eukaryotes or rotates (in prokartotes) to move the cell through an aqueous enviornment. See axoneme.

Fimbria (fimbriae)

A long, needlelike projection from the cell membrane of bacteria that is involved in attachment to nonliving surfaces or other cells.

Cytosol

The fluid portion of the cytoplasm,excluding the contents of membrane-enclosed organelles.

Nucleus

1. The center of an atom, containing protons and neutrons.
2. In eukaryotic cells, the large organelle containing the chromosomes and surrounded by a double membrane.
3. A discrete clump of neuron cell bodies in the brain, usually sharing a distinct function.

Nuclear Envelope

The double-layered membrane enclosing the nucleus of a eukaryotic cell.

Nuclear Lamina

A lattice-like sheet of fibrous nuclear lamins, which are one type of intermediate filament. Lines the inner membrane of the nuclear envelope, stiffening the envelope and helping to organize the chromosomes.

Nucleolus

In eukaryotic cells, a specialized structure in the nucleus where ribosomal RNA processing occurs and ribosomal subunits are assembled.

Endoplasmic Reticulum (ER)

A network of interconnected membranous sacs and tubules found inside eukaryotic cells that functions in lipids and proteins that reside in the endomembrane system and the plasma membrane or are secreted from the cell. Seerough and smooth endoplasmic reticulum.

Rough Endoplasmic Reticulum (RER) (rough ER)

The portion of the endoplasmic reticulum that is dotted with
ribosomes. Involved in synthesizing plasma membrane proteins, secreted proteins, and proteins localized to the ER, Golgi apparatus, and lysosomes. Compare with smooth endoplasmic reticulum.

Lumen

The interior space of any hollow structure (e.g., the rough ER) or organ stomach).

Smooth Endoplasmic Reticulum (SER) (smooth ER)

The portion endoplasmic reticulum that lacks attached ribosomes. Involved in lipids and removing toxic molecules. Compare with rough endoplasmic reticulum.

Golgi apparatus

A eukaryotic organelle, consisting of stacks offlattened membranous sacs (cisternae), that functions in processing and sorting proteins and lipids
destined to be secreted or directed to other organelles. Also called Golgi complex.