Evolution
Evolution is the process of change that has transformed life on Earth
DNA
Deoxyribonucleic acid: a long linear polymer found in the nucleus of a cell and formed from nucleotides and shaped like a double helix
Biology
The scientific study of life
Eukaryotic Cell
A type of cell with a membrane-enclosed nucleus and membrane-enclosed organelles. Organisms with eukaryotic cells (protists, plants, fungi, and animals) are called eukaryotes.
Prokaryotic Cell
A type of cell lacking a membrane-enclosed nucleus and membrane-enclosed organelles. Organisms with prokaryotic cells (bacteria and archaea) are called prokaryotes.
Biosphere
The entire portion of Earth inhabited by life; the sum of all the planet's ecosystems.
Ecosystems
All the organisms in a given area as well as the abiotic factors with which they interact; one or more communities and the physical environment around them
Community
All the organisms that inhabit a particular area; an assemblage of populations of different species living close enough together for potential interaction.
Population
A group of individuals of the same species that live in the same area and interbreed, producing fertile offspring.
Organism
a creature such as a plant, animal or a single-celled life form, or something that has interdependent parts and that is being compared to a living creature
Organs
A specialized center of body function composed of several different types of tissues.
Organ Systems
A group of organs that work together in performing vital body functions.
Tissues
An integrated group of cells with a common structure, function, or both.
Organelles
Any of several membrane-enclosed structures with specialized functions, suspended in the cytosol of eukaryotic cells.
Cell
The part of a neuron that houses the nucleus and most other organelles.
Molecule
Two or more atoms held together by covalent bonds.
Negative Feedback
A form of regulation in which accumulation of an end product of a process slows the process; in physiology, a primary mechanism of homeostasis, whereby a change in a variable triggers a response that counteracts the initial change.
Positive Feedback
A form of regulation in which an end product of a process speeds up that process; in physiology, a control mechanism in which a change in a variable triggers a response that reinforces or amplifies the change.
Adaptation
Inherited characteristic of an organism that enhances its survival and reproduction in a specific environment.
What are the 7 Characteristics of Life?
1. Order2. Regulation3. Energy Processing4. Evolutionary Adaptation 5. Response to the Environment 6. Reproduction 7. Growth and Development
Metabolism
The totality of an organism's chemical reactions, consisting of catabolic and anabolic pathways, which manage the material and energy resources of the organism.
What are the three domains by which all living organisms are classified?
Domain Bacteria Domain Archaea Domain Eukarya
What are the 4 kingdoms in the Domain Eukarya?
Plantae Animalia FungiProtista
What are Bacteria?
All unicellular prokaryotic (no nucleus) organisms with peptidoglycan in their cell walls
What is the Theory of Natural Selection?
A process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than other individuals because of those traits.
Why is evolution considered the core theme of biology?
Evolution accounts for the unity and diversity of life and it explains the most fundamental aspects of all life on earth. It accounts for the common features shared by all forms of life due to the descent from a common ancestor.
Define Biology? What is the definition of Biology
Biology is the scientific study of life
What is the molecule that can account for both the unity and the diversity of life?
DNA
What is the appropriate term for an interacting group of individuals of a single type occupying a defined area?
A Population
How would you define a Eukaryotic cell?
A eukaryotic cell has membrane-enclosed organelles, the largest of which is usually the nucleus
How would you define a prokaryotic cell?
A prokaryotic cell is simpler and usually smaller, and does not contain a nucleus or other membrane-enclosed organelles
What are the 7 Properties/Characteristics of Life
1. Order2. Regulation3. Energy Processing4. Evolutionary Adaptation 5. Response to the Environment 6. Reproduction 7. Growth and Development
What are the 10 levels of Biological Organization?
1. Biosphere2. Ecosystem3. Communities4. Populations5. Organisms6. Organs and Organ Systems7. Tissues8. Cells 9. Organelles10. Molecules
Cell
The lowest level of organization that can perform all activities required for life
Of the three domains Bacteria, Archaea, and Eukarya, which one is prokayotic?
Archaea
The energy used by most organisms for metabolism and growth ultimately comes from....
The sun
Eukaryotic organisms that decompose dead organisms and absorb the nutrients are generally found in which kingdom?
Fungi
Primary Structure
-Sequence of AAs attached by peptide bonds
Secondary Structure
- Arises through hydrogen bonding between carbonyl oxygen and amino hydrogens located on the peptide backbone (main chain)- Two most common are alpha helices and beta sheets- DOES NOT involve H-bonding of side chains, but the type of secondary structure that's formed can be influenced by side chains
Tertiary Structure
- Refers to interactions of secondary structures- Side chain and main chain H-bonding are important - Also ionic, hydrophobic, and van der Waals
Quaternary Structure
- Interactions between different polypeptide chains- Interactions mediated by same forces important for tertiary structure- Relative orientation of subunits can change to regulate function of the complex
Interactions Governing S,T, and Q Structures of Protein
1. H-Bonds- Especially important for secondary structure2. Ionic- Between side chains of charged AAs - "salt bridges"3. Hydrophobic- Hydrophobic side chains exclude water and get packed together - E favorable, an entropic effect4. Van der Waals - not strong on own but yes in aggregate- Between any two atoms - Important in tightly packed regions of the protein
H-Bonding in an Alpha Helix
- Alpha helix stabilized by main chain H-bonds- Occurs between every fourth residue (red arrows)- Happens between partially negative O and hydrogens on partially positive N (due to partial double bond character of peptide bond)- Turns once ever 3.6 AAs- Though side chains ARE NOT directly involved in forming H-bonds, the nature of the side chain helps determine which secondary structure will form
Structure of Alpha Helix
- All opportunities for H-bonding in a peptide backbone are satisfied- This makes alpha helix E favorable for spanning a lipid bilayer - the H on the N and the Carbonyl O are already interacting with each other - dont need to interact with water
Protein Structure
- A series of secondary structure elements linked together by flexible connectors (loops or unstructured regions)- NOT ALL AAs in a protein are part of a secondary structure - some just exist as a short segment connecting one 2ndary to another
Parallel Beta Sheets
- All strands run in same direction- Notice that H-Bond alignment is slightly different
H-Bonds and Tertiary Structure
1. Bonds between main chains of 2 different strands2. Bonds between the peptide bond and a side chain3. Bonds between two side chains
Ionic and van der Waals Interactions
1. Ionic (salt bridges)- Important in tertiary and quaternary structures- Negative AA interacts with Positive AA2. Van der Waals- Occur by close packing of AA side chains- Often important in stabilization at center of protein
Hydrophobic Interactions
- In terms of E, strongest force driving protein folding is hydrophobic interaction - in the interior of a protein- Just want to get away from water - move to center of protein to do so - then have van der Waal interactions
Hypothetical Protein Folding Pathway
1. Secondary structures acquired2. Tertiary structures acquired
Proteins composed of Beta Sheets
Immunoglobulin Fold - found in IgG and other proteinsB-propeller - 4-7 blades and is important for mediating protein protein interactionB-Barrel - found in natrually fluorescent protein from jellyfish (GFP) - barrel shields the fluorophore from water
hydroxyl group
consists of a hydrogen bonded to an oxygen.
carbonyl group
a carbon linked by a double bond to an oxygen atom. also called an aldehyde or a ketone depending on its location.
carboxyl group
consists of a carbon double-bonded to both an oxygen and a hydroxyl group
amino group
composed of a nitrogen bonded to two hydrogen atoms and the carbon skeleton
phosphate group
consists of a phosphorus atom bonded to four oxygen atoms
aldehyde
the name for a carbonyl group (c=o) located at either end of a carbon skeleton.
ketone
the name for a carbonyl group (c=o) located near the middle of a carbon skeleton.
Element,
a substance that cannot be broken down to other substances by chemical reactions. (92)
essential elements,
the 20-25% of natural elements that an organism needs to live a healthy life and reproduce.
Trace elements,
elements required by an org. in only minute quantities
Dalton,
1.7 x 10^-24 g. same as amu (atomic mass unit). The mass of a proton or neutron.
atomic number,
The number of protons in an element. 2He means there are 2 protons in the nucleus of helium. Equal number of electrons unless noted.
mass number,
The sum of protons plus neutrons in the nucleus of an atom. 4/2He means there are 2 neutrons
atomic mass,
Total mass of an atom. = approximately the mass number.
isotope,
A different atomic forms of the same element. All atoms of same element have same number of protons, but isotopes have more neutrons giving greater mass.
Radioactive isotope,
Isotope in which the nucleus decays spontaneously, giving off particles and energy. If # of protons changes it changes into a different element.
Energy,
Capacity to cause change.
Potential energy:
The energy matter possesses because of its location or structure. (Water on a hill has potential energy because of it's altitude)
Electron Shells:
Different levels (like a staircase) where electrons can be found. The higher the level (father the distance) the more potential energy on the electron.
Valence electrons,
Electrons in the outermost shell of an atom.
Valence shell,
The outermost electron shell of an atom.
Valence,
The bonding capacity of an atom; the number of unpaired electrons required to complete the valence shell. Oxygen has a valence of 2.
Completed valence shell,
The atom with a full valence shell will not react readily with other atoms. Called inert.
Shell limits,
1:2, 2:8, 3:8
Orbital,
The 3dimensional space where an electron is found 90% of the time.
Molecule,
Two or more atoms held together by COVALENT bonds.
Compound,
Combination of two or more different elements.
Electronegativity,
The attraction of an atom for the electrons of a covalent bond. Greater atom's elecneg, the more it pulls electrons toward itself.
Ion,
A charged atom or molecule
Cation,
A positively charged Ion
Anion,
A negatively charged Ion
Ionic Bond
attraction between anions and cations
Ionic compounds are called,
Salts
Polar molecule,
the overall charge of a molecule is unevenly distributed
Cohesion,
ex. water has high cohesion because of the abundance of hydrogen bonds. capacity to hold itself together.
Adhesion,
the clinging of one substance to another.
kinetic energy,
the energy of motion. anything that moves has kinetic energy. Atoms and molecules have kinetic energy.
heat,
a form of energy. the measure of a matter's total kinetic energy due to motion of its molecules; depends in part on the matter's volume. not temperature
Light Microscope,
visible light is passed through the specimen and then through the glass lenses. up to x1000
Organelles,
membrane-enclosed structures within eukaryotic cells.
Electron microscope,
Uses a beam of electrons instead of light. Elecron microscopes kill the cells in preparation unlike light microscopes.
Scanning electron microscope,
electron beam scans the surface of the sample, usually coated with gold.results in a 3d image of the specimen's surface.
Transmission Electron Microscope,
used to study internal structure of cells.
Cell fractionation,
takes cells apart and separates major organelles and other subcellular structures.
eukaryotic cell,
most of DNA inside nucleus, bounded by a double-membrane.
prokaryotic cell,
DNA is concentrated in a region that is not membrane enclosed, called the nucleoid.
cytoplasm,
interior of a cell, in euk cells: the region between the nucleous and plasma membrane.
plasma membrane,
selective barrier that allows passage of enough oxygen, nutrients, and wastes to service the entire cell.
nucleus,
contains most of the genes in a eukaryotic cell (also in mitochondria and chloroplasts).
nuclear envelope,
encloses the nucleus seperating its contents from the cytoplasm. Double membrane.
chromosomes,
structures that carry genetic information. discrete units of dna. each chromosome contains one long DNA molecule associated with many proteins.
Chromatin,
the complex of DNA and proteins making up chromosomes.
Nucleolus,
mass of densely stained granules and fibers adjoining part of the chromatin. RNA is synthesized here.
Ribosomes,
the cellular components that carry out protein synthesis.
Free Ribosomes,
suspended in the cytosol
Bound Ribosomes,
attached to the outside of the endoplasmic reticulum or nuclear envelope.
Flagellum,
motility structure prestent in some animal cells.
Endoplasmic Reticulum,
network of membranous sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes; has rough and smooth regions.
Golgi apparatus,
organelle active in synthesis, modification, sorting, and secretion of cell products.
Lysosome,
digestive organelle where macromolecules are hydrolyzed.
Mitochondrion,
organelle where cellular respiration occurs and most ATP is generated.
Peroxisome,
organelle with various specialized metabolic functions; produces hydrogen peroxide as a by-product then converts it to water.
Microvilli,
projections that increase the cell's surface area.
Cytoskeleton,
reinforces cell's shape; functions in cell movement; components are made of protein. Includes: Microfilaments, Intermediate filaments, Microtubules.
Centrosome,
region where the cell's microtubules are initiated; contains a pair of centrioles.
In Animal cells not Plant,
Lysosomes, centrosomes, with centrioles, Flagella (but in some plant sperm).
In Plant cells not Animal,
Chloroplasts, central vacuole, cell wall,
Central vacuole,
prominent organelle in older plant cells; storage, breakdown of waste products, hydrolysis of macromolecules; enlargement of vacuole major mechanism of plant growth.
Chloroplast,
photosynthetic rganelle; converts energy of sunlight to chemical energy stored in sugar molecules.
Plasmodesmata,
cytoplasmic chanels through cell walls that connect the cytoplasms of adjacent cells.
Cell wall,
outer layer that maintains cell's shape and protects cell from mechanical damage; made of cellulose, other polysaccharides and protein.
Metabolic function,
the processes necessary for the maintenance of a living organism.
covalent bond
a chemical bond that involves sharing a pair of electrons between atoms in a molecule
ionic bond
a chemical bond in which one atom loses an electron to form a positive ion and the other atom gains to electron to form a negative ion
hydrogen bond
a chemical bond consisting of a hydrogen atom between two electronegative atoms (e.g., oxygen or nitrogen) with one side be a covalent bond and the other being an ionic bond
Four base pairs found in DNA and how they pair.
Adenine:Thymine Guanine:Cytosine
MRNA
the template for protein synthesis The form of RNA that carries information from DNA in the nucleus to the ribosome sites of protein synthesis in the cell
RNA
(biochemistry) a long linear polymer of nucleotides found in the nucleus but mainly in the cytoplasm of a cell where it is associated with microsomes
transcription
(genetics) the organic process whereby the DNA sequence in a gene is copied into mRNA
chromosome
in a eukaryotic cell, one of the structures in the nucleus that are made up of DNA and protein; in a prokaryotic cell, the main ring of DNA
nonpolar covalent bond
A covalent bond in which the bonding electrons are shared equally by the bonded atoms, resulting in a balanced distribution of electrical charge
polar covalent bond
A covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive.
single, double, and triple covalent bonds
two, four and six electrons are shared respectively
hydrogen bonds
the weak bond bridging hydrogen atoms and atoms of the opposite charge
solvent
substance doing the dissolving
dissolve
A mixture in which particles of one or more substances (the solute) are distributed uniformly throughout another substance (the solvent), so that the mixture is homogeneous.
heat capacity
The amount of heat required to raise the temperature of a specified amount of a substance by 1°C or 1 K. The degree to which a substance changes temperature in response to a gain or loss of heat.
capillary action
A proccess powered by adhesion that causes water molecules to move upward through a narrow tube such as the stem of a plant.
organic molecules are those that have
carbon atoms
macromolecules
large molecules such as proteins, carbohydrates, nucleic acids, or lipids. hundreds or thousands of atoms. usually polymers
polymer
a naturally occurring or synthetic compound consisting of large molecules made up of a linked series of repeated simple monomers
monomer
The subunit that serves as the building block of a polymer.
functional groups
A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.
monosaccharide
A single sugar molecule such as glucose or fructose, the simplest type of sugar.
disaccharide
Consists of two monosaccharides joined by a glycosidic linkage. During the process of joining, a water molecule is lost. this is a condensation reaction, or specifically a dehydration reaction.
glucose+fructose
sucrose
glucose+galactose
lactose
glucose+glucose
maltose
polysaccharide
macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glyco- sidic linkages
starch
polymer of a-glucose molecules. the principal energy storage molecule in plant cells.
glycogen
polymer of a-glucose molecule. major energy storage molecule in animal cells.
cellulose
polymer of b-glucose molecules. serves as a structural molecule in the walls of plant cells and is the major component of wood.
chitin
polymer similar to cellulose (b-glucose molecules), structural molecule in walls of fungus cells and in the exoskeleton of insects, other arthropods, and mollusks.
lipids
a class of substances that are insoluble in water (and other polar solvents, but are soluble in nonpolar substances (like ether or chloroform). Three major types.
Triglyceride
glyceride occurring naturally in animal and vegetable tissues; it consists of three individual fatty acids bound together in a single large molecule; an important energy source forming much of the fat stored by the body
triglycerides: saturated fatty acid
A fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, thus maximizing the number of hydrogen atoms that can attach to the carbon skeleton.
triglycerides: monounsaturated fatty acid
has one double covalent bond and each of the two carbons in this bond had only one hydrogen atom bonded to it.
triglycerides: polyunsaturated fatty acid
like a monounsaturated fatty acid except that there are two or more double covalent bonds.
phospholipid
looks just like a lipid except that one of the fatty acid chains is replaced by a phosphate group. The two fatty acid tails are nonpolar and hydrophobic and the phosphate head is polar and hydrophilic.
amphipathic molecule
a molecule with both polar (hydrophilic) and nonpolar (hydrophobic) regions.
steroids
characterized by a backbone of four linked carbon rings. ex. cholesterol, hormones like testosterone and estrogen.
structural proteins
Proteins that are important for holding cells and organisms together, silk in cocoons and webs; collagen and elastin in animal connective tissue; keratin in hair
storage proteins
Function: storage of amino acidsExamples: -ovalbumin: in egg white, source of amino acids- Casein: found in milk, provide amino acis for baby animals (mammals)
transport proteins
transport specific substances between cells (e.g., hemoglobin transports oxygen in red blood cells); move specific substances (e.g., ions, glucose, amino acids) across cell membranes
Defensive proteins
provide protection against foreign substances that enter the bodies (antibodies)
Enzyme
a globular protein that activate or accelerate metabolic reactions (act as catalysts) in either direction. enzymes are unchanged as a result of this reaction. It can perform it's function repeatedly. standard suffix of "ase".
peptide bonds
The bonds connecting amino acids together to form polypeptide chains.
primary structure
The level of protein structure referring to the specific sequence of amino acids. ex: cys-tyr-phe-gln
secondary structure
3d shape. The localized, repetitive coiling or folding of the polypeptide backbone of a protein due to hydrogen bond formation between peptide linkages.
alpha helix
the spiral shape resulting from the coiling of a polypeptide in a protein's secondary structure
beta pleated sheet
One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.
fibrous proteins
proteins whose shape is dominated by alpha helix and beta pleated sheets
tertiary structure
includes 3dimensional shaping and often dominates the structure of globular proteins. factors contributing to structure: hydrogen bonding between R groups of amino acids, Ionic bonding between R groups... hydrophobic effect that occurs when hydrophobic R groups move toward the center of the protein, formation of disulfide bonds (disulfide bridge)
quaternary structure
protein that is assembled by two or more separate peptide chains.
nucleic acids
DNA and RNA
nucleotide
3 parts: a nitrogen base, a 5-carbon sugar called deoxyribose, and a phosphate group. there are 4 dna nucleotides: adenine: a double ring base, thymine: a singe ring base, cytosine: a single ring base, guanine: a double ring base. Single ring: purine, double ring: pyrimidine.
RNA differences
Sugar is ribose (not deoxyribose), adenine pairs with uracil (not thymine), and is single stranded.
activation energy
the energy that an atomic system must acquire before a process (such as an emission or reaction) can occur. "catalysts are said to reduce the energy of activation during the transition phase of a reaction
catalysts
substance that speeds up (reduces the activation energy of) a chemical reaction but is not used up itself or permanently changed
metabolism
chemical reactions that occur in biological systems. Includes the breakdown of substances (catabolism), the formation of new products (synthesis or anabolism) or the transferring of energy from one substance to another.
chemical equilibrium
the condition where the rate of reaction in the forward direction equals the rate in the reverse direction and so there is no net production of reactants or products.
substrate
the substance or substances upon which the enzyme acts. ex. the enzyme amylase catalyzes the substrate amylose. enzymes are substrate specific... work only in a particular way with a particular substrate.
efficiency of an enzyme is effected by
temperature and pH
denatured
loss of an enzyme's normal shape so that it no longer functions; caused by a less than optimal pH and temperature
cilia
Short, hair-like structures made of microtubules that enable movement of cells or movement of materials outside a cell
centrioles and basal bodies are? and they act as?
act as microtubule organizing centers. centrioles are one of two small cylindrical cell organelles composes of 9 triplet microtubules. basal bodies are centrioles forming the bases of cilia and flagella
vacuoles and vesicles are
fluid filled membrane bound bodies.
transport vesicles
move materials between organelles or between organelles and the plasma membrane.
food vacuoles
temporary receptacles of nutrients. Food vacuoles often merge with lysosomes, whose digestive enzymes break down the food.
Storage vacuoles
in plants. store starch, pigments, and toxic substances.
contractile vacuoles
specialized organelles in single-celled organisms that collect and pump excess water out of the cell.
cell wall is composed mainly of?
cellulose
chitin
found in cell walls of fungi.
extracellular matrix
found in animals, in the area between adjacent cells. provides mechanical support and helps bind adjacent cells together. common substance found here: protein collagen.
Cell junctions
anchor cells to one another or provide a passageway for cellular exchange.
Anchoring junctions
protein attachments between adjacent animal cells.
Desmosome
a type of intercellular junction in animal cells that functions as an anchor
tight junctions
(in animal cells) membranes of neighboring cells are actually fused forming continuous belts around cell to prevent leakage of extracellular fluid
Communicating junctions
passageways between cells that allow the transfer of chemical or electrical signals.
Gap junctions
a type of communicating junction between animal cells that consist of proteins called connexins which allow passage of ions and small molecules but prevent the cytoplasms of each cell from mixing.
plasmodesmata
Open channels in the cell wall of a plant through which strands of cytosol connect from an adjacent cell.
hypotonic
having a lower concentration of solute than another solution
hypertonic
When comparing two solutions, the solution with the greater concentration of solutes
isotonic
(used of solutions) having the same or equal number of solutes (osmotic pressure)
osmotic pressure
the pressure exerted by a solution necessary to prevent osmosis into that solution when it is separated from the pure solvent by a semipermeable membrane
bulk flow
the collective movement of substances in the same direction in response to a force or pressure. example: blood moving through a blood vessel
Passive transport
movement of substances from regions of higher to lower concentrations, so not require expenditure of energy.
diffusion
process by which molecules tend to move from an area where they are more concentrated to an area where they are less concentrated
osmosis
diffusion of water through a selectively permeable membrane
dialysis
diffusion of solutes across a selectively permeable membrane. term used usually when different solutes are separated by a selectively permeable membrane.
plasmolysis
the movement of water out of a cell (osmosis) that results in the collapse of the cell.
facilitated diffusion
the transport of substances through a cell membrane along a concentration gradient with the aid of carrier proteins
countercurrent exchange
the opposite flow of adjacent fluids that maximizes transfer rates; for example, blood in the gills flows in the opposite direction in which water passes over the gills, maximizing oxygen uptake and carbon dioxide loss.
active transport
movement of solutes against a gradient and requires expenditure of energy (usually ATP).
vesicular transport
uses vesicles or other bodies in the cytoplasm to move macromolecules or large particles across the plasma membrane.
Exocytosis
vesicles fusing with the plasma membrane and releasing their contents to the outside of the cell. Common when a cell produces substances for export.
Endocytosis
capture of a substance outside the cell when the plasma membrane merges to engulf it. The substance then enters the cytoplasm enclosed in a vesicle.
Phagocytosis
(Endocytosis)"cellular eating" occurs when -undissolved- material enters the cell. The plasma membrane merges to engulf it, forming a phagocytic vesicle.Phagocytic cells attack and engulf bacteria in this manner.
Pinocytosis
(endocytosis) "cellular drinking" occurs when -dissolved- substances enter a cell. plasma membrane folds inward to form a channel allowing the liquid to enter. plasma membrane then closes off the channel, encircling the liquid inside a vesicle.
Receptor-mediated endocytosis
occurs when -specific molecules- in the fluid surrounding the cell bind to specialized receptors that concentrate in coated pits in the plasma membrane. The membrane pits, receptors, and their specific molecules (ligands) flod inward and the formation of a vesicle follows.
Primary Structure
Sequence of AAs attached by peptide bonds
Secondary Structure
- Arises through hydrogen bonding between carbonyl oxygen and amino hydrogens located on the peptide backbone (main chain)- Two most common are alpha helices and beta sheets- DOES NOT involve H-bonding of side chains, but the type of secondary structure that's formed can be influenced by side chains
Tertiary Structure
- Refers to interactions of secondary structures- Side chain and main chain H-bonding are important - Also ionic, hydrophobic, and van der Waals
Quaternary Structure
- Interactions between different polypeptide chains- Interactions mediated by same forces important for tertiary structure- Relative orientation of subunits can change to regulate function of the complex
Interactions Governing S,T, and Q Structures of Protein
1. H-Bonds- Especially important for secondary structure2. Ionic- Between side chains of charged AAs - "salt bridges"3. Hydrophobic- Hydrophobic side chains exclude water and get packed together - E favorable, an entropic effect4. Van der Waals - not strong on own but yes in aggregate- Between any two atoms - Important in tightly packed regions of the protein
H-Bonding in an Alpha Helix
- Alpha helix stabilized by main chain H-bonds- Occurs between every fourth residue (red arrows)- Happens between partially negative O and hydrogens on partially positive N (due to partial double bond character of peptide bond)- Turns once ever 3.6 AAs- Though side chains ARE NOT directly involved in forming H-bonds, the nature of the side chain helps determine which secondary structure will form
Structure of Alpha Helix
- All opportunities for H-bonding in a peptide backbone are satisfied- This makes alpha helix E favorable for spanning a lipid bilayer - the H on the N and the Carbonyl O are already interacting with each other - dont need to interact with water
Protein Structure
- A series of secondary structure elements linked together by flexible connectors (loops or unstructured regions)- NOT ALL AAs in a protein are part of a secondary structure - some just exist as a short segment connecting one 2ndary to another
Parallel Beta Sheets
- All strands run in same direction- Notice that H-Bond alignment is slightly different
H-Bonds and Tertiary Structure
1. Bonds between main chains of 2 different strands2. Bonds between the peptide bond and a side chain3. Bonds between two side chains
Ionic and van der Waals Interactions
1. Ionic (salt bridges)- Important in tertiary and quaternary structures- Negative AA interacts with Positive AA2. Van der Waals- Occur by close packing of AA side chains- Often important in stabilization at center of protein
Hydrophobic Interactions
- In terms of E, strongest force driving protein folding is hydrophobic interaction - in the interior of a protein- Just want to get away from water - move to center of protein to do so - then have van der Waal interactions
Hypothetical Protein Folding Pathway
1. Secondary structures acquired2. Tertiary structures acquired
Proteins composed of Beta Sheets
Immunoglobulin Fold - found in IgG and other proteinsB-propeller - 4-7 blades and is important for mediating protein protein interactionB-Barrel - found in natrually fluorescent protein from jellyfish (GFP) - barrel shields the fluorophore from water
hydroxyl group
consists of a hydrogen bonded to an oxygen.
carbonyl group
a carbon linked by a double bond to an oxygen atom. also called an aldehyde or a ketone depending on its location.
carboxyl group
consists of a carbon double-bonded to both an oxygen and a hydroxyl group
amino group
composed of a nitrogen bonded to two hydrogen atoms and the carbon skeleton
phosphate group
consists of a phosphorus atom bonded to four oxygen atoms
aldehyde
the name for a carbonyl group (c=o) located at either end of a carbon skeleton.
ketone
the name for a carbonyl group (c=o) located near the middle of a carbon skeleton.
Element,
a substance that cannot be broken down to other substances by chemical reactions. (92)
essential elements,
the 20-25% of natural elements that an organism needs to live a healthy life and reproduce.
Trace elements,
elements required by an org. in only minute quantities
Dalton,
1.7 x 10^-24 g. same as amu (atomic mass unit). The mass of a proton or neutron.
atomic number,
The number of protons in an element. 2He means there are 2 protons in the nucleus of helium. Equal number of electrons unless noted.
mass number,
The sum of protons plus neutrons in the nucleus of an atom. 4/2He means there are 2 neutrons
atomic mass,
Total mass of an atom. = approximately the mass number.
isotope,
A different atomic forms of the same element. All atoms of same element have same number of protons, but isotopes have more neutrons giving greater mass.
Radioactive isotope,
Isotope in which the nucleus decays spontaneously, giving off particles and energy. If # of protons changes it changes into a different element.
Energy,
Capacity to cause change.
Potential energy:
The energy matter possesses because of its location or structure. (Water on a hill has potential energy because of it's altitude)
Electron Shells:
Different levels (like a staircase) where electrons can be found. The higher the level (father the distance) the more potential energy on the electron.
Valence electrons,
Electrons in the outermost shell of an atom.
Valence shell,
The outermost electron shell of an atom.
Valence
The bonding capacity of an atom; the number of unpaired electrons required to complete the valence shell. Oxygen has a valence of 2.
Completed valence shell
The atom with a full valence shell will not react readily with other atoms. Called inert.
Shell limits
1:2, 2:8, 3:8
Orbital
The 3dimensional space where an electron is found 90% of the time.
Molecule
Two or more atoms held together by COVALENT bonds.
Compound
Combination of two or more different elements.
Ion,
A charged atom or molecule
Cation,
A positively charged Ion
Anion,
A negatively charged Ion
Ionic Bond
attraction between anions and cations
Ionic compounds are called,
Salts
Polar molecule,
the overall charge of a molecule is unevenly distributed
Cohesion,
ex. water has high cohesion because of the abundance of hydrogen bonds. capacity to hold itself together.
Adhesion
The clinging of one substance to another. Cohesion refers to water molecules sticking to each other, while adhesion refers to water molecules sticking to other substances. Other liquids have fewer interactions between the molecules.
kinetic energy,
the energy of motion. anything that moves has kinetic energy. Atoms and molecules have kinetic energy.
heat,
a form of energy. the measure of a matter's total kinetic energy due to motion of its molecules; depends in part on the matter's volume. not temperature
Light Microscope,
visible light is passed through the specimen and then through the glass lenses. up to x1000
Organelles,
membrane-enclosed structures within eukaryotic cells.
Electron microscope,
Uses a beam of electrons instead of light. Elecron microscopes kill the cells in preparation unlike light microscopes.
Scanning electron microscope,
electron beam scans the surface of the sample, usually coated with gold.results in a 3d image of the specimen's surface.
Transmission Electron Microscope,
used to study internal structure of cells.
Cell fractionation,
takes cells apart and separates major organelles and other subcellular structures.
eukaryotic cell,
most of DNA inside nucleus, bounded by a double-membrane.
prokaryotic cell,
DNA is concentrated in a region that is not membrane enclosed, called the nucleoid.
cytoplasm,
interior of a cell, in euk cells: the region between the nucleous and plasma membrane.
plasma membrane,
selective barrier that allows passage of enough oxygen, nutrients, and wastes to service the entire cell.
nucleus,
contains most of the genes in a eukaryotic cell (also in mitochondria and chloroplasts).
nuclear envelope,
encloses the nucleus seperating its contents from the cytoplasm. Double membrane.
chromosomes,
structures that carry genetic information. discrete units of dna. each chromosome contains one long DNA molecule associated with many proteins.
Chromatin,
the complex of DNA and proteins making up chromosomes.
Nucleolus,
mass of densely stained granules and fibers adjoining part of the chromatin. RNA is synthesized here.
Ribosomes,
the cellular components that carry out protein synthesis.
Free Ribosomes,
suspended in the cytosol
Bound Ribosomes,
attached to the outside of the endoplasmic reticulum or nuclear envelope.
Flagellum,
motility structure prestent in some animal cells.
Endoplasmic Reticulum,
network of membranous sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes; has rough and smooth regions.
Golgi apparatus,
organelle active in synthesis, modification, sorting, and secretion of cell products.
Lysosome,
digestive organelle where macromolecules are hydrolyzed.
Mitochondrion,
organelle where cellular respiration occurs and most ATP is generated.
Peroxisome,
organelle with various specialized metabolic functions; produces hydrogen peroxide as a by-product then converts it to water.
Microvilli,
projections that increase the cell's surface area.
Cytoskeleton,
reinforces cell's shape; functions in cell movement; components are made of protein. Includes: Microfilaments, Intermediate filaments, Microtubules.
Centrosome,
region where the cell's microtubules are initiated; contains a pair of centrioles.
In Animal cells not Plant,
Lysosomes, centrosomes, with centrioles, Flagella (but in some plant sperm).
In Plant cells not Animal,
Chloroplasts, central vacuole, cell wall,
Central vacuole,
prominent organelle in older plant cells; storage, breakdown of waste products, hydrolysis of macromolecules; enlargement of vacuole major mechanism of plant growth.
Chloroplast,
photosynthetic rganelle; converts energy of sunlight to chemical energy stored in sugar molecules.
Plasmodesmata,
cytoplasmic chanels through cell walls that connect the cytoplasms of adjacent cells.
Cell wall,
outer layer that maintains cell's shape and protects cell from mechanical damage; made of cellulose, other polysaccharides and protein.
Metabolic function,
the processes necessary for the maintenance of a living organism.
ionic bond
a chemical bond in which one atom loses an electron to form a positive ion and the other atom gains to electron to form a negative ion
hydrogen bond
a chemical bond consisting of a hydrogen atom between two electronegative atoms (e.g., oxygen or nitrogen) with one side be a covalent bond and the other being an ionic bond
Four base pairs found in DNA and how they pair.
Adenine:Thymine Guanine:Cytosine
MRNA
the template for protein synthesis The form of RNA that carries information from DNA in the nucleus to the ribosome sites of protein synthesis in the cell
RNA
(biochemistry) a long linear polymer of nucleotides found in the nucleus but mainly in the cytoplasm of a cell where it is associated with microsomes
transcription
(genetics) the organic process whereby the DNA sequence in a gene is copied into mRNA
chromosome
in a eukaryotic cell, one of the structures in the nucleus that are made up of DNA and protein; in a prokaryotic cell, the main ring of DNA
nonpolar covalent bond
A covalent bond in which the bonding electrons are shared equally by the bonded atoms, resulting in a balanced distribution of electrical charge
polar covalent bond
A covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive.
single, double, and triple covalent bonds
two, four and six electrons are shared respectively
hydrogen bonds
the weak bond bridging hydrogen atoms and atoms of the opposite charge
solvent
substance doing the dissolving
dissolve
A mixture in which particles of one or more substances (the solute) are distributed uniformly throughout another substance (the solvent), so that the mixture is homogeneous.
heat capacity
The amount of heat required to raise the temperature of a specified amount of a substance by 1°C or 1 K. The degree to which a substance changes temperature in response to a gain or loss of heat.
capillary action
A proccess powered by adhesion that causes water molecules to move upward through a narrow tube such as the stem of a plant.
organic molecules are those that have
carbon atoms
macromolecules
large molecules such as proteins, carbohydrates, nucleic acids, or lipids. hundreds or thousands of atoms. usually polymers
polymer
a naturally occurring or synthetic compound consisting of large molecules made up of a linked series of repeated simple monomers
monomer
The subunit that serves as the building block of a polymer.
functional groups
A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.
monosaccharide
A single sugar molecule such as glucose or fructose, the simplest type of sugar.
disaccharide
Consists of two monosaccharides joined by a glycosidic linkage. During the process of joining, a water molecule is lost. this is a condensation reaction, or specifically a dehydration reaction.
glucose+fructose
sucrose
glucose+galactose
lactose
glucose+glucose
maltose
polysaccharide
macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glyco- sidic linkages
starch
polymer of a-glucose molecules. the principal energy storage molecule in plant cells.
glycogen
polymer of a-glucose molecule. major energy storage molecule in animal cells.
cellulose
polymer of b-glucose molecules. serves as a structural molecule in the walls of plant cells and is the major component of wood.
chitin
polymer similar to cellulose (b-glucose molecules), structural molecule in walls of fungus cells and in the exoskeleton of insects, other arthropods, and mollusks.
lipids
a class of substances that are insoluble in water (and other polar solvents, but are soluble in nonpolar substances (like ether or chloroform). Three major types.
Triglyceride
glyceride occurring naturally in animal and vegetable tissues; it consists of three individual fatty acids bound together in a single large molecule; an important energy source forming much of the fat stored by the body
triglycerides: saturated fatty acid
A fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, thus maximizing the number of hydrogen atoms that can attach to the carbon skeleton.
triglycerides: monounsaturated fatty acid
has one double covalent bond and each of the two carbons in this bond had only one hydrogen atom bonded to it.
triglycerides: polyunsaturated fatty acid
like a monounsaturated fatty acid except that there are two or more double covalent bonds.
phospholipid
looks just like a lipid except that one of the fatty acid chains is replaced by a phosphate group. The two fatty acid tails are nonpolar and hydrophobic and the phosphate head is polar and hydrophilic.
amphipathic molecule
a molecule with both polar (hydrophilic) and nonpolar (hydrophobic) regions.
steroids
characterized by a backbone of four linked carbon rings. ex. cholesterol, hormones like testosterone and estrogen.
structural proteins
Proteins that are important for holding cells and organisms together, silk in cocoons and webs; collagen and elastin in animal connective tissue; keratin in hair
storage proteins
Function: storage of amino acidsExamples: -ovalbumin: in egg white, source of amino acids- Casein: found in milk, provide amino acis for baby animals (mammals)
transport proteins
transport specific substances between cells (e.g., hemoglobin transports oxygen in red blood cells); move specific substances (e.g., ions, glucose, amino acids) across cell membranes
Defensive proteins
provide protection against foreign substances that enter the bodies (antibodies)
Enzyme
a globular protein that activate or accelerate metabolic reactions (act as catalysts) in either direction. enzymes are unchanged as a result of this reaction. It can perform it's function repeatedly. standard suffix of "ase".
peptide bonds
The bonds connecting amino acids together to form polypeptide chains.
primary structure
The level of protein structure referring to the specific sequence of amino acids. ex: cys-tyr-phe-gln
secondary structure
3d shape. The localized, repetitive coiling or folding of the polypeptide backbone of a protein due to hydrogen bond formation between peptide linkages.
alpha helix
the spiral shape resulting from the coiling of a polypeptide in a protein's secondary structure
beta pleated sheet
One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.
fibrous proteins
proteins whose shape is dominated by alpha helix and beta pleated sheets
tertiary structure
includes 3dimensional shaping and often dominates the structure of globular proteins. factors contributing to structure: hydrogen bonding between R groups of amino acids, Ionic bonding between R groups... hydrophobic effect that occurs when hydrophobic R groups move toward the center of the protein, formation of disulfide bonds (disulfide bridge)
quaternary structure
protein that is assembled by two or more separate peptide chains.
nucleic acids
DNA and RNA
nucleotide
3 parts: a nitrogen base, a 5-carbon sugar called deoxyribose, and a phosphate group. there are 4 dna nucleotides: adenine: a double ring base, thymine: a singe ring base, cytosine: a single ring base, guanine: a double ring base. Single ring: purine, double ring: pyrimidine.
RNA differences
Sugar is ribose (not deoxyribose), adenine pairs with uracil (not thymine), and is single stranded.
activation energy
the energy that an atomic system must acquire before a process (such as an emission or reaction) can occur. "catalysts are said to reduce the energy of activation during the transition phase of a reaction
catalysts
substance that speeds up (reduces the activation energy of) a chemical reaction but is not used up itself or permanently changed
metabolism
chemical reactions that occur in biological systems. Includes the breakdown of substances (catabolism), the formation of new products (synthesis or anabolism) or the transferring of energy from one substance to another.
chemical equilibrium
the condition where the rate of reaction in the forward direction equals the rate in the reverse direction and so there is no net production of reactants or products.
substrate
the substance or substances upon which the enzyme acts. ex. the enzyme amylase catalyzes the substrate amylose. enzymes are substrate specific... work only in a particular way with a particular substrate.
efficiency of an enzyme is effected by
temperature and pH
denatured
loss of an enzyme's normal shape so that it no longer functions; caused by a less than optimal pH and temperature
cilia
Short, hair-like structures made of microtubules that enable movement of cells or movement of materials outside a cell
centrioles and basal bodies are? and they act as?
act as microtubule organizing centers. centrioles are one of two small cylindrical cell organelles composes of 9 triplet microtubules. basal bodies are centrioles forming the bases of cilia and flagella
vacuoles and vesicles are
fluid filled membrane bound bodies.
transport vesicles
move materials between organelles or between organelles and the plasma membrane.
food vacuoles
temporary receptacles of nutrients. Food vacuoles often merge with lysosomes, whose digestive enzymes break down the food.
Storage vacuoles
in plants. store starch, pigments, and toxic substances.