Introduction (Week1-5) Test 1 Flashcards
Proteins are made up of which functional groups?
Carboxyl & Amino
What is the cell membrane’s structure?
-Lipids
-Proteins
-Carbohydrates
What is the function of the cell membrane?
-Transport
-Diffusion
-Osmosis
What is the structure of enzymes?
-Proteins
-Nucleic acids (ribozyme)
What is the function of enzymes?
Catalyze chemical reactions
What do binding sites do?
Bind and orient substrate(s)
What do catalytic sites do?
Reduce chemical activation energy
What are the 3 types of respiration?
1) Aerobic respiration
2) Anaerobic respiration
3) Fermentation
What are monomers?
Basic structural unit of polymers
Ex: Carbohydrate, amino acid and nucleotides
What are polymers?
Molecule made up of a large number of identical or similar units (monomers) attached by covalent bonds
Can lipids make polymers?
No
What are macromolecules?
Thousands of atoms united by covalent bonds
What is dehydration (condensation)?
The synthesis of polymers
What are the steps to dehydration (condensation)?
-Monomers (substrates) are joined to form polymers (product)
-This reaction needs energy (ATP) and is usually catalyzed by an enzyme
-The type of metabolism involved in the formation of polymers using monomers is called anabolism
What is hydrolysis?
The degradation of polymers
How does hydrolysis occur?
-Breakdown of polymer (substrates) in smaller molecules (product) by the addition of water
-This reaction produces a net quantity of energy (ATP) and is usually catalyzed by an enzyme
-The type of metabolism involved in the degradation of polymers is called catabolism
What are organic molecules?
Molecules that contain carbon atoms (except CO2)
What are functional groups?
Specific molecular groups that bond to carbon-hydrogen cores
What are characteristics of functional groups?
-Each group has unique chemical properties
-The different functional groups will interact between each others in a molecule, in addition to the environment, creating the 3D structure of the functioning bio-molecules.
-3D structure determines the function
True or false? The properties of functional groups are retained, wherever they attach, and influence behaviour of entire molecules in reactions?
True
Are polar functional groups hydrophobic?
No, they are hydrophilic (love water)
Polar functional groups tend to make _______ bonds between the electronegative element, such as oxygen, and hydrogen
Hydrogen
Are nonpolar functional groups hydrophobic?
Yes, thus they tend to rearrange themselves together and away from water molecules when in aqueous solution
Which functional groups are polar?
Hydroxyl and carbonyl
Which functional groups are nonpolar?
Methyl
Which functional groups are slightly polar?
Sulfhydryl (tends to bond with itself)
Which functional group are acidic?
Carboxyl & phosphate
Which function group is basic?
Amino group
Synthesis of disaccharide by dehydration between 2 ________ groups makes it possible to form a covalent bond called _________ bond.
-Hydroxyl
-Glycosidic
What are amino acids composed of?
-An amino group
-A carboxyl group
-Single hydrogen
-Central alpha carbon where there is a side chain (R)
Are amino acids organic molecules?
Yes
What is the backbone of amino acids?
N-C-C
What are characteristics of non-polar amino acids?
-Have hydrophobic side chains (such as methyl functional group).
-Tend to rearrange themselves away from water molecules.
-Helps the protein fold and will create hydrophobic interaction (aka exclusion) or Van der Waals attraction.
What are characteristics of polar uncharged amino acids?
-Have side chains that contain oxygen as a hydroxyl or carbonyl functional group.
-Tend to make hydrogen bonds between the electronegative element, such as oxygen and hydrogen.
-Are hydrophilic
What are characteristics of charged amino acids?
-Have side chains that contain acids or bases that can ionize
-Opposite charged side chain of amino acids can interact and create ionic bonds with each other
-Same charged repel each other
What are characteristics of aromatic amino acids?
-have side chains that are non-polar
-hydrophobic
-Van der Waals attraction/Hydrophobic exclusion
What is significant about Methionine?
It is always the first amino acid of a polypeptide in Eukaryote and Archaea
What is significant about Proline?
It causes kinks in polypeptides
What is significant about Cysteine?
It contains a side chains with a sulfhydryl functional group, which links chains together to make disulphide bridge
What is disulphide bridge?
A type of covalent bond that is the strongest of the bonds between side chains
What are monomers and polymers of amino acids called?
Monomers: amino acids
Polymers: polypeptides (composed of monomers of unbranched amino)
What is a protein made up of?
One or more polypeptides with a function
How are amino acids joined?
Dehydration synthesis
How are peptide bonds formed?
Between the amino end and carboxyl end of two adjacent amino acids
Is the peptide bond able to rotate?
No, it is planar and does not permit rotation.
However, the Ca-C bond can rotate
What is the primary structure of amino acids?
Sequence of amino acids linked by peptide bonds
What is the secondary structure of amino acids?
Interaction of atoms in the peptide backbone (NCC)
-Hydrogen bonds between amino acids of the backbone (not the side chain)
-Only the H of the amine and O atom of the carbonyl group of the backbone participate in the hydrogen bonds.
What are the 2 structures found in the secondary structure of an amino acid?
-Alpha helix: coiled spiral
-Beta pleated sheet: planar structure (always composed of a minimum of 2 or more beta strands)
What is the tertiary structure of an amino acid?
3D structure formed by the interaction between the side chains (R) of the other amino acids and also with the environment
One polypeptide with a ________ structure can form a functioning protein
Tertiary
What are the tertiary structure bonds?
-Van der Waals/Hydrophic exclusion
-Hydrogen bonds
-Ionic bonds
Disulphide bridge
What is the quaternary structure of amino acids?
Arrangement of 2 or more polypeptides chains in a functional protein
Which bonds/interactions are involved in the quaternary structure of amino acids?
-Van der Waals/hydrophobic exclusion
-Hydrogen bonds
-Ionic bonds
-Disulphide bridge
The same bonds and interactions keeps the 2 polypeptides together
What are motifs?
Similarities between otherwise dissimilar proteins (motifs are also known as super-secondary structure)
What are examples of motifs?
1) Helix-turn-helix
2) Beta barrel motif
3) Beta-alpha-beta motif
What is the significance of the helix-turn-helix motif?
-Major structural motif capable of binding DNA
-Each monomer incorporates two alpha helices, joined by a short strand of amino acids, that bind to the major groove of DNA
-The HTH motif occurs in many proteins that regulate gene expression
What is the significance of the beta barrel motif?
-The beta sheet folded around to form a tube
-Are involved in membrane transport
What is beta-alpha-beta motif?
-Motif contains 2 beta-sheets which are connected by an alpha helix
-Creates a fold or crease at the core of nucleotide-binding sites in a wide variety of proteins
-For example, proteins that bind nucleotides, such as enzyme cofactors FAD, NAD+, and NADP+
What are domains of proteins?
-Functional units within a larger structure
-They can be thought of as substructures within the tertiary structure of a protein
True or false? Most proteins are made up of multiple domains that perform different parts of the protein’s function.
True,in many cases, these domains can also be physically separated
What happens if the DNA-binding region changes (different gene)?
The specificity of the factor for DNA can be changed without changing its ability to stimulate transcription
What are the protein functions?
1) Enzyme catalysis
2) Defense
3) Transport
4) Support
5) Motion
6) Regulation
What is enzyme catalysis?
Biological catalysts that facilitate specific chemical reactions
What is defense (protein function)?
Proteins use their shapes to ‘’recognize’’ foreign microbes and cancer cells. These cell-surface receptors form the core of the body’s immune systems.
Ex: antibody
What is transport (protein function)?
A variety of proteins that transport small molecules and ions
Ex: membrane transport proteins help move ions and molecules across the membrane
What is support (protein function)?
Protein fibres play structural roles. These fibres include keratin in hair, fibrin in blood clots and collagen
What two protein filaments are needed for muscle contraction?
Actin and myosin
What is regulation (protein function)?
Small proteins called hormones serve as intercellular messengers in animals. For example, insulin is a hormone that promotes the absorption of glucose from the blood into liver, fat and skeletal muscle cells
What are factors that affect the structure and function of proteins?
1) Temperature
2) pH
3) Organic solvent
4) Detergent
How does temperature affect structure and function of proteins?
-The 3D structures of proteins change with temperature
-Since the function of a protein depends on its 3D shape, the function of the protein will be altered if outside of its normal temperature range
How does pH affect protein structure and function?
-Acids react with amino acid side chains that are negatively charged and bases react with the amino acid side chains that are positively charged resulting in the disruption of the ionic bond.
-In addition, hydrogen bonds are also disrupted
How does high ion concentration (salt) affect protein structure and function?
-Salt ions form strong bonds with the charge functional group of amino acids, disrupting ionic bonds
How does preservation of food work?
High slat content and lactic acid produce during fermentation of cabbage and pickles denature the proteins of bacteria that could spoil the food
What is denaturation of protein?
When environmental conditions exceed the limitations of a protein the secondary, tertiary and quaternary bonds are overcome (broken).
If the change is extreme the..
-The protein will no longer function
Damage can be permanent
What is keratin?
Structural protein for hair, wool, feathers, nails, scales, hooves, horns and skin.
It is very strong and water insoluble:
-long alpha-helix with hydrophobic amino acids
-Disulphide bonds, more S-S bonds the harder the structure
-Permanent wave (perm), is made by the reducing of disulphide bond and generation of new disulphide bonds
What are characteristics of lipids?
-Loosely defined group of molecules with one main chemical characteristic
-Insoluble in water
-High proportion of non-polar C-H bonds causes the molecule to be hydrophobic
-Doesn’t form polymers
-Good source of energy due to high C-H with 9kcal per g compared to carbohydrates’ 4kcal per g.
What are the 3 family of lipids?
1) Triglycerides
2) Phospholipids
3) Steroids
What are characteristics of triglycerides?
-Composed of one glycerol and three fatty acids
-The hydrocarbons chains of fatty acids vary in length (usually even-numbered chains of 14-20 carbons)
-The three fatty acids of a triglyceride are often very different from one another
-The many C-H bonds of fats serve as a form of long-term energy storage
What are characteristics of saturated triglycerides?
-No double bonds between carbon
-Higher melting point, animal origin
What are characteristics of unsaturated triglycerides?
-One or more double bonds
-Low melting point, plant origin
What are monounsaturated triglycerides?
Fatty acids with one double bond
What are polyunsaturated triglycerides?
Fatty acids with more than one double bond
What are cis fatty acids?
Most naturally occurring unsaturated fatty acids have double bonds with a cis configuration
What are trans fatty acids?
Fats that are partially hydrogenated (not natural). Trans fats have been linked to elevated levels of low-density lipoprotein (LDL) ‘’bad cholesterol’’ and lowered levels of high-density lipoprotein (HDL) ‘’good cholesterol.
What are trans fatty acids associated with?
An increased risk for coronary heart disease
What are phospholipids?
The molecule that composes the membranes of the cell (outer and inner membranes)
What are phospholipids composed of?
1) Phosphate group - hydrophilic (usually choline, ethanolamin, or serine)
2) Glycerol - forms the backbone of the phospholipid molecule
3) Fatty acids - two fatty acids attached to the glycerol backbone (hydrophobic)
True or false? Phospholipids are amphipathic?
True (that means they are both hydrophilic and hydrophobic)
What are micelles?
Lipid molecules orient with polar (hydrophilic) head toward water and non-polar (hydrophobic) tails away from water
Why is plasma membrane more fluid for unsaturated fatty acids?
They have double bonds between carbon atoms, which bend/kink in the fatty acid tails
Therefore, there is less packing between the fatty acids tails (this makes the plasma membrane fluid)
What is the function of steroids?
-Chemical signalling (hormones like testosterone)
-Have an impact on fluidity of plasma membrane (cholesterol)
What are steroids composed of?
4 carbon rings
What is cholesterol’s impact on fluidity of the plasma membrane (At body temp. And at lower temp)
At body temperature:
-Lower membrane fluidity
At lower temperature:
-Increase in membrane fluidity so that it doesn’t solidify
What are oligosaccharides?
Small chains of about three to ten monosaccharides linked together
What is the function of an oligosaccharide?
-Found on cell surfaces acting as identification markers
What are glycolipids?
Sugar on a lipid
What are glycoproteins?
Sugar on a protein
What are prokaryotic cells?
They have an outer plasma membrane but no internal membranes
What are eukaryotic cells?
Have extensive amounts of membranes, consisting of an outer plasma membrane and some internal membranes around the different organelles (endomembrane)
Why are cell membranes important?
Living cells are encased within a lipid membrane, which permit the physical separation between the inside of the cell (where biochemical reactions take place) and the outside of the cell.
The plasma membrane has selective permeability where the cell can generally control what goes in and out
In addition, eukaryotes have organelles, which membrane permit to further compartmentalize the biochemical reactions.
What are the 3 molecular constituents of the cell membrane?
1) Phospholipid bilayer
2) Protein (Transmembrane protein and interior protein network)
3) Surface markers (mainly carbohydrates)
What is the fluid mosaic model by Singer and Nicolson (1976)?
-A model of the plasma membrane where the proteins are inserted into the lipid bilayer, with their non-polar segments in contact with the non-polar interior of the bilayer (fatty acids tails) and their polar portions protruding out from the membrane surface
In this model, a mosaic of proteins floats in or on the fluid lipid bilayer
What are integral membrane proteins?
They are inserted into the phospholipid bilayer.
An integral protein that crosses the bilayer completely is called a _________ protein.
Transmembrane
What are peripheral membrane proteins?
They are attached to the surface of the phospholipid bilayer or to an integral protein
What are transmembrane domains?
-Protein region that is composed of hydrophobic amino acids, which anchor the protein to the membrane since the fatty acids of the phospholipids are also hydrophobic
How are integral membrane proteins usually arranged?
Into alpha-helices
(They can also be beta-sheet which form the pore through the membrane)
The primary difference in terms of integral membrane proteins lies in…….
The number of times that the protein crosses the membrane
(Ex: single transmembrane domains can be used to anchor the cytoskeleton to the cell)
Multiple transmembrane domains can be used as…
Cell-surface receptors for external molecules, such as the hormone
What do transporter proteins do?
Form channels or carriers to control movement of material in and out of the cell. Membrane are very specific at what goes in and out
What do potassium channels do?
Function to conduct potassium ions according o the concentration gradient. They are found in most cells, most notable neurons
What are aquaporins?
Water channel proteins that facilitate transport of water in and out of the cell
What are channel proteins?
Have a hydrophilic interior that provides an aqueous channel through which polar molecules can pass when the channel is open
What are carrier proteins?
Bind specifically to the molecule they assist to carry through the membrane (ions, sugars, amino acids, etc.)
True or false?
Both the channels and carriers are selectively permeable
True!
Both channels and carriers are usually selective for one type of molecule and thus the cell membrane is said to be selectively permeable
What are enzymes?
Protein involved in the catalytic reactions of chemical, lowering the activation energy
What is ATP synthase?
A protein present in the membrane of mitochondria that catalyzes the formation of the energy storage molecule Adenosine Triphosphate (ATP) using Adenoside Diphosphate (ADP) and inorganic phosphate (P)
What do cell surface receptors do?
Detective chemical messages (ex: insulin receptors allow glucose into the cell)
What do cell surface markers do?
Membranes have carbohydrates (usually oligosaccharides) on the outer surface and permit to ID a cell type and self.
What is cell-to-cell adhesion?
Binds cells together
What is an example of cell-to-cell adhesion?
Tight junctions in epithelial cells of the intestine prevent the content of your intestine to leak in between your cell. The absorption of nutrients is done by the selective permeability of the epithelial cells
What is attachment for proteins?
Anchor cells to the cytoskeleton and extracellular matrix
What do spectrins do (interior protein network)?
-Determines the shape of the cell
-Form supporting scaffold beneath membrane, anchored to both membrane and cytoskeleton
What do clathrins do ( interior protein network)?
-Anchor certain proteins to specific sites, especially on the exterior plasma membrane in receptor-mediated endocytosis
-Proteins line coated pits and facilitate binding to specific molecules
What is the function of the cell membrane?
-Allows some substances to move in and out of the cell but stops others (selective permeability)
-Transmits signals between intra and extracellular spaces
What are the 2 types of membrane transport?
1) Passive transport
2) Active transport
What are characteristics of passive transport (membrane transport)?
-Requires no energy
-Molecules move in response to a concentration gradient
(Simple diffusion,
Facilitated diffusion,
Osmosis)
What are characteristics of active transport (membrane transport)?
-Requires energy
-Can move substances from low to high concentration
What is simple diffusion?
The molecules will always disperse from a high concentration to a low concentration until all the solution reaches the same concentration
How does simple diffusion affect nonpolar molecules, very small polar molecules, small polar molecules and larger polar molecules and ions?
1) Nonpolar (such as steroids): will move until the concentration is equal on both sides
2) Very small polar: can also pass through the membrane (ex: O2 and CO2)
3) Small polar: limited permeability (ex: H2O)
4) Larger polar molecules/ions: very limited permeability
What is facilitated diffusion?
Molecules that cannot cross the membrane easily may move through proteins
What are 3 characteristics of facilitated diffusion?
1) Specific transport: only transport certain molecules or ions
2) Passive transport: move by diffusion from region of higher to lower concentration (no energy require)
3) Saturation: the transport protein can get saturated
What are the 2 types of facilitated diffusion?
1) Channel proteins
2) Carrier proteins
(Both carrier and channel proteins are usually selective for one type of molecule and thus the cell membrane is said to be selectively permeable)
Both the channel and carrier proteins can get saturated
What are channel proteins?
Have a hydrophilic interior that provides an aqueous channel through which polar molecules can pass when the channel is open
What are carrier proteins?
Bind specifically to the molecule they assist to carry through the membrane (ions, sugars, amino acids, etc.)
What are aquaporins?
Aquaporins open channels permit water to cross the plasma membrane according to concentration (osmosis)
What are ion channels?
-Ion channels allow the passage of ions through nonpolar interior of plasma membrane according.
-The channel pores, containing amino acids with hydrophilic side chains must be narrow enough to allow only ions with the appropriate size and charge to pass through the channel.
-Some are gated channels — open or close in response to stimulus (nerve impulse)
True or false? Ion channels have ion selectivity, permitting some inorganic ions to pass, but not others.
True
What is the relationship between concentration and rate of transport for carrier proteins? (Facilitated diffusion)
-Must bind to the molecule they transport, so the relationship between concentration and rate of transport differs from simple diffusion
-As concentration increases, transport by simple diffusion shows a linear increase in rate of transport. But when a carrier proteins is involved, a concentration increases means that more of the carriers are bound to the transported molecule.
-At high enough concentration, all carriers will be occupied, and the rate of transport will be constant. This means that the carrier exhibits saturation
What is osmosis?
The net diffusion of water across a selective membrane toward a higher solute concentration
How does osmosis work?
-When a selectively permeable membrane separates two concentrations of solutes but only lets water pass through the membrane but not the solute
-The side with higher solute concentration has tied up more water molecules in hydration shells and thus has fewer free water molecules
-Thus, the high amt of free water (low solute) moves towards hte lower amt of free water molecule (high solute concentration)
What is osmolarity of solutions? (3)
-Hypotonic solution: the solution has a lower solute concentration than the cell
-Isotonic solution: the solution has the same solute concentration than the cell
-Hypertonic solution: the solution has a higher solute concentration than the cell
What is an example of hypotonic solution?
A red blood cell placed in a hypotonic solution (such as distilled water) will have a higher amount of solutes (salt) inside the cell than the pure distilled water (no salt).
Since the cell has a selectively permeable membrane, water will rush into the cell. The cell can bust
What is an example of isotonic solution?
A red blood cell placed in an isotonic solution will not have any osmotic pressure
What is an example of hypertonic solution?
A red blood cell placed in a hypertonic solution will lose its water (bc it has a higher solute concentration than the cell)
What is osmoregulation and turgor pressure?
Osmoregulation: how some organisms maintain osmotic balance
Turgor pressure: plant cells use turgor pressure to push the cell membrane against the cell wall and keep the cell rigid, thus blocking entry of too much water and giving the plant their rigidity.
What is extrusion?
Excess water is collected and ejected from the cell through contractile vacuoles in some protists (paramecium)
What is isosmotic regulation?
Some organisms that live in the ocean adjust their internal concentration of solutes to match that of the surrounding seawater. Because they are isosmotic with respect to their environment, no net flow of water occurs into or out of these cells.
How do terrestrial animals do isosmotic regulation?
Circulating a fluid through their bodies that matches cells in an isotonic solution. The blood in your body, for example, contains a higher amount concentration of the high albumin, which elevates the solute concentration of the blood to match that of your cells’ cytoplasm.
Why don’t cells of prokaryotes, fungi, plants, and many protists need to maintain osmotic balance?
They are surrounded by strong cell walls, which can withstand high internal pressures without bursting
How does active transport work?
-Move substances from a region of lower concentration to a region of higher concentration across a membrane against a concentration gradient
-Requires an energy source, often under the form of adenosine triphosphate (ATP).
-Requires the use of carrier proteins
-The carrier proteins can get saturated
What are the three types of active transport protein?
1) Uniport: transports one substance in one direction
2) Symport: Transports two different substances in the same direction
3) Antiport: Transports two different substances in opposite directions
What are the 2 types of active transport?
-Primary active transport: Energy (ATP) is used to transport a chemical, for example sodium (Na+), outside the cell against its concentration
-Secondary active transport: The passive movement of one solute with its concentration gradient (diffusion of Na+) induce the movement of another solute (glucose) against its concentration gradient
Energy i. Used indirectly to establish a concentration gradient (Na+) resulting in movement of the second solute (glucose)
What are the 2 types of transport (bulk transport)?
Endocytosis: movement of bulk substances into the cell
Exocytosis: movement of bulk materials out of the cell
Note: endocytosis does not bring the substance directly into the cytoplasm of a cell. The material taken in is still separated from the cytoplasm by the membrane of the vesicle
When does endocytosis occur?
When the plasma membrane envelops food particles and/or liquids to bring them into the cell. Like active transport, endocytosis requires energy to work
What are the 3 types of endocytosis?
1) Phagocytosis: the material the cell takes in is particulate (made up of discrete particles), such as an organism or some other fragment of organic matter.
2) Pinocytosis: The material the cell takes in is dissolved substances or fluids
3) Receptor-mediated endocytosis: these molecules first bind to specific receptors in the plasma membrane - they have a conformation that fits snugly into the receptor. It acts like a molecular mousetrap, closing over to form an internal vesicle
When does exocytosis occur?
When material is discharged from the cell
Vesicles in the cytoplasm fuse with the cell membrane and release their contents to the exterior of the cell
-Used indirectly plants to export cell wall material
-Used in animals to secrete hormones, neurotransmitters, digestive enzymes and expel waste.
What are enzymes?
Enzymes are macromolecules (generally proteins, but sometimes RNA) that catalyze the biological reactions within the cell by lowering the activation energy
The unique three-dimensional shape of an enzyme enables the reaction by… (2)
-Bringing two substrates together in the correct orientation to lower the activation energy required to form bonds (anabolism)
-Stressing particular chemical bonds of a substrate to lower the activation energy required to break the bonds (catabolism)
True or false? The enzyme is changed/consumed in the reaction.
False, it is not changed or consumed in the reaction, so only a small amount of an enzyme is needed, and it can be used repeatedly
Which suffixes generally indicate that a molecule is an enzyme?
‘’-ase’’ or ‘’-zyme’’
What are ribozyme?
-Non-protein enzymes made of RNA
-They have catalytically active segments of RNA
-Not necessarily in ribosome (even if it sounds similar)
What can ribozymes do?
-catalyze the dehydration synthesis of peptide bonds in ribosome
-They can also be used to cleave RNAs
What is peptidyl transferase?
A ribozyme that forms peptide bonds between adjacent amino acids
What do catabolic enzymes and anabolic enzymes do?
Catabolic enzymes: breakdown molecules
Anabolic enzymes: build molecules
(Note: they both need activation energy to work)
What is induced fit (for enzymes)?
The enzyme will adjust its shape slightly to properly bind to the substrate forming the enzyme-substrate complex
What happens to the products when a reaction is complete?
They dissociate (detach from the enzyme)
(Note: the enzyme is uncharged after the rxn and can thus be reused)
How do enzymes lower activation energy?
During the enzymatic rxn, the side chain of the enzyme protein interacts chemically with the substrates, usually stressing or distorting a particular bond and consequently lowering the activation energy needed to make or break the bond
After the bonds of the substrates are broken, or new bonds are formed, the substrates…
Have been converted to products
Are enzymes specific to their substrates?
Yes, their specificity is determined by the active site
How does citrate form?
The methyl of acetylene CoA needs to form a covalent bond with the carbon atom of the carbonyl group of oxaloacetate.
The active site of the enzyme citrate synthase permits these groups (methyl and carbonyl) to be adjacent to each other and react
How does lysozyme destroy bacteria?
By cleaving/hydrolysing peptidoglycans in their cell walls
The active site of the lysozyme stretches the bonds between the glycan monomers
The bonds between the glycans become more unstable due to stretching and can be more reactive to water, breaking the bonds (hydrolysing, cutting with water)
What are cofactors?
-One or more non-protein components required by enzymes in order to function
-Can be an inorganic metal ion (Zn, Fe, Mg, Ca) or organic molecule (coenzyme)
What are coenzymes?
A non-protein organic molecule that plays an accessory role in enzyme-catalyzed processes, often by acting as a donor or acceptor of electrons
-usually not permanently found to the enzymes
-they enter into the rxn as a ‘’co-substrate’’, as they are changed by the rxn and released from the enzyme
What is an example of coenzymes?
-Vitamin B6 and B12
-Nucleic acid such as NAD (nicotinamide adenine dinucleotide) is a coenzyme involved in the respiration process (transfer electrons and protons).
How do electrons get transferred between enzymes and coenzymes?
The electrons pass in pairs from the active site of the enzyme to a coenzyme that serves as the electron acceptor. The coenzyme then transfers the electrons to a different enzyme, which releases them (and the energy they bear) to the substrates in another reaction
What are enzyme inhibitors?
Chemicals that bind to enzymes which slow down the rate of rxn being catalyzed/reduce the rate of an enzymatic rxn (or stopping it)
What are enzyme activators?
Bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme’s active site(s) for its substrate(s)
What are the 2 ways that enzyme inhibition occurs?
-Competitive inhbitors
-Non-competitive inhibitors
How does competitive inhibition occur?
The inhibitor competes with the substrate for the same active site, occupying the active site and thus preventing substrates from binding
What is reversible inhibition?
The non-covalent binding of inhibitors to the active sites of enzymes is not permanent and after a moment it dissociates with the active site
How can competitive inhibition be reversed?
Adding mo substrate than their inhibitors, since the chance the enzyme will encounter the substrate is greater than the inhibitor
How does non-competitive inhibition occur?
Bind to the enzyme in a location other than the active site (allosteric site), changing the shape of the enzyme and making it unable to bind to the substrate
-This is called an allosteric inhibitor
What do allosteric activators do?
Bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme’s active site(s) for its substrate(s).
How does enzyme velocity relate to the concentration of substrate?
Enzyme velocity is the speed at which the enzyme catalyzes the rxn
-At low substrate concentration, the initial velocity rises almost linearly with substrate concentration
-But when the substrate concentration reaches a certain level, enzyme velocity plateaus
-The plateau represents the maximum velocity of the rxn, designated Vmax
-At Vmax, the enzymes are saturated with substrate and thus cannot go faster
(Note: this is for a fixed concentration of enzyme)
How does the presence of competitive inhibitors affect enzyme velocity?
It takes a higher substrate concentration to achieve the same velocities that were reached with sufficient substrate available
How does non-competitive inhibition affect enzyme velocity?
Enzyme molecules that have been bound by the inhibitor are taken out of the game so enzyme rate (velocity) is reduced for all values of substrate concentration
What are biochemical pathways?
There are thousands of different enzymes that catalyze a variety of reactions
Many of these rxns in a cell occur in sequences called biochemical pathways
In such pathways, the product of one reaction becomes the substrate for the next
What are the organizational units of metabolism?
Biochemical pathways
What are multienzyme complexes?
Made up of several enzymes attached together
These are groups of related enzymes speed up sequential steps within the same biochemical pathways
What are benefits of multienzyme complexes?
-The product of one rxn can be directly delivered to the next enzyme (little drifting)
-Unwanted side-rxns are eliminated
-Makes controlling the pathway easier since pathway can be controlled as a unit
What is feedback inhibition and regulation of biochemical pathways?
-For a biochemical pathway to operate efficiently, its activity must be coordinated and regulated by the cell
-Prevents synthesizing a compound when plenty is already present (save energy and materials)
-The regulation of simple biochemical pathways often depends on an elegant feedback mechanism
-The product of the pathway binds to an allosteric site and inhibits one of the previous enzymes in the pathway. This mode of regulation is called feedback inhibition
What is the rate of an enzyme-catalyzed reaction affected by?
Concentration of both the substrate and the enzyme that works on it
-Chemical or physical factors that alters the enzyme’s three-dimensional shape — such as temperature, pH, and the binding of regulatory molecules — can affect the enzyme’s ability to catalyze the rxn
How does pH affect enzymes?
-Change in pH can alter enzyme activity, where enzyme activity is the highest at a specific pH (optimal pH) and declines at a lower or higher pH.
-pH has an effect on the 3D structure of an enzyme by, for example, perturbing ionic interactions between oppositely charged amino acid residues (ionic bonds)
-Enzymes have an optimum pH that usually ranges from pH 6 to 8 in the human body, however certain enzymes are adapted low pH such as pepsin in the stomach
What are extremophiles?
Certain organisms that have evolved to sustain extreme conditions
What does photosynthesis do?
Uses energy absorbed from sunlight to combine small molecules (water and carbon dioxide) into complex organic molecules (sugars)
Energy from sunlight is stored as ______ energy in the ______ bonds between atoms in the organic molecules (sugar)
(FOR PHOTOSYNTHESIS^)
1) Potential energy
2) Covalent
What is energy?
The capacity to do work
What are the 2 states of energy?
1) Potential: stored energy (physical, chemical)
2) Kinetic: energy of motion
What is the first law of thermodynamics?
Law of conservation of energy states that energy is not created nor destroyed, simply transformed
What is the second law of thermodynamics?
Energy cannot be transformed with 100% efficiency and the unavailable energy manifests as an increase in randomness or disorder, which is named entropy
All rxns in the universe will tend to go from ______ to ________
(ENTROPY QUESTION)
1) ordered
2) disordered
Meaning that order is a much less stable state than disorder
(Order requires more energy to produce than disorder)
What is G (Gibb’s free energy)?
Free energy (energy available to do work)
Reactions that require G (Gibb’s free energy) to be carried out are called…
Endergonic
Note:positive deltaG = products have more free energy than reactants. Not spontaneous (requires input of energy) and is endergonic
Reactions that release G (energy in the bonds of products is lower than energy in bonds of reactants) are called…
Exergonic
Note: negative deltaG = products have less free energy that reactants, spontaneous (may not be instantaneous) and is exergonic
Because of the 2nd law of thermodynamics, exergonic reactions will happen ________ because….
1)Spontaneously
2) they increase disorder and endergonic will not, as they increase order
What is oxidation and reduction?
Oxidation: process by which an atom or molecule that loses an electron is said to be oxidized
Reduction: process by which an atom or molecule that gains an electron is said to be reduced
What is activation energy?
The energy required to destabilize existing bonds in order to start a chemical reaction
True or false? Rate of exergonic reactions is independent on the activation energy required
False
Rate can be increased in 2 ways…
1) increasing energy of reacting molecules (heating)
2)lowering activation energy (catalyst: enzyme)
What are catalysts?
Substances that influence chemical bonds in a way that lowers activation energy. Catalyst are not consumed in the rxn
What are the 2 types of metabolism?
1) Catabolic rxns (catabolism): chemical rxns that harvest energy by breaking down molecules
2) Anabolic rxns (anabolism): chemical rxns that use energy to build up molecules
What is ATP?
Adenosine Triphosphate
-Primary energy currency used by cells
-Created by catabolism
-Composed of ribose (five carbon sugar), adenine, and a chain of three phosphates.
-Key to energy storage
-PO4 groups are highly negatively charged and strongly repel each other
-Bonds between PO4 are thus unstable, release energy when broken
-ATP have low activation energy
Why is ATP not suitable for long-term energy storage?
-Phosphate bonds are too unstable
-Fats and carbohydrates better to store energy
-Cells store only a few seconds worth of ATP
ATP hydrolysis drives ________ rxns
Endergonic
What are characteristics of carbohydrates?
-Molecules with a 1:2:1 ratio of carbon, hydrogen, oxygen
-Empirical formula of C1nH2nO1n
-C—H covalent bonds holds energy and thus carbohydrates can be used to store energy
What are monosaccharides?
One sugar
-Monomer of carbohydrates that is composed of 3 to 7 carbons
-The majority of monosaccharides have 5 to 6 carbons and have a cyclic form in aqueous solution
Monosaccharides, especially _____, are an essential source of ______ in the cells during processes of respiration and fermentation
1) Glucose
2) Energy
What are disaccharides?
Two monosaccharides linked together
(Synthesis of disaccharides by dehydration (2 hydroxyl groups), which makes it possible to make a covalent bond (called a glycosidic bond))
What are oligosaccharides and what is their function?
Small chains of about three to ten monosaccharides linked together
-Found on cell surfaces acting as identification markers
What are polysaccharides and what are their functions?
Long chains of more than ten monosaccharides linked together
-Energy storage: plants use starch, animals use glycogen
-Structural support: plants use cellulose, arthropods and fungi use chitin
When alpha glucose forms a polymer it creates _____
Starch
Note: you have an enzyme that can break down the alpha glycosidic bond of starch
When beta glucose forms a polymer, it creates ______
Cellulose
Note: you don’t have the enzyme that can break the beta glycosidic bond of cellulose. Thus, you cannot digest it and access the glucose sugar
How are polysaccharides linked together?
Unbranched chain linkage occurs between the carbon 1 (C-1) of the glucose molecule and the C-4 of another, making them at 1->4 linkages
Branched chains linkage occurs between the carbon 1 (C-1) of one glucose molecule and the C-6 of another, making them at 1->6 linkages Branched chains
What are autotrophs?
Organisms that produce complex organic compounds using carbon from simple substances such as carbon dioxide and a source of energy
What are photoautotrophs?
They use photosynthesis to gather energy from light
What are heterotrophs?
They use organic molecules produced by autotrophs or other heterotrophs as a source of energy
Most (but not all) of the ATP is produced in the ______
Mitochondria
Energy metabolism is based on _____ reactions
Redox
(to understand the process of energy metabolism, we must follow the fate of the electrons lost from the food molecules)
Note: these rxns are not the simple transfer of electrons, they are also usually dehydrogenations
What is respiration?
The process by which energy is harvested. The oxidation of compounds to extract energy from chemical bonds.
For respiration, energy must be converted from the nutrients ingested by the organism to ___
ATP
One of the main metabolites used by organisms for the production of ATP is ______
Glucose
About how much of your water needs are created by your own metabolism?
8-10%
During aerobic respiration, glucose is oxidized to ___
CO2
True or false? In respiration, during each transfer of electrons, energy is released.
True
When NAD+ acquired 2 electrons and 1 proton from the active site of the enzyme, t is reduced to…
NADH
What is the final electron in the following:
1) Aerobic respiration
2)Anaerobic respiration
3) Fermentation
1) Oxygen
2) Inorganic molecules other than O2
3) Organic molecules
What is substrate-level phosphorylation?
ATP is formed by transferring a phosphate group directly to ADP from an organic substrate containing a phosphate.
During glycolysis, the initial breakdown of glucose the chemical bonds of glucose are shifted around in reactions that provide the energy required to form ATP by substrate-level phosphorylation
What is oxidative phosphorylation?
ATP is synthesized by the enzyme ATP synthase, using energy from a proton (H+) gradient
-This gradient is formed by high-energy electrons from the oxidation of glucose passing down an electron transport chain
-These electrons, with their energy depleted, are then donated to oxygen, hence the term oxidative phosphorylation (for aerobic respiration)
In eukaryote, pyruvate oxidation occurs inside the (…) after transport of pyruvate in the mitochondria via the ______________ pyruvate translocase from the ____.
1)Mitochondrial matrix
2) transport protein/enzyme
3) cytosol
Since you have 2 pyruvates that are produced by glycolysis, you will have a total of (…) at the end of pyruvate oxidation
2x CO2
2x NADH
2x Acetyl CoA
The oxidation of pyruvate is carried out by the pyruvate _________ enzyme complex in _ steps.
1) dehydrogenase
2) 3
How does oxidative phosphorylation work? (Generally)
NADH and FADH2 associate with the electron transport chain on the inner membrane of the mitochondrion.
The electron transport chain uses the electrons energy from NADH and FADH2 to pump the H+ from the matrix to the inter-membrane space (proton motor force)
What is an electron transport chain?
(Oxidative phosphorylation)
A series of electron carrier protein complexes (I to IV) that accomplish a series of redox rxns
What is the first rxn in oxidative phosphorylation?
Electrons from the carriers are passed through the electron transport chan.
-The first rxn is where NADH passes its electron to NADH dehydrogenase (I).
-A series of redox rxns will generate energy whereby NADH dehydrogenase will pump one proton (H+) into the inner membrane space.
FADH2 will give their electrons to complex __, Which will transfer them to _______ (Q)
(Oxidative phosphorylation)
1) II
2) Ubiquinone
Ubiquinone (Q) will transport the electrons coming from complex _ and __ to __ complex (__), which will pump the H+ from the matrix to the intermembrane space
(Oxidative phosphorylation)
1) I
2) II
3) bc1
4) III
After bc1, ________ (Cyt c) carries electrons to the _____________ complex (IV) (much like ubiquinone) where the H+ will pump to the inter-membrane space
(Oxidative phosphorylation)
1) cytochrome c
2) cytochrome oxidase
In aerobic respiration, the final electrons acceptor is ____, which combine with hydrogen to produce ___
1) oxygen
2) water (H2O)
The protons (H+) that have been pumped in the inter-membrane space using the electron transport chain, will re-enter the …… using the protein ATP synthase because a ____ ______ has been formed
1) mitochondrial matrix
2) concentration gradient
The energy released by the transport of __ allows for the formation of ___ and ____ and __
This is specifically known as __________
(Oxidative phosphorylation)
1) H+
2) ADP
3) ATP
4) Pi (inorganic phosphate)
5) chemiosmosis
The combined processes of the electron transport chain and chemiosmosis are known as ___________
Oxidative phosphorylation
What is the total yield for aerobic respiration? (Total amt of ATP for eukaryote)
1 glucose yield 32 ATP, but in eukaryote 1 ATP per NADH is needed to transport the NADH produced by glycolysis in the mitochondrion
-Eukaryotes aerobic respiration 1 glucose will yield a total of 30 ATP
How does regulation of aerobic respiration occur?
When ATP levels are high, cells do not need to be generating large amounts of ATP by cellular respiration
-ATP production is controlled via a negative and positive feedback loop of the multienzyme complexes
Some of the product of the respiration process, ATP and citrate, can become an ______ of phosphofructokinase in glycolysis. While the NADH can become an _____ of pyruvate dehydrogenase in the ________ step.
(Regulation of aerobic respiration)
1) inhibitor
2) inhibitor
3) pyruvate oxidation step
ADP is an ____ of phosphofructokinase of glycolysis, which makes the enzyme sensitive to levels of both ___ and ___.
1) Activator
2) ADP
3) ATP
During anaerobic respiration, the protons and electrons are combined to…
An element other than oxygen
What is the role of NAD+?
The cell transfers electrons and protons to it
Fermentation uses organic matter to dump the proton and electron and regenerate ____
NAD+
What happens if there is no oxygen? (Aerobic respiration/fermentation)
Many organisms in the absence of oxygen (or other inorganic electron acceptors) can use organic compounds as electron acceptors
Therefore, allowing for the recycling of NADH to NAD+.
When fermentation occurs, only ______ is used as an energy/ATP generation mechanism.
Glycolysis
If you exercise too intensely, your muscle can run out of oxygen and go into ____ fermentation process to keep giving you energy (for a short time)
Lactic
