Biology exam 2

substrate

(1) A reactant that interacts with a catalyst, such as an enzyme or ribozyme, in a chemical reaction. (2) A surface on which a cell or organism sits.

They could differ in

(1) location of linkages (e.g., 1,4 or 1,6); (2) types of linkages (e.g., αα or ββ); (3) the sequence of the monomers (e.g., two galactose and then two glucose, versus alternating galactose and glucose); and/or (4) whether the four monomers are linked in a line or whether they branch.

Carbohydrates have diverse functions in cells: Besides serving as precursors to other molecules, they

(1) provide fibrous structural materials, (2) mark cell identity, and (3) store chemical energy.

What is the chemical formula for a monosaccharide (simple sugar)?

(CH2O)n

In Organisms, Potential Energy Is Stored in the Bonds of Molecules

(a) Carbon dioxide has low potential energy because the electrons involved in covalent bonds are held tightly by oxygen atoms. (b)Carbohydrates, such as the sugar shown here, have high potential energy because many of the covalent bonds are weak and the electrons are held equally between C and H atoms

What transporters are playing roles here? Na+/glucose symporter:

- Brings glucose into cell - Indirect active transport

Chemical work

- Building polymers (proteins, nucleic acids, polysaccharides), needs energy

Most common reversible modification of enzymes is the addition of phosphate groups (phosphorylation)

- Causes a change in shape - May activate or inactivate the enzyme

Hydrolysis of the bond between the two outermost phosphate groups results in:

- Formation of ADP and Pi - A highly exergonic reaction Releases 7.3 kilocalories of energy per mole of ATP

Diffusion down a concentration gradient:

- Increases entropy - Is spontaneous

Phospholipid bilayers have fluidity

- Lipids move freely within the single layer - The more fluid a membrane is, the more permeable

Equilibrium occurs when the solutes are evenly distributed

- Molecules are still moving randomly - But there is no more net movement

Mechanical work

- Muscle contraction - Moving chromosomes - Beating flagella

Phosphdiester bond

- Phosphate group (PO43-) attached to carbon - two oxygens from the phosphate group are attached to carbons - strong covalent bond between phosphate group and two 5-carbon ring carbohydrates over two ester bonds -covalent -linkage between 3' carbon of a sugar and 5'

If the products of a chemical reaction have shorter, stronger covalent bonds than the reactants:

- Potential energy in the bonds decreases - Change in potential energy is transformed to thermal energy (heat) - Heat is released - ∆H is negative (potential energy of products - potential energy of reactants) - Reaction is exothermic

Adenosine triphosphate (ATP) is the energy currency for cells

- Provides the fuel for most cellular activities - Contains three negatively charged phosphate groups - Negative charges repel each other

Transport work

- Pump molecules against their gradient, need energy

What transporters are playing roles here? Na+/K+ pump:

- Re-establishes Na+/K+ gradient - Direct active transport

Phospholipid bilayers are selectively permeable

- Small, nonpolar molecules move across phospholipid bilayers quickly - Charged or large polar substances cross slowly, if at all

In an isotonic solution:

- There will be no net water movement - The cell size will remain the same

What transporters are playing roles here? GLUT1 carrier:

- Transports glucose out to extracellular fluid - Facilitated diffusion

In a hypotonic solution:

- Water will move into the cell by osmosis -The cell will swell

Carrier proteins

- bind to a specific solute to be transported and undergo a conformational change to transfer the bound solute across the membrane

Direct active transport

- energy from ATP hydrolysis is used to transport solutes against their electrochemical gradients. Transport proteins used are called transport ATPases or pumps.

Direct active transport part 2

- energy from ATP hydrolysis is used to transport solutes against their electrochemical gradients. Transport proteins used are called transport ATPases or pumps.

Channel proteins

- form a hydrophilic pore that extends across the membrane - e.g., - Na+ channels (Na+ moves into cells) - Aquaporins (facilitates rapid mvmt of water across membranes)

Active Transport

- membrane proteins move solutes across membranes against their electrochemical gradient; requires energy This allows cells to: • Take up essential nutrients from the environment •Maintain constant, nonequilibrium concentrations of specific ions (e.g., K+, Na+)

Facilitated diffusion

- movement of an ion or molecule across a membrane with the help of a membrane protein; does not require input of energy because the solute is moving down its electrochemical gradient

Lipid bilayers

- phospholipids with two fatty acid chains

Oligosaccharides

- short complex polymers of monosaccharides -Display information on the outer surface of cells

Micelles

- single fatty acid chain

Indirect (secondary) active transport

- transport proteins couple the uphill (or against electrochemical gradient) transport of one solute across the membrane to the downhill transport of another.

fat

-A large lipid molecule made from an alcohol called glycerol and three fatty acids; a triglyceride. Most fats function as energy-storage molecules. -Composed of three fatty acids linked to glycerol -Also called triacylglycerols or triglycerides -When their fatty acids are polyunsaturated, they are liquid and form oils -Primary role = energy storage

ion channel

-A type of channel protein that allows certain ions to diffuse across a plasma membrane down an electrochemical gradient. -Ion channels form pores, or openings, in a membrane. Ions diffuse through these pores in a predictable direction: from regions of high concentration to regions of low concentration and from areas of like charge to areas of unlike charge.

Steroid

-A type of lipid characterized by a carbon skeleton consisting of four rings with various functional groups attached. -Distinguished by a four-ring structure -Steroids differ from one another by the functional groups attached to carbons in the rings

How Enzymes Work

-Activation energy is the amount of kinetic energy required to reach the transition state of a reaction. -Enzymes are catalysts. They speed reaction rates but do not affect the change in free energy of the reaction. -Enzymes have active sites that bring substrates together and may change shape to stabilize the transition state. -Enzymes speed up a reaction by lowering the activation energy, often with the help of cofactors, coenzymes, or prosthetic groups.

The concentration of a solution outside a cell may differ from the concentration inside:

-An outside solution with a higher concentration is hypertonic to the inside of a cell -An outside solution with a lower concentration is hypotonic to the cell -If solute concentrations are equal on the outside and inside of a cell, solutions are isotonic to each other

Paradoxical Effect of Cholesterol on Membrane Fluidity

-Animal cells contain up to 50% cholesterol in their membranes

Enzymes:

-Are catalysts -Are not altered during the course of the reaction -Have no effect on the thermodynamics of the reaction

Reduction-oxidation reactions (redox reactions) Oxidation: loss of an electron(s)

-Are chemical reactions that involve electron transfer -loss of an electron(s) -Always occur together -Electrons are transferred from an electron donor to an electron acceptor - Oxidation often "removes Hs"

How do structural differences in the lipid membrane contribute to adaptations in the domains of life?

-Bacteria, Eukarya - phospholipids with fatty acid tails -Archaea - phospholipids with isoprenoid tails -Branched isoprenoid chains provide greater membrane stability and help withstand harshenvironments (high temp)

Energetic coupling

-Between exergonic and endergonic reactions -Allows energy released from one reaction to drive another reaction

An isoprenoid is a branched hydrocarbon chain

-Build from isoprene -Function as pigments, scents, vitamins, sex hormone precursors -Building blocks for more complex lipids -Usually unsaturated (has C double bonds)

A fatty acid is an unbranched hydrocarbon chain bonded to a carboxyl group (-COOH)

-Building blocks for more complex lipids -Can be saturated or unsaturated

Why do thermodynamically favorable reactions not proceed on their own in the absence of energy?

-Chemical reactions require that certain covalent bonds between the atoms of the reactant molecules be broken -For this to occur, the reactants must contain sufficient kinetic energy (energy of motion) to overcome a barrier (the activation energy).

Gram Staining

-Crystal violet stain developed by Dr. Gram -Used to distinguish between two types of cell walls found in bacteria

DNA Structure and Function

-DNA's primary structure consists of a sequence of linked deoxyribonucleotides. -The secondary structure of DNA consists of two DNA strands running in opposite directions that are twisted into a double helix. -The tertiary structure of DNA forms compact structures by twisting the double helix into supercoils or wrapping around histone proteins. -DNA is an extremely stable molecule that serves as a superb archive for information in the form of base sequences. Its secondary structure is stabilized by hydrogen bonds and base-stacking interactions between bases inside of the helix. -DNA is readily copied via complementary base pairing. Complementary base pairing in DNA occurs between A-T and G-C bases.

Introduction to Biological Membranes: Functions

-Define boundaries and serve as permeability barriers -Serve as sites of specific functions -Regulate the transport of molecules -Cell signaling -Cell adhesion

How Substances Move across Lipid Bilayers: Diffusion and Osmosis

-Diffusion is the random movement of ions or molecules owing to their thermal energy. -If a membrane separates solutions that differ in concentration or charge, passive transport results in the net directional movement of solutes across the membrane that makes the environments on both sides of the membrane more similar. This is a spontaneous process driven by an increase in entropy. -The diffusion of water across a membrane in response to a concentration gradient is called osmosis.

The energy-storage molecules, like starch, are being hydrolyzed to release glucose.

-Disaccharides like the lactose in milk would be hydrolyzed to release glucose and galactose. -These sugars may be further broken down to produce ATP and raw materials for building other molecules, such as glycolipids and glycoproteins. -The insoluble cellulose that makes up dietary fiber does not get broken down, but it will help retain water and support the digestion and passage of fecal material.

How does an enzyme lower the activation energy barrier?

-Enzyme provides surface where reactants can bind in an arrangement that brings the reactive parts of the molecules close to each other -This ensures that a higher proportion of molecules have enough energy to undergo the reaction Enzymes lower activation energy by simply providing a suitable surface and environment to facilitate the reaction.

This claim is likely correct because carbohydrates have the potential for greater structural variation than proteins.

-Glycosidic linkages between sugar monomers can vary more in location and geometry than can peptide-bond linkages between amino acid residues, which are completely standardized. -The different monosaccharide monomers vary extensively in their size, the position of the carbonyl group, the orientations of hydroxyl groups, and the presence of modifications in the polymerized forms (e.g., modified sugar residues in chitin and peptidoglycan).

Endothermic reactions

-Heat energy is taken up -ΔH > 0 -Products have higher potential energy than reactants

Fats and Food

-Highly saturated lipids (like butter) are solid at room temp -Saturated lipids with long hydrocarbon tails (like waxes) form stiff solids at room temp -Polyunsaturated lipids (like plant oils) are liquid at room temp -Unsaturated plant oils may be hydrogenated to make margarine and Crisco Break double bonds and add H atoms Creates "trans fat"

When amphipathic lipids are placed in water:

-Hydrophilic heads interact with water -Hydrophobic tails interact with each other, away from the water

What Do Carbohydrates Do?

-In carbohydrates, as in proteins and nucleic acids, structure correlates with function. -Cellulose, chitin, and peptidoglycan are polysaccharides that function in support. They are made up of monosaccharide monomers joined by β-1,β-1,4-glycosidic linkages. When individual molecules of these polysaccharides align side by side, bonds form between them—resulting in strong, flexible fibers or sheets that resist hydrolysis. -The oligosaccharides on cell-surface glycoproteins and glycolipids can function as specific signposts or identity tags because their constituent sugar residues are so diverse in geometry and composition. -Both starch and glycogen function as energy-storage molecules. They are made up of glucose molecules that are joined by α-glycosidicα-glycosidic linkages. These linkages are readily hydrolyzed to release glucose for the production of ATP and raw materials for building new molecules.

Enzymes Can Work Together in Metabolic Pathways

-In cells, enzymes often work together in metabolic pathways that sequentially modify a substrate to make a product. -Feedback inhibition may be used to regulate a pathway, often by controlling the activity of the first enzyme in the pathway. -Metabolic pathways were vital to the evolution of life, and new pathways continue to evolve in cells.

Both are mechanisms that regulate the interaction between enzymes and their substrates.

-In competitive inhibition, the regulatory molecule binds directly to the active site and interferes with substrate binding. -In allosteric regulation, the regulatory molecule binds to a different region and causes the enzyme to change conformation and either open or close the active site.

Phospholipid Bilayers

-In solution, phospholipids spontaneously assemble into bilayers that can serve as a physical barrier between an internal and external environment. -Small nonpolar molecules tend to move directly across lipid bilayers readily; ions cross rarely, if at all. -The permeability and fluidity of lipid bilayers depend on the temperature, the concentration of cholesterol, and the chemical structure of the lipids present, such as the saturation status and length of the hydrocarbon chains. Phospholipids with longer or saturated tails form a dense and highly hydrophobic interior that lowers bilayer permeability, relative to phospholipids containing shorter or unsaturated tails.

Potential energy of molecules:

-Is stored in chemical bonds -Depends on the configuration & position of its shared electrons -Weaker bonds with equally shared electrons have -HIGH potential energy Stronger bonds with unequally shared electrons have LOW potential energy

Sodium-potassium (Na+/K+) pump: 3 Na+ out , 2 K+ in

-Keeps the [Na+] outside the cell HIGHER than inside -Keeps the [K+] inside the cell HIGHER than outside -Accounts for 30% of total ATP consumption

RNA Structure and Function

-Like DNA, RNA's primary structure consists of a sequence of linked ribonucleotides. -Compared to DNA, in RNA, thymine (T) is replaced by uracil (U) so that complementary base pairing occurs between A-U and C-G bases. -RNA's secondary structure includes a variety of configurations including short regions of complementary base pairing within a single strand to form double-helical stems and unpaired loops. -The secondary structures in a strand of RNA can further fold into more complex shapes via complementary base pairing to give the molecule tertiary structure. -RNA is versatile and can function as an information-carrying molecule and a catalyst.

Lipid Structure and Function

-Lipids are largely hydrophobic compounds due to their high number of nonpolar C—H bonds. -The three main types of lipids found in cells are fats, steroids, and phospholipids. These molecules vary considerably in structure and function. Fats store chemical energy; certain steroids and phospholipids are key components of cell membranes. -In hydrocarbon chains, the length and degree of saturation profoundly affect their physical properties. -All lipids have a hydrophobic region, but amphipathic lipids also possess a distinct hydrophilic region containing polar or charged groups. -Phospholipids have a polar or charged head and a nonpolar tail. The nonpolar tail usually consists of fatty acids or isoprenoids.

All biological membranes have a common general structure:

-Made up of lipids and proteins, held together by noncovalent interactions -Composed of lipid molecules arranged as a double layer (= a lipid bilayer) -Composed of proteins embedded in the lipid bilayer -Are dynamic, fluid structures -Are asymmetric; lipid/protein composition different in each monolayer

Cholesterol acts as a fluidity buffer:

-Makes membrane less fluid at higher temps (immobilizes FA's) -Makes membrane more fluid at lower temps (prevents tight packing)

Regulatory molecules control when / where an enzyme functions

-Might change the enzyme's structure - Might change its ability to bind its substrate -Might activate or inactivate the enzyme's function

Sugars as Monomers

-Monosaccharides are organic compounds that have a carbonyl group and several hydroxyl groups. -The molecular formula for a sugar is typically (CH2O)n,(CH2O)n, but the number of "carbon-hydrate" groups may vary between sugars, as indicated by the subscript n.n. -Monosaccharides have either an aldose or ketose configuration, depending on whether the carbonyl group is located at the end or within the carbon chain. -Although some monosaccharides may have the same molecular formula, the spatial arrangement of their functional groups leads to differences in their molecular structures and therefore functions. -In solution, monosaccharides can form ring structures that may differ from one another in the orientation of a hydroxyl group, even among molecules of the same monosaccharide

The Structure of Polysaccharides

-Monosaccharides can be covalently bonded to one another via glycosidic linkages, which join hydroxyl groups on adjacent molecules. -In contrast to proteins and nucleic acids, polysaccharides do not always form a single uniform backbone structure. The numerous hydroxyls found in each monosaccharide allow glycosidic linkages to form at different sites and new strands to branch from existing chains. -The types of monomers involved and the geometries of the glycosidic linkages between monomers distinguish different polysaccharides from one another. -The most common polysaccharides in organisms today are starch, glycogen, cellulose, and chitin; peptidoglycan is an abundant polysaccharide that consists of sugar monosaccharides and short chains of attached amino acids.

What Factors Affect Enzyme Function?

-Most enzymes are proteins, and thus their activity can be directly influenced by environmental factors, such as temperature and pH, or by modifications that alter their three-dimensional structure. -Enzyme activity may be regulated by molecules that compete with substrates to occupy the active site or whose binding alters the enzyme shape. -Protein cleavage and phosphorylation may regulate enzyme activity by modifying the primary structure of the enzyme.

What Is a Nucleic Acid?

-Nucleic acids are polymers of nucleotide monomers, which consist of a sugar, a phosphate group, and a nitrogenous base. Ribonucleotide monomers polymerize to form RNA. Deoxyribonucleotide monomers polymerize to form DNA. -Ribonucleotides have a hydroxyl (—OH)(—OH) group on their 2′ carbon; deoxyribonucleotides have a hydrogen (—H)(—H) instead. -Nucleic acids polymerize when condensation reactions join nucleotides together via phosphodiester linkages. -Nucleic acids are directional: they have a 5′ end and a 3′ end. During polymerization, new nucleotides are added only to the 3′ end.

Many factors influence the behavior of the membrane:

-Number of double bonds between the carbons in the phospholipid's hydrophobic tail (saturated vs. unsaturated) -Length of the tail (how many carbons it has) -Number of cholesterol molecules in the membrane -Temperature

Polysaccharides: Antibiotics

-Peptidoglycan is a structural polymer found in bacterial cell walls Long backbones of alternating monosaccharides (N- acetylglucosamine; NAG and N-acetylmuramic acid; NAM) -Short amino acid chains form peptide bonds between adjacent strands​

Polysaccharides

-Polysaccharides are polymers of monosaccharide monomers -Sugars are linked when a condensation reaction occurs between two hydroxyl groups - A covalent glycosidic linkage forms The bonds can be broken by hydrolysis reactions

Nonspontaneous Reactions May Be Driven Using Chemical Energy

-Redox reactions transfer energy by coupling exergonic oxidation reactions to endergonic reduction reactions. -Bonds with high potential energy may be formed during the reduction step of a redox reaction. Many of these bonds form when an electron is transferred along with a proton (H+).(H+). -The potential energy in ATP is used to drive a variety of cellular processes. -When a phosphate group from ATP is added to a substrate, it increases the potential energy of the substrate and may be used to convert endergonic reactions into exergonic reactions.

Exothermic reactions

-Release heat energy -ΔH < 0 -Products have less potential energy than reactants

Main factors that affect the diffusion of solutes across membranes:

-Size (smaller = more permeable) -Polarity (nonpolar = more permeable) -Charge (ions = NOT permeable) O2 > H2O > glycerol >>>>> glucose>>>>>>Cl- K+ Na+

Why do you think activity goes up and then down in these graphs? What is happening to the enzyme at different temperatures and pHs?

-The activity goes up as the enzyme reaches its optimal temp or pH and goes down as it moves further away from that optimal temp/pH. -The enzyme at diff temps/pH might have less kinetic energy or be unfolding/denaturing.

electrochemical gradient

-The combined effect of an ion's concentration gradient and electrical (charge) gradient across a membrane that affects the diffusion of ions. -Electrochemical gradients are established when ions build up on one side of a membrane. -In response to electrochemical gradients, ions will diffuse in a directional manner if an appropriate channel exists.

transition state.

-The free energy of the transition state is high because the bonds that existed in the original reactants must be destabilized. Once products form, the free energy drops sharply. -The transition state is the intermediate point between breaking old bonds and forming new ones. - free energy rises dramatically when the reactants combine to form an intermediate configuration called the

Proteins Alter Membrane Structure and Function

-The permeability of lipid bilayers can be altered significantly by membrane proteins. -Channel proteins form pores in the membrane that may have highly regulated closed and open conformations, and facilitate the diffusion of specific solutes into and out of the cell. -Carrier proteins undergo conformational changes that facilitate the diffusion of specific molecules into and out of the cell. -Pumps use energy to actively move ions or molecules in a single direction, often against the electrical or chemical gradient. -In combination, the selective permeability of phospholipid bilayers and the specificity of transport proteins make it possible to create an environment inside a cell that is radically different from the exterior environment.

What Happens to Energy in Chemical Reactions?

-The standard free-energy change for a chemical reaction is an equation used to measure the overall change in Gibbs free energy (ΔG)(∆G)—that is, to calculate the combined effects of changes in enthalpy (ΔH)(∆H) and entropy (ΔS).(∆S). -Reactions with a negative ΔG∆G are exergonic and will occur spontaneously. -Reactions with a positive ΔG∆G are endergonic and will not occur without an input of energy.

The energy profile shows changes in free energy that occur during a hypothetical reaction between a molecule A and a molecule containing parts B and C. The overall reaction would be written as A+BC→AB+C.A+BC→AB+C. EaEa is the activation energy of the reaction.

-The ΔG∆G label on the graph indicates the overall change in free energy in the reaction—that is, the energy of the products minus the energy of the reactants. -In this case, the products have lower free energy than the reactants, meaning that the reaction is exergonic. But because the activation energy for this reaction, symbolized by Ea,Ea, is high, the reaction would proceed slowly—even at high temperature. -Here is an important point: The more unstable the transition state, the higher the activation energy and the less likely a reaction is to proceed quickly. -Reaction rates, then, depend on both the kinetic energy of the reactants and the activation energy of the particular reaction—meaning the free energy of the transition state. -If the kinetic energy of the reactants is high, such as at high temperatures, then molecular collisions are more likely to overcome the activation energy barrier. -At this point, the transition state is formed and the reaction takes place.

Gram-positive bacteria

-Thick layer of the peptidoglycan -Dye is retained inside the cell (= bacteria appear dark purple)

Gram-negative bacteria

-Thin layer of peptidoglycan -Layer of peptidoglycan is sandwiched between the -outer membrane and the plasma membrane -Thin layer of peptidoglycan does not retain the stain (= bacteria appear pink)

In Search of the First Life-Form

-To test the RNA world hypothesis, researchers have attempted to synthesize new ribozymes in the laboratory. Using artificial selection strategies, they have succeeded in identifying RNAs that catalyze several different reactions. -One origin-of-life theory holds that ribozymes that catalyzed reactions necessary for the production of ribonucleotides may have preceded the evolution of RNA replicases.

Osmosis: A Special Type of Diffusion

-Water can move across lipid bilayers - Osmosis is the diffusion of water (a special type of diffusion) - Only occurs across selectively permeable membranes -Water moves from regions of low solute concentration to regions of high solute concentration - It equalizes the concentration on both sides of the bilayer

In a hypertonic solution:

-Water will move out of the cell by osmosis -The cell will shrink

Feedback inhibition

-When an enzyme in a pathway is inhibited by the final product of that pathway -The final product binds to an allosteric site on an enzyme earlier in the pathway and causes a shape change that inhibits the enzyme -Inhibits the pathway when enough product is made

Entropy (S) is the amount of disorder

-When the products of a chemical reaction become less ordered than the reactant molecules: -Entropy increases ΔS > 0

Cellulose

-a structural polysaccharide in plants Forms a protective layer around plant cells called the cell wall -Made of β-glucose monomers joined by β-1,4-glycosidic linkages -Every other glucose is flipped, so it: Forms a linear molecule rather than a helix Permits hydrogen bonds to -form between adjacent, parallel strands

Sodium-potassium (Na+/K+) pump:

-aka Na+/K+ ATPase -Uses ATP -Transports Na+ and K+ against their concentration gradients 3 Na+ ions out 2 K+ ions in -Creates concentration gradients for both ions

Reduction-oxidation reactions (redox reactions) Reduction: gain of an electron(s)

-always occur together -Electrons are transferred from an electron donor to an electron acceptor -Electrons are usually accompanied by a proton (H+) Reduction often "adds Hs"

According to the RNA world model, a ribozyme would replicate by creating a double-stranded RNA intermediate. Would you expect the intermediate to have the same catalytic activity as the original ribozyme? Justify your answer with an explanation.

-catalytic activity depends on the tertiary structure generated from folding single stranded molecules -fully stranded forms of RNA would not be in the tertiary structure

Hydrocarbons are molecules that

-contain only carbon and hydrogen -Electrons are shared equally in C-C and C-H bonds (nonpolar bonds) -They are hydrophobic

lipid bilayer

-is created when lipid molecules align in paired sheets. -the hydrophilic heads in each layer face the surrounding solution while the hydrophobic tails face one another inside the bilayer. -In this way, the hydrophilic heads interact with water while the hydrophobic tails interact with one another.

tertiary structure in DNA

-less dependent on primary structure, and so it is far less variable between different sequences. Two forms of DNA tertiary structure are commonly found in cells. When DNA becomes wound too tightly or loosely with respect to the number of base pairs per helical turn, it can twist on itself to form compact, three-dimensional structures called supercoils -DNA in the cells of eukaryotes and certain archaea will form tertiary structures by wrapping around specialized DNA-binding proteins called histones. The resulting DNA-protein complexes compact the DNA into discrete, movable units during cell division

Glycogen

-storage polysaccharide in animals -Nearly identical to amylopectin; more frequent branches

Starch

-storage polysaccharide in plants -Composed of α-glucose monomers -Forms a helix -Amylose—unbranched starch with only α-1,4-glycosidic linkages -Amylopectin—branched starch with some α-1,6-glycosidic linkages

Enthalpy (H)

-the potential energy of the molecule -(heat content) -Changes in enthalpy -(ΔH) are primarily based on the difference in potential energy -ΔH -(Exothermic): Products have less potential energy than reactants +ΔH -(Endothermic): Products have higher potential energy than reactants

-In solution, molecules exist in a state of random movement, each possessing a certain amount of kinetic energy in any given moment -For a reaction to occur, the energy of the molecule must exceed the EA -So to increase the rate of a reaction, the proportion of molecules with sufficient energy must be increased. This can be achieved by two means:

1) increase the kinetic energy of the reactants (increase temperatures) 2) lower the activation energy (lower the barrier, so more molecules reach it)

Two types of active transport:

1. Direct active transport 2. Indirect (secondary) active transport

Monosaccharide monomers are simple sugars that structurally vary in 4 primary ways:

1. Number of carbon atoms present (3-8) Five = pentose Six = hexose 2. Location of the carbonyl group At the end = aldose In the middle = ketose 3. Spatial arrangement of their atoms Different arrangement of the hydroxyl groups 4. Alternative ring forms Sugars typically form ring structures in aqueous solutions

purines

1.) Adenine 2.) Guanine Bigger, double rings formed from 9 atoms

Two major types of integral membrane transport proteins that allow solutes to cross the membrane in facilitated diffusion:

1.) Carrier proteins 2.)Channel proteins

Glycoproteins and glycolipids are important in:

1.) Cell-cell recognition: Identify cells as "self" (blood types) 2.) Cell-cell signaling: Communication between cells

Cell theory

1.) Cells are the basic unit of life 2.) All organisms are made of 1 or more cells 3.) All cells come from other cells

Joining Nucleotides Together to Make Nucleic Acids

1.) Each strand is a single molecule, with nucleotides joined by phosphodiester bonds 2.) A condensation reaction is used 3.) Phosphodiester bonds are covalent

Which of the following describe the differences between isoprenoids and fatty acids? (check all that apply)

1.) Fatty acids have a carboyxl group at one end, and isoprenoids do not. 2.) soprenoids are found in the tails of lipids that make up Archaea cell membranes, while fatty acid are found in the tails of lipids that make up animal cell membranes.

Two types of regulation:

1.) Noncovalent - involves regulatory molecule interacting with the enzyme through noncovalent interactions 2.) Covalent - involves making or breaking of covalent bonds

Nucleic Acids in Cells

1.) Nucleic acids carry genetic (heritable) information in living cells 2.) Although proteins perform a variety of functions in cells, including catalysis, they are not a unit of heredity

Which of the following are examples of active transport? (check all that apply)

1.) The movement of glucose into the cell using energy from the movement of Na+ ions into the cell. 2.) ATP hydrolysis driving the movement of molecules against their concentration gradient.

Chemical evolution

1.) The theory of life and the first cell's origin 2.) The first cell needed a molecule that could carry heritable information, replicate and catalyze reactions

Which of the following is true about starch and cellulose? (check all that apply)

1.) They are both found in plants. 2.) Starch is made up of alpha-glucose, while cellulose 3.) is made up of beta-glucose.

Which of the following are true of monosaccharides? (check all that apply)

1.) They are polar and dissolve in water. 2.) They can have between 3 and 8 carbons. 3.) They polymerize to form polysaccharides.

The fluidity of a membrane ____________. (check all that apply)

1.) affects the permeability of the membrane. 2.) is affected by temperature. 3.) is affected by the length of the phospholipid tails (fatty acids).

Proteins that span a membrane ________________. (check all that apply)

1.) are typically amphipathic. 2.) have a transmembrane domain that is made of mostly nonpolar amino acids. 3.) are called integral membrane proteins.

What two conditions must be present for osmosis to occur?

1.) concentration gradient 2.) a membrane that allows water to pass but not the solute

pyramids

1.) cytosine 2.) Uracil- found in RNA 3.) Thymine- found in DNA single ring, only 6 atoms

Chitin and peptidoglycan differ in that chitin is _________. (check all that apply)

1.) found in fungi and peptidoglycan is found in bacteria. 2.) doesn't have amino acids attached to it, but peptidoglycan does. 3.) is found in insect exoskeletons and peptidoglycan is not.

ATP hydrolysis ___________. (check all that apply)

1.) is often coupled to endergonic reactions. 2.) is an exergonic reaction. 3.) is the conversion of ATP to ADP and Pi.

Match the correct type of lipid with its function. (check all that apply)

1.) phospholipids: cell membrane 2.) steroids: cell membrane

Diffusion is __________. (check all that apply)

1.) spontaneous and increases entropy. 2.) the movement of a molecule from a high concentration to low concentration region.

What are three ways monosaccharides differ from one another?

1.) the location of their carbonyl group 2.)the number of carbon atoms they contain 3.)the orientation of their hydroxyl groups

DNA has 16% G how much A?

16+16= 32 68+32=100 68/2= 34 A=34%

Deoxyribose has an H bonded where?

2' carbon

Ribose has a -OH group bonded where?

2' carbon

he ββ-1,4-glycosidic linkages in these molecules result in insoluble fibers that most organisms cannot break down with enzymes.

2: When individual molecules of these carbohydrates align, bonds form between them and produce fibers or sheets that resist pulling and pushing forces.

What temperature do you think enzymes in our body work best? What pH?

37ºC and pH 7.2 (approximately neutral)

What is the structure of a steroid?

4 fused carbon rings

QUANTITATIVE If nucleotides from the DNA of a human were quantified and 30 percent of them contained the base adenine, what percentage of them would contain the base guanine? 20 percent 30 percent 40 percent 70 percent

40%

3 parts of a nucleotide

5 carbon sugar, phosphate group, nitrogenous base

What would be the sequence of the strand of DNA that is made from the following template: 5′-GATATCGAT-3′? (Your answer must be written 5'→3'5'→3'.) How would the sequence be different if RNA were made from this DNA template?

5'ATCGATATC3'

RNA World hypothesis states that RNA was the first "living molecule"

A "living molecule" must store info and have the ability to copy that info to make new molecules - RNA stores info in its nucleotide sequence - One RNA strand can serve as a template to copy new strands - RNA can also act as an enzyme, catalyzing chemical reactions

gated channel

A channel protein that opens and closes in response to a specific stimulus, such as the binding of a particular substance or a change in voltage across the membrane.

Lipids:

A diverse group of carbon-containing compounds that are largely nonpolar Lipids are mostly hydrocarbons

What is a glycolipid? What is a glycoprotein?

A glycolipid is a lipid molecule covalently linked to sugars. A glycoprotein is a protein covalently linked to sugars.

A Cell

A highly organized compartment bound by a membrane and containing concentrated chemicals in an aqueous solution

What is a lipid?

A lipid is a carbon-containing compound that is largely nonpolar and mostly contains hydrocarbon.

vesicle

A membrane-enclosed compartment with an aqueous interior that is often used in cells to transport cargo between organelles or to the plasma membrane for secretion.

Phospholipids

A molecule that is a constituent of the inner bilayer of biological membranes, having a polar, hydrophilic head and a nonpolar, hydrophobic tail. -Consist of a glycerol linked to: A phosphate group bonded to a charged or polar molecule Two hydrocarbon chains -Fatty acids in Bacteria and Eukarya Isoprenoids in Archaea • Primary role = form cell membranes

feedback inhibition

A type of control in which high concentrations of the final product of a metabolic pathway inhibit one of the enzymes early in the pathway. A form of negative feedback.

hydrogen bond

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

If you were to expose glucose to oxygen on your lab bench, why would you not expect to see it burn as described by the reaction in

Activation energy is required for the sugar and oxygen to reach their transition state.

Nucleotides are activated by linking additional phosphates to an existing 5′ phosphate.

Activation increases the chemical energy in the nucleotides enough to offset the decrease in entropy that will result from the polymerization reaction so that the polymerization proceeds spontaneously.

Passive transport does not require an input of energy—it happens because of energy already present in an existing gradient.

Active transport is active in the sense of requiring an input of energy from, for example, ATP.

Cholesterol Affects Membrane Fluidity and Permeability part 2

Adding cholesterol to membranes increases the density of the hydrophobic section -Makes membrane more stiff and decreases fluidity

Purines

Adenine and Guanine

The complementary base pairing in the secondary structure of DNA allows each strand to serve as a template.

After separating the strands of a DNA double helix, each template strand can be copied to make two identical double-stranded DNA molecules.

What's the difference between α-glucose and β-glucose?

Alpha-glucose has the C1 hydroxyl below the plane of the ring while beta-glucose has the C1 hydroxyl above the plane of the ring

In lab, you isolated (or read about isolating) bacteria that are able to breakdown starch. What enzyme do they produce? This enzyme breaks the starch down into disaccharides. What is the disaccharide? Do animals produce the enzyme? Where in the body is it found?

Amylase breaks down starch into the disaccharide maltose. Animals produce amylase, which is present in saliva, the pancreas, and the small intestine.

What's the difference between an aldose and a ketose?

An aldose is an aldehyde sugar with the carbonyl at the end while a ketose is a ketone sugar with the carbonyl in the middle of the carbon chain

liposome

An artificial vesicle formed by mixing amphipathic lipids, such as phosopholipids, together in an aqueous solution.

Compare and contrast isoprenoids and fatty acids with respect to structure and function.

An isoprenoid is a branched hydrocarbon chain built from isoprene. They function as pigments, scents, vitamins, sex hormone precursors, and as building blocks for more complex lipids. They are usually unsaturated. A fatty acid is an unbranched hydrocarbon chain bonded to a carboxyl group. They function as building blocks for more complex lipids and can be either saturated or unsaturated.

peripheral membrane protein

Any membrane protein that does not span the entire lipid bilayer but instead binds to only one side of the bilayer.

integral membrane protein

Any membrane protein that spans the entire lipid bilayer. Also called transmembrane protein.

catabolic pathway

Any set of chemical reactions that breaks down large, complex molecules into smaller ones, releasing energy in the process. Those that break down molecules for sources of energy and carbon building blocks

anabolic pathway

Any set of chemical reactions that synthesizes large molecules from smaller ones. Generally requires an input of energy. those that use energy and carbon building blocks to synthesize molecules

example of facilitated diffusion

Aquaporins are channel proteins that allow the passage of water molecules

If the regulated enzyme is at the start of a metabolic pathway, then when it is turned off, there will be no product to serve as a substrate for the following reaction.

As a result, none of the subsequent reactions would occur, including the formation of the final product.

Packed saturated hydrocarbon tails have fewer spaces and more van der Waals interactions.

As the length of saturated hydrocarbon tails increases, the forces that hold them together also increase, making the membrane even denser.

Gram-positive bacteria

Bacteria that have a thick peptido glycan cell wall, and no outer membrane. They stain very darkly (purple) in Gram stain.

Most RNA is single-stranded, so its nucleotide sequence (primary structure) affects the ability of complementary base-pairing interactions to form stems and loops (secondary structures) and fold the molecule into a specific higher-order shape (tertiary structure).

Because most DNA exists in double-stranded form, the secondary and tertiary levels of structure do not demonstrate the sequence-based variability seen in RNA.

Which of the reactions is most likely to be endergonic?

Breaking a polar covalent bond and forming a non-polar covalent bond

Which of the following pair by three hydrogen bonds in DNA?

C and G

induced fit

Change in the shape of the active site of an enzyme, as the result of initial weak binding of a substrate, so that it binds substrate more tightly.

Regulation may involve covalent modifications

Changes the enzyme's primary structure - Can be reversible or irreversible

What is chitin? What reaction do you think chitinase catalyzes?

Chitin is a polysaccharide found in the exoskeleton of insects and the cell walls of fungi. Chitinase likely catalyzes the breakdown of chitin (glycosidic bonds)

Cholesterol decreases membrane fluidity at high temperatures and increases membrane fluidity at low temperatures. Thinking about the structure of cholesterol, can you explain how this may occur?

Cholesterol's structure allows it to immobilize fatty acids at high temperatures and disrupts tight packing at lower temperatures.

Example of low potential energy

Co2

Which would have the highest?

Co2

amphipathic

Containing hydrophilic and hydrophobic regions

pyrimidines

Cytosine and Thymine

Cells follow the central dogma:

DNA encodes RNA, RNA encodes proteins

What is responsible for the increased stability of DNA compared to RNA?

DNA is more stable than RNA because it lacks a hydroxyl group on the 2' carbon

Primary structure of DNA

DNA molecules have a sugar-phosphate backbone, created by phosphodiester linkages, and a sequence of any of four nitrogenous bases that extend from it.

secondary vs primary structure DNA

DNA's secondary structure consists of two antiparallel strands twisted into a double helix. The double helix is shaped and stabilized by hydrogen bonding between the complementary base pairs, hydrophobic interactions, and van der Waals interactions.

Nucleic Acids function:

DNA: Storage, transmission, and expression of genetic information RNA: Gene expression & others

Spatial arrangement of their atoms

Different arrangement of the hydroxyl groups

Define diffusion

Diffusion is movement of molecules down their concentration gradient

passive transport

Diffusion of a substance across a membrane. When this event occurs with the assistance of membrane proteins, it is called facilitated diffusion.

Regulation via noncovalent interactions:

Does not permanently affect the enzyme structure and is "reversible" - Competitive inhibition occurs when a molecule competes with the substrate for the active site - Allosteric regulation occurs when a molecule binds at a location other than the active site -Causes a change in enzyme shape -Can activate or deactivate the enzyme

Bond Saturation Affects Membrane Fluidity and Permeability

Double bonds in a hydrocarbon chain cause a "kink" - Prevents the close packing of hydrocarbon tails - Reduces hydrophobic interactions Membranes are much more permeable and more fluid Saturated hydrocarbon chains have fewer spaces and stronger hydrophobic interactions - Membranes are denser, less permeable, and less fluid

Nucleic Acids structure:

Double-stranded helix (DNA) or single-stranded (RNA) Antiparallel strands when double-stranded Each strand has a 5' end and a 3' end Complementary base pairing Hydrogen bonds in base pairing: A=T (or A=U), G≡C

Which of the following describes the effect of temperature on enzyme-catalyzed reactions?

Enzymes have an optimal temperature at which they work and the reaction will proceed the fastest at this temperature.

T/F The products always have lower entropy than the reactants.

F, exergonic reactions can occur if the products have lower entropy if there is a large drop in enthalpy

T/F The reaction always occurs quickly.

F, the reaction rate depends on the activation energy and it may be high and result in a exergonic reaction happening slowly if at all

The Gibbs free energy change ( G) states:

G (kcal/mol) = H - T S

Fat structure

Glycerol (3C alcohol) + fatty acid - fatty acid: hydrocarbon chain with carboxyl group "head"

Sodium Potassium ATPase

Helps maintain Na/K levels inside the cell:

How does cholesterol stay in place in the plasma membrane?

Hydrogen bonding and hydrophobic interactions

All of the sugars would be deoxyribose instead of ribose, so the 2′ carbon would be bonded to a hydrogen instead of a hydroxyl.

In addition, the uracil base at the 5′ end would be replaced with a thymine base.

energetic coupling

In cellular metabolism, the mechanism by which energy released from an exergonic reaction (commonly, hydrolysis of ATP) is used to make an endergonic reaction spontaneous.

In what ways can monosaccharides differ from each other?

In the number of carbons present (3-8), the type of carbonyl (aldose vs. ketose), the spatial arrangement of -OH groups around each carbon, and the formation of different ring forms

The retro-evolution hypothesis starts with a single key reaction and then evolves additional enzyme-catalyzed reactions to generate more of the substrate for the original reaction.

In the patchwork hypothesis, the evolution of a new pathway occurs by repurposing enzymes from other already existing pathways. New activities may arise in the process.

Peripheral membrane proteins are associated with one of the two hydrophilic surfaces of the membrane, but do not cross through the hydrophobic interior. .

Integral membrane proteins completely pass through the membrane via a series of adjacent nonpolar amino acids

Examples would include (1) the production of nucleotides, and (2) polymerization of RNA.

It is thought that nucleotides were scarce during chemical evolution, so their catalyzed synthesis by a ribozyme would have been advantageous. Catalysis by an RNA replicase would have dramatically increased the reproductive rate of RNA molecules.

If a solution surrounding a cell is hypertonic relative to the inside of the cell, how will water move?

It will not move, because equilibrium exists

Suppose a cell is placed in a solution with a high concentration of potassium and no sodium. How would the cellular sodium-potassium pump function in this environment?

It would continue using ATP to pump sodium out of the cell and potassium into the cell.

Label the tonicity for each solution below (isotonic, hypotonic, or hypertonic).

Left - hypotonic, Center - isotonic, Right - hypertonic

Hydrocarbons are nonpolar because electrons are shared equally in C—HC—H bonds owing to the similar electronegativities of carbon and hydrogen. Since C—HC—H bonds form no partial charges, hydrocarbons do not dissolve in water.

Lipids, therefore, are mostly hydrophobic because they have a significant hydrocarbon component.

Temperature Affects Membrane Fluidity and Permeability

Membrane fluidity decreases as temperature drops - Molecules in the bilayer move more slowly - Hydrophobic tails pack together more tightly -Decreased membrane fluidity causes decreased permeability

Hydrophobic interactions become stronger as saturated hydrocarbon tails increase in length

Membranes containing phospholipids with longer tails are less permeable and less fluid

An experiment is set up in which two solutions are divided by a planar bilayer. On side A: 0.4M of a solute that can cross the bilayer (is permeable); On side B: 0.8M of a different solute that can also cross the bilayer (is permeable).

Molecules on side A will move to side B - final concentration will be 0.2M on each side.

Predict the flow of molecules. Predict the final concentration of each solute on each side.

Molecules on side B will move to side A - final concentration will be 0.4M on each side

Carbohydrates include:

Monosaccharide ("one sugar") - monomers Disaccharide ("two sugars) Oligosaccharide ("few sugars") - small polymers Polysaccharide ("many sugars") - large polymers

Are monosaccharides polar? Do they dissolve in water? Why or why not?

Monosaccharides are polar and dissolve in water due to their hydroxyl (OH) and carbonyl (C=O) functional groups

Where would you find the highest Na+ concentrations? Lowest?

Na+ concentrations are highest outside of the cell and lowest inside of the cell.

Which of the following is NOT an example of passive transport?

Na+ ions being pumped out of the cell.

Best studied example of indirect active transport:

Na+/glucose symporter

Which of the following molecules would most readily cross a cell membrane?

O2

what molecule is transported via simple diffusion?

O2

Reaction rate is based primarily on the activity of the enzyme.

Once the temperature reaches a level that causes unfolding and inactivation of the enzyme, the rate decreases to the uncatalyzed rate.

Define osmosis:

Osmosis is the diffusion of water

Make experimental outcome predictions based on these two hypotheses:

PREDICTION OF HYPOTHESIS: The carbohydrate component of the glycoprotein will bind to sperm and block their attachment to eggs. PREDICTION OF ALTERNATE HYPOTHESIS: The protein component of the glycoprotein will block sperm attachment to eggs.

How is the structure of peptidoglycan different from other polysaccharides?

Peptidoglycan has modified sugars, some with amino acids

The bridge formed by the phosphate group is called?phosphdiester

Phosphdiester linkage

How is potential energy and disorder represented in the Gibbs Free Energy Equation? When are they positive or negative?

Potential energy is represented by ΔH. Disorder is represented by ΔS. When products have less potential energy than reactants, ΔH is negative; when they have more, ΔH is positive. When disorder increases, ΔS is positive; when it decreases, ΔS is negative.

What does it mean for a fatty acid to be unsaturated vs. saturated? Draw the structure of a saturated fatty acid and an unsaturated fatty acid.

Saturated fatty acids consist of only single bonds between the carbons. Unsaturated fatty acids have one or more double bonds in the hydrocarbon chain.

DNA primary structure is based on covalent bonds and has greater variability compared to the secondary and tertiary levels.

Secondary structure is based on complementary base pairing and involves two strands of DNA. The tertiary structure of DNA often includes proteins.

RNA World hypothesis

Self-replicating RNA molecules may have been the precursor to all life (could carry heritable information, catalyze reactions that promote its own replication)

Most organisms can regulate their membrane fluidity by changing the lipid composition of the membrane. This is especially important for organisms that can't regulate their temperature, like cold-blooded animals, plants, protists, fungi, and bacteria. What kind of change would you expect to see in the cell membranes of hibernating animals? Why?

Since hibernating animals will be at colder temperatures, you would expect more unsaturated fatty acids & shorter fatty acid chains and possibly an increase in cholesterol composition of membranes.

What would happen to a patient's blood cells if given an I.V. drip of saline?

Since saline would likely have the same salt concentration, the blood cells would be in an isotonic solution so there would be no shrinking or swelling of blood cells.

Solutes =

Small molecules and ions in a solution - Have thermal energy & are in constant random motion

Given the results on the right, what conclusion would you make about how sperm recognize and bind to an egg?

Sperm recognize and bind to an egg by attaching to carbohydrates

Alternative ring forms

Sugars typically form ring structures in aqueous solutions

T/F Activation energy is required for the reaction to proceed.

T

T/F The products have lower Gibbs free energy than the reactants.

T

Temperature (T)

Temperature in Kelvin

Membrane fluidity depends on:

Temperature- cells cannot regulate - Higher temperature, greater fluidity Type of fatty acids- cells can regulate ⬇️ - Unsaturated increase fluidity Length of fatty acids - Shorter, more fluid Cholesterol - Fluidity "buffer"

We know that termites contain the enzyme cellulase (the enzyme that degrades cellulose) in their guts. Interestingly, upon sequencing the termite genome it was shown that they don't contain the gene for cellulase. Remember that genes (DNA) code for proteins/enzymes. How can termites have the enzyme, but not the gene?

Termites have symbiotic bacteria in their gut that make the enzyme cellulase.

Like proteins, single-stranded RNA molecules will fold into different shapes that have different properties.

The additional hydroxyl on the ribose sugar also makes RNA more reactive, such that it can support catalytic functions.

Gibbs free energy

The amount of energy in the reaction available to do work—what chemists call

How are the carbohydrates covalently linked to lipids or proteins on the outside of cells different from the polysaccharides starch and cellulose?

The carbohydrates linked to lipids or proteins tend to have structural diversity and different linkages compared to the repetitive structure and linkage of starch and cellulose.

Which of the following is true when comparing an uncatalyzed reaction to the same reaction with a catalyst?

The catalyzed reaction has the same ΔG.

How does pH affect enzyme-catalyzed reactions?

The concentration of protons affects an enzyme's folded structure and reactivity.

The αα-glucose residues would all be oriented the same (no longer flipped across the glycosidic linkages) and the molecule would coil into a helix.

The hydrogen bonds that were present between adjacent ββ-glucose polymers would no longer occur with the αα-glucose polymer, so multi-strand fibers would not be formed.

active site

The location in an enzyme molecule where substrates (reactant molecules) bind and react.

Every reaction has an activation energy (EA):

The minimum amount of energy that molecules must have before collision between them will be successful in leading to the reaction

enzyme are catalysts

The only reactions that occur at any appreciable rates in a cell are those for which the appropriate enzymes are present and active. Without enzymes, metabolic reactions would proceed too slowly to sustain life.

In the G-T pair, only one hydrogen bond could form—between the bottom N-H in guanine and one of the carbonyl groups (C═O)(C═O) of thymine.

The other two potential H-bonding sites in guanine would repel the similar partial charges in the aligned groups extending from the thymine base. No hydrogen bonding would be possible in an A-C pair.

Penicillin (an antibiotic discovered by Alexander Fleming) in an antibiotic that acts by inhibiting the enzymes that catalyze the peptide bond formation in peptidoglycan, weakening the cell wall.

The penicillin doesn't work very well on E.coli, but does on S. aureus Why? E. coli are Gram (-) bacteria with a thin peptidoglycan layer S. aureus are Gram (+) bacteria with a thick layer of peptidoglycan layer

selective permeability

The property of a membrane that allows some substances to diffuse across it much more readily than other substances.

If the products of a reaction have stronger, more polar covalent bonds than the reactants, what is true about the reaction?

The reaction has a negative ΔH.

Which of the following is true of all exergonic reactions?

The reaction has a net release of free energy.

A chemical reaction has a ∆G of -5.6 kcal/mol. Which of the following would most likely be true?

The reaction would result in an increase in entropy (S) and a decrease in the enthalpy content (H) of the system.

This type of interaction is called allosteric ("different-structure") regulation because the binding event changes the shape of the enzyme in a way that makes the active site available or unavailable

The regulatory molecule binds at a location other than the active site and changes the shape of the enzyme.

This tactic is called competitive inhibition because the molecule involved competes with the substrate for access to the enzyme's active site

The regulatory molecule is similar in size and shape to the enzyme's natural substrate and inhibits catalysis by binding to the enzyme's active site.

understand The three phosphate groups in ATP have four negative charges in close proximity.

The repulsive forces from the clustered negative charges result in weak, unstable bonds that have high potential energy.

You have discovered an enzyme that appears to function only when a particular sugar accumulates. Which of the following scenarios would you predict to be responsible for activating this enzyme?

The sugar phosphorylates the enzyme to form the active conformation

When unsaturated hydrocarbon tails are packed into a lipid bilayer, kinks created by double bonds produce spaces among the tails.

These spaces reduce the number of van der Waals interactions that help hold the hydrophobic tails together, weakening the barrier to solutes.

Free fatty acids are amphipathic because their hydrocarbon tails are hydrophobic but their carboxyl functional groups are hydrophilic. In fats, the charged carboxyl groups of fatty acids are converted to ester linkages.

This change reduces the difference in polarity across the molecule, making it more uniformly nonpolar. As a result, fats are not considered amphipathic.

The Mg2+Mg2+ ion carries positive charges that will interact with the negative charges on ATP.

This interaction helps the enzyme transfer a phosphate from ATP to its substrate.

What about water? What diagram does that represent?

This is a hypotonic solution and water would rush into the cells causing the cells to burst. (left diagram)

DNA Structure and Complementary Strands

This model suggests that each DNA strand can act as a template for the synthesis of its complementary strand

he energy that's released when sugars are processed is used to synthesize ATP from a precursor called adenosine diphosphate (ADP) plus a free inorganic phosphate (Pi)(Pi) molecule. The overall reaction can be written as follows:

To put this in terms of bonds, some of the chemical energy stored in the C—HC—H and C—CC—C bonds of carbohydrate [(CH2O)n][(CH2O)n]is released as new C═OC═O bonds are formed in CO2.CO2. This energy is then transferred to a new bond linking a third phosphate group to ADP to form ATP.

Which of the following is true of trans fat?

Trans fat is made by an industrial process called hydrogenation of oils.

secondary structure of DNA

Two anti-parallel strands twist into a double helix, stabilized by hydrogen bonding between complementary bases (A-T & G-C) and hydrophobic interactions. Although each base has polar groups involved in the hydrogen bonds, the bases' carbon-nitrogen rings are mostly nonpolar. This is a key point, because in aqueous solution (the environment inside a cell) hydrophobic interactions cause double-stranded DNA to twist into a helix to minimize contact between the hydrophobic bases and surrounding water molecules

Unsaturated fat is different from saturated fat in that _______

Unsaturated fat has one or more C double bonds.

How does glucose go from an area of low concentration in the gut lumen (open area of small intestine) to high concentration in the intestinal epithelium? Does this require energy?

Using a sodium-glucose symporter. The energy from Na+ moving down its concentration gradient supplies the energy for the active transport of glucose.

How does glucose go from an area of high concentration in the intestinal epithelium to low concentration outside of those cells to get distributed to other tissues? Does this require energy?

Using glucose carriers such as GLUT1. This is facilitated diffusion and does not require energy.

Which of the following is true with respect to osmosis?

Water will move out of a cell when placed in a hypertonic solution

energetic coupling

When ATP is hydrolyzed it can transfer a cleaved phosphate group to a substrate

Note that the term "activated" means something different when used to describe the effect of phosphorylation on an enzyme versus a substrate. When a substrate is activated, its potential energy has been increased, and this extra energy is used to convert an endergonic reaction to one that is exergonic

When an enzyme is activated, its catalytic function has been turned on—but any change in the potential energy of the enzyme is not directly used to drive the catalytic reaction.

Phospholipids are amphipathic, so their hydrophilic end will interact with water and their hydrophobic end will not. Water molecules are more ordered when surrounding the hydrophobic regions.

When phospholipids are brought together to form a membrane, the hydrophobic regions are tucked away from water and thus the entropy in water increases. Events that increase entropy tend to be spontaneous.

When nucleotides polymerize to form a nucleic acid ________

a covalent bond forms between the sugar of one nucleotide and the phosphate of a second.

In all reactions, even spontaneous ones, a certain minimum amount of kinetic energy—called the_____________—is required to sufficiently strain the chemical bonds in molecules so they can react to form products

activation energy

Glucose moving into the cell against its concentration gradient

active transport

Na+ ions moving from inside to outside the cell

active transport

What are the four nitrogenous bases found in RNA?

adenine, cytosine, guanine, uracil (A, C, G, U)

Proteins can be

amphipathic

The enzymes involved in breaking the α-glycosidicα-glycosidic linkages in starch are called

amylases

Pumps

are membrane proteins that provide active transport of molecules across the membrane using ATP hydrolysis

Micelles

are tiny spherical aggregates created when the hydrophilic heads of a set of lipids face outward and interact with the water, while the hydrophobic tails interact with each other in the interior, away from the water.

The fluid-mosaic model was a radical departure from the sandwich hypothesis.

at least some proteins span the membrane instead of being found only outside the lipid bilayer.

Isoprenoid =

branched hydrocarbon chain

aldose

carbonyl group at end of carbon chain

ketose

carbonyl group in middle of carbon chain

Glut-1

carrier protein

Glut-1 is a?

carrier protein

glucose transporter

carrier protein

RNA provides a template that can be copied and can also

catalyze the polymerization reaction required for its own replication.

What are the primary functions of carbohydrates in cells?

cell identity, energy storage, raw material source for synthesis, and structure

aquaporin

channel protein

calcium channel

channel protein

Irreversible changes often result from

cleavage of peptide bonds

The antibiotic sulfanilamide inhibits the synthesis of folic acid by binding to dihydropteroate synthetase. Given what you know about the structure of sulfanilamide and the structure of the substrate, what type of enzyme regulation is this an example of?

competitive inhibition

reaction that forms glylosdic linkage

condensation

Name of bond when nucleotides join together to make nucleic acid?

condensation reaction between hydroxyl on the sugar and the phosphate the reaction forms a new covalent bond between the nucleotides and a molecule of water is released

The difference between the sugar in DNA and the sugar in RNA is that the sugar in DNA ________.

contains one less oxygen atom.

DNA deoxyribonucleotides- monomer

deoxyribonucleic acid- polymer the sugar is deoxyribose

What determines the primary structure of a DNA molecule?

deoxyribonucleotide sequence

enzymes lower activation energy by

destabilizing bonds in the substrates and promoting the formation of the transition state.

Gibbs free energy (G)

determines whether a reaction is spontaneous or requires added energy to proceed

Movement down their concentration gradient =

diffusion

Na+/K+ ATPase

direct (ATP driven) active transport

Simple diffusion

direct, unaided movement through the lipid bilayer. Movement is dictated by the molecule's concentration gradient.

When just two sugars link together, the resulting molecule is known as a

disaccharide

the recipient molecule is called the

electron acceptor

the molecule giving up an electron is called the

electron donor

A chemical reaction that has a positive ΔG is best described as

endergonic

kinetic energy

energy of motion

The concentration of protons in a solution, as measured by pH, also affects

enzyme structure and function. pH affects the charge on acidic and basic groups in residue side chains, and also the active site's ability to participate in reactions that involve the transfer of protons or electrons.

Explain the lock-and-key model of enzyme activity. What is incorrect about this model?

enzymes are actually flexible and not rigid

how do enzymes affect activation energy?

enzymes lower the activation energy to speed up the reaction

Glucose moving into the cell down its concentration gradient

facilitated diffusion

Na+ ions moving from outside to the inside of the cell

facilitated diffusion

Water moving through aquaporins

facilitated diffusion

increased disorder with stack of papers

falling down

T/F Ribonucleotides are added to the 3′ end of a DNA strand.

false

T/F The red blood cell liposomes are more hypertonic relative to water than the frog egg liposomes.

false

T/F The red blood cell liposomes are more hypotonic relative to water than the frog egg liposomes.

false

T/F There is a difference in the number of carbons

false

T/F There is a difference in the position of the carbonyl group in the linear form.

false

true or false, unsaturated fatty acids only have single bonds?

false

T/F Complementary pairing between sugars is required for copying nucleic acids.

false, pairing occurs between bases not sugars

Temperature affects the

folding and movement of an enzyme as well as the kinetic energy of its substrates

There is a net movement

from high-concentration regions to low-concentration regions

Which of the following is a storage polysaccharide?

glycogen

store polysaccharide in animals

glycogen

Sugars are linked by

glycosidic bonds

Monosaccharides polymerize when a condensation reaction occurs between two hydroxyl groups, resulting in a covalent connection (—O—)(—O—) called a

glycosidic linkage

What type of bond is formed between two sugars in a disaccharide?

glycosidic linkage

Monosaccharides are linked together by what type of bond to form polysaccharides? What type of reaction is this?

glycosidic linkages (bonds) condensation (dehydration) reaction

glucose that's coursing through your bloodstream right now is a six-carbon sugar, or a

hexose

What holds cellulose molecules together in bundles large enough to form fibers?

hydrogen bonds

Where is energy stored in molecules?

in covalent bonds

A catalyst

increases the rate of a reaction

Na+/glucose symporter

indirect, coupled active transport

amphipathic proteins can

integrate into lipid bilayers

A concentration gradient

is created by a difference in solute concentrations

potential energy

is energy that is stored in position - EX: chemical bonds, gravitational, chemical gradients

Entropy (S)

is the amount of disorder: + ΔS: breakdown molecules - ΔS: build molecules

Facilitated diffusion across a membrane ____

is when membrane proteins assist in passive transport.

what is true about allosteric regulation?

it causes a conformational change

Galactosemia is a potentially fatal disease that occurs in humans who lack the enzyme that converts galactose to glucose. If you were a physician treating a person with this disease, which of the following would you have them exclude from their diet?

lactose

Steroids have a distinctive four-ring structure with variable side groups attached; fats consist of three fatty acids linked to glycerol; many phospholipids also have a glycerol linked to fatty acids, but instead of three fatty acids, they have two plus a hydrophilic, phosphate-containing "head" region.

lipid

These variations give each monosaccharide a unique structure and function.

many distinct monosaccharides exist because so many aspects of their structure are variable: aldose or ketose placement of the carbonyl group, the number of carbons, and the different arrangements of hydroxyl groups in space. Ring forms of the same molecule also have alternative shapes.

Facilitated diffusion

membrane proteins bind specific solutes and facilitate their movement across membranes. Movement is dictated by the molecule's concentration/charge (electrochemical) gradient.

Active transport

membrane proteins move solutes across membranes against their electrochemical gradient, so the transport requires an input of energy

A linked series of biochemical reactions that sequentially changes an initial substrate to form a final product; the product of one reaction is the substrate of the next reaction.

metabolic pathway

Thinking about the membrane protein, what types of amino acids were probably in contact with the phospholipid fatty acid tails?

non polar

Integral membrane proteins are anchored in lipid bilayers. Which of the following groups of amino acid residues would likely be found in the portion that crosses the lipid bilayer?

nonpolar

nucleic acid monomer

nucleotide (in both RNA and DNA), phosphate+sugar+base

Nucleic acids are polymers made up of which of the following monomers?

nucleotides

Diffusion (a type of passive transport)

occurs when substances diffuse across a membrane in the absence of an outside energy source

Single strands of nucleic acids are directional, meaning that there are two different ends. What functional groups define the two different ends of a strand?

one end has a free phosphate group on the 5' carbon and one has a free hydroxyl group bonded to the 3' carbon

Unsaturated hydrocarbon chains have

one or more double bonds in the hydrocarbon chains (C=C) H atoms are removed to make a double bond Forms a "kink" in the chain - Monounsaturated chains have 1 double bond - Polyunsaturated chains have many double bonds

Saturated hydrocarbon chains consist of

only single bonds between the carbons (C-C) Has the maximum number of H atoms ("saturated" with hydrogens)

The movement of substances through channel proteins is

passive—meaning it does not require an input of energy.

Ribose, which acts as a building block for nucleotides, has five carbons and is called a

pentose

The most important enzyme involved in catalyzing the hydrolysis of α-glycosidicα-glycosidic linkages in glycogen molecules is a protein called

phosphorylase

What types of amino acids would be associated with the phospholipid heads

polar uncharged, basic

What types of amino acids would be associated with the cytoplasm and environment

polar uncharged, basic, acidic

what is not part of a nucleotide structure

protein

Cellular reactions are mediated by

protein catalysts (enzymes) and, in some cases, RNA catalysts (ribozymes)

Which reaction would benefit the most from energetic coupling? How does hydrolysis of ATP work in energetic coupling?

reaction 2 The hydrolysis of ATP is exergonic - the energy of hydrolysis can be coupled to do work of an endergonic reaction

RNA ribonucleotides- monomer

ribonucleic acid- polymer the sugar is ribose

Saturated vs. Unsaturated Lipids

saturated: fatty acids with no CC double bonds, solids derived from animals unsaturated: fatty acids with 2 or more CC double bonds, liquids derived from plants

What kinds of changes in phospholipid composition would you expect if single-celled organisms were moved from a warm environment to a cold environment, while still maintaining the same membrane fluidity?

shorter, more unsaturated hydrocarbon tails

Oxygen moving through the lipid bilayer

simple diffusion

Water moving through the lipid bilayer

simple diffusion

A detergent is a

small amphipathic molecule that can form micelles. However, unlike amphipathic lipids, detergents are water soluble

what moves quickly across plasma membranes?

small, non polar substances

understand Electrons in C—HC—H bonds are not held as tightly as electrons in C—OC—O bonds

so they have higher potential energy.

what does spontaneous mean in chemical reactions

spontaneous reactions run in the direction that lowers the free energy

Second law of thermodynamics

states that total entropy always increases in a system

What factor increases membrane fluidity?

temperature increase

Although cellulose and starch are identical in terms of stored chemical energy, our ability to harvest the energy from these two polysaccharides differs considerably. What is responsible for this difference?

the a linkages in starch are easily hydrolyzed and the b linkages in cellulose resist hydrolysis

Explain how feedback inhibition regulates metabolic pathways.

the final product of a pathway inhibits the activity of an enzyme early in the same pathway, thus reducing the activity of all movements

What is a transition state?

the intermediate complex formed as covalent bonds in the reactants are being broken and re-formed during a reaction

glycosidic linkages form between hydroxyl groups, and because every monosaccharide contains at least two hydroxyls

the location and geometry of glycosidic linkages can vary widely among different oligosaccharides and polysaccharides.

Lysozyme, an enzyme found in human saliva, tears, and other secretions, catalyzes the hydrolysis of the β-1,β-1,4-glycosidic linkages in peptidoglycan. Predict the effect of this enzyme on bacteria and how it may be involved in human health.

the peptidoglycan in cell walls starts to degrade, leading to the death of bacteria

Changes in enthalpy (ΔH)

the total energy of a molecule, are primarily based on the difference in potential energy

Delta G is 5.6 kal/mol, what's true?

there is an increase of S and a decrease of H in the system

what is not true about catalysts?

they go through a chemical change during the reaction

How do the phospholipids in archaea differ from those in other cells?

they have isoprenoid tails instead of fatty acid tails.

Which of the following is a pyrimidine found in DNA?

thymine

What is not true about the Na+/K+/ATPase

transport Na+ in

Three-carbon sugars

trioses

T/F Polymerization of nucleic acids occurs by the formation of phosphodiester bonds.

true

T/F Strands in a double helix are synthesized in an antiparallel orientation.

true

T/F The frog egg liposomes contain ion channels, which are not present in the red blood cell liposomes.

true

T/F The red blood cell liposomes contain more aquaporins than the frog egg liposomes.

true

T/F There is a difference in the orientation of a hydroxyl group in the ring form.

true

T/F There is a difference in the overall shape of the molecule—one is a ring and the other is linear.

true

True or False, active transport requires ATP?

true

in general, unsaturated lipids are more fluid than saturated lipids at a given temperature.

true

true or false, a higher concentration of a solution outside of the cell is hypertonic?

true

true or false, nucleic acid is directional?

true, 5' to 3' direction

osmosis and diffusion

two types of passive transport

Simple diffusion

unassisted movement of a solute from a region of higher concentration to a region of lower concentration

Fatty acid =

unbranched hydrocarbon chain bonded to -COOH functional group

RNA

undergoes hydrogen bonding with complementary bases on the same strand

Enzymes determines

whether a spontaneous reaction (ΔG<0) will occur at an appreciable rate, BUT NOT WHETHER A REACTION IS SPONTANEOUS!

base stacking

which results from van der Waals interactions between the tightly packed adjacent bases.

The mathematical expression for the change in free energy of a system is ΔG= ΔH-TΔS. Which of the following is correct?

ΔG is the change in free energy.

Enzyme catalysis has three steps:

​1.) Initiation—substrates bind to active site 2.) Transition state facilitation—interactions between the substrate and active site R-groups lower the activation energy - many enzymes undergo a conformational change (induced fit model) ​3.) Termination—products are released from the enzyme

Glycolipids

—lipids with oligosaccharides attached

Glycoproteins

—proteins with oligosaccharides attached