Biology 1107 Exam 1
Describe 4 ways carbon skeletons may vary, and explain how this variation contributes to the diversity and complexity of organic molecules.
Covalent bonds link carbon atoms together in long chains that form the skeletal framework for organic molecules. These carbon skeletons may vary in: -Length -Shape -Number and Location of double bonds -Other elements covalently bonded to available sites
List four conditions under which proteins may be denatured.
1 Extreme heat 2. high or low pH 3. ionization of liquid medium 4. A change in environment. The last one needs a little more explanation. If a protein is meant for a liquid-liquid environment, and it is brought into an air-liquid environment, it may denature. Proteins form because of the folds created from hydrophilic and hydrophobic folding. If there is no water in which these bonds form, the protein will denature.
Distinguish between a protein and a polypeptide.
1. A polypeptide is a linear polymer of amino acids, linked together by peptide bonds. 2. Proteins are functional entities composed primarily of one or more polypeptides and often non-polypeptide cofactors. A protein without its co-factors is known as an apoprotein.
List four characteristics of water that are emergent properties resulting from hydrogen bonding.
1. Cohesive 2 Adhesive 3. Denser as a liquid than as a solid 4. Able to absorb large amounts of energy
What three things can an open system exchange with the environment?
1. Information 2. Energy 3. Materials
What two things does energy have to do to be a thermodynamic system?
1. The thermodynamic system uses energy to create itself 2. The thermodynamic system must make room for itself by displacing it's environment and establishing its volume and pressure.
List and describe the four major components of an amino acid. Explain how amino acids may be grouped into 4 groups according to the physical and chemical properties of the R group.
1. amino group, 2. hydrogen 3. R group 4. carboxyl group (1) non-polar and neutral, (2) polar and neutral, (3) acidic and polar, (4) basic and polar.
Name the products of the dissociation of water and give their concentration in pure water.
2 H2O OH− + H3O+ H3O^+1 = hydronium ion OH^-1 = hydroxide ion Concentration in pure water 1x10^-7 mol/L
Explain how you would make up a one molar (1M) solution of ethyl alcohol.C2H6O.
2 carbons - 24 grams, 6 hydrogens, 6 grams, 1 oxygen, 14 grams, 24 + 14 + 6 = ethanol has a molar weight of 44. Ethanol is 0.789 grams per milliliter, so 55.8 milliliters of ethanol in 1 liter of water will create a 1 molar solution of ethanol.
Define electronegativity.
A chemical property that describes the tendency of an atom or a functional group to attract electrons (or electron density) towards itself.[1] An atom's electronegativity is affected by both its atomic number and the distance that its valence electrons reside from the charged nucleus. The higher the associated electronegativity number, the more an element or compound attracts electrons towards it.
Distinguish between each of the following pairs of terms: a. Neutron and proton
A neutron has a neutral charge and a proton has a positive charge. A neutron has slightly more mass than a proton.
Distinguish between nonpolar covalent, polar covalent and ionic bonds.
A nonpolar covalent bond is a bond where electrons are shared equally between two atoms. A polar covalent bond is a chemical bond where the shared electrons spend more time closer to the nucleus of the more electronegative atom. In an ionic bond, the electrons are completely transferred from one atom to another rather than shared.
Distinguish between b. nucleotide and nucleoside
A nucleoside contains a nitrogenous base and a sugar. A nucleotide is a nucleoside, plus the phosphate group that comprises the "backbone" of DNA.
Describe the mechanisms by which enzymes lower activation energy
ALL enzymes lower the activation energy by lowering the potential energy(stabilizing) of the transition state. The electrons in a transition state can be stabilized by the enzyme when they interact with another ion, atom, or molecule. Some but not all enzymes catalyze reactions by providing an alternate mechanism for the reaction, a new, lower energy pathway. In this case the enzyme produces intermediate(s) (that is eventually used up) to synthesize a product. For example: Substrate + enzyme --> C C + B --> product + enzyme C represents an intermediate, B is a another substrate Then again only some enzymes provide alternate mechanisms, but ALL enzymes stabilize transition states.
What is a buffer? In your explanation, use as a model acetic acid and acetate in solution
Acetic acid and acetate maintain a pH equilibrium. Acetic acid is an acid and acetate is a base. The two function together as a buffering system. CH3COOH <==> CH3COO- + H2 When the concentration of protons increases slightly, the protons react with acetate ions to form acetic acid and pH does not change. If the concentration of protons decreases slightly, acetic acid gives up protons and pH stays the same
If you place a paper towel so that it touches spilled water, the towel will draw in the water.
Adhesion
Describe and draw the basic structure of the Amino functional group and outline the chemical properties of the organic molecules in which they occur.
Amines act as a base, they tend to attract a proton in solution, form with carboxyls to make amino acids
Name the 6 major functional groups found in organic molecules. ACCHPS
Amino, Carbonyl, Carboxyl, Hydroxyl, Phosphate, Sulfhydryl
`Explain how a peptide bond forms between two amino acids.
An amino acid links with another amino acid through a condensation reaction to form a peptide bond A peptide bond (amide bond) is a covalent chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, causing the release of a molecule of water (H2O), hence the process is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acid
Identify an ester linkage and describe how it is formed.
An ester linkage is the bonding between fatty acids and glycerol that characterizes true fats. It is formed by dehydration synthesis (when two small molecules join together by removing H2O)
Distinguish between an isolated and an open system. Explain why an organism is considered an open system.
An isolated system is a physical system without any external exchange. It's total energy and mass stay constant. An open system is a system which continuously interacts with its environment. The interaction can take the form of information, energy, or material transfers into or out of the system boundary, depending on the discipline which defines the concept (see below). An open system should be contrasted with the concept of an isolated system which exchanges neither energy, matter,nor information with its environment.
Explain how substrate concentration affects the rate of an enzyme-catalyzed reaction.
As the concentration of substrate increases, the rate of reaction also increases until the point saturation occurs. It means as you increase the concentration, rate keeps increasing and then one point comes when the maximum rate is achieved and there is no free enzyme to bind with substrate and all the active sites of enzyme are bound to the substrate. So after that point, increasing the concentration wont have any effect.
Explain how weak interactions and disulfide bridges contribute to tertiary protein structure.
As you know that hydrogen bonding aids the formation of the secondary structures. Once these structures are formed (ie alpha helix, beta-sheet, beta-turn), the R groups now can interact with other R groups. In the tertiary structure, the weak interactions (ie hydrogen bonding, ionic bonding, van der waals interactions) aid in the 3D structure of the protein. Disulfide bonds form in the tertiary structure which add extra stability to the overall 3D shape of the protein.
atomic number
Atomic number is only the number of protons in the nucleus of the atom, giving the atom it's identity as a particular element
How Many Bonds Can an Atom Have?
Atoms with more than one unpaired electron can form multiple single bonds with multiple atoms or double or triple bonds with a single atom.
Compare and contrast the structure of DNA vs. RNA.
DNA Double stranded no OH at the 2' end which is why it is deoxyribonucleic found in the nucleus contain thymine RNA single stranded OH presence ...ribonucleic acid found in the nucleus and ribosomes contains uracil DNA and RNA both essential in living organisms both replicate from 5'----------------------3' DNa represents the genetic materia....and RNA represents the protein make up of the body
Briefly describe the three-dimensional structure of DNA
DNA is double helical in structure. each spiral strand, composed of a sugar phosphate backbone and attached bases, is connected to a complementary strand by hydrogen bonding (non- covalent) between paired bases, adenine (A) with thymine (T) and guanine (G) with cytosine (C).
The Double Helix contains antiparallel strands of DNA. What does antiparallel mean in this context?
DNA is made of antiparallel strands, meaning that while one strand runs from 3' to 5', its complementary strand (the other half of the double helix, in other words) runs from 5' to 3'. The two strands are "parallel", but running in opposite directions. By way of analogy, you could say that the northbound lane and southbound lane of a major interstate are antiparallel.
ΔH > 0 or change in enthalpy is positive, is reaction endothermic or exothermic?
Endothermic, because it gained energy, energy was put into it.
What is enthalpy?
Enthalpy is a measure of the total energy of a thermodynamic system
ΔH < 0 in other words, change in enthalpy is negative. Is reaction endothermic or exothermic
Exothermic, because it lost energy, therefore the energy was given off.
Explain the first and second laws of thermodynamics in your own words.
First -- energy cannot be created or destroyed, but can be transformed from a more useful form to a less useful form, such as from wood to smoke and ashes Second -- Energy moves towards entropy -- the potential energy of a system will be less than the initial energy, if there are no inputs of energy.
Define heat of vaporization
Heat of Vaporization-the amount of heat required to convert unit mass of a liquid into the vapor without a change in temperature.
Humans sweat and dogs pant to cool themselves on hot days.
High specific heat Water absorbs latent heat in order to evaporate, and this absorption of heat causes a cooling for sweating humans and panting dogs.
What does ΔG stand for?
How much energy, both mechanical and heat, that was either added to or subtracted from a system.
Name two types of secondary protein structure. Explain the role of hydrogen bonds in maintaining secondary structure.
Hydrogen bonding between the carbonyl oxygen of one amino acid residue and the hydrogen on the amino group of another. Two types are: 1. ά-helix Formed from Hydrogen Bonds There are 3.6 amino acid residues per turn of the helix. Notice the regular helix shape. This is drawn as a helix that follows the -N-C-C-N-C- backbone of the polymer Alpha helices are often the basis of fibrous polymers (see below). The Alpha helix was first discovered by Linus Pauling. Right handed helix.
Describe and draw the basic structure of the Hydroxyl functional group and outline the chemical properties of the organic molecules in which they occur.
Hydroxyl groups act as weak acids. Highly polar, molecules with hydroxyl groups are soluble. Defining functional group of alcohols such as ethanol and methanol
What is the significance of an atoms valence in the construction of molecules and compounds?
If the valence shell of an atom is filled, the element is stable and less likely to form a chemical bond with another atom. If the valence (outer) shell of an atom is missing one or more electrons, it is likely to fill those shells by sharing electrons with other atoms that also have unfilled valence shells.
Explain why metabolic disequilibrium is one of the defining features of life.
If there was metabolic equilibrium, no work would be able to be performed, no energy would be transferred, and life would not be possible. Thus metabolic disequilibrium. This can be expressed as a ΔG of zero
Distinguish between exergonic and endergonic reactions in terms of free energy change.
In an exergonic reaction, energy leaves the system and the reaction is spontaneous, ΔG is negative. In an endergonic reaction, ΔG is positive -- energy was added to the system and it is not spontaneous. If ΔG is zero, the equation is in equilibrium
Distinguish between the glycosidic linkages found in starch and cellulose. Explain why the difference is biologically important.
In starch the linkage is alpha (1-4) and in cellulose is beta (1-4) linkage. Animals have the enzyme to digest alpha linkage but not beta linkages. so that explains why we cant digest cellulose. Animals like cows can because they have bacteria that help digest it. whenever we say alpha it means the OH group (Carbon 1) is on the opposite side of the OCH3 group (Carbon 6) which is pointing down. Beta just means theyre both on the same side with OH pointing down.
Explain how carbon's electron configuration explains its ability to form large,complex and diverse organic molecules.
It has four valence electrons which can form many covalent bonds, of different combinations of single and double bonds,and multiple carbon atoms can form long chains such as gasoline.
Describe the formation of a glycosidic linkage
It's the bond that forms between two monosaccharides (sugars) when larger carbohydrates (disaccharides and polysaccharides) are synthesised. It involves the reaction of two -C-OH groups, producing water, and a -C-O-C- bond. This -C-O-C- bond is called the glycosidic link. The formation of the glycosidic link is known as a condensation reaction, because water is formed.
How does water's cohesion and adhesion contribute to the movement of water from the roots to the leaves of a tree.
The cohesion of water allows a long string of water molecules to be hydrogen bonded to all the way from the roots to the leaves in a long train of water molecules. Adhesion helps this process with capillary action, where the water that is attracted to the side of the of the xylem vessels, which allows other water molecules to move further up. Finally, transpiration acts as a water "pump" against gravity, by having water molecules evaporate out through the stomata on the leaves of plants, and this evaporation action pulls the chain of water molecules up behind it.
Describe the basic structure of the Phosphate functional group and outline the chemical properties of the organic molecules in which they occur.
Phosphate groups carry two negative charges and they go from one molecule to another, the two negative charges often greatly affects the receiving molecule When several phosphate groups are linked together, breaking O-P bonds between them releases large amounts of energy.
Distinguish between kinetic and potential energy
Potential energy is stored energy; kinetic energy is energy in motion that is doing work.
Explain what determines protein structure and why it is important.
Protein structure is determined first by the gene that codes for that protein, and then by non-covalent interactions such as hydrogen bonding, ionic interactions, Van Der Waals forces, and hydrophobic packing. Proteins serve many different functions because they are diverse in size and shape -- form follows function.
Explain the role of catabolic and anabolic pathways in cellular metabolism.
Reactions that break down molecules and produce ATP are called catabolic pathways. Reactions that synthesize larger molecules from smaller components are called anabolic pathways.
Distinguish between ribose and deoxyribose
Ribose is a single-ring pentose [5-C] sugar. The numbering of the carbon atoms runs clockwise, following organic chemistry rules. Note the absence of the hydroxyl (-OH) group on the 2' carbon in the deoxy-ribose sugar in DNA as compared with the ribose sugar in RNA
Explain why strong covalent bonds and weak bonds are both essential in living organisms.
Strong covalent bonds are needed for living organisms so that organism bodies can form and hold together and not fall apart. Water is made of weak hydrogen bonds, which make it a solvent, and water is needed for life to dissolve nutrients for ingestion or wastes for excretion, to transport important chemicals or even be used as one.
Explain how the atomic number and mass number of an atom can be used to determine the number of neutrons
Subtract atomic number from mass number and you will have the number of neutrons
Describe and draw the basic structure of the Sulfhydryl functional group and outline the chemical properties of the organic molecules in which they occur.
Sulfhydryl groups are a sulfur atom bonded to a hydron atom, they link up with disulfides S-S bonds. In proteins, they form disulfide bonds that contribute to protein structure
Explain how temperature, pH, cofactors, and enzyme inhibitors can affect enzyme activity.
Temperature affects enzyme activity because enzymes are made of proteins and as the temperature raises, the protein's molecular structure will be more and more unstable until it denatures and breaks apart. The pH works essentially the same where the enzyme will denature if it is in too acidic or too basic of an environment. Cofactors are molecules that will fit into the active site of an enzyme and active/deactivate. Enzyme inhibitors are little molecules that will fit into an enzyme and prevent the cofactor from reaching it and activating it.
What is the difference between "heat" and "temperature?" Give examples.
Temperature is an intensive property, measured in degrees, while heat is an extensive property measured in BTU's. An intensive property is not dependent on the amount of substance present -- water boils at a temperature of 100 degrees, whether it's a gallon or a million gallons. Heat is an extensive property, measured in BTU's. it is the amount of heat energy required to increase the temperature of 1 pound of water from 3.8 degrees to 4.4 degrees Celsius.
Insects like water striders can walk on the surface of a pond without breaking the surface.
The cohesive property of water -- the tendency of water to be attracted to water, makes the top layer of water molecules that don't have any water above them are pulled inward to other molecules, so when a water strider steps on water, the force of the top layer of water coheres to itself and resists the foot of the water strider from separating water molecules from each other.
If you slightly overfill a water glass, the water will form a convex surface above the top of the glass.
The cohesive property of water -- the water at the top of the overfilled glass is more attracted to the the water than to the side of the glass, creating a convex meniscus.
Describe the electron-sharing continuum
The degree to which electrons are shared in chemical bonds forms a continuum, from equal sharing in nonpolar covalent bonds, to unequal sharing in polar covalent bonds, to the transfer of electrons in ionic bonds.
Draw and label a simplified model of an atom. Explain how this model misrepresents our understanding of atomic structure
The electrons don't actually go around in a circular orbit, but rather they appear in places around the nucleus that can be predicted with probability.
Ice floats on water.
Water expands as it changes from a liquid to a solid, becoming less dense rather than more dense.
What happens with energy when electrons go from a higher potential to a more stable configuration?
energy is released; exothermic
Explain the following observations by referring to the properties of water: Ocean temperatures fluctuate much less than temperatures on land.
Water is able to absorb large amounts of energy, including heat, and is denser as a liquid than a solid. Therefore, it takes a lot of energy to heat water, and water does not give up it's heat as quickly as air does -- high specific heat and high heat of vaporization
Explain how enzyme structure determines enzyme specificity.
its like a lock and key mechanism. where the substrate (this substance the enzyme acts on) is the lock and the enzyme is the key. so only the enzymes with the structure that fits perfectly into the substrate can act on the substrate. hence specific enzymes act on specific substrates. this is how enzyme structure determine enzyme specificity..
Distinguish between: a. pyrimidine and purine
purines - A and G pyrimidines - C and T (and U) purines have two rings, pyrimidines have one
Define pH
the measure of concentration and activity of hydronium atoms in a solution
Describe the function of enzymes in biological systems
they act as catalysts to reactions, thus lowering the energy required for a reaction to proceed to formation of product.
Explain the following observations by referring to the properties of water: • Coastal areas have milder climates than adjacent inland areas.
Water is able to absorb large amounts of energy, including heat. So the ocean absorbs heat in the summer because the water is cooler than the air, sucking the heat out of the air, thus cooling the air in summer. In the winter, the air is cooler than water, so the heat moves from the water to the air, warming the air in winter.
Define adhesion as regards to water
Water is attracted to other materials besides water. This is adhesion
Define cohesion as regards to water
Water is attracted to other water. This is cohesion
Explain how acids and bases may directly or indirectly alter the hydrogen ion concentration of a solution.
When an acid interacts with a solution, it can donate protons. When an alkaline interacts with a solution, it can accept protons.
Identify the four elements that make up 96% of living matter
CHNO -- Carbon, Hydrogen, Nitrogen, Oxygen
What does ΔH stand for?
Change in enthalpy, or change in energy in the system.
What is the difference between a compound and a molecule?
Chemical bond = molecule crystalline structure or atom by itself -- not a molecule 1 A molecule consists of two more atoms, which can be the same or different types of atom, that are linked by a chemical bond. A molecule of H2 or O2 is still a molecule, but not a compound. 2. A compound is usually a molecule as well. To be a compound, it has to have two different types of atoms, such as H2O. 3. Some compounds like NaCl are not molecules because they are linked together in a crystalline structure, rather than being molecularly bonded.
Explain why highly ordered living organisms do not violate the second law of thermodynamics.
this increase in organization over time in no way violates the second law. The entropy of a particular system, such as an organism, may actually decrease, so long as the total entropy of the universe-the system plus its surroundings-increases. Thus, organisms are islands of low entropy in an increasingly random universe. The evolution of biological order is perfectly consistent with the laws of thermodynamics.
List the major components of a nucleotide, and describe how these monomers are linked to form a nucleic acid.
A nucleotide is a monomer of a nucleic acid (thus multiple nucleotides will form a nucleic acid such as DNA or RNA). A nucleotide is consisted of a nitrogenous base (A, T, C, or G in DNA .... and A, "U", C, or G in RNA). These nitrogenous bases can be grouped as Pyrimidines ( which will be the C, U, or T) and Purines (which will be A and G). The pyrimidines are smaller in molecular size and purines are larger. The second component is a phosphate group (PO4 3-). Third will be the pentose sugar (either deoxyriboose, which will have one less oxygen b/c the prefix "de" and then oxy meaning less oxygen..... or ribose sugar, which will have an extra oxgen). As these nucleic acids are joined together (thus making a polymer, either DNA or RNA) via phosphodiester linkages, the phophate and sugar components will be have interacting forces between them (to bind them), forming a sugar-phosphate backbone. This polymer will have two distinct ends, with the top part (consisting of a phosphate group) serving as the 5' end and the bottom end (with hydroxyl group, OH, from the pentose sugar) serving as the 3' end.
Define a base
A solution in which the concentration of hydronium atoms is less than 10^-7 moles per liter.
Define acid
A solution in which the concentration of hydronium ions is greater than 10^-7 moles per liter.
Describe the building-block molecules, structure, and biological importance of fats, phospholipids, and steroids.
Lipids are diverse group of hydrophobic molecules, all hydrophobic; includes waxes and pigments not discussd A. Fats - not polymers, large molecules assembled from smaller molecules - glycerol and fatty acids 1. glycerol = alcohol w/ 3 C, each with a OH group 2. fatty acid = long C skeleton, 16-18 C long (fig 5.11) a. carboxyl group at end b. long chain of hydrocarbons - C-Hbonds are nonpolar, producing hydrophobic molecule c. 3 fatty acids join to the carbon skeleton, making a triglyceride, aka triglycerol d. fatty acids attached to the chain can be the same or different e. if there are no double bonds btn C, chain is straight - saturated fatty acid - solid =fats f. if double bonds occur, chain is kinked- unsaturated - will be liquid = oils g. cis bonds vs. trans bonds in hydrogenated products 1. trans fats in hydrogenated products may contribute more to atherosclerosis than saturated fats h. fat is very useful - a gram of fat stores more than 2x as much energy as a gram of polysac 1. compact storage for animals on the move (Plants don't have to move) 2. storage, warmth and cushioning B. Phospholipids -similar to fat, but only 2 fatty acids 1. 3rd hydroxyl group of glycerol attaches to negatively charged phosphate group (Fig. 5.13) a. other small charged molecules can attach to phosphate group to form phospholipids 2. head is hydrophilic, tail is hydrophobic (fig 5.14) a. in water, phospholipids self assemble into bilayers to shield hydrophobic portions from H2O 3. cell membranes are made of this, form a boundary btn cell and environment that is semipermeable C. Steroids - lipids w/ 4 fused rings for C skeleton (f.g 5.15) 1. functional groups vary 2. cholesterol a. common in cell membranes b. precurser of other steroids, eg. sex hormones and other hormones c. cholesterol is important, too much is bad
Distinguish between each of the following pairs of terms c Atomic weight and mass number
Mass number is an absolute -- it is the total number of protons and neutrons in an atom Atomic weight is the ratio of the average mass of the atom relative to 1/12 of the weight of a carbon atom.
mass number
Mass number is the total number of protons and neutrons in the most common isotope of an atom
Distinguish between each of the following pairs of terms b. Atomic number and mass number
Mass number is the total number of protons and neutrons in the most common isotope of an atom Atomic number is only the number of protons in the nucleus of the atom, giving the atom it's identity as a particular element
Explain how molecular chaperones may assist in proper folding of proteins.
Molecular chaperones are proteins that assist the non-covalent folding or unfolding and the assembly or disassembly of other macromolecular structures, but do not occur in these structures when the structures are performing their normal biological functions having completed the processes of folding and/or assembly
Explain why an investment of activation energy is necessary to initiate a spontaneous reaction.
Molecules are stable, but it is a question of how stable. In order to take them from stable to reactive, energy must be added to the molecule. Many reactions can proceed on the thermal energy bouncing the molecules together at room temperature. These reactions will run more slowly at lower temperatures as less molecules have enough energy to react.
Distinguish between monosaccharides, disaccharides, and polysaccharides. Give examples of each.
Monosaccharides: have a chemical formula of C6H12O6. -the basic unit of carbohydrates -the simplest form of sugar -Glucose, Galactose, Fructose Disaccharides: have the chemical formula C12H22O11, consist of two monosaccharides which are joined by the process of dehydration synthesis (during while a molecule of water is formed) -Maltose, Lactose, Sucrose Polysaccharides: polymers of carbohydrates, three or more monosaccharides joined together through the process of dehydration synthesis. -Cellulose, Glycogen, Starch
Distinguish between competitive and non-competitive or allosteric inhibition.
Non-competitive inhibition involves an inhibitor molecule binding to the enzyme at a different area, changing the conformation of the enzyme and altering the shape of the active site. As a result the catalytic efficiency of the enzyme is reduced and the shape of the active site may be so altered that the reaction cannot occur. This type of inhibition may or may not be reversible. Inhibition is usually reversible unless the inhibitor is some kind of poison. Penicillin, for example, causes the death of bacteria due to irreversible inhibition of an enzyme needed to form the bacterial cell wall. In humans, hydrogen cyanide irreversibly binds to cytochrome oxidase present in all cells with lethal consequences Allosteric regulation is the regulation of an enzyme or protein by binding an effector molecule at the protein's allosteric site (that is, a site other than the protein's active site). Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are called allosteric inhibitors. The term allostery comes from the Greek allos, "other," and stereos, "space," referring to the regulatory site of an allosteric protein's being separate from its active site. Allosteric regulation is a natural example of feedback control. Allosteric inhibitors are modulator molecules which bind somewhere besides the active site, change the enzyme's shape and "turn off" the catalytic activity
Explain the induced-fit model of enzyme function. What is a cofactor?
The favored model for the enzyme-substrate interaction is the induced fit model.[1] This model proposes that the initial interaction between enzyme and substrate is relatively weak, but that these weak interactions rapidly induce conformational changes in the enzyme that strengthen binding. A cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. These proteins are commonly enzymes, and cofactors can be considered "helper molecules" that assist in biochemical transformations.
With the use of a diagram or diagrams, explain why water molecules are: b. capable of hydrogen bonding with 4 neighboring water molecules
The oxygen atom is charged as 2- .And the two hydrogen atoms are charged as 1+ each.Therefore the oxygen atom can attract two hydrogen atoms of other two water molecules and the two hydrogen atoms can attrat two oxygen atoms of another two water molecules
Explain how the primary structure of a protein is determined.
The primary structure refers to amino acid sequence of the polypeptide chain. The primary structure is held together by covalent or peptide bonds, which are made during the process of protein biosynthesis or translation. The two ends of the polypeptide chain are referred to as the carboxyl terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity. Counting of residues always starts at the N-terminal end (NH2-group), which is the end where the amino group is not involved in a peptide bond. The primary structure of a protein is determined by the gene corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, which is read by the ribosome in a process called translation. The sequence of a protein is unique to that protein, and defines the structure and function of the protein.
Define specific heat
The specific heat is the amount of heat per unit mass required to raise the temperature by one degree Celsius.
5′ end and 3′ end of a nucleotide
The terms 5' and 3' (read as "five prime" and "three prime") refer to the carbon atoms in a sugar molecule. Every nucleotide is made of three parts: a phosphate group, a five-carbon (pentose) sugar, and a nitrogenous base. The 5 carbon atoms in the pentose sugar are numbered 1 - 5 for reference. In both sugars, the number 5 carbon is the one that is NOT part of the main ring. It is found in the upper left part of each molecule in these diagrams. The number 3 carbon is the lower left carbon. When these sugars are included in a nucleotide, a phosphate group is attached to the number 5 carbon. This becomes the 5' end. The hydroxyl group shown in the above diagrams remains attached to the number 3 carbon. This is the 3' end of the nucleotide. When DNA or RNA form from individual nucleotides, the 5' (phosphate) end of one nucleotide joins to the 3' (hydroxyl) end of the next nucleotide. This gives the growing polymer directionality; the 5' end will always have a phosphate group while the 3' end always has a hydroxyl group. This directionality is vitally important when DNA is being replicated or transcribed, or when RNA is being used to make proteins.
Explain how two isotopes of an element are similar. Explain how they are different.
The two isotopes of an element have the same number of protons but different numbers of neutrons
With the use of a diagram or diagrams, explain why water molecules are: a. polar
The water molecule is polar because the shared electrons are closer to the oxygen atom rather than the hydrogen atoms.
Describe and draw the basic structure of the Carboxyl functional group and outline the chemical properties of the organic molecules in which they occur.
acidic, tends to drop a proton, forms with amines to make amino acids Amino acids are linked together by covalent bonds that are formed between amino and carboxyl containing groups
Do carboxyl functional groups function as acids or bases? Do carboxyl functional groups tend to attract or drop a proton?
acids and they tend to drop a proton
Describe and draw the basic structure of the Carbonyl functional group and outline the chemical properties of the organic molecules in which they occur.
acts as an acid, tends to lose a proton in solution. found on aldehyde and ketone molecules. The carbonyl functional group is the site of reactions that link these molecules into more complex compounds like ribose
Do amino functional groups function as acids or bases? Do amino functional groups attract or drop a proton?
bases, and they attract a proton
Why is RNA so versatile?
because RNA simply takes a copy of the DNA for proteins that have to be made. then it goes to the cytoplasm and attaches to ribosomes to create these proteins. the DNA can't fit out of the nucleus there for the smaller RNA have to go in and get the "codes" for the protein production.
Second type of secondary protein structure
beta pleated sheet Beta-pleated sheets are so called because of the 'pleated' or folds when view form the side. The polypeptide chain is much more stretched out in comparison to the alpha helix. This Beta-pleated sheet was discovered by Pauling and Corey. This 'sheet' often has twists that increase the strength and rigidity of the structure. (Try twisting a sheet of paper to see this effect).
What are the roles of Carbohydrates as structural molecules?
cellulose in plants and chitin in Arthropods
What does ΔS stand for?
change in entropy
Write and define each component of the equation for Gibbs free-energy change.
ΔG = ΔH - TΔS Gibbs free energy equation determines if a chemical equation will be spontaneous or not. If ΔG comes out negative, it is spontaneous, if positive, it's not spontaneous. ΔH is change in enthalpy, or energy in a system, and TΔS is difference in entropy multiplied by temperature, and entropy is the energy that is not used for work and accumulates as waste heat. So if difference in enthalpy is greater than difference in entropy times temperature, that means that energy was added to the system, and if difference in enthalpy is less than difference in temperature times difference in entropy, that means that energy left the system.
