Chemical [blank] are pure substances consisting of a single type of atom

elements

Atoms contain a nucleus made up of [blank] with positive charges and [blank] that are without charge.

proton and neutron

The nucleus is surrounded by [blank] that have [blank] charges and occur in discrete regions called [blanks] that are grouped into "shells"

electron; negative; orbital

The chemical properties of an atom, that is, the kinds of chemical reactions it has with other atoms or molecules, are determined by properties of its outermost orbitals or [blank] shell

valence

Two atoms will react with each if it leads to a more stable state, specifically so that they both have [blank] valence shells.

filled/full

In a Eukaryotic Cell: A double membrane-bound organelle that contains genetic information encoded on chromosomes

Nucleus

In a Eukaryotic Cell: A complex of RNA and protein that is the site of protein synthesis

Ribosomes

In a Eukaryotic Cell: Network of membranes containing enzymes that are responsible for synthezing lipids

Smooth ER

In a Eukaryotic Cell: Organelle that contains membranes called cristae, it is responsible for producing most of the cell's ATP

Mitochondria
(only animal cells/ chloroplast = plant/algal cells)

In a Eukaryotic Cell: Digests food items or autodigests damaged organelles through acid hydrolysis

Lysosomes
(only animal cells)

In a Eukaryotic Cell: Stacks of flattened membranes called cisternae, in which proteins are modified (for example, glycosylated) after they are synthesized

Golgi Apparatus

In a Eukaryotic Cell: Site of reactions that fix inorganic carbon (CO2) onto organic compounds using the energy from light

Chloroplasts
(Plant and algal cells)

In a Eukaryotic Cell: Structural support for the cell, it is made up of microtubules, microfilaments and intermediate filaments

Cytoskeleton

Chloroplast in plant cells

-sunlight is converted to chemical energy during photosynthesis
-double membrane, exterior for structure and interior contains Thylakoids
-THYLAKOIDS dominates by hundreds of membrane bound flattened vesicles and staked into piles called GRANA
-Many of the pigments, enzymes, and molecular machinery responsible for converting light energy into carbohydrates are embedded in the thylakoid membranes, certain enzymes found in STROMA

Peroxisomes all eukaryotic cells

-single membrane contains transporters for selected macromolecules
-components: enzymes that catalyze oxidation reactions and catalase (processes peroxide)
-function:oxidation of fatty acids, ethanol, or other compounds

Vacuoles (Plant and Algal cells)

-single membrane contains transporters for selected molecules
-components: varies, pigments, oils, carbohydrates, water, or toxins
-function: varies, coloration, storage of oils, carbohydrates, water, or toxins

Plasma Membrane (all Eukaryotic Cells)

-single membranes contains transport and receptor proteins
-components: phospholipid bilayer with transport and receptor proteins
-function: selective permeability maintains intracellular environment

Cell Wall (plant cells)

no membrane
-components: carbohydrate fibers running through carbohydrate or protein matrix
-function: protection and structural support

Roles of hydrogen bonds

1)making water a good solvent for polar or charged molecules
2)causing water to have a high heat of vaporization
3)causing water to have strong cohesion and adhesion
4)causing water to have a high surface tension

A solution contains 1 X 10-12 moles of OH- per liter what is the pH? and is the solution acidic or basic?

pH=2
solution is acidic

Two atoms with different electronegativities react to form a compound in which they share electrons

Polar Covalent Bond

Two or more atoms react to form a stable compound in which electrons are transferred completely from one atom to another

Ionic Bond

Two completely independent (there has been no chemical reaction between them) polar molecules, each containing atoms with partial charges, can be held together by this kind of bond

Hydrogen Bond

The atoms in a compound that is hydrophobic are bonded in this manner

Non-Polar Covalent Bond

The movement of water across a semipermeable membrane (selectively permeable)

Osmosis

Transport of a molecule across a membrane against its concentration gradient; this requires the use of energy; usually in the form of ATP

Active Transport

-the energy needed to move the substances against their gradient is provided by a phosphate group from adenosine triphosphate (ATP)

Transport of a molecule that otherwise could not pass easily (or at all) through a membrane, down its concentration gradient through a protein channel

Facilitated Diffusion

Channel Proteins=Ion channels

-facilitated diffusion
-channel proteins are selective
-each channel protein has a structure that allows it to admit a particular type of ion or small molecule

Movement of molecules across a semipermeable membrane, down an electrochemical gradient, without the aid of a protein channel

Simple Diffusion

Facilitated Diffusion

-ions cross membranes through specialized membrane proteins called ion channels
-ion channels forms pores of holes in a membrane
-ions move from areas of high concentration to low concentration and areas of like char to areas of unlike charge
-ions move in response to a combined concentration and electrochemical gradient

Electrochemical Gradient

-is a combined concentration and electrical gradient
-established when ions build up on one side of a membrane

Facilitated Diffusion via carrier proteins

-facilitated diffusion can also occur through carrier proteins or transporters, that change shape during the process to allow the molecule to be released inside the cell when the conformation change of the protein occurs

Phospholipid Membrane

-membrane forming lipids have a polar (hydrophilic region) and a non-polar (hydrophobic region)
-the charges and polar bonds in the head region interact with water molecules when a phospholipid is placed in solution
-the long isoprene or fatty-acid tails of a phospholipid are non-polar hydrophobic

Lipid Bilayers show selective permeability

High to Low

-small non-polar molecules: O2, CO2, N2
-small uncharged polar molecules: H20, glycerol
-large uncharged polar molecules: glucose, sucrose
-ions: Cl-, K+, Na+

Outside solution HYPERtonic to inside

net flow of water out of cell; cell shrivels and shrinks

Outside solution HYPOtonic to inside

net flow of water into cell; cell swells or even bursts

Isotonic solutions

no change

-solute concentrations are equal on either side of the membrane, the liposome will maintain its size
-when outside solution does not affect the membranes shape

A wall-less protozoan is removed from the marine environment, where the predominant solute is NaCl. The protozoan has been going hungry and has no sugar left in its cytoplasm. It is placed into a laboratory beaker that is isotonic with the inside of the cell, but the only solute present is glucose. Which of the following will happen?

Glucose will very slowly diffuse through the membrane into the cell, making the cell hypertonic and causing water to flow into the cell as well

Fluid-Mosaic Model

-proposed that some proteins span the membrane instead of being found only outside the lipid bilayer (sandwich model)

*Suggested that membranes are a mosaic of phospholipids and different types of proteins; the overall structure was proposed to be dynamic and fluid

Integral membrane proteins

-some proteins span the membrane and have segments facing both the interior and exterior surfaces

aka: transmembrane proteins

Peripheral membrane proteins

found only on one side of the membrane

the major component of cell membranes

Phospholipids

A hydrocarbon chain covalently bonded to a carboxyl group

fatty acid

three fatty acids, each with double bonds between carbons; bonded to a glycerol molecule by ester linkages

unsaturated fats

A cell membrane would be highly permeable to this inorganic molecule

CO2 = small non-polar molecules

A triglyceride with no double bonds in its tail

saturated fat

A steroid molecule that is a important component to the cell membrane in animal cells but not plant cells

Cholesterol

What would INCREASE the fluidity and permeability of the cell membrane

increasing the percent of unsaturated fatty acids

Temperature and Fluidity of membrane

-as temperature decreases the fluidity and permeability of the membrane decreases
-at ver low temperatures lipid bilayers begin to solidify
-increasing temperature = increasing permeability
-how quickly molecules move within and across membranes is a function of temperature and the structure of the hydrocarbon tails in the bilayer

Diffusion

-molecules and ions move randomly in all direction when a concentration gradient exists, but there is a net movement from regions of high concentration to regions of low concentration

*diffusion along a concentration gradient is a spontaneous process because it results in an increase in entropy

Amino Acids

-All have a carbon atom bonded to an amino group, a hydrogen atom, and a carboxyl group, and a R group
-but each R group is unique
-the properties of amino acids vary because their R groups vary

Protein

-is a macromolecule (large molecule made up of smaller molecules)
-a polymer (many parts)
-consist of linked amino acid monomers (one part)

Condensation/Dehydration reactions

-monomers polymerize
-reactions are named bc the newly formed bond results in the loss of a water molecule

Hydrolysis

-reverse reaction of condensation/dehydration
-breaks polymers apart by adding a water molecule
-water molecule reacts with the bond linking the monomers, separating one monomer from the polymer chain

Amino Acids polymerize

-when a bond forms between the carboxyl group of one amino acid and the amino group of another

bond b/t carboxyl group of one amino acid and amino group of another

-the C-N bond that results from the condensation reaction is called a peptide bond

Amino Acid ionic bonding

-between electrically charged side chains
-charged side chains from hydrogen bonds; highly soluble in water

*Acidic and Basic*

Amino Acid Covalent bonding

-between two cysteine
-for a disulfide bond

Amino Acid Hydrophobic Interaction

-between a polar side chains (partial charges can form hydrogen bonds; soluble in water)
&
-Non-polar side chains (no charges or electronegative atoms to form hydrogen bonds; not soluble in water)

Amino Acid Hydrogen bonding

-between two polar side chains
-both: partial charges can form hydrogen bonds; soluble in water

-Serine and Glutamine

Tertiary Structure

-hydrogen bonding
-hydrophobic interactions
-van der Waal interactions
-covalent bonding
-ionic bonding

van der Waals interations

-once hydrophobic side chains are close to one another, they are stabilized by electrical attractions
-weak attractions
-the partial minute charge on one molecule induces an opposite partial charge in the nearby molecule and causes an attraction
-occurs in polypeptide when many hydrophobic residues congreate

Covalent bonding (tertiary structure)

-covalent bonds can form between sulfur atoms when a reaction occurs between the sulfur-containing R groups of two cysteines
-the two cysteines form a DISULFIDE=(two sulfur) bonds are frequently referred to as bridges because they create strong links between distinct regions of the same polypeptide

Microtubules are composed of this protein

-Tubulin; two separate protein tubulin dimers
~a-tubulin and b-tubulin
-in function microtubes are similar to actin filaments: they provide stability and are involved in movement

The ATPase motor protein that interacts with microfilaments

Myosin:

-is a motor protein; a protein converts the chemical energy in ATP into the mechanical work of movement

Microfilaments are made of this protein

Actin:

-globular protein that make fibrous structures of actin filaments
-is often the most abundant of all proteins

A transport vesicle moving through the cell along a microtubule would be carried by this ATPase motor protein

Kinesin

-when ATP is added to kinesin or drops off the protein moves

One of many different proteins that make up intermediate filaments

Keratin ( or vimentin or lamin)

-lines surfaces inside your body and skin
-these intermediate filaments provide the mechanical strength required for these cells to resist pressure and abbrasion

The sliding of microtubules that cause the beating of cilia and flagella in a eukaryotic cell is driven by this ATPase motor protein

Dynein

Which level or levels of structure shown is/are stabilized either totally or partially by hydrogen bonds

-secondary
-tertiary
-quaternary

Which level or levels of protein structure shown contain(s) peptide bonds?

-All four structures: primary; secondary; tertiary; and quaternary

Secondary Structure

-created part by hydrogen bonding between portions of the peptide-bonded backbone
-the bending that aligns parts of the backbone and allows these bonds to form occur in two ways:
1)a helix: alpha helix in which the polypeptide's backbone is coiled
OR
2)B-pleated sheets: beta pleated sheet in which segment of a peptide chain bend 180 deg and then fold in the same plane

The protein structure in which more than one discrete polypeptide must be present

Quaternary Structure:

-the combination of polypeptide subunits gives protein structure
-the individual polypeptides may be held together by bonds or other interactions among R-groups or sections of their peptide backbones

Porin

Forms a stable opening in cell membranes to allow certain hydrophilic molecules to pass through

Hemoglobin

A protein with quaternary structure consisting of 2 alpha and 2 beta subunit polypeptides

Tata box binding protein

A protein that binds to certain regions of DNA in the nucleus

Prion protein

A protein that can act as an infectious agent and cause various diseases called spongiform encephalopathies

Hexokinase

An enzyme that catalyzes a reaction that attaches a phosphate group to a six-carbon sugar

Heat shock protein

A molecular chaperone protein that helps other proteins fold into their proper tertiary structures

Create watertight seals between adjacent animal cells

Tight Junctions

A matrix of cellulose fibers with spaces filled mostly by pectin

Primary Cell Wall

Plasmodesmata

Connections that link the cytoplasms of adjacent plant cells

Protein channels that form connections between cytoplasms of adjacent animal cells

Gap Junctions

Desmosomes

Protein complexes that form “rivet-like” structures anchored on both sides by the cytoskeletons of adjacent animal cells

Extracellular Matrix

Collagen fibers surrounded by a gelatinous matrix formed mostly by proteoglycans

Cadherins

Proteins that are specific to cell types and mediate cell-cell interactions that lead to formation of tissues in animals

Hormones

Molecules used to signal between cells at a distance in multicellular eukaryotic organisms

events that would occur for an enzyme that carries out its function either inside the endomembrane system: place in correct order

1)Ribosome binds to mRNA and initiates translation
2)Signal sequence of polypeptide is synthesized
3)Signal recognition particle (SRP) binds to the signal sequence
4)Signal recognition particle binds to an SRP receptor, bringing the ribosome to the endoplasmic reticulum (ER) membrane
5)Protein is moves into the rough endoplasmic reticulum (RER) as it is translated
6)Oligosaccharides are added to some individual amino acids of the protein
7)Glycoproteins are further modified as they move from the cis to the trans face of the Golgi apparatus
8)A vesicle containing an enzyme is released at the trans face of the Golgi apparatus
9)A vesicle fuses with the outer membrane of a late endosome, releasing an enzyme and resulting in a lysosome
10)Proteins in a bacterium are digested enzymatically

Lipid Soluble Hormone

Binds to a cytosolic receptor and generally initiates a long-term change in gene expression in a cell

cAMP

A common second messenger in transduction, it generally activates protein kinases

G protein

This kind of protein is activated by membrane-bound signal receptors, and gets its name from the observation that it is regulated by the nucleotide GTP

Lipid Insoluble Hormone

Binds to a membrane bound receptor and usually results in a more rapid physiological response in a cell