Biology 151

Three types of cytoskeletal element, subunits and explain

(a) Microtubule subunit: tubulin dimers -A hollow, tubelike polymer of tubulin dimers that helps make up the cytoskeleton -enable the movement of substances within cells (figela, cilia) -helps maintain shape and internal structure -polymers of protein dimers -vesicle transport in the cell -cell division (chromosome segregation) -dynamic structure and can assemble and dissemble quickly (called dynamic instability) -associate with the motor proteins dynein and kinesin to transport substances in the cell. (b) microfilament subunit: actin monomers -A helical polymer of actin monomers, present in various locations in the cytoplasm, that helps make up the cytoskeleton. -enable the movement of substances (crawling) -help maintain shape -cell division (cytokinesis) -muscle contraction -transport vesicle -associate with the motor protein myosin to transport vesicles in the cell and to cause cell shape changes, such as muscle contraction (c) intermediate filament. subunit: diverse -A polymer of proteins, which vary according to cell type, that combine to form strong, cable-like filaments that provide animal cells with mechanical strength. function: cell shape and support -dynamic structure and can assemble and dissemble quickly All three of these cytoskeletal elements are long chains, or polymers, made up of protein subunits

ATP

(adenosine triphosphate) main energy source that cells use for most of their work -the universal "currency" of cellular energy -ATP is composed in part of adenosine, which is made up of the base adenine and the five-carbon sugar ribose -The chemical energy of ATP is held in the bonds connecting the phosphate groups. At physiological pH, these phosphate groups are negatively charged and have a tendency to repel each other. The chemical bonds connecting the phosphate groups therefore store chemical energy. This energy is released when new, more stable bonds are formed that contain less chemical energy

basal lamina

- is a specialized layer of extracellular matrix that is present beneath all epithelial tissues, -The role of the basal lamina is to provide a structural foundation for these epithelial tissues. The basal lamina is made of several proteins textbook def: the basal lamina. The basal lamina, found beneath epithelial tissue, is a specialized form of extracellular matrix.

hydrogen bond

-A hydrogen bond results when a hydrogen atom covalently bonded to an electronegative atom interacts with an electronegative atom of another molecule. weak attraction between a hydrogen atom (with a slight positive charge) and another atom(electronegative atom) -weaker than covalent bonds

Endergonic versus exergonic reactions

-An endergonic reaction requires an input of energy Describes reactions with a positive ΔG that are not spontaneous and so require an input of energy. - exergonic reaction releases energy Describes reactions with a negative ΔG that release energy and proceed spontaneously. ex)hydrolysis of apt

Cellular respiration

-Cellular respiration is a series of catabolic reactions that converts the energy stored in food molecules, such as glucose, into the energy stored in ATP, and produces carbon dioxide as a waste or by-product. - It can occur in the presence of oxygen (termed aerobic respiration) or in the absence of oxygen (termed anaerobic respiration). -In most organisms, cellular respiration consumes oxygen and produces ATP by substrate-level phosphorylation and oxidative phosphorylation, as well as carbon dioxide and water. -in cellular respiration, electron carriers transport electrons released during the catabolism of organic molecules to the respiratory electron transport chain. -During cellular respiration, sugar molecules like glucose are broken down in the presence of oxygen to produce carbon dioxide and water - releases energy because the potential energy of the reactants is greater than that of the products. - is an oxidation-reduction reaction.

what forms local secondary structures?

-Interactions between stretches of amino acids in a protein -result from hydrogen bonding in the polypeptide backbone

pigmants

-Pigments are molecules that absorb some wavelengths of visible light (Fig. 8.8). Pigments look colored because they reflect light enriched in the wavelengths that they do not absorb. Chlorophyll is the major photosynthetic pigment; it appears green because it is poor at absorbing green wavelengths. The chlorophyll molecule consists of a large, light-absorbing "head" containing a magnesium atom at its center and a long hydrocarbon "tail"

nucleus

-houses the genome -the site of RNA synthesis -innner most organelle of the endomembrane system -stores dna -has a nuclear envelope which defines its boundaries

how is glycine different from other amino acids? How is proline opposite?

-its R group is hydrogen and therefore assymetric ( all others are symmetric) -also it is non polar and its R group is small enough to fit places where not all r groups can fit, making its backbone flexible proline- its change restricts rotation and flexibility

cell membrane

-lipids are the main component * phospholipid is the most common* made up of hydrophilic head and hydrophobic tail -they are amphipathic -They have properties that allow them to form a barrier in an aqueous (watery) environment. -proteins are often embedded in or associated with the membrane -Carbohydrates can also be found in cell membranes, usually attached to lipids (glycolipids) and proteins (glycoproteins). -are dynamic

cortex

-the area of the cytoplasm just beneath the plasma membrane. -At the cortex, microfilaments reinforce the plasma membrane and organize proteins associated with it.

movement of vesicles from ER to Golgi -biosyntheic pathway

-vesicles carry lipids and proteins, either within the vesicle interior or embedded in their membranes it goes from ER to Golgi and then to the rest of the cell and is a part of a biosynthetic pathway in which lipids and proteins are sequentially modified and delivered to their final destinations -while traffic usually travels from the ER to the Golgi apparatus, a small amount of traffic moves in the reverse direction, from the Golgi to ER. the reverse pathway is important to retrieve proteins in the ER or Golgi that were accidentally moved forward and to recycle membrane component

active transport primary active transport (gradient def) secondary active transport

-• The "uphill" movement of substances against a concentration gradient, called active transport, requires energy. Many cells maintain size and composition using active transport -primary uses energy directly from ATP -secondary is driven by electrochemical gradient • A gradient that has both charge and chemical components is known as an electrochemical gradient • Because the movement of the coupled molecule is driven by the movement of protons and not by ATP directly, this form of transport is called secondary active transport

fatty acids differ in

1)chain length (number of carbons) 2)saturation -unsaturated: Describes fatty acids that contain carbon-carbon double bonds. -saturated: Describes fatty acids that do not contain double bonds; the maximum number of hydrogen atoms is attached to each carbon atom, "saturating" the carbons with hydrogen atoms. *The chains of saturated fatty acids are straight, while the chains of unsaturated fatty acids have a kink at each double bond.*

What percentage of carbon's orbitals are spherical in conformation?

40%

epithelial tissue

A body tissue that covers the surfaces of the body, inside and out

double bond

A chemical bond formed when atoms share two pairs of electrons

covalent bond

A chemical bond formed when two atoms share electrons

In chemical reactions atoms .........

A chemical reaction. Atoms retain their identity during a chemical reaction as bonds are broken and new bonds are formed to yield new molecules.

Centrosome

A compact structure that is the microtubule organizing center for animal cells.

intermediate filaments

A component of the cytoskeleton that includes all filaments intermediate in size between microtubules and microfilaments - polymers of proteins that vary according to cell type.

polar covalent bond versus non polar covalent bond

A covalent bond in which electrons are not shared equally as a result of a difference in the ability of the atoms to attract electrons, a property called electronegativity. -ex) h20 because... In a molecule of water, the electrons are more likely to be located near the oxygen atom. Electronegativity tends to increase across a row in the periodic table; as the number of protons across a row increases, electrons are held more tightly to the nucleus. Therefore, oxygen is more electronegative than hydrogen and attracts electrons more readily than does hydrogen. non polar covalent bond- A covalent bond between atoms that have the same, or nearly the same, electronegativity. -ex) gaseous hydrogen (H2) Oxygen (O2) carbon bonds (C-C)

Differentiate between covalent bonds and generally weaker interactions such as polar covalent, hydrogen, and ionic bonds.

A covalent bond is present when two atoms share their valence electrons (the electrons in the outermost orbital of an atom). Each shared pair of valence electrons make a covalent bond that is depicted by a single line connecting the two chemical symbols for the atoms. A polar covalent bond is present when the valence electrons are not shared equally by the two atoms, thus giving areas of the molecule a positive or negative charge. A hydrogen bond forms when a hydrogen atom covalently bound to an electronegative atom (giving the hydrogen a partial positive charge) interacts with an electronegative atom of another molecule. A hydrogen bond is typically depicted by a dotted line. An ionic bond is formed by the attraction between a molecule that has a positive charge (due to the loss of one electron) and a molecule that has a negative charge (due to the gain of one electron). The two molecules are not covalently bound, but they associate with each other due to their opposite charges.

glysocidic bonds

A covalent bond that attaches one monosaccharide to another.

Nucleoid

A dense region of DNA in a prokaryotic cell. - In prokaryotes, a cell structure with multiple loops formed from supercoils of DNA.

chemical energy

A form of potential energy that is stored in chemical bonds between atoms. -strong bonds do not contain very much chemical energy bc when you consider that strong bonds have a very stable arrangement of orbitals and therefore do not require a lot of energy to remain intact. Examples of molecules with strong covalent bonds that contain relatively little chemical energy are carbon dioxide (CO2) and water (H2O). -Conversely, some covalent bonds are relatively weak. These bonds are easily broken because the arrangement of orbitals in these molecules is only somewhat more stable than if the two atoms did not share any electrons. As a result, weak covalent bonds require a lot of energy to stay intact and contain a lot of chemical energy -Organic molecules such as carbohydrates, lipids, and proteins contain relatively weak covalent bonds, including many carbon-carbon (C-C) bonds and carbon-hydrogen (C-H) bonds. Therefore, organic molecules are rich sources of chemical energy and are called fuel molecules. Page 119

Molecule

A group of atoms bonded together -the atoms interact to form a chemical bond!

accessory pigment

A light-absorbing pigment other than chlorophyll in the photosynthetic membrane; carotenoids are important accessory pigments.

Electronegativity

A measure of the ability of an atom in a chemical compound to attract electrons

electron carrier

A molecule that carries electrons (and energy) from one set of reactions to another.

Polypeptide

A polymer of amino acids connected by peptide bonds.

fermentation

A process of breaking down pyruvate through a wide variety of metabolic pathways that extract energy from fuel molecules such as glucose; the partial oxidation of complex carbon molecules to molecules that are less oxidized than carbon dioxide. - Glucose can be broken down in the absence of oxygen by fermentation, producing a modest amount of ATP. -Pyruvate, the end product of glycolysis, is processed differently in the presence and the absence of oxygen. -In the absence of oxygen, pyruvate enters one of several fermentation pathways. -In lactic acid fermentation, pyruvate is reduced to lactic acid. -In ethanol fermentation, pyruvate is converted to acetaldehyde, which is reduced to ethanol. -During fermentation, NADH is oxidized to NAD+, allowing glycolysis to proceed. -does not rely on oxygen or any other electron acceptor. Fermentation is accomplished through a wide variety of metabolic pathways that extract energy from fuel molecules such as glucose. -Fermentation occurs in the cytoplasm and does not require proteins embedded in specialized membranes.

photosystem

A protein-pigment complex that absorbs light energy to drive redox reactions and thereby sets the photosynthetic electron transport chain in motion.

oxidation-reduction reaction

A reaction involving the loss and gain of electrons between reactants. In biological systems these reactions are often used to store or release chemical energy. LEO GER -electrons are transferred from one molecule to another.

photosynthetic electron transport chain

A series of redox reactions in which light energy absorbed by chlorophyll is used to power the movement of electrons; in oxygenic photosynthesis, the electrons ultimately come from water and the terminal electron acceptor is NADP+.

oxidative phosphorylation

A set of metabolic reactions that occurs by passing electrons along an electron transport chain to the final electron acceptor, oxygen, pumping protons across a membrane, and using the proton electrochemical gradient to drive synthesis of ATP.

basal lamina

A specialized form of extracellular matrix that underlies and supports all epithelial tissues.

cofactor

A substance that associates with an enzyme and plays a key role in its function. -Metallic cofactors also bind to enzymes used in the transport of electrons for cellular respiration and photosynthesis, processes that are discussed in the next two chapters

activator

A synthesized compound that increases the activity of an enzyme.

Macromolecules

A very large organic molecule composed of many smaller molecules - the order the macromolecule is arranged changes the entire molecules

substrate-level phosphorylation

A way of generating ATP in which a phosphate group is transferred to ADP from an organic molecule, which acts as a phosphate donor or substrate. AKA a phosphate group is transferred to ADP from an enzyme substrate, in this case an organic molecule.

ADP is an energy ___________ and ATP an energy __________

ADP is an energy acceptor and ATP an energy donor

ATP synthase

ATP synthase An enzyme that couples the movement of protons through the enzyme with the synthesis of ATP.

ADP and AMP

ATP's chemical relatives ADP-two phosphate groups AMP- one phosphate group

Absorption of light energy by chlorophyll...

Absorption of light energy by chlorophyll. Absorption of light energy by (a) an isolated chlorophyll molecule in the lab and (b) an antenna chlorophyll molecule.

Actin microfilaments associate with ________ to transport various types of cellular cargo, such as vesicles, inside of cells. Furthermore, _________ are responsible for changes in the shape of many types of cell. One of the most dramatic examples of cell shape change is the shortening (contraction) of a muscle cell. Muscle contraction depends on the interaction of myosin with microfilaments, and is powered by ATP

Actin microfilaments associate with myosin to transport various types of cellular cargo, such as vesicles, inside of cells. Furthermore, microfilaments are responsible for changes in the shape of many types of cell. One of the most dramatic examples of cell shape change is the shortening (contraction) of a muscle cell. Muscle contraction depends on the interaction of myosin with microfilaments, and is powered by ATP

Identify the cytoskeletal element that interacts with adherens junctions, desmosomes, and hemidesmosomes.

Adherens junctions interact with microfilaments. Desmosomes and hemidesmosomes interact with intermediate filaments.

All of the oxygen in Earth's atmosphere results from ..........

All of the oxygen in Earth's atmosphere results from photosynthesis by organisms containing two photosystems.

amino acid residues

Amino acids that are incorporated into a protein are often referred to as amino acid residues.

cyclic electron transport

An alternative pathway for electrons during the Calvin cycle that increases the production of ATP. -To increase ATP production, some electrons from photosystem I cycle back into the electron transport chain. -Cyclic electron transport involves the redirection of electrons from ferredoxin back into the electron transport chain and increases ATP production.

cholesterol

An amphipathic lipid that is a major component of animal cell membranes. -Cholesterol molecules embedded in the lipid bilayer affect the fluidity of the membrane. - At temperatures typically found in a cell, cholesterol decreases membrane fluidity. However, at low temperatures, cholesterol increases membrane fluidity because it prevents phospholipids from packing tightly with other phospholipids. Thus, cholesterol helps maintain a consistent state of membrane fluidity by preventing dramatic transitions from a fluid to solid state.

name and describe the component of an atom

An atom is made up of positively charged particles called protons, neutral particles called neutrons, and negatively charged particles called electrons. The dense central nucleus of an atom is made up of protons and neutrons. Electrons orbit around the nucleus, and the regions of space where they are most likely to be found are called orbitals.

liposomes

An enclosed bilayer structure spontaneously formed by phospholipids in environments with neutral pH, like water.

allosteric enzyme

An enzyme whose activity is affected by binding a molecule at a site other than the active site. Typically, allosteric enzymes change their shape on binding an activator or inhibitor. -Allosteric enzymes regulate key metabolic pathways. Allosteric enzymes bind activators and inhibitors at sites other than the active site, resulting in a change in their shape and activity. Allosteric enzymes are often found at or near the start of a metabolic pathway or at the crossroads of multiple pathways

Explain how protein folding allows for enzyme specificity.

An enzyme's three-dimensional shape is very important for its specificity. The enzyme has to fold into its correct shape in order for the active site (the portion of the enzyme that binds substrate and converts it to product) to be in the right area and shape. An enzyme will only recognize its substrate if its active site is in the right conformation due to the correct three-dimensional folding.

an enzyme-catalyzed reaction

An enzyme-catalyzed reaction. An enzyme accelerates a reaction by lowering the activation energy, EA.

An imbalance between the light-harvesting reactions and the Calvin cycle can lead to......

An imbalance between the light-harvesting reactions and the Calvin cycle can lead to the formation of reactive oxygen species

anchoring cell junction

Anchoring cell junctions include adherens junctions and desmosomes. -Adherens junctions form a belt around the circumference of a cell. They are composed of cell adhesion molecules called cadherins and connect to microfilament -Desmosomes are button-like points of adhesion between cells. They are composed of cadherins and connect to intermediate filaments.

Antenna chlorophyll molecules transfer......

Antenna chlorophyll molecules transfer absorbed light energy to the reaction center.

motor proteins

Any of various proteins that are involved in intracellular transport or cause muscle contraction by moving the actin microfilaments inside muscle cells.

At the end of glycolysis, but before the subsequent steps in cellular respiration, which molecules contain some of the energy held in the original glucose molecule?

At the end of glycolysis, the energy in the original glucose molecule is contained in pyruvate, ATP, and NADH.

At the end of the citric acid cycle, but before the subsequent steps of cellular respiration, which molecules contain the energy held in the original glucose molecule?

At the end of the citric acid cycle, the energy in the original glucose molecule is held in ATP, NADH, and FADH2.

hydrophilic

Attracted to water -polar -readily dissolve in water

Atom

Basic unit of matter. -can combine to form molecules

why is the membrane fluid

Because membrane lipids are able to move in the plane of the membrane, the membrane is said to be fluid -the degree depends on the type of lipids that make up the membrane ex), which have no double bonds, are straight and tightly packed—again reducing mobility ex)he double bonds in unsaturated fatty acids introduce kinks in the fatty acid tails, reducing the tightness of packing and enhancing lipid mobility in the membrane

Which of the following is an example of a hydrogen bond? Please choose the correct answer from the following choices, and then select the submit answer button. A)The bond that forms between two oxygen atoms within different water molecules B)the bond that forms between two hydrogen atoms within the same water molecule C)The bond that forms between hydrogen and oxygen atoms within different water molecules D)the bond that forms between two hydrogen atoms within different water molecules E)the bond that forms between a hydrogen and oxygen atom within the same water molecule

C

question: Predict the effects of interfering with the function of cadherins and integrins.

Cadherins are transmembrane proteins that are clustered together in adherens junctions and desmosomes. The extracellular domains of the cadherins associate with cadherins from another cell, attaching one cell to another. In adherens junctions, the cytosolic domains of these cadherins associate with microfilaments. This establishes a physical connection among the actin cytoskeletons of all cells present in the tissue. Unlike adherens junctions, the cytosolic domains of the cadherins in desmosomes bind to intermediate filaments of the cytoskeleton, also holding together adjacent cells. Interfering with the function of adherens junctions and desmosomes would lead to defects of cell‒cell adhesion. Hemidesmosomes anchor epithelial cells to the basal lamina. They are composed of transmembrane proteins called integrins. The integrin extracellular domain binds to extracellular matrix proteins in the basal lamina, and the integrin cytosolic domain binds to intermediate filaments. This results in a firmly anchored cell. Defects in integrins would interfere with the ability of cells to adhere to the basal lamina.

Carbohydrate synthesis takes place in the...

Carbohydrate synthesis takes place in the stroma, whereas sunlight is captured and transformed into chemical energy by the photosynthetic electron transport chain in the thylakoid membrane.

Distinguish between catabolism and anabolism

Catabolism is the set of chemical reactions that break down macromolecules into smaller units, producing energy (ATP). Anabolism is the set of chemical reactions that build macromolecules from smaller units and require an input of energy (usually in the form of ATP).

Enzymes

Catalysts for chemical reactions in living things -reduce the activation energy Although an enzyme accelerates a reaction by reducing the activation energy, the difference in free energy between reactants and products (ΔG) does not change. In other words, an enzyme changes the path of the reaction between reactants and products, but not the starting or end point -An important characteristic of enzymes is that, as catalysts, they participate in a chemical reaction but are not consumed in the process. -enzymes form a complex with the reactants and products. -Enzymes are folded into three-dimensional shapes that bring particular amino acids into close proximity -highly specific for its substrate and for the types of reaction it catalyzes.

Cell junctions

Cell junctions connect cells to one another to form tissues. -Cell junctions anchor cells to each other and to the extracellular matrix, allow sheets of cells to act as a barrier, and permit communication between cells in tissues. -Tight junctions prevent the passage of substances through the space between cells and divide the plasma membrane into apical and basolateral regions. Gap junctions (in animals) and plasmodesmata (in plants) allow cells to communicate rapidly with one another.

whats the difference between prokaryotes or eukaryotes

Cells can be classified as prokaryotes or eukaryotes, which differ in the degree of internal compartmentalization.

How are Cellular respiration and photosynthesis are complementary metabolic processes?

Cellular respiration and photosynthesis are complementary metabolic processes. Cellular respiration breaks down carbohydrates in the presence of oxygen to supply the energy needs of the cell, producing carbon dioxide and water as byproducts, while photosynthesis uses carbon dioxide and water in the presence of sunlight to build carbohydrates, releasing oxygen as a byproduct.

Cellular respiration is an _______________- reaction.

Cellular respiration is an oxidation-reduction reaction.

why does cellular respiration release a large amount of energy?

Cellular respiration releases a large amount of energy because the sum of the potential energy in all of the chemical bonds of the reactants (glucose and oxygen) is higher than that of the products (carbon dioxide and water).

Cellular respiration ____------ energy because the potential energy of the reactants is --------- than that of the products.

Cellular respiration releases energy because the potential energy of the reactants is greater than that of the products.

Challenges to the efficiency of photosynthesis include ......

Challenges to the efficiency of photosynthesis include excess light energy and the oxygenase activity of rubisco.

Explain the relationship between strength of a covalent bond and the amount of chemical energy it contains.

Chemical energy in molecules is stored as potential energy of the electrons in atoms, occupying orbitals at various distances from the nucleus. The stronger the covalent bond, the less chemical energy it contains. The weaker the covalent bond, the more chemical energy it contains. Carbohydrates, lipids, and proteins have many carbon‒carbon and carbon‒hydrogen bonds. These bonds are relatively weak and are therefore rich sources of chemical energy.

Chemical reactions involve __________

Chemical reactions involve the breaking and forming of bonds.

Chlorophyll molecules in chloroplasts normally only fluoresce a very small amount compared to chlorophyll that has been extracted into a solvent solution. What iis the best explanation for this difference?

Chlorophyll molecules in chloroplasts normally only fluoresce a very small amount compared to chlorophyll that has been extracted into a solvent solution. Which of the following is the best explanation for this difference? Question 1 choices Choice A., In chloroplasts, the molecules are held close together and oriented to allow transfer of excitation energy between molecules.

Compare the overall reactions of photosynthesis and cellular respiration.

Compare the overall reactions of photosynthesis and cellular respiration. Self-Assessment 2 Answer In photosynthesis, energy from sunlight is captured in chemical forms (ATP and NADPH) that are used to synthesize carbohydrates from CO2. In cellular respiration, carbohydrates are oxidized to CO2, releasing energy that is ultimately used to synthesize ATP. In photosynthesis, H2O is the ultimate electron donor and O2 is produced as a by-product. In cellular respiration, O2 is the ultimate electron acceptor and H2O is produced as a by-product.

animal connective tissue

Connective tissue is composed of protein fibers in a gel-like polysaccharide matrix. -dominated by the extracellular matrix and has a low cell density.

Contrast what happens when antenna chlorophylls absorb light energy with what happens when the reaction center absorbs light energy. Why are antenna chlorophylls so important in photosynthesis?

Contrast what happens when antenna chlorophylls absorb light energy with what happens when the reaction center absorbs light energy. Why are antenna chlorophylls so important in photosynthesis? Self-Assessment 5 Answer Antennae chlorophyll transfer absorbed light energy to adjacent chlorophyll molecules; reaction center molecules transfer energy and electrons to an adjacent electron acceptor molecule.

The formation of which one of the following large organic molecules from their respective building blocks does not result in the release of at least one water molecule? Please choose the correct answer from the following choices, and then select the submit answer button. proteins phospholipids polysaccharides nucleic acids All of these large organic molecules form with the loss of a water molecule.

Correct: phospholipids

Amino acids can be spontaneously generated in vitro, but only under anaerobic conditions. Please choose the correct answer from the following choices, and then select the submit answer button. true false

Correct: true

Cyanobacteria evolved two photosystems either by the ...... or ......

Cyanobacteria evolved two photosystems either by the transfer of genetic material, or by gene duplication and divergence.

dynamic instability

Cycles of shrinkage and growth in microtubules. -hese cycles of depolymerization and polymerization are called dynamic instability.They allow spindle microtubules to quickly find and attach to chromosomes during cell division

Cyclic electron transport increases.........

Cyclic electron transport increases the production of ATP.

Describe how a proton gradient is used to generate ATP.

Describe how a proton gradient is used to generate ATP. Self-Assessment 8 Answer The protons accumulated in the intermembrane space cannot passively diffuse across the membrane, so they diffuse through a transport channel called ATP synthase. This enzyme is composed of two subunits: Fo (the channel through which protons flow) and F1 (the catalytic unit that synthesizes ATP). Proton flow through the channel causes it to rotate, which converts the energy of the proton gradient into mechanical rotational energy (kinetic energy). The rotation of the Fo subunit leads to rotation of the F1 subunit. Rotation causes conformational changes in the F1 subunit that allow it to catalyze the synthesis of ATP from ADP and Pi.

Describe how the movement of electrons along the electron transport chain leads to the generation of a proton gradient.

Describe how the movement of electrons along the electron transport chain leads to the generation of a proton gradient. Self-Assessment 7 Answer The movement of electrons along the electron-transport chain in the inner mitochondrial membrane is coupled to the transfer of protons through several enzyme complexes and electron carriers. Electrons donated by NADH enter through complex I, and electrons donated by FADH2 enter through complex II. From complexes I and II, coenzyme Q (CoQ) picks up electrons and transfers them to complex III. Complex III donates electrons to cytochrome c, which in turn transfers them to complex IV, which then donates them to the final electron acceptor, oxygen. As the electrons pass through the complexes, protons are pumped into the intermembrane space. This creates a concentration and charge gradient, providing a source of potential energy that is then used to drive the synthesis of ATP

Describe the three major steps in the Calvin cycle and the role of the key enzyme rubisco.

Describe the three major steps in the Calvin cycle and the role of the key enzyme rubisco. Self-Assessment 4 Answer See Fig. 8.6. Briefly, in the first step, CO2 enters the Calvin cycle and is added to the 5- carbon compound RuBP in a reaction catalyzed by the enzyme rubisco, generating 3-phosphoglycerate (3-PGA). In the second step, the 3-PGA is reduced through conversion of ATP to ADP and NADPH to NADP+, producing triose phosphate, the carbohydrate. Some of the triose phosphate molecules exit the cycle to be used as an energy source for the cell. In the final step of the cycle, triose phosphate molecules that did not exit the cell are used to regenerate RuBP through reactions with ATP. Then the cycle starts again with more CO2.

Describe two different metabolic pathways that pyruvate can enter.

Describe two different metabolic pathways that pyruvate can enter. Self-Assessment 5 Answer In the first pathway, pyruvate is converted to acetyl-CoA, which is the starting substrate for the citric acid cycle. During the citric acid cycle, the chemical energy in the bonds of acetyl-CoA is transferred to ATP by substrate-level phosphorylation and to the electron carriers NADH and FADH2. The second pathway is fermentation, a reaction that happens without oxygen. There are many fermentation pathways but all rely on oxidation of NADH to NAD+ when pyruvate or a derivative of pyruvate is reduced. Two major fermentation pathways are lactic acid fermentation and ethanol fermentation. In the lactic acid pathway, electrons from NADH are transferred to pyruvate to produce lactic acid and NAD+. In the ethanol fermentation pathway, pyruvate releases carbon dioxide to form acetaldehyde, and electrons from NADH are transferred to the molecule to produce ethanol and NAD+.

Describe two different ways in which ATP is generated in cellular respiration.

Describe two different ways in which ATP is generated in cellular respiration. Self-Assessment 3 Answer ATP is generated by substrate-level phosphorylation and oxidative phosphorylation. In substrate-level phosphorylation, a phosphorylated organic molecule directly transfers a phosphate group to ADP. This pathway produces only a small amount of the total ATP generated in the process of cellular respiration. In contrast, most of the ATP generated in cellular respiration is produced through oxidative phosphorylation (stage 4 of cellular respiration). In these reactions, ATP is generated indirectly through the reduction of electron carriers, the transfer of electrons from electron carriers to the electron-transport chain, and the subsequent synthesis of ATP from ADP and inorganic phosphate

Describe two strategies that plants use to limit the formation and effects of reactive oxygen species.

Describe two strategies that plants use to limit the formation and effects of reactive oxygen species. Self-Assessment 9 Answer Two strategies that plants use to limit the formation and effects of reactive oxygen species are antioxidants and xanthophylls. Antioxidants like ascorbate and beta-carotene neutralize reactive oxygen species. Xanthophylls are yellow-orange pigments that slow the formation of reactive oxygen species by reducing excess light energy. They accept absorbed light energy directly from chlorophyll and convert this energy to heat.

tubuline

Dimers (composed of an α tubulin and a β tubulin) that assemble into microfilaments. -One α tubulin and one β tubulin combine to make a tubulin dimer and the tubulin dimers are assembled to form the microtubule.

Describe how diversity is achieved in polymers, using proteins as an example.

Diversity is achieved in polymers through endless combinations of subunits. A protein, for example, is a polymer of amino acid subunits. As we will discuss in Chapter 4, there are 20 different kinds of amino acids. Thus, there are numerous combinations of subunits that could be made, each resulting in a different protein. In this way, polymers are capable of displaying virtually limitless diversity.

anaerobic respiration

Does not use oxygen

Evidence exists that atmospheric CO2 has increased over the last several decades due to human activities. How does increased CO2 levels affect the pH of Earth's waters?

Due to the formation of carbonic acid, increased CO2 levels decrease the pH of Earth's waters.

During catalysis, the ____________ and -______ form a complex with the ---------. - What are Transient covalent bonds and what do they do

During catalysis, the substrate and product form a complex with the enzyme. Transient covalent bonds and/or weak noncovalent interactions stabilize the complex.

Electron carriers

Electron carriers -transfer electrons to an electron transport chain, which harnesses the energy of these electrons to generate ATP.

valence electrons

Electrons on the outermost energy level of an atom -highest energy level -determine the ability of an atom to combine with other atoms to form molecules

Name and describe the two forms of energy and provide an example of each.

Energy is a system's capacity to do work. One form of energy is kinetic energy (the energy of motion). Moving objects perform work that results in their movement and the movement of surrounding matter. Examples of kinetic energy are flexing a muscle, throwing a ball, and basically any kind of movement. The other form of energy is potential energy (stored energy). Potential energy depends on the structure of the object or its position relative to its surroundings, and it is released by a change in the object's structure or position. A ball sitting on the top of the stairs has a great deal of potential energy, which is released when the ball starts to roll down the stairs (at which point, the energy is converted into kinetic energy).

Which of the following do enzymes change? ΔG; reaction rate; types of product generated; activation energy; the laws of thermodynamics.

Enzymes increase the reaction rate and decrease the activation energy. The other parameters are not changed by enzymes.

Enzymes reduce the ______________ of the transition state between reactants and products, thereby reducing the ___________________________, required for a chemical reaction to proceed

Enzymes reduce the free energy level of the transition state between reactants and products, thereby reducing the energy input, or activation energy, required for a chemical reaction to proceed

Estimate the overall efficiency of photosynthesis and describe where in the pathway energy is dissipated.

Estimate the overall efficiency of photosynthesis and describe where in the pathway energy is dissipated. Self-Assessment 11 Answer Because chlorophyll can only absorb visible light, most of the sun's output (~60%) is not absorbed by chlorophyll. Some of the visible light energy is reflected off the leaf or passes through it (~8%). Some of the light energy is absorbed but not transferred to the reaction center and is consequently given off as heat (~8%). Thus, the photosynthetic electron-transport chain captures at most about 24% of the sun's usable energy. An additional energy loss comes during the Calvin cycle, in part from photorespiration (~20%). In all, the maximum energy conversion efficiency of photosynthesis is about 4%.

Eukaryotic organisms are believed to have gained photosynthesis by ...

Eukaryotic organisms are believed to have gained photosynthesis by endosymbiosis.

Explain the trade-off that rubisco faces in terms of selectivity and enzymatic speed.

Explain the trade-off that rubisco faces in terms of selectivity and enzymatic speed. Self-Assessment 10 Answer The ability of rubisco to favor CO2 over O2 requires a high degree of selectivity (because carbon dioxide and oxygen look very similar to a large enzyme). This selectivity makes the reaction rate of rubisco very slow.

Explain what an oxidation-reduction reaction is and why the breakdown of glucose in the presence of oxygen to produce carbon dioxide and water is an example of an oxidation-reduction reaction.

Explain what an oxidation-reduction reaction is and why the breakdown of glucose in the presence of oxygen to produce carbon dioxide and water is an example of an oxidation-reduction reaction. Self-Assessment 2 Answer Oxidation‒reduction reactions are used to store or release chemical energy. Oxidation is the loss of electrons and reduction is the gain of electrons. This gain and loss always happens in a single reaction in which electrons are transferred from one molecule to another. In many reactions, electrons are not completely transferred between molecules. Instead, there is a change in electron density around an atom. This happens in the breakdown of glucose in the presence of oxygen to produce carbon dioxide and water. The carbon atoms in glucose are oxidized because they go from sharing electrons equally in the carbon‒carbon bonds to partially losing electrons in the carbon‒oxygen bonds of the carbon dioxide molecule. The opposite is true for oxygen, which is reduced in the same reaction. The oxygen atoms go from sharing electrons equally to partially gaining electrons when water is formed.

Explain why using water as an electron donor requires a photosynthetic electron transport chain with two photosystems.

Explain why using water as an electron donor requires a photosynthetic electron transport chain with two photosystems. Self-Assessment 6 Answer Photosystem II is needed to pull electrons from water, whereas Photosystem I can harness enough light energy to convert NADP+ to NADPH.

Extracellular matrix proteins influence _________ and ________

Extracellular matrix proteins influence cell shape and gene expression.

how is cell shape determined by the structure of the extracellular matrix?

Fibroblasts adopt different shapes depending on whether they are grown on a two-dimensional or a three-dimensional matrix.

two photosystems working together

For the two photosystems to work together to move electrons from water to NADPH, they must have distinct chemical properties. Photosystem II supplies electrons to the beginning of the electron transport chain. When photosystem II loses an electron (that is, when it is itself oxidized), it is able to pull electrons from water. In contrast, photosystem I energizes electrons with a second input of light energy so they can be used to reduce NADP+. The key point here is that photosystem I when oxidized is not a sufficiently strong oxidant to split water, whereas photosystem II is not a strong enough reductant to form NADPH.

Glucose can be broken down in the absence of _______ by ___________, producing a modest amount of ______.

Glucose can be broken down in the absence of oxygen by fermentation, producing a modest amount of ATP.

what happens with the change in free energy in cellular respiration

Glucose is oxidized through a series of chemical reactions, releasing energy in the form of ATP and reduced electron carriers.

Glycolysis

Glycolysis is the partial oxidation of glucose and results in the production of pyruvate, as well as ATP and reduced electron carriers. -takes place in the cytoplasm -Glycolysis is a series of 10 reactions in which glucose is oxidized to pyruvate. -Glycolysis consists of preparatory, cleavage, and payoff phases. -The breakdown of glucose to pyruvate; the first stage of cellular respiration. -the most common fuel molecule in animals, plants, and microbes -Glycolysis literally means "splitting sugar," an apt name because in glycolysis a 6-carbon sugar (glucose) is split in two, yielding two 3-carbon molecules. The process is anaerobic because oxygen is not consumed. -there are 3 main phases of glycosides -For each molecule of glucose broken down during glycolysis, a net gain of two molecules of ATP and two molecules of NADH is produced. -The synthesis of ATP in glycolysis results from the direct transfer of a phosphate group from a substrate to ADP, a process called substrate-level phosphorylation -glycolysis begins with a single molecule of glucose (six carbons) and produces two molecules of pyruvate (three carbons each). These reactions yield four molecules of ATP and two molecules of NADH. However, two ATP molecules are consumed during the initial phase of glycolysis, resulting in a net gain of two ATP molecules and two molecules of NADH

Hemidesmosomes

Hemidesmosomes are composed of cell adhesion molecules called integrins and connect cells to the extracellular matrix and intermediate filaments.

Fatty acids and melting points

Higher melting points = saturated (all single bonds), greater the length Lower melting points = unsaturated (at least one double bond: cis) -- chains do not "fit" next to each other well due to kinks. More unsaturated, lower MP (fewer hydrophobic interactions to overcome via kinetic energy).

How do antenna chlorophylls differ from reaction center chlorophylls?

How do antenna chlorophylls differ from reaction center chlorophylls? Quick Check 3 Answer Antenna chlorophyll molecules transfer absorbed energy from one antenna chlorophyll molecule to another, and ultimately to the reaction center. Reaction center chlorophylls transfer electrons to an electron acceptor, resulting in the oxidation of reaction center chlorophyll molecules.

How does cyclic electron transport lead to the production of ATP?

How does cyclic electron transport lead to the production of ATP? As the electrons from ferredoxin are picked up by plastoquinone, additional protons are transported from the stroma to the lumen. As a result, there are more protons in the lumen that can be used to drive the synthesis of ATP.

From their positions in the periodic table, can you predict how many lithium atoms and hydrogen atoms can combine to form a molecule?

Hydrogen and lithium are in the same column, or group, in the periodic table. Each has one valence electron in their outer orbital. As a result, one atom of lithium combines with one atom of hydrogen to make lithium hydride, with a full complement of two electrons in the single molecular orbital.

hydrolysis reactions

Hydrolysis reactions often break down polymers into their subunits, and in the process one product gains a proton and the other gains a hydroxyl group. -Keep in mind that the release of free energy during ATP hydrolysis comes from breaking weaker bonds (with more chemical energy) in the reactants and forming more stable bonds (with less chemical energy) in the products.

If phospholipids are added to a test tube of water at neutral pH, they _______

If phospholipids are added to a test tube of water at neutral pH, they spontaneously form spherical bilayer structures called liposomes that surround a central space

In 1953, Stanley Miller and Harold Urey demonstrated that_______ can be generated in the laboratory in conditions that mimic___________ Other experiments have shown that _____, _____ and _____can be generated in the laboratory. Once the building blocks were synthesized, they could join together in the presence of clay minerals to form ______

In 1953, Stanley Miller and Harold Urey demonstrated that amino acids can be generated in the laboratory in conditions that mimic those of the early Earth. page 45 Other experiments have shown that sugars, bases, and lipids can be generated in the laboratory. page 46 Once the building blocks were synthesized, they could join together in the presence of clay minerals to form polymers. page 46

In a chemical reaction, atoms themselves do not change, but ............

In a chemical reaction, atoms themselves do not change, but which atoms are linked to each other changes, forming new molecules.

In eukaryotes, photosynthesis takes place in --------- The Calvin cycle takes place in the ---------, and the light-harvesting reactions take place in the ----------.

In eukaryotes, photosynthesis takes place in chloroplasts: The Calvin cycle takes place in the stroma, and the light-harvesting reactions take place in the thylakoid membrane.

lumen

In eukaryotes, the continuous interior of the endoplasmic reticulum; in plants, a fluid-filled compartment enclosed by the thylakoid membrane; generally, the interior of any tubelike structure.

In photosynthesis, water is _______, releasing --------, and carbon dioxide is _________, forming carbohydrates.

In photosynthesis, water is oxidized, releasing oxygen, and carbon dioxide is reduced, forming carbohydrates.

coenzyme Q (CoQ)

In respiration, a mobile electron acceptor that transports electrons from complexes I and II to complex III in the electron transport chain and moves protons from the mitochondrial matrix to the intermembrane space.

In the Calvin cycle, the reduction of 3-PGA involves what two steps?

In the Calvin cycle, the reduction of 3-PGA involves two steps: (1) ATP donates a phosphate group to 3-PGA, and (2) NADPH transfers two electrons plus one proton (H+) to the phosphorylated compound, which releases one phosphate group (Pi).

grana

Interlinked structures that form the thylakoid membrane.

whats the difference between isotopes and isomers?

Isotopes are two atoms with the same number of protons, but a different number of neutrons. Because they have the same number of proton they are atoms of the same element, but with different masses. For example, most carbon is C-12 (with 6 protons and 6 neutrons); the radioactive isotope used for carbon dating is C-14 (with 6 protons and 8 neutrons). Isomers are two molecules with the same atoms joined together in a different shape. For example, butane is C4H10, with the four carbon atoms joined in a straight chain; methylpropane is also C4H10, but with the carbon atoms joined in a T shape.

Keratinocytes

Keratinocytes in the epidermis are specialized to protect underlying tissues and organs. They are able to perform this function in part because of their elaborate system of cytoskeletal filaments. These filaments are often connected to the cell junctions that hold adjacent keratinocytes together.

Kinetic versus Potential energy

Kinetic energy is energy of motion, and potential energy is stored energy.

lipid raft

Lipids assembled in a defined patch in the cell membrane.

List the products of linear electron transport and cyclic electron transport, and describe the role of cyclic electron transport.

List the products of linear electron transport and cyclic electron transport, and describe the role of cyclic electron transport. Self-Assessment 8 Answer Linear electron transport makes both NADPH and ATP; cyclic electron transport produces only ATP. The role of cyclic electron transport is to increase the production of ATP to the ratio required by the Calvin cycle. These electrons are routed into an alternative pathway (the cyclic electron-transport system) that creates ATP by setting up a proton gradient that drives the conversion of ADP to ATP by the enzyme ATP synthase.

List three major steps that are hypothesized to have occurred in the evolutionary history of photosynthesis.

List three major steps that are hypothesized to have occurred in the evolutionary history of photosynthesis. Self-Assessment 12 Answer (1) The earliest step was the evolution of pigments that can use light energy to drive the movement of electrons. (2) Cyanobacteria incorporated two different photosystems in their photosynthetic electron-transport chain. One hypothesis is that an ancestral cyanobacterium with one photosystem gained the second photosystem through the transfer of genetic material from another bacterium. Another hypothesis is that a single photosystem was duplicated and then the copy diverged in sequence and function. (3) Photosynthesis is hypothesized to have evolved in eukaryotic cells through an endosymbiotic event during which a cyanobacterium was incorporated into a plant cell and eventually evolved to be the chloroplast.

Complex Carbrohydrates

Long, branched chains of monosaccharides

Metabolic pathways

Metabolic pathways are integrated, allowing control of the energy level of cells.

Metabolism

Metabolism is the set of biochemical reactions that transforms biomolecules and transfers energy.

Question: Explain how the dynamic nature of microtubules and microfilaments is important for their functions.

Microtubules and microfilaments are dynamic in structure because they can become longer or shorter with the addition or subtraction of their subunits. This addition or deletion is influenced by many factors, including the concentration of free subunits and the activity of regulatory proteins. The dynamic nature of microtubules in spindles allows them to explore the space of a cell and find chromosomes during cell division. The dynamic nature of microfilaments is important for some forms of cell movement.

what makes up the spindles that attach to chromosomes during cell division.

Microtubules make up the spindles that attach to chromosomes during cell division.

Mitochondria and chloroplasts are organelles involved in......

Mitochondria and chloroplasts are organelles involved in harnessing energy, and likely evolved from free-living prokaryotes.

aldoses

Monosaccharides with an aldehyde group in their linear form are referred to as aldoses.

Most chemical reactions in cells are .........

Most chemical reactions in cells are readily reversible -the direction of a reaction can be influenced by the concentrations of reactants and products. For example, increasing the concentration of the reactants or decreasing the concentration of the products favors the forward reaction.

_________ associate with microtubules and microfilaments to cause movement.

Motor proteins associate with microtubules and microfilaments to cause movement.

The Calvin cycle requires both ATP and NADPH. Which of these molecules provides the major input of energy needed to synthesize carbohydrates?

NADPH supplies the major input of energy that is used to synthesize carbohydrates in the Calvin cycle.

Name the major inputs and outputs of the Calvin cycle.

Name the major inputs and outputs of the Calvin cycle. Self-Assessment 3 Answer The major inputs of the Calvin cycle are CO2 (from the atmosphere) and ATP and NADPH (from the photosynthetic pathway). The major outputs of the Calvin cycle are ADP, NADP+, and carbohydrates (triose phosphates). Larger sugars such as glucose and sucrose are synthesized from triose phosphates in the cytoplasm.

Name the products of the citric acid cycle.

Name the products of the citric acid cycle. Self-Assessment 6 Answer In two turns of the citric acid cycle (one for each acetyl-CoA), 2 ATP, 6 NADH, and 2 FADH2 are produced. Carbon dioxide and oxaloacetate are also produced.

Cold air has less entropy than hot air. The second law of thermodynamics states that entropy always increases. Do air conditioners violate this law?

No, because the second law of thermodynamics applies to the universe as a whole. This means that we have to consider not just the air in the room but the heat released to the outdoors as well. An air conditioner produces more hot air than cold air, and therefore total entropy increases, as described by the second law of thermodynamics.

Name and describe ways that organisms obtain energy and carbon from the environment.

Organisms obtain energy from the environment in two ways: (1) by harvesting energy from sunlight (phototrophs), and (2) by harvesting energy from chemical compounds (chemotrophs). These groups are further distinguished by how they obtain carbon. Autotrophs obtain carbon directly from inorganic sources—such as carbon dioxide—and convert it into an organic source of carbon, like glucose. Heterotrophs obtain carbon from organic compounds made by other organisms

chemoautotrophs

Other microorganisms extract energy from inorganic sources but build their own organic molecules; these organisms are called chemoautotrophs. They are often found in extreme environments, such as deep-sea vents, where sunlight is absent and inorganic compounds such as hydrogen sulfide are plentiful.

Animals breathe in air that contains more oxygen than the air they breathe out. Where is oxygen consumed?

Oxygen is consumed in cellular respiration. Oxygen is the final electron acceptor in the electron transport chain and is converted to water.

cytochrome-b6 f complex (cyt)

Part of the photosynthetic electron transport chain, through which electrons pass between photosystem II and photosystem I.

Phospholipids can form ________, ____________, or ________when placed in water.

Phospholipids can form (a) micelles, (b) bilayers, or (c) liposomes when placed in water.

Photosynthesis consists of two sets of reactions which are.......

Photosynthesis consists of two sets of reactions: (1) the Calvin cycle, in which carbon dioxide is reduced to form carbohydrates, and (2) light-harvesting reactions, in which ATP and NADPH are generated to drive the Calvin cycle

Photosynthesis

Photosynthesis is the major pathway by which energy and carbon are incorporated into carbohydrates. - biochemical process for building carbohydrates using energy from sunlight and carbon dioxide (CO2) taken from the air. These carbohydrates are used both as starting points for the synthesis of other molecules and as a means of storing energy that can be converted into ATP through cellular respiration. -CO2 molecules are reduced to form higher-energy carbohydrate molecules. This requires both an input of energy from ATP and the transfer of electrons from an electron donor. In photosynthesis, energy from sunlight is used to produce ATP and electron donor molecules capable of reducing CO2

Photosystem II pulls electrons from _---, resulting in _-----------. Photosystem I passes electrons to ___________, producing ______________

Photosystem II pulls electrons from water, resulting in the production of oxygen and protons on the lumen side of the membrane. Photosystem I passes electrons to NADP+, producing NADPH for use in the Calvin cycle.

Protection from excess light energy includes .......

Protection from excess light energy includes antioxidant molecules that neutralize reactive oxygen species and xanthophyll pigments that dissipate excess light energy as heat.

List essential functions of proteins, nucleic acids, carbohydrates, and lipids.

Proteins act as catalysts to facilitate chemical reactions and also provide structural support of the cell. Nucleic acids encode and transmit genetic information. Carbohydrates provide a source of energy and make up the cell wall in bacteria, plant, and algae cells. Lipids store energy, act as signaling molecules, and make up the membranes of the cell.

Proteins are polymers of --------- nucleic acids are polymers of --------- , and carbohydrates such as starch are polymers of ----

Proteins are polymers of amino acids, nucleic acids are polymers of nucleotides, and carbohydrates such as starch are polymers of simple sugars.

Oxidation of Pyruvate

Pyruvate is oxidized in the mitochondrial matrix, forming acetyl-CoA, the first substrate in the citric acid cycle.

Pyruvate

Pyruvate is oxidized to acetyl-CoA, connecting glycolysis to the citric acid cycle. -In the presence of oxygen, pyruvate can be further oxidized to release more energy, first to acetyl-CoA and then even further in the series of reactions in the citric acid cycle. Pyruvate oxidation is a key step that links glycolysis to the citric acid cycle. In eukaryotes, this is the first step that takes place inside the mitochondria. -The conversion of pyruvate to acetyl-CoA results in the production of one molecule of NADH and one molecule of carbon dioxide. -Pyruvate oxidation occurs in the mitochondrial matrix.

Reaction centers are _--_____________.Special chlorophyll molecules in the reaction center transfer ------------- to an -----------, thus initiating the photosynthetic electron transport chain

Reaction centers are located within pigment-protein complexes known as photosystems. Special chlorophyll molecules in the reaction center transfer excited-state electrons to an electron-acceptor molecule, thus initiating the photosynthetic electron transport chain

molecular orbital

Region in a molecule where atomic orbitals overlap

Rubisco can act ... Rubisco has evolved to.........

Rubisco can act catalytically on oxygen as well as on carbon dioxide. When it acts on oxygen, there is a loss of energy and of reduced carbon from the Calvin cycle. page 168 Rubisco has evolved to favor carbon dioxide over oxygen, but the cost of this selectivity is reduced speed

question: Most animal fats are solid at room temperature, whereas plant and fish oils tend to be liquid. Both contain fatty acids. Can you predict which type of fat contains saturated fatty acids, and which type contains unsaturated fatty acids?

Saturated fatty acids are less mobile within the membrane compared to unsaturated fatty acids. As a result, saturated fatty acids tend to be solid at room temperature, whereas unsaturated fatty acids tend to be liquid. Margarine and many other animal fats contain saturated fatty acids and are solid, whereas many plant and fish oils contain unsaturated fatty acids and are liquid at room temperature.

Show in a diagram how energy from sunlight is used to produce ATP.

Show in a diagram how energy from sunlight is used to produce ATP. Self-Assessment 7 Answer Diagram should show the two ways in which electron transport results in a high concentration of protons in the lumen: (1) as a result of water splitting and (2) the coupled movement of electrons and protons that involves both plastoquinone and the cytochrome b6f complex and results in protons being moved across the thylakoid.

Metastic cancer cells

Some cancer cells spread from the original site of cancer formation to the bloodstream and then to distant organs of the body.

reaction center .

Specially configured chlorophyll molecules where light energy is converted into electron transport. -(a) Antenna chlorophylls deliver absorbed light energy to the reaction center, allowing electrons to be transferred to an electron acceptor molecule. (b) After the reaction center has lost an electron, it is reduced by gaining an electron, so it is ready to absorb additional light energy. -The reaction center is where light energy is converted into chemical energy as a result of the excited electron's transfer to an adjacent molecule.

Starch formation provides......

Starch formation provides chloroplasts with a way of storing carbohydrates that will not cause water to enter the cell by osmosis.

The Calvin cycle

The Calvin cycle is a three-step process that uses carbon dioxide to synthesize carbohydrates. -(1) addition of CO2 (carboxylation); (2) reduction; and (3) regeneration. -The first step is the addition of CO2 to the 5 carbon sugar RuBP. This step is catalyzed by the enzyme rubisco, considered the most abundant protein on Earth. The resulting 6-carbon compound immediately breaks down into two 3-carbon compounds. page 157 -The second step is the donation of a phosphate group to the 3 carbon compounds by ATP followed by reduction by NADPH to produce 3 carbon triose phosphate molecules. Some of these triose phosphates are exported from the chloroplast to the cytosol, where they are used to build larger sugars. page 158 -The third step is the regeneration of RuBP from five 3-carbon triose phosphates.

The Calvin cycle requires ------- molecules of NADPH and ------ molecules of ATP for each CO2 incorporated into carbohydrates

The Calvin cycle requires two molecules of NADPH and three molecules of ATP for each CO2 incorporated into carbohydrates -These electrons reenter the photosynthetic electron transport chain by plastoquinone. Because these electrons eventually return to photosystem I, this alternative pathway is cyclic in contrast to the linear movement of electrons from water to NADPH.

The R groups of the basic and acidic amino acids are _________. At the pH of a cell, the R groups of the basic amino acids __________ and become ________charged, whereas those of the acidic amino acids ________ and become ___________ charged.

The R groups of the basic and acidic amino acids are strongly polar. At the pH of a cell, the R groups of the basic amino acids gain a proton and become positively charged, whereas those of the acidic amino acids lose a proton and become negatively charged.

The ability to use water as an electron donor in photosynthesis evolved in ......

The ability to use water as an electron donor in photosynthesis evolved in cyanobacteria

The accumulation of protons in the thylakoid lumen...

The accumulation of protons in the thylakoid lumen drives the synthesis of ATP.

If the difference between the enthalpy of the products and that of the reactants is positive and the difference between the entropy of the products and reactants is negative, predict whether the reaction is spontaneous or not.

The amount of energy available to do work is called Gibbs free energy (G). In a chemical reaction, you compare the free energy of the reactants and products to determine whether there is energy available to do work. This difference is called ΔG. ΔG = ΔH ‒ TΔS. If the enthalpy difference (ΔH) is negative and the entropy difference (ΔS) is positive, then ΔG is negative and free energy is released. This kind of reaction is exergonic and occurs spontaneously.

van der walls

The binding of temporarily polarized molecules because of the attraction of opposite charges. -The van der Waals forces come into play only when atoms are sufficiently close to one another, and they are weaker than hydrogen bonds, but many van der Waals forces acting together help to stabilize molecules.

The buildup of protons in the lumen......

The buildup of protons in the lumen drives the production of ATP by oxidative phosphorylation. The ATP synthase is oriented such that ATP is produced on the stroma side of the membrane.

The change of free energy in a chemical reaction is described by

The change of free energy in a chemical reaction is described by ΔG = ΔH - TΔS.

peptide bond

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid - The formation of a peptide bond involves the loss of a water molecule since in order to form a C-N bond, -its a C-N bond The covalent linkage joining two amino acids together

metabolism -catabolism -anabolism

The chemical reactions occurring within cells that convert molecules into other molecules and transfer energy in living organisms. -its broken down into catabolism and anabolism catabolism-The set of chemical reactions that break down molecules into smaller units and, in the process, produces ATP to meet the energy needs of the cell. Catabolic reactions have a negative ΔG and release energy, often in the form of ATP. -cellular respiration is catabolic anabolism-The set of chemical reactions that build molecules from smaller units utilizing an input of energy, usually in the form of ATP. Anabolic reactions result in net energy storage within cells and the organism. Anabolic reactions have a positive ΔG and require an input of energy, often in the form of ATP. For example, carbohydrates can be broken down, or catabolized, into sugars, fats into fatty acids and glycerol, and proteins into amino acids. These initial products can be broken down further to release energy stored in their chemical bonds. The synthesis of macromolecules such as carbohydrates and proteins, by contrast, is anabolic.

The citric acid cycle results in..... and it is..

The citric acid cycle results in the complete oxidation of fuel molecules and the generation of ATP and reduced electron carriers. -it is the third stage of cellular respiration, in which acetyl-CoA is broken down and more carbon dioxide is released. -citric acid cycle supplies electrons to the electron transport chain, leading to the production of much more energy in the form of ATP than is obtained by glycolysis alone. -citric acid cycle takes place in the mitochondrial matrix. It is composed of eight reactions and is called a cycle because the starting molecule, oxaloacetate, is regenerated at the end -The acetyl group of acetyl-CoA is completely oxidized, with the net production of one ATP, three NADH, and one FADH2. -The citric acid cycle is a cycle because the acetyl group of acetyl-CoA combines with oxaloacetate, and then a series of reactions regenerates oxaloacetate. -A complete turn of the citric acid cycle results in the production of one molecule of GTP (which is converted to ATP), three molecules of NADH, and one molecule of FADH2. -Citric acid cycle intermediates are starting points for the synthesis of many different organic molecules. from textbook: In the first reaction, the 2-carbon acetyl group of acetyl-CoA is transferred to a 4-carbon molecule of oxaloacetate to form the 6-carbon molecule citric acid or tricarboxylic acid (hence the variant names "citric acid cycle" and "tricarboxylic acid cycle"). The molecule of citric acid is then oxidized in a series of reactions. The last reaction of the cycle regenerates a molecule of oxaloacetate, joining to a new acetyl group and allowing the cycle to continue.

endomembrane system

The collection of membranes inside and around a eukaryotic cell -includes the nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, plasma membrane and the vesicles that move between them -it compartmentalizes the cell

The complete oxidation of glucose during the first three stages of cellular respiration results in ..... Legit just notes: The energy in these electron carriers is released in a series of redox reactions that occur as electrons pass through a chain of protein complexes in the inner mitochondrial membrane to the final electron acceptor, oxygen, which is reduced to water. The energy released by these redox reactions is not converted directly into the chemical energy of ATP, however. Instead, the passage of electrons is coupled to the transfer of protons (H+) across the inner mitochondrial membrane, creating a concentration and charge gradient (Chapter 5). This electrochemical gradient provides a source of potential energy that is then used to drive the synthesis of ATP.

The complete oxidation of glucose during the first three stages of cellular respiration results in the production of two kinds of reduced electron carriers: NADH and FADH2.

=. The cytoskeleton is composed of ............that help maintain ........

The cytoskeleton is composed of microtubules, microfilaments, and intermediate filaments that help maintain cell shape.

energetic coupling

The driving of a non-spontaneous reaction by a spontaneous reaction. -It requires that the net ΔG of the two reactions be negative. In addition, the two reactions must occur together. In some cases, this coupling can be achieved if the two reactions share an intermediate. - A spontaneous (exergonic) reaction drives a non-spontaneous (endergonic) reaction. (a) The hydrolysis of ATP drives the formation of glucose 6-phosphate from glucose. (b) The hydrolysis of phosphoenolpyruvate drives the synthesis of ATP.

The electron transport chain consists of

The electron transport chain consists of a series of electron transfer or redox reactions that take place within both protein complexes and diffusible compounds. Water is the electron donor and NADP+ is the final electron acceptor.

The electron transport chain

The electron transport chain transfers electrons from electron carriers to oxygen, using the energy released to pump protons and synthesize ATP by oxidative phosphorylation. -NADH and FADH2 donate electrons to the electron transport chain -electrons move from one redox couple to the next. -The electron transport chain is made up of four complexes. Complexes I and II accept electrons from NADH and FADH2, respectively. The electrons are transferred from these two complexes to coenzyme Q. -Reduced coenzyme Q transfers electrons to complex III and cytochrome c transfers electrons to complex IV. Complex IV reduces oxygen to water. -The transfer of electrons through the electron transport chain is coupled with the movement of protons across the inner mitochondrial membrane into the intermembrane space. -The electron transport chain. (a) The electron transport chain consists of four complexes (I to IV) in the inner mitochondrial membrane. (b) Electrons flow from electron carriers to oxygen, the final electron acceptor. (c) The proton gradient formed from the electron transport chain has potential energy that is used to synthesize ATP. -Electrons also must be transported between the four complexes -These electron transfer steps are each associated with the release of energy as electrons are passed from the reduced electron carriers NADH and FADH2 to the final electron acceptor, oxygen. Some of this energy is used to reduce the next carrier in the chain, but in complexes I, III, and IV, some of it is used to pump protons (H+) across the inner mitochondrial membrane, from the mitochondrial matrix to the intermembrane space (Fig. 7.10). Thus, the transfer of electrons through complexes I, III, and IV is coupled with the pumping of protons. The result is an accumulation of protons in the intermembrane space.

Regulation of threonine dehdyratase, an allosteric enzyme........

The enzyme is inhibited by the final product, isoleucine, which binds to a site distinct from the active site.

cytochrome c

The enzyme to which electrons are transferred in complex III of the electron transport chain.

The evolutionary history of photosynthesis

The evolutionary history of photosynthesis. (a) Hypotheses for the origin of the two photosystems in cyanobacteria. (b) Later, by endosymbiosis, free-living cyanobacteria became the chloroplasts of eukaryotic cells.

question: Describe two effects that the extracellular matrix can have on the cells that synthesize it.

The extracellular matrix can influence the shape of cells that grow in or on it. For example, fibroblasts take on different shapes depending on whether they are grown on a two-dimensional or three-dimensional extracellular matrix. The extracellular matrix can also affect the expression of genes of the cells that grow in or on it. For example, the expression of the milk-protein β-casein by mammary epithelial cells grown in cell culture is strongly influenced by the type and composition of the extracellular matrix.

The extracellular matrix

The extracellular matrix provides structural support and informational cues.

Describe the first and second laws of thermodynamics and how they relate to chemical reactions.

The first law of thermodynamics is the law of conservation of energy. It states that energy can be neither created nor destroyed; it can only be transformed from one form into another. The second law of thermodynamics states that the transformation of energy is associated with an increase in the disorder of the universe. The degree of disorder is called entropy. Chemical reactions are subject to the laws of thermodynamics (like everything else). As a result, the total amount of energy remains the same before and after a chemical reaction, but some of the energy is used to increase the entropy of the system, and only some of the energy is available to do the work of the cell.

The first versus second law of thermodynamics

The first law of thermodynamics states that energy cannot be created or destroyed -the universe contains a constant amount of energy . The second law of thermodynamics states that there is an increase in entropy in the universe over time. -Because the amount of disorder increases when energy is transformed from one form to another, some of the total energy is not available to do work.

List the four most common elements in organic molecules and state which common macromolecules always contain all four of these elements.

The four most common elements in organic molecules in order of decreasing abundance by dry mass are carbon, oxygen, hydrogen, and nitrogen. All four of these elements are found in proteins and nucleic acids because they are parts of the building blocks of these polymers.

The hydrolysis of ATP is an ________ reaction that drives many __________ reactions in a cell.

The hydrolysis of ATP is an exergonic reaction that drives many endergonic reactions in a cell.

Describe how the hydrolysis of ATP can drive non-spontaneous reactions in a cell.

The hydrolysis of ATP releases energy. This energy can be used to drive nonspontaneous reactions in a cell if the total ΔG for the entire pathway is negative.

The laws of thermodynamics govern _____________

The laws of thermodynamics govern energy flow in biological systems.

The light-harvesting reactions

The light-harvesting reactions use sunlight to produce the ATP and NADPH required by the Calvin cycle.

The linear transport of electrons from water to NADPH requires......

The linear transport of electrons from water to NADPH requires the energy input of two photosystems.

dermis

The main type of cell in the dermis is the fibroblast, which synthesizes the extracellular matrix. The dermis is strong and flexible because it is composed of tough protein fibers of the extracellular matrix. The dermis also has many blood vessels and nerve endings.

The major component of the plant cell wall is __________

The major component of the plant cell wall is cellulose, a polymer of glucose.

Chloyophyll

The major photosynthetic pigment contained in the thylakoid membrane; it plays a key role in the chloroplast's ability to capture energy from sunlight. Chlorophyll appears green because it is poor at absorbing green wavelengths. -Chlorophyll molecules are bound by their tail region to integral membrane proteins in the thylakoid membrane. These protein-pigment complexes, referred to as photosystems, are the functional and structural units that absorb light energy and use it to drive electron transport. -The large number of alternating single and double bonds in the head region explains why chlorophyll is so efficient at absorbing visible light. -When visible light is absorbed by a chlorophyll molecule, one of its electrons is elevated to a higher energy state

The major protein complexes of the photosynthetic electron transport chain include.....

The major protein complexes of the photosynthetic electron transport chain include the two photosystems as well as the cytochrome-b6 f complex (cyt), through which electrons pass between photosystem II and photosystem I (Fig. 8.14).

The maximum theoretical efficiency of photosynthesis is approximately///

The maximum theoretical efficiency of photosynthesis is approximately 4% of total incident solar energy.

intracellular transport

The motor protein kinesin interacts with microtubules to move vesicles in the cell.

The movement of protons back into the mitochondrial matrix through the Fo subunit of ATP synthase is coupled with.............

The movement of protons back into the mitochondrial matrix through the Fo subunit of ATP synthase is coupled with the formation of ATP, a reaction catalyzed by the F1 subunit of ATP synthase

osmosis

The net movement of a solvent such as water across a selectively permeable membrane such as the plasma membrane

explain how the periodic table is arranged

The periodic table of elements is organized by the increasing atomic number of each atom. The atomic number is the number of protons an atom has in its nucleus.

The phosphate head group is __________because it is _________. By contrast, the two fatty acid tails are ________because _______. Molecules with both hydrophilic and hydrophobic regions in a single molecule are termed ________.

The phosphate head group is hydrophilic ("water-loving") because it is polar, enabling it to form hydrogen bonds with water. By contrast, the two fatty acid tails are hydrophobic ("water-fearing") because they are nonpolar and do not form hydrogen bonds with water. Molecules with both hydrophilic and hydrophobic regions in a single molecule are termed amphipathic.

phosphodiester bond

The phosphodiester bond. Phosphodiester bonds link successive deoxyribonucleotides, forming the backbone of the DNA strand.

The photosynthetic electron transport chain connects -------------

The photosynthetic electron transport chain connects two photosystems.

photosystem I

The photosystem that energizes electrons with a second input of light energy so they have enough energy to reduce NADP+.

photosystem II

The photosystem that supplies electrons to the beginning of the electron transport chain. When photosystem II loses an electron, it can pull electrons from water.

plasma membrane

The plasma membrane is a selective barrier that controls the movement of molecules between the inside and the outside of the cell -• It is the boundary that defines the space of the cell, separating its internal contents from the surrounding environment -• Phospholipids with embedded proteins make up the membrane surrounding all cells -maintains homeostasis by being semipermeable

active sight

The portion of the enzyme that binds substrate and converts it to product. -The specificity of enzymes can be attributed to the structure of their active sites. The enzyme active site interacts only with substrates having a precise three-dimensional structure. -The size of the active site of an enzyme is small compared to the size of the enzyme as a whole and the active site amino acids occupy a very specific spatial arrangement.

From the summary: What evidence is there for the hypothesis that life originated on Earth by the creation and polymerization of small organic molecules by natural processes?

The principal molecules found in organisms are themselves made of simpler molecules joined together. So if we want to understand how proteins emerged on Earth, then we first have to understand the synthesis of amino acids. Stanley Miller conducted experiments that showed that when a mixture of gases―which were thought to have been present in the early atmosphere―were ignited with a spark, amino acids were generated. Other scientists have subsequently shown that the other building blocks of life—sugars, bases, and lipids—can also be formed in laboratory conditions that simulate the early atmosphere. Analyses of meteorites that provide samples of the early solar system have also shown the presence of diverse amino acids, lipids, and other organic compounds, which supports Miller's initial hypothesis. Building off of Miller's work, Leslie Orgel performed experiments that showed how nucleotides would spontaneously join to synthesize nucleic acids. Many years later, John Sutherland and his colleagues were able to synthesize nucleotides themselves under conditions thought to be like those on the early Earth.

Calvin Cycle

The process in which carbon dioxide is reduced to synthesize carbohydrates, with ATP and NADPH as the energy sources. -The Calvin cycle consists of 15 chemical reactions that synthesize carbohydrates from CO2. These reactions can be grouped into three main steps: (1) carboxylation, in which CO2 is added to a 5-carbon molecule; (2) reduction, in which energy and electrons are transferred to the compounds formed in step 1; and (3) regeneration of the 5-carbon molecule needed for carboxylation -The Calvin cycle is capable of producing more carbohydrates than the cell needs or, in a multicellular organism, more than the cell is able to export. excess carbohydrates are converted to starch, a storage form of carbohydrates Because starch molecules are not soluble, they provide a means of carbohydrate storage that does not lead to osmosis. The formation of starch during the day provides photosynthetic cells with a source of carbohydrates that they can use during the night

endosymbiosis versus endosymbiotic hypothesis.

The process in which one cell takes up residence inside of another cell is called endosymbiosis. Therefore, the idea that chloroplasts and mitochondria (Chapter 7) arose in this way is called the endosymbiotic hypothesis.

The rate at which protein subunits are added depends on _________. explain what happens at high and low conc -faster assembling end is called -slower end is called

The rate at which protein subunits are added depends on the concentrations of tubulin and actin in that region of the cell. At high concentrations of subunits, microtubules and microfilaments can become longer at both ends, although the subunits are assembled more quickly on one end than the other. The faster-assembling end is called the plus end and the slower-assembling end is called the minus end

The rate of a chemical reaction is defined as......

The rate of a chemical reaction is defined as the amount of product formed (or reactant consumed) per unit of time.

The rate of biochemical reactions is increased by __________________

The rate of biochemical reactions is increased by protein catalysts called enzymes.

For each of the following pairs of molecules, indicate which member of the pair is reduced and which is oxidized, and which has more chemical energy and which has less chemical energy: NAD+/NADH; FAD/FADH2; CO2/C6H12O6.

The reduced molecules are NADH, FADH2, and C6H12O6, and the oxidized molecules are NAD+, FAD, and CO2. The reduced forms have more chemical energy than their corresponding oxidized forms.

stroma

The region surrounding the thylakoid, where carbohydrate synthesis takes place.

Question: A mutation leads to a change in one amino acid in a protein. The result is that the protein no longer functions properly. How is this possible?

The sequence of amino acids in a protein determines how a protein folds, so a change in even a single amino acid can affect the way the protein folds and can disrupt its function. For example, if the hydrophobic R groups of two amino acids must aggregate for proper structure and function, then a mutation that changes one of the hydrophobic amino acids for an acidic or a basic amino acid will prevent this aggregation and disrupt structure and function. Similarly, if proper folding requires interaction between the R groups of an acidic and a basic amino acid, then, if either one of them is changed to a hydrophobic amino acid, proper folding will not take place.

The shape of the structure of phospholipids is determined by the ____________. Also what are micelles versus bilayer

The shape of the structure is determined by the bulkiness of the head group relative to the hydrophobic tails. For example, lipids with bulky heads and a single hydrophobic fatty acid tail are wedge-shaped and pack into spherical structures called micelles (Fig. 5.3a). By contrast, lipids with less bulky head groups and two hydrophobic tails form a bilayer

inter membrane

The space between the inner and outer mitochondrial membranes.

the sugar/nucleotide in RNA is..... the sugar/nucelotide in DNA is... they differ how?

The sugar in RNA is ribose, and the sugar in DNA is deoxyribose. The sugars differ in that ribose has a hydroxyl (OH) group on the second carbon (designated the 2′ carbon), whereas deoxyribose has a hydrogen atom at this position (hence, deoxyribose).

photic zone

The surface layer of the ocean through which enough sunlight penetrates to enable photosynthesis.

The synthesis of carbohydrates through the Calvin cycle results in ....

The synthesis of carbohydrates through the Calvin cycle results in significant energy losses, which are due in part to photorespiration. page 169

Question:Describe the functions of the three major motor proteins and state which cytoskeletal element each interacts with.

The three major motor proteins are myosin, kinesin, and dynein. Myosin binds to microfilaments in the cell and can cause these filaments to move relative to each other, as in muscle cell contraction. Myosin can also attach to various types of cellular cargo and move along a microfilament, transporting these materials from one part of the cell to another. Kinesin transports cargo toward the plus end of microtubules, while dynein transports cargo in the opposite way, toward the minus end of the microtubule. Dynein also associates with microtubules to cause movement of cilia and flagella.

Question:Describe three major types and functions of cell junctions.

The three major types of cell junctions are anchoring junctions (adherens junctions, desmosomes, and hemidesmosomes); barrier junctions (tight junctions); and communicating junctions (gap junctions and plasmodesmata). Anchoring junctions allow cells to adhere to one another. Barrier junctions prevent the passage of substances between cells. Communicating junctions permit substances to flow from the cytoplasm of one cell to the cytoplasm of a neighboring cell.

The Z scheme

The use of water as an electron donor requires input of light energy at two places in the photosynthetic electron transport chain. -Another name for the photosynthetic electron transport chain, so called because the overall energy trajectory resembles a "Z."

A man has ordered a glass of soda in a restaurant. When his drink arrives, he notices that quite a bit of ice is floating at the top of the glass. Why does the ice float? Please choose the correct answer from the following choices, and then select the submit answer button. A)The water molecules in the soda are arranged in a lattice pattern, providing a "net" on which ice can sit. B)he water molecules in ice are arranged in a lattice pattern, and the water molecules in the soda are more densely packed compared to the water molecules in the ice, causing ice to float. C)The water molecules in ice are arranged in a lattice pattern, causing ice to float. D)The water molecules in the ice are more densely packed compared to the water molecules in the soda. E)The water molecules in the soda are more densely packed compared to the water molecules in the ice.

The water molecules in ice are arranged in a lattice pattern, and the water molecules in the soda are more densely packed compared to the water molecules in the ice, causing ice to float.

relationship between the rate of a reaction and height of an energy barrier

There is an inverse correlation between the rate of a reaction and the height of the energy barrier: the lower the energy barrier, the faster the reaction; the higher the barrier, the slower the reaction.

Which of the following best describes a role that microfilaments play in the structure and function of red blood cells

They maintain the biconcave shape to maximize gas exchange.

Three thermodynamic parameters that define a chemical reaction are....

Three thermodynamic parameters define a chemical reaction: Gibbs free energy (G), enthalpy (H), and entropy (S)

Question: Name three types of cytoskeletal element, the subunits they are composed of, their relative sizes, and the major functions of each type.

Three types of cytoskeletal elements are microtubules, microfilaments, and intermediate filaments. Microtubules are made up of α- and β-tubulin dimers; microfilaments are made up of actin monomers; and intermediate filaments are made up of intermediate filament protein subunits. Microtubules have the largest diameter (25 nm); microfilaments have the smallest diameter (7 nm); and intermediate filaments have an intermediate diameter (10 nm). Microtubules help to maintain cell shape, provide tracks for vesicles and other cargo inside of cells, and make up the spindles that attach to chromosomes during cell division. Microfilaments also help to maintain cell shape and associate with myosin to cause muscle contraction. Intermediate filaments provide cells with mechanical strength.

Threonine dehydratase can also adjust the rate of the reaction, depending on the ______ At a low concentration of threonine, the rate of the reaction __________ . As the concentration of threonine increases, the _________ . At a particular threshold, a small increase in threonine concentration results in a large increase in reaction rate. Finally, when there is excess substrate, the reaction rate __________

Threonine dehydratase can also adjust the rate of the reaction, depending on the concentration of substrate. At a low concentration of threonine, the rate of the reaction is very slow. As the concentration of threonine increases, the activity of the enzyme increases. At a particular threshold, a small increase in threonine concentration results in a large increase in reaction rate. Finally, when there is excess substrate, the reaction rate slows down.

Thylakoid membranes structure

Thylakoid membranes form structures that resemble flattened sacs, and these sacs are grouped into structures called grana (singular, granum) that look like stacks of interlinked pancakes. Grana are connected to one another by membrane bridges in such a way that the thylakoid membrane encloses a single interconnected compartment called the lumen The region surrounding the thylakoid membrane is called the stroma.

Tissues and organs

Tissues and organs are communities of cells that perform specific functions. -two or more tissues form organs

True or False? The atomic mass can be used to differentiate between different isotopes of the same element.

True

How did eukaryotic cells evolve?

Two hypotheses for the origin of the eukaryotic cell. Both hypotheses lead to the evolution of a mitochondrion-bearing protist.

binding of inhibitors

Two mechanisms of inhibitor function. (a) Some inhibitors bind to the active site of the enzyme and (b) other inhibitors bind to a site that is different from the active site. Both types of inhibitor reduce the activity of an enzyme and therefore decrease the rate of the reaction.

Two motor proteins that associate with these microtubule tracks are _____ and ____. explain the difference between the two

Two motor proteins that associate with these microtubule tracks are kinesin and dynein. Kinesin transports cargo toward the plus end of microtubules, located at the periphery of the cell (Fig. 10.7). By contrast, dynein carries its load away from the plasma membrane toward the minus end, located at the centrosome in the interior of the cell. Movement along microtubules by kinesin and dynein is driven by conformational changes in the motor proteins and is powered by energy harvested from ATP.

______________ is absorbed by chlorophyll

Visible light is absorbed by chlorophyll

Water -----------electrons to one end of the photosynthetic electron transport chain, whereas -------- ------------- electrons at the other end.

Water donates electrons to one end of the photosynthetic electron transport chain, whereas NADP+ accepts electrons at the other end.

List three unusual properties of water and explain why these properties make water conducive to life.

Water has unusual properties and is conducive to life in the following ways: Water is a polar molecule, and because of its regions of positive and negative charge, some molecules are attracted to water (hydrophilic) and some are repelled by it (hydrophobic). It is this property that allows things like lipid cellular membranes, and thus cells, to exist. The polar nature of water also makes it a good solvent—hydrophilic compounds dissolve readily in water. Water also has a neutral pH (around 7), the pH of most cells. Since many chemical reactions can only be carried out in a solution around a neutral pH, it is important that the cell remain in this range to function. Water resists temperature changes better than other substances due to its extensive network of hydrogen bonding. This is important for a variety of reasons. This phenomenon allows chemical reactions, which produce heat as a by-product, to occur inside the cell without changing the internal temperature. In a similar way, but on a global scale, the oceans act as a temperature regulator and keep the Earth in a temperature range that supports life. The network of hydrogen bonds that forms when water freezes makes ice less dense than liquid water. As a result, ice floats on water, which allows aquatic life to survive below the ice in the winter. Finally, the cohesive properties and surface tension of water facilitate water transportation in plants

question: A container is divided into two compartments by a membrane that is fully permeable to water and small ions. Water is added to one side of the membrane (side A), and a 5% solution of sodium chloride (NaCl) is added to the other (side B). In which direction will water molecules move? In which direction will sodium and chloride ions move? When the concentration is equal on both sides, will diffusion stop?

Water molecules move in both directions, but the net movement of water molecules is from side A to side B. Water moves from regions of higher water concentration to regions of lower water concentration. Likewise, sodium and chloride ions move in both directions, but the net movement of sodium and chloride ions is from side B to side A. Movement of water and ions results from diffusion, the random motion of substances. Even when the concentration of all molecules is the same on the two sides, diffusion still occurs, but there is no net movement of water molecules or ions.

When chlorophyll in solution returns to its ground state via energy release, it is ready to absorb another photon. How is this different in the reaction center chlorophyll in the chloroplast?

When chlorophyll in solution returns to its ground state via energy release, it is ready to absorb another photon. How is this different in the reaction center chlorophyll in the chloroplast? Question 4 choices Choice A., The reaction center chlorophyll must obtain a replacement electron.

why would the citric acid cycle go in reverse? what molecules generally are produced by the citric acid cycle?

Why would an organism run the citric acid cycle backward? The answer is that running the cycle in reverse allows an organism to build, rather than break down, organic molecules. Whether the cycle is run in the reverse or forward direction, the intermediates generated step by step as the cycle turns provide the building blocks for synthesizing the cell's key biomolecules -Molecules produced by the citric acid cycle. Many organic molecules can be synthesized from citric acid cycle intermediates.

within each protein complex of the electron transport chain.....

Within each protein complex of the electron transport chain, electrons are passed from electron donors to electron acceptors. Each donor and acceptor is a redox couple, consisting of an oxidized and a reduced form of a molecule. The electron transport chain contains many of these redox couples. When oxygen accepts electrons at the end of the electron transport chain, it is reduced to form water: this reaction is called complex IV

Write the overall chemical equation for glycolysis, noting the starting and ending products and highlighting the energy-storing molecules that are produced.

Write the overall chemical equation for glycolysis, noting the starting and ending products and highlighting the energy-storing molecules that are produced. Self-Assessment 4 Answer The starting product is glucose and the end product is pyruvate. Energy-storing molecules that are produced are ATP and NADH. Glucose + 2NAD+ + 2ADP + 2Pi → 2 pyruvate + 2ATP + 2NADH + 2H+ + 2H2O

Write the overall photosynthetic reaction and identify which molecules are oxidized and which molecules are reduced.

Write the overall photosynthetic reaction and identify which molecules are oxidized and which molecules are reduced. Self-Assessment 1 Answer The overall photosynthetic reaction is CO2 + H2O → C6H12O6 + O2, in which the CO2 is reduced to C6H12O6 and the H2O is oxidized to O2.

Bread making involves ethanol fermentation and typically uses yeast, sugar, flour, and water. Why are yeast and sugar used?

Yeast cells are eukaryotes. In bread making, yeast can use sugar as a food source for ethanol fermentation. The carbon dioxide produced in the process causes the bread to rise. The ethanol is removed in the baking process.

plant cells have......

a cell wall outside the plasma membrane, vacuoles specialized for water uptake, and chloroplasts that convert energy of sunlight into chemical energy

extracellular matrix

a collection of extracellular molecules secreted by cells that provides structural and biochemical support to the surrounding cells. -an insoluble meshwork composed of proteins and polysaccharides

proton gradient

a potential source of energy -The proton gradient has two components: a chemical gradient due to the difference in concentration and an electrical gradient due to the difference in charge between the two sides of the membrane. To reflect the dual contribution of the concentration gradient and the electrical gradient, the proton gradient is also called an electrochemical gradient. -t stores energy much in the same way that a battery or a dam does. Through the actions of the electron transport chain, protons have a high concentration in the intermembrane space and a low concentration in the mitochondrial matrix. As a result, there is a tendency for protons to diffuse back to the mitochondrial matrix, driven by a difference in concentration and charge on the two sides of the membrane.

Cytoskeleton

a protein scaffold. -helps cells maintain their shape and serves as a network of tracks for the movement of substances within cells

Acid versus Base

acid: molecule that releases a proton (H+) base: a molecule that accepts a proton in aqueous solution.

activation energy (EA)

activation energy (EA) The energy input necessary to reach the transition state. -enzymes do not act by supplying heat. Instead, they reduce the activation energy by stabilizing the transition state and decreasing its free energy (the red curve in Fig. 6.13). As the activation energy decreases, the speed of the reaction increases

how are proteins, carbohydrates, and nucleic acids different from lipids?

all are polymers made up of smaller, repeating units with a defined structure. Lipids are different. Instead of being defined by a chemical structure, they share a particular property: Lipids are all hydrophobic. They share a property and not a structure. they are a chemically diverse group of molecules

Microtubules form from dimers of _____and ______ subunits that polymerize into a ____________

alpha-tubulin; beta-tubulin; hollow tube

signal sequence

amino acid sequences that allow them to be recognized and sorted

Proteins

amino acids -provide structural support and act as catalysts that facilitate chemical reactions.

signal recognition particle (srp)

an RNA-protein complex -binds to both the signal sequence and the free ribosome, and brings about a pause in translation -then it binds with a receptor on the RER so that the ribosome is now associated with the RER -the SRP receptor brings the ribosome to a channel in the membrane of the RER -The SRP then dissociates and translation continues, allowing the growing polypeptide chain to be threaded through the channel

Nuceleotide

are composed of three components: a 5-carbon sugar, a nitrogen-containing compound called a base, and one or more phosphate groups assemble to form nucleic acids, which store and transmit genetic information./

bilayer ex) liquid bilayer

bilayer-A two-layered structure of the cell membrane with hydrophilic "heads" pointing outward toward the aqueous environment and hydrophobic "tails" oriented inward, away from water. liquid bilayer-A lipid bilayer is a structure formed of two layers of lipids in which the hydrophilic heads are the outside surfaces of the bilayer and the hydrophobic tails are sandwiched in between, isolated from contact with the aqueous environment.

The transition state is that portion of the progress of a chemical reaction with a large amount of energy found in ___________BLANK reactions.

both endergonic and exergonic

Microtubules can grow by addition of tubulin dimers to _______________, and they can shorten by removal of dimers from ______________.

both plus and minus ends; both plus and minus ends

amino acids

building blocks of proteins -linked by covalent bonds to form proteins -An amino acid contains four groups attached to a central carbon atom. -Each amino acid contains a central carbon atom, called the α (alpha) carbon, covalently linked to four groups: an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (H), and an R group, or side chain, that differs from one amino acid to the next. on summary: An amino acid consists of a carbon atom (the α carbon) attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain.

Cell movement can be facilitated by microfilaments in what way?

by dynamic growing and shrinking at the ends

______________ is the backbone of organic molecules

carbon

Name the elements that constitute 94% of the total dry mass of human cells -which is the most abundant element

carbon, hydrogen, oxygen, nitrogen -carbon is the most abundant

organic molecules

carbon-based molecules

carbonyl group versus amide group in peptide bonds

carbonyl group: C=O amide group:N-H electron is more attracted to the co then the NH group bc of the EN and therefore the peptide bonds tend to take on characteristics of double bonds

carboxylation vs reduction vs regeneration

carboxylation: The first step of the Calvin cycle, in which carbon dioxide absorbed from the air is added to a 5-carbon molecule, called ribulose 1,5-bisphosphate (RuBP). side note: This step is catalyzed by the enzyme ribulose bisphosphate carboxylase oxygenase, or rubisco for short. An enzyme that adds CO2 to another molecule is called a carboxylase, explaining part of rubisco's long name. Page 158 Before rubisco can act as a carboxylase, RuBP and CO2 must diffuse into its active site. Once the active site is occupied, the addition of CO2 to RuBP proceeds spontaneously in the sense that no addition of energy is required. The product is a 6-carbon compound that immediately breaks into two molecules of 3-phosphoglycerate (3-PGA). These 3-carbon molecules are the first stable products of the Calvin cycle. reduction: A reaction in which a molecule gains electrons. regeneration: In the context of photosynthesis, the third step of the Calvin cycle, in which the 5-carbon molecule needed for carboxylation is produced.

chemiosmotic hypothesis

chemiosmotic hypothesis The hypothesis that the gradient of protons across a membrane provides a source of potential energy that is converted into chemical energy stored in ATP.

cilia and flagella

cilia-A hairlike organelle that propels the movement of cells or of substances within cells or out of the body; shorter than a flagellum. -short flagella-An organelle that propels the movement of cells or of substances within cells; longer than a cilium. -long In these organelles, microtubules associate with the motor protein dynein, which causes movement.

plant cell wall

composed of as many as three layers: 1)the outermost middle lamella -synthesized first -It is composed of a gluelike complex carbohydrate, and it is the main mechanism by which plant cells adhere to one another. 2)the primary cell wall, -The primary cell wall is formed next and consists mainly of cellulose, but it also contains a number of other molecules, including pectin. The primary cell wall is laid down while the cells are still growing. It is assembled by enzymes on the surface of the cell and remains thin and flexible. O 3)the secondary cell wall, located closest to the plasma membrane -once cell growth has stopped -It also is made largely of cellulose but in addition contains a substance called lignin. Lignin hardens the cell wall and makes it water resistant. In woody plants, the cell wall can be up to 25% lignin.

Lysosomes

contain enzymes that break down macromolecules such as proteins, nucleic acids, lipids, and complex carbs -degrade macromolecules -specialized vesicles derived from the Golgi apparatus that degrade damaged or unneeded macromolecules -contain a variety of enzymes that break down macromolecules such as proteins, nucleic acids, and complex carbohydrates -demonstrates the Golgi apparatus' ability to sort and dispatch proteins to particular destinations

Peroxisomes

contain many different enzymes that are involved in important metabolic reactions, including breakdown of fatty acids and the synthesis of certain types of phospholipids

nucelar envelope

defines the boundary of the nucleus -consists of two membraneS: inner and outer membranes -each is lipid bilayer with associated proteins -these two membranes are continuous with each other at nuclear pores

The ability of microtubules to undergo rapid ___________ and slower ____________ is associated with the ability of the ______________ to explore the cell and locate chromosomes.

depolymerization; polymerization; spindle apparatus

organelles

divide cell contents into smaller spaces for different functions - many of the organelles inside the cells are not isolated entities, but instead communicate with one another. in fact, the membrane of the organelles are either physically connected by bridges or they are transiently connected by vesicles

Microtubules and microfilaments are _____ structures. They become longer by the ________of ________ to their ends, and become ______ by the loss of subunits

dynamic They become longer by the addition of subunits to their ends, and become shorter by the loss of subunits

Microtubules are __________ because they __________ and depolymerize at their ends.

dynamic; polymerize

The basis for movement of cilia and flagella is the interaction of the motor protein __________with the cytoskeletal elements called ____________

dynein; microtubules

List features of carbon that allow it to form diverse structures.

eatures of carbon that allow it to form diverse structures are the following: A carbon atom behaves as if it has four unpaired electrons, allowing it to form covalent bonds with up to four different atoms. Each of these bonds can also rotate freely, contributing to the structural diversity of carbon-based molecules. Carbon atoms can bond with other carbon atoms to form large carbon chains that branch or form rings, also giving rise to a great diversity of structures. Carbon can also form double bonds (sharing two electrons). A double bond does not freely rotate, which limits the flexibility of the molecule and its structural options.

electron donor

electron donor A molecule that loses electrons.

electron transport chain

electron transport chain The system that transfers electrons along a series of membrane-associated proteins to a final electron acceptor, using the energy released as electrons move down the chain to produce ATP. - Electron transport chains are used in respiration to harness energy from fuel molecules such as glucose and in photosynthesis to harness energy from sunlight

When the atoms join into a molecule, the two orbitals merge into a single molecular orbital containing two _____________ that are shared by the ______________. A ____________________ between atoms is denoted by a single line connecting the two chemical symbols for the atoms

electrons hydrogen atoms covalent bond

negatively charged _______ move around the nucleus in whats called

electrons orbitals

nuclear localization signals

enable proteins to move through pores in the nuclear envelope

nucleic acids

encode and transmit genetic information.

endomembrane system is

endomembrane system is an interconnected system of membranes that includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, and plasma membrane.

endosymbiosis -an example of chloroplast endosymbiosis

endosymbiosis -A symbiosis in which one partner lives within the other. -A second example of chloroplast endosymbiosis. The photosynthetic amoeba Paulinella chromatophora acquired photosynthesis by endosymbiosis independently of and more recently than the endosymbiosis that gave rise to chloroplasts in green plants and other eukaryotes.

energy

energy A property of objects that can be transferred from one object to another, and that cannot be created or destroyed -the capacity to do work

enthalpy vs entropy vs absolute temperature what is the equation and how does anabolic and catabolic reactions play a role in the equation

enthalpy- The total amount of energy in a system. entropy-The degree of disorder in a system. absolute temperature- Temperature measured on the Kelvin scale. ΔG = ΔH - TΔS -Catabolic reactions have a negative ΔG and release energy, often in the form of ATP. Anabolic reactions have a positive ΔG and require an input of energy, often in the form of ATP. -If the conversion of reactant A into product B is spontaneous, the reverse reaction converting reactant B into product A is not. The ΔG's for the forward and reverse reactions have the same absolute value but opposite signs.

Give three characteristics of enzymes and describe how they permit chemical reactions to occur in cells.

enzymes reduce the activation energy of a chemical reaction (or the energy input necessary to reach the transition state) by stabilizing the transition state and decreasing its free energy. See Fig. 6.13. Enzymes are catalysts that participate in a chemical reaction, forming complexes with products and reactants, but are not themselves consumed in the process. See Fig. 6.14. Enzymes are also highly specific. They typically catalyze only one reaction, recognizing a specific substrate. Finally, inhibitors and activators can influence enzyme activity. Inhibitors decrease the activity of enzymes, whereas activators increase this activity.

Lipids

fats and oils -make up cell membranes, store energy, and act as signaling molecules. -chemically diverse -hydrophobic -Lipids freely associate with one another because of extensive van der Waals forces between their fatty acid tails. These weak interactions are easily broken and re-formed, so lipid molecules are able to move within the plane of the membrane, sometimes very rapidly:

in the absence of oxygen, pyruvate can be broken down by...

fermentation

phases of glycosis

first phase: The first phase prepares glucose for the next two phases by the addition of two phosphate groups to glucose. This phase requires an input of energy. To supply that energy and provide the phosphate groups, two molecules of ATP are hydrolyzed per molecule of glucose. In other words, the first phase of glycolysis is an endergonic process. second phase:The second phase is the cleavage phase, in which the 6-carbon molecule is split into two 3-carbon molecules. For each molecule of glucose entering glycolysis, two 3-carbon molecules enter the third phase of glycolysis. third phase:The third and final phase of glycolysis is sometimes called the payoff phase because ATP and the electron carrier NADH are produced. Later, NADH will contribute to the synthesis of ATP during oxidative phosphorylation. This phase ends with the production of two molecules of pyruvate.

carbon atoms form.......

four covalent bonds

4 stages of cellular respiration

glycolysis pyruvate oxidation citric acid cycle oxidative phosphorylation 1)In stage 1, glucose is partially broken down to make pyruvate and energy is transferred to ATP and reduced electron carriers, a process known as glycolysis. 2)In stage 2, pyruvate is oxidized to another molecule called acetyl-coenzyme A (acetyl-CoA), producing reduced electron carriers and releasing carbon dioxide. 3)Acetyl-CoA enters stage 3, the citric acid cycle, also called the tricarboxylic (TCA) cycle or the Krebs cycle. In this series of chemical reactions, the acetyl group is completely oxidized to carbon dioxide and energy is transferred to ATP and reduced electron carriers. The amount of energy transferred to ATP and reduced electron carriers in this stage is nearly twice that of stages 1 and 2 combined. 4)Stage 4 is oxidative phosphorylation. In this series of reactions, reduced electron carriers generated in stages 1-3 donate electrons to the electron transport chain and a large amount of ATP is produced.

Gibbs free energy (G)

he amount of energy available to do work. -In a chemical reaction, we can compare the free energy of the reactants and products to determine whether the reaction releases energy that is available to do work. The difference between two values is denoted by the Greek letter delta (Δ). In this case, ΔG is the free energy of the products minus the free energy of the reactants (Fig. 6.8). If the products of a reaction have more free energy than the reactants, then ΔG is positive and a net input of energy is required to drive the reaction forward (Fig. 6.8a). By contrast, if the products of a reaction have less free energy than the reactants, ΔG is negative and energy is released and available to do work

chaperones

help proteins fold correctly -they help protect slow folding or denatured proteins until they can attain their proper 3d structures

water forms hydrogen bonds which explains its properties of....

high cohesion, surface tension, and resistance to rapid temperature change.

nuclear pores

holes in the nuclear envelope that allow materials to pass in and out of the nucleus -the transfer of information encoded by DNA depends on the movement of RNA molecules out of the nucleus through these pores

how does hydrogen bonds affect temperature

hydrogen bonds make water more resistant to temperature change -long story short when there is more hydrogen bonds some of the energy used to heat up the water goes to breaking those hydrogen bonds. if there were no hydrogen bonds, then all the energy would go into raising the temperature

the proton pump involves....

in photosynthesis, the proton pump involves: (1) the transport of two electrons and two protons, by the diffusion of plastoquinone, from the stroma side of photosystem II to the lumen side of the cytochrome-b6 f complex and (2) the transfer of electrons within the cytochrome-b6 f complex to a different molecule of plastoquinone, which results in additional protons being picked up from the stroma and subsequently released into the lumen.

Plasmodesmata

in plants, the endomembrane system is actually continuous between cells through these connecting pores

The plus ends of both microtubules and microfilaments differentiate from the minus ends:

in that new tubulin or actin subunits are added more quickly.

Where is the highest-energy electron found in an atom of hydrogen?

in the spherical orbital closest to the nucleus

How does increasing the temperature affect the change in free energy (ΔG) of a chemical reaction?

increasing the temperature increases the value of TΔS, which decreases ΔG, since ΔG = ΔH - TΔS. As a result, an increase in temperature makes it more likely that a reaction will proceed without a net input of energy.

nucleic acids and examples

informational molecules—that is, they are large molecules that carry information in the sequence of nucleotides that make them up. ex) DNA- genetic material in all organisms RNA-key player in protein synthesis and the regulation of gene expression.

Inhibitor

inhibitor A synthesized compound that decreases the activity of an enzyme. -There are two classes of inhibitors. Irreversible inhibitors usually form covalent bonds with enzymes and irreversibly inactivate them. Reversible inhibitors form weak bonds with enzymes and therefore easily dissociate from them.

integral versus peripheral membrane proteins

integral- permanently associated with cell membranes and cannot be seperated from the membrane experimentally without destroying the membrane itself -Most integral membrane proteins are transmembrane proteins that span the entire lipid bilayer peripheral- temporarily associated with lipid bilayer or with integral membrane proteins through weak noncovalent interactions

the sequence of amino acids is... dictates.... it determines...

it is a proteins primary stucture it dictates protein folding which determines its function

kinetic versus potential energy

kinetic energy- the energy of motion, and it is perhaps the most familiar form of energy. ex) A moving object, such as a ball bouncing down a set of stairs, possesses kinetic energy. Kinetic energy is associated with any kind of movement, such as a person running or a muscle contracting. potential energy- Stored energy that is released by a change in an object's structure or position. ex)Potential energy depends on the structure of the object or its position relative to its surroundings, and it is released by a change in the object's structure or position. For example, the potential energy of a ball is higher at the top of a flight of stairs than at the bottom.Similarly, an electrochemical gradient of molecules across a cell membrane is a form of potential energy. Given a pathway through the membrane, the molecules move down their concentration and electrical gradients from higher to lower potential energy -the more stable electron configuration will always be the one with lower potential energy. ENERGY CAN BE CONVERTED EX: The ball at the top of the stairs has a certain amount of potential energy because of its position. As it rolls down the stairs, this potential energy is converted to kinetic energy associated with movement of the ball and the surrounding air. When the ball reaches the bottom of the stairs, the remaining energy is stored as potential energy.

lactic acid fermentation versus ethanol fermentation

lactic acid fermentation- The fermentation pathway in animals and bacteria during which electrons from NADH are transferred to pyruvate to produce lactic acid and NAD+. ethanol fermentation- The fermentation pathway in plants and fungi during which pyruvate releases carbon dioxide to form acetaldehyde and electrons from NADH are transferred to acetaldehyde to produce ethanol and NAD+. In both fermentation pathways, NADH is oxidized to NAD+. However, NADH and NAD+ do not appear in the overall chemical equations because there is no net production or loss of either molecule. NAD+ molecules that are reduced during glycolysis are oxidized when lactic acid or ethanol is formed.

Polymers

large compound formed from combinations of many monomers - complex molecules made up of repeated simpler units connected by covalent bonds. EX) Proteins are polymers of amino acids,

Steroids

lipid such as cholestoral -hydrophobic

cell membranes are composed of

lipids, proteins, and carbohydrates

The photosynthetic electron transport chain

located in the thylakoid membrane.

Animal Extracellular Matrix

made of mostly protein -the matrix is negatively charged, attracting positively charged ions and water molecules that provide protection against compression and other physical stress.

Microfilaments help a cell ____________________

maintain its size and shape.

Lingnin

makes cell walls hard half is in cell walls, half is in the glue that holds fibers together

hydrogenosomes

many eukaryotes that lack mitochondria contain small organelles called hydrogenosomes that generate ATP by anaerobic processes (Fig. 27.6). These organelles have little or no DNA, but genes of mitochondrial origin in the cells' nuclei code for proteins that function in the hydrogenosome. Thus, hydrogenosomes appear to be highly altered mitochondria adapted to life in oxygen-poor environments.

pH and what the numbers are

measures the proton concentration 0-7 acidic ( H is greater than OH) 7 neutral (concentrations of H and OH is equal) 7-14 basic (OH is greater than H)

mitochondria versus chloroplast

mitochondria (singular, mitochondrion) -Specialized organelles that harness energy for the cell from chemical compounds like sugars and convert it into ATP. -Mitochondria synthesize most of the ATP required to meet the cell's energy needs. - they have a double membrane (rod-shaped organelles with an outer membrane and a highly convoluted inner membrane whose folds project into the interior) -in the process of breaking down sugar and synthesizing ATP, oxygen is consumed and carbon dioxide is released (its the sight of cellular respiration) chloroplast An organelle that converts energy of sunlight into chemical energy by synthesizing simple sugars. --has three membranes: an outer membrane, inner membrane, and thylakoid membrane -Chloroplasts contain highly folded thylakoid membranes. -Both of these organelles are specialized to harness energy for the cell. Interestingly, they are both semi-autonomous organelles that grow and multiply independently of the other membrane-bound compartments, and they contain their own small genomes.

mitochondrial matrix

mitochondrial matrix The space enclosed by the inner membrane of the mitochondria.

Golgi apparatus

modifies and sorts proteins and lipids -the next stop for vesicles that bud off the ER -golgi apparatus has 3 primary roles 1) it further modifies proteins and lipids produced by the ER 2)it acts as a sorting station as these proteins and lipids move to their final destinations 3) it is the site of synthesis of most of the cells carbohydrates -under the microscope the Golgi apparatus looks like stacks of flattened membrane sacs, called cistern, surrounded by small vesicles

Golgi apparatus

modifies proteins and lipids produced by the ER and act as a sorting station as they move to their final destinations

difference in potential energy between carbs, lipids, co2, water

molecules such as carbohydrates and lipids have a large amount of potential energy in their chemical bonds. In contrast, molecules like carbon dioxide and water have less potential energy in their bonds.

Monosaccharides versus disaccaride versus polysaccharides

mono is one simple sugar di is two simple sugars poly is many (polymers)

collagen

most abundant protein -collagen is composed of intertwined fibers - A collagen molecule consists of three polypeptides wound around one another in a triple helix -A bundle of collagen molecules forms a fibril, and the fibrils are assembled into fibers textbook def: Type I collagen molecules are organized in a triple helix and grouped into bundles called fibrils, which in turn are grouped into bundles called fibers. This type of arrangement, seen in fibers and steel cables, imparts tremendous strength.

functional pairs

mostly polar -the nitrogen, oxygen, phosphorous, and sulfur in a functional group make it polar

Contraction of muscles is an example of how the motor protein _______ interacts with the cytoskeletal elements called _____________ to produce movement.

myosin; actin filaments

question: Name two places where the extracellular matrix can be found in plants and animals.

n plants, the extracellular matrix makes up the cell wall, which is composed of proteins like cellulose and lignin. The interconnected cell walls of the plant support the entire organism. In animals, one example of the extracellular matrix is connective tissue. Here, proteins like collagen, elastin, and laminin provide support and protection to the tissues surrounding them. Another example is the basal lamina. This is a specialized layer of extracellular matrix that is present beneath all epithelial tissues and provides a structural foundation.

negative feedback

negative feedback Describes the effect in which the final product of a biochemical pathway inhibits the first step; the process in which a stimulus acts on a sensor that communicates with an effector, producing a response that opposes the initial stimulus. Negative feedback is used to maintain steady conditions, or homeostasis.

nicotinamide adenine dinucleotide phosphate (NADPH)

nicotinamide adenine dinucleotide phosphate (NADPH)- An important cofactor in many biosynthetic reactions; the reducing agent used in the Calvin cycle. -NADPH transfers the electrons that allow carbohydrates to be synthesized from CO2 -NADPH can move freely within the stroma of the chloroplast. Although NADPH is a powerful reducing agent, energy and electrons are transferred from NADPH only under the catalysis of a specific enzyme, thus providing a high degree of control over the fate of these electrons. -NADPH provides most of the energy incorporated in the bonds of the carbohydrate molecules produced by the Calvin cycle

to reach the transition state, the reactant ..................As a result, all chemical reactions, even spontaneous ones that release energy, require .............

o reach the transition state, the reactant must absorb energy from its surroundings (the uphill portion of the curve in Fig. 6.13). As a result, all chemical reactions, even spontaneous ones that release energy, require an input of energy that we can think of as an "energy barrier."

The photosynthetic reaction center becomes _______ when it passes its __________ to the ______________, which is thus ___________.

oxidized; excited electron; electron acceptor; reduced

Which of the following gases did Stanley Miller not use in his experiment to recapitulate the Earth's early atmosphere? water vapor (H2O) ammonia (NH3) hydrogen gas (H2) methane (CH4) oxygen gas (O2)

oxygen gas

The covalent linkage joining two amino acids together is referred to as a(n) ______ bond.

peptide

Successive amino acids in proteins are connected by __________

peptide bonds

oxidation of water

photosynthesis - linked with the reduction of CO2 through a series of redox reactions in which electrons are passed from one compound to another. -The process begins with the absorption of sunlight by protein-pigment complexes. The absorbed sunlight provides the energy that drives electrons through the photosynthetic electron transport chain. In turn, the movement of electrons through this transport chain is used to produce ATP and NADPH. And finally, ATP and NADPH are the energy sources needed to synthesize carbohydrates using CO2 in a process called the Calvin cycle

Photosynthesis

photosynthesis -The biochemical process in which carbohydrates are built from carbon dioxide and the energy of sunlight. -results in the release of oxygen as a waste product.

photosynthetic electron transport chain leads to..

photosynthetic electron transport chain leads to the formation of NADPH.

All organisms either get energy from the sunlight which is ________ or from chemical compounds which is_____

phototrophs get it from the sunlight chemotrophs get it from chemical compounds

phototrophs versus chemotrops -subgroups of both phototrophs and chemotrophs

phototrophs- get energy from the sunlight -example: plants subgroups: autotrophs: they are able to convert carbon dioxide into glucose, thus providing its own organic source of carbon (ex; vascular plants) heterotrophs: An organism that obtains its carbon from organic molecules synthesized by other organisms. (ex:helipbacteria) chemotrophs- get energy from chemical compounds ex: animals bc they ingest other things that give them energy autotrophs: they are able to convert carbon dioxide into glucose, thus providing its own organic source of carbon (ex: hydrogen bacteria) heterotrophs:An organism that obtains its carbon from organic molecules synthesized by other organisms. (ex:animals)

Is water polar or non-polar?

polar -uneven distribution of electrons

primary, secondary, tertiary and quaternary sequences of amino acids

primary-The sequence of amino acids in a protein. The sequence of amino acids ultimately determines how a protein folds. Secondary- interactions between stretches of amino acids in a protein form local secondary structures. Tertiary- Longer-range interactions between these secondary structures in turn support the overall three-dimensional shape of the polypeptide Quaternary-some proteins are made up of several individual polypeptides that interact with each other, and the resulting ensemble is the quaternary structure. (picture of this on my desktop)

Prokaryotes versus Eukaryotes

prokaryotes- include bacteria and archaeans and lack a nucleus -also lack internal compartmentalization bc there is no physical barrier separating the genetic material from the rest of the cell. instead the DNA is concentrated in the nucleoid eukaryotes- include animals, plants, fungi, and protists, have nucleus and specialized internal structures (membrane that include organelles) -the presence of the nucleus allows for the processes of transcription and translation to be seperated in time and space. the separation in turn allows for more complex ways to regulate gene expression than are possible in prokatroyes

Actin

protein subunit that makes up microfilaments; used by both striated and smooth muscles to contract and generate force. -they are the thinnest of the three cytoskeletal fibers, and are present in various locations in the cytoplasm (Fig. 10.3b). They are relatively short and extensively branched in the cell cortex

Organic molecules include....

proteins, nucleic acids, carbohydrates, and lipids

Carbohydrates

provide a source of energy and make up the cell wall in bacteria, plants, and algae -composed of c,h,o atoms usually a 1;2;1 ratio -most simple carbohydrate is called saccharide -most are 6 carbon sugars

Bases of nucleotides are _______ and _____ -what is incorporated in those categories

pyrimidines (cytosine, thymine, and uracil) and purines (guanine and adenine)

When light is absorbed by chlorophyll in solution, it _________ releases the energy in the form of ____________.

rapidly; heat and light

Microfilaments are composed of ____________ in ____________arrangement.

repeating actin subunits; a thin double-helix

aerobic respiration

requires oxygen -Oxygen is consumed in aerobic respiration, and carbon dioxide and water are produced -In aerobic respiration, oxygen is the final electron acceptor, resulting in the formation of water. This way of generating ATP is called oxidative phosphorylation.

tertiary structure of a protein results from

result from interactions between amino acid side chains.' the three-dimensional conformation of a single polypeptide chain, usually made up of several secondary structure elements -it determines function

ribulose 1,5-bisphosphate (RuBP) versus ribulose bisphosphate carboxylase oxygenase (rubisco)

ribulose 1,5-bisphosphate (RuBP) The 5-carbon sugar to which carbon dioxide is added by the enzyme rubisco. ribulose bisphosphate carboxylase oxygenase (rubisco) The enzyme that catalyzes the carboxylation reaction in the Calvin cycle. -responsible for the addition of the carbon atoms needed for the formation of carbohydrates, but by itself rubisco does not increase the amount of energy stored within the newly formed bonds. -For this energy increase to take place, the carbon compounds formed by rubisco must be reduced. Nicotinamide adenine dinucleotide phosphate (NADPH) is the reducing agent used in the Calvin cycle. NADPH transfers the electrons that allow carbohydrates to be synthesized from CO2 -Rubisco can act catalytically on oxygen as well as on carbon dioxide. When it acts on oxygen, there is a loss of energy and of reduced carbon from the Calvin cycle. page 168 Rubisco has evolved to favor carbon dioxide over oxygen, but the cost of this selectivity is reduced speed

alpha helix and beta helix

secondary structures found in proteins alpha helix- backbone tightly twisted - Hydrogen bonding between carbonyl and amide groups in the backbone stabilizes the helix. beta helix- backbone folds back and forth on itself but looks more like a line makes a pleaded sheet Hydrogen bonds between neighboring strands stabilize the structure.

proteins in membranes... -transporters versus receivers etc

serve different functions -some act as transporters, moving ions or other molecules across the membrane -other membrane proteins act as receptors that allow the cell to receive signals from the environment -others are enzymes that catalyze chemical reactions or anchors that attach to other proteins and help to maintain cell structure and shape -these membrane proteins can be classified into two groups depending on how they associate with cell membranes (integral versus peripheral)

Cells differ in

shape and are well adapted for their various function

_______ determines the property of amino acids

side chain

ribosomes

sites of protein synthesis, in which amino acids are assembled into polypeptides guided by the information stores in mRNA

Smooth ER

small amount of ER is smooth because it lacks ribosomes. -its the site of fatty acid and phospholipid biosynthesis -this type of ER predominates in cells specialized for the production of lipids (ex: cells that synthesize steroid hormones have. a well developed SER that produces large quantities of cholesterol.) -enzymes within the SER convert cholesterol into steroid hormones

Plasmids

small circular DNA molecules that carry a few genes -are commonly transferred between bacteria through the action of threadlike structures known as pilli , which extend from one cell to another

Vesicles

small membrane sacs that transport substances within a cell or form the interior to the exterior of the cell -not only bud off from and fuse with organelles but also w the plasma membrane

mitochondria

specialized organelles that harness energy for the cell -rod-shaped organelles surrounded by a double membrane

amphipathic. molecules in water .....

spontaneously arrange themselves into various structures in which the polar head groups on the outside interact with water and the nonpolar tail groups come together on the inside away from water. This arrangement results from the tendency of polar molecules like water to exclude nonpolar molecules or nonpolar groups of molecules.

Catalysts

substances that speed up chemical reactions

substrate (S)

substrate (S) A molecule acted upon by an enzyme. -In such a reaction, the substrate (S) is converted to a product (P) In the presence of an enzyme (E), the substrate first forms a complex with the enzyme While still part of the complex, the substrate is converted to product .Finally, the complex dissociates, releasing the enzyme and product.

symbiont

symbiont -An organism that lives in closely evolved association with another species.

symbiosis

symbiosis (plural, symbioses) -Close interaction between species that live together, often interdependently.

symbiosis between a heterotrophic host and a photosynthetic partner is common throughout the __________________________

symbiosis between a heterotrophic host and a photosynthetic partner is common throughout the eukaryotic domain.

the shape of a protein is determined by

the R group

ionic bond

the attraction between oppositely charged ions -ex) NaCl

cytoplasm

the entire contents of a cell other than the nucleus

spontaneous reactions

the free energy of the reactant is higher than the free energy of the product and ΔG is negative.

cytosol

the jelly-like internal environment of the cell that surrounds the organelles inside the plasma membrane

the large size of many enzymes is required at least in part to ......

the large size of many enzymes is required at least in part to bring the catalytic amino acids into very specific positions in the active site of the folded enzyme.

base pairing of DNA

the nearly perfect fit between A-T and G-C nucleotides -results from hydrogen bonding

Endoplasmic Reticulum

the organelle where proteins and lipids are synthesized then it goes to the Golgi apparatus -the ER consists of a complex network of interconnected tubules and flattened sacs -the interior of the ER Is continuous throughout and is called the lumen -er has two diff appearances (some look rough when viewed because they are studded with ribosomes which is the RER; then theres the smooth ER, SER because it lacks ribosomes)

the oxidation of the electron carriers ------ and ------- formed during ------, ---------, and the --------- leads to the generation of a ______________, which is a source of potential energy. This source of potential energy is used to synthesize _______

the oxidation of the electron carriers NADH and FADH2 formed during glycolysis, pyruvate oxidation, and the citric acid cycle leads to the generation of a proton electrochemical gradient, which is a source of potential energy. This source of potential energy is used to synthesize ATP.

protein sorting

the process by which proteins end up where they need to be to perform their function -directs proteins to their proper location in or out of the cell -directs proteins to the cytosol, the lumen of organelles, the membranes of the endomembrane system, or even out of the cell entirely

pyrimidine versus cytosine bases

the pyrimidine bases (Fig. 2.19a) have a single ring and include cytosine (C), thymine (T), and uracil (U). The purine bases (Fig. 2.19b) have a double-ring structure and include guanine (G) and adenine (A). DNA contains the bases A, T, G, and C, and RNA contains the bases A, U, G, and C. Just as the order of amino acids provides the information carried in proteins, so, too, does the sequence of nucleotides determine the information in DNA and RNA molecules. -Pyrimidines have a single-ring structure, and (b) purines have a double-ring structure.

rough endoplasmic reticulum (RER)

the rough ER synthesizes transmembrane proteins, proteins that end up in the interior of organelles, and proteins destined for secretion - as a result, cells that secrete large quantities of protein have extensive rough ER, including cells of the gut that secrete digestive enzymes and cells of the pancreas that produce insulin

the stable association of animal cells with one another and with the extracellular matrix is made possible by_____________, and that these junctions are reinforced by the _________________.

the stable association of animal cells with one another and with the extracellular matrix is made possible by cell junctions, and that these junctions are reinforced by the cytoskeleton.

Cohesion - what is it -what type of bonds cause it

the sticking together of particles of the same substance. -hydrogen bonds cause this -leads to high surface tension

endosymbiotic theory

theory that eukaryotic cells formed from a symbiosis among several different prokaryotic organisms

thylakoid membrane

thylakoid membrane -in a chloroplast -A highly folded membrane in the center of the chloroplast that contains light-collecting pigments and that is the site of the photosynthetic electron transport chain. -The thylakoid membrane contains specialized light-collecting molecules called pigments, of which chlorophyll is the most important.

Exocytosis versus endocytosis

together exo and endocytosis provides a way to move material into and out of the cells without passing through the cell membrane exo:when a vesicle fuses with a plasma membrane -provides a way for a vesicle to empty its contents to the extracellular space or to deliver proteins embedded in the vesicle membrane to the plasma membrane endo: a vesicle can bud off from the plasma membrane, enclosing material from outside the cell and bring it into the cell interior

transition state

transition state reaction in which chemical bonds in the reactants are broken and new bonds in the product are formed. -It is highly unstable and therefore has a large amount of free energy.

3 main lipids

triglycerol, phospholipids, steroids

triglycerol versus fatty acid versus glycerol

triglycerol: -lipid used for energy storage -made up of three fatty acids joined to glycerol -hydrophobic and form oil droplets inside of the cell and because they exclude water molecules, they are great for storage because they can compact s lot of molecules into a small volume fatty acid:long chain of carbon atoms attached to a carboxyl group (-COOH) at one end -have weak non-covalent van Der walls charges. because of these charges, their melting points depends on their length and level of saturation -either saturated or unsaturated glycerol:A 3-carbon molecule with OH groups attached to each carbon.

triose phosphate

triose phosphate A 3-carbon carbohydrate molecule, produced by the Calvin cycle and exported from the chloroplast. -Triose phosphates are the true products of the Calvin cycle and they are the principal form in which carbohydrates are exported from the chloroplast during photosynthesis.

what're the two features of the photosynthetic electron transport chain that are responsible for the buildup of protons in the thylakoid lumen

two features of the photosynthetic electron transport chain are responsible for the buildup of protons in the thylakoid lumen (Fig. 8.14c). First, the oxidation of water releases protons and O2 into the lumen. Second, the cytochrome-b6 f complex, the protein complex situated between photosystem II and photosystem I, and plastoquinone together function as a proton pump that is functionally and evolutionarily related to proton pumping in the electron transport chain of cellular respiration

Monosaccharides

unbranched carbon chains with either an aldehyde (HC = O) or a ketone (C = O) -In both types of monosaccharide, the other carbons each carry one hydroxyl (-OH) group and one hydrogen (H) atom. -in ring form -attaches by glysocidic bonds In summary: Monosaccharides assemble to form disaccharides or longer polymers called complex carbohydrates.

Hydrophobic

water hating -nonpolar -ex) oil

Why is liquid water denser than ice?

when liquid turns into solid ice, it causes a hard crystalline structure which has more space between molecules. when it is liquid, the molecules can become tighter and closer together

ΔG of common hydrolysis reactions in a cell

ΔG of common hydrolysis reactions in a cell. ATP hydrolysis has an intermediate value of ΔG compared to other common hydrolysis reactions.

intracellular environment

• Human red blood cells avoid shrinking or bursting by maintaining an intracellular environment isotonic with the extracellular environment, like blood • But what about a single-celled organism, like paramecium, swimming in a freshwater lake? • In this case, the extracellular environment is hypotonic compared with the concentration in the cell's interior • As a result, paramecium faces the risk of bursting from water moving in by osmosis • Paramecium and some other single-celled organisms contain contractile vacuoles that solve this problem

in ________, the total surface areas of intracellular membranes is about _________ than that of the plasma membrane

• In eukaryotes, the total surface area of intracellular membranes is about tenfold greater than that of the plasma membrane

• Proteins produced on free ribosomes are _________ • These proteins often contain amino acid sequences, called____________ • Proteins with no signal sequence remain in the ________ • Proteins destined for mitochondria or chloroplasts often have a signal sequence at their _______ • Proteins targeted to the nucleus usually have signal sequences located ______ • These nuclear signal sequences, called nuclear localization signals, enable proteins to move through pores in the nuclear envelope • If the polypeptide contains no other signal sequence, it continues into the _______ • If it contains a second sequence, called a signal-anchor sequence, it ---------- • Proteins destined for the ER lumen or secretion have an _______

• Proteins produced on free ribosomes are sorted after they are translated • These proteins often contain amino acid sequences, called signal sequences, that allow them to be recognized and sorted • Proteins with no signal sequence remain in the cytosol • Proteins destined for mitochondria or chloroplasts often have a signal sequence at their amino ends • Proteins targeted to the nucleus usually have signal sequences located internally • These nuclear signal sequences, called nuclear localization signals, enable proteins to move through pores in the nuclear envelope • If the polypeptide contains no other signal sequence, it continues into the lumen • If it contains a second sequence, called a signal-anchor sequence, it does not continue all the way into the lumen and ends up in the membrane • Proteins destined for the ER lumen or secretion have an amino-terminal signal sequence

Homeostasis

• The active maintenance of a constant environment is known as homeostasis, and it is a critical attribute of cells and life itself

membrane transports are of two types which are ... and explain

• The first type is a channel, which provides an opening between the inside and outside of the cell within which certain molecules can pass, depending on their shape and charge • The second type of transporter is a carrier, which binds to and then transports specific molecules • Membrane carriers exist in two conformations, one that is open to one side of the cell, and another that is open to the other side of the cell • Many cells have specific protein channels, known as aquaporins, for transporting water molecules • These channels allow water to move more readily across the plasma membrane by facilitated diffusion than is possible by simple diffusion

1) hydrostatic pressure/ tutor pressure 2) The pressure exerted by water inside the cell on the cell wall provides _______ that is similar in function to the support provided by _______ • In addition, plant and fungal cells have another structure, called the ________ that can ____________

• The force exerted by water pressing against an object is called hydrostatic pressure, or turgor pressure • The pressure exerted by water inside the cell on the cell wall provides structural support for man organisms that is similar in function to the support provided by animals' skeletons • In addition, plant and fungal cells have another structure, called the vacuole that can absorb water and also contribute to turgor pressure

anger and Nicolson fluid mosaic model

• The idea that lipids are proteins coexist in the membrane, and that both are able to move in the plane of the membrane, led American biologists Singer and Nicolson to propose the fluid mosaic model in 1972 According to this model, the lipid bilayer is a fluid structure within which molecules move laterally, and is a mosaic (mixture) of two types of molecules, lipids and proteins

The principle that structure determines function can be demonstrated by many observations. For example,

• The principle that structure determines function can be demonstrated by many observations. For example, the most proteins can be unfolded, or denatured, by chemical treatment or high temperature that disrupts the hydrogen and ionic bonds holding the tertiary structure together

passive transport

• The simplest form of movement into and out of cells is passive transport • Passive transport works by diffusion, which is the random movement of molecules • Some molecules cannot move across the lipid bilayer directly can move passively toward a region of lower concentration through protein transporters • When a molecule moves by diffusion through a membrane protein and bypasses the lipid bilayer, the process is called facilitated diffusion

cell wall

• the cells of many organisms have a cell wall external to the plasma membrane • The cell wall plays an important role in maintaining the shape of these cells