BIO 311C exam 1
What is a peptide bond? Through what reaction is it formed?
A peptide bond is a bond formed between the carboxyl group and the amino group in an amino acid to form a protein. They are formed through condensation reactions.
What is a peptide bond? Through what reaction is it formed?
A peptide bond is the bond that holds a polypeptide chain together. It is formed through dehydration synthesis, or a condensation reaction between a Hydrogen atom in an amino acid's amino group and a hydroxyl group in the carboxyl group of an amino acid.
What are the three components of a nucleotide? Where are the covalent bonds joining these three parts, and through what reaction are nucleotides joined to make polymers (nucleic acids)?
A phosphate group, a 5 carbon sugar, and a nitrogenous base. Nucleotides are joined to make polymers by a dehydration reaction (condensation)
What is the basic structure of a phospholipid? Is it a polar molecule or nonpolar or what?
A phospholipid consists of a hydrophilic head containing a phosphate group and two hydrophobic, hydrocarbon tails; the molecule is amphipathic as it consists of both polar and nonpolar regions (head=polar, tails=nonpolar).
Tell the 'life story' of a membrane protein (e.g., 'birth, maturation, placement & function, death').
A protein begins with the synthesis of a signal peptide that attracts a free ribosome towards the rough endoplasmic reticulum. Once it becomes bound, the ribosome continues synthesizing a polypeptide and cuts off the signal peptide and undergoes chemical changes and folding (secondary/tertiary structure.) A polypeptide then is transported through a vesicle to the Golgi Apparatus where it undergoes further chemical changes. Once this is complete, a vesicle transports it to its destination, which could be one of three options: the plasma membrane, becomes a lymphocyte (specialized digestion protein), or to a destination outside of the cell (such as testosterone or estrogen)
What is an acid? What is a base? Give examples of each. What is the pH scale?
Acid is a H+ donor, Base is a H+ acceptor or an OH- donor, H+ and OH- = 10-14 pH scale consists of the scale of acid smallest nuclear mber to base largest number. The pH scale is based on H+ concentration, however it also implies OH- concentration. Each pH unit represents a tenfold difference in H+ and OH- concentrations. An example of an acid is gastric acid in our stomachs, and an example of a base is our blood, ammonia, and bleach.
Tell how the bonds that link monomers in simple starch (amylose) differ from the bonds between monomers in cellulose, even though in both cases the monomer is glucose.
Alpha bonds occur when linking monomers in a simple starch (amylose), while beta bonds occur between the monomers in cellulose. The beta bonds in cellulose are at a bond angle that makes it difficult for enzymes to break the monomers apart, resulting in a strong bond that most organisms cannot break down.
Describe and distinguish among the four levels of structure that can occur in a protein
Primary - the peptide bonds holding the amino acids together, sequence of amino acids Secondary - hydrogen bonds between the carboxyl and amino groups in a protein chain. They are created by right-handed coiling of the primary protein structure. The coiling is caused by hydrogen bond interactions between the amino acids within the protein. Tertiary - bonds between the R groups in a protein chain, which can include polar and nonpolar bonds, hydrophobic interactions, hydrogen bonding, ionic interactions, and disulfide bridges (which are this strongest). Quaternary - Bonds between separate polypeptides
In order to function, a particular enzyme must bind snugly to a spherical, positively charged particle. The enzyme should have a pocket of what shape and lined with R groups of what property?
The pocket should be rounded like a semi-circle and have R groups that can be negatively charged.
What bonds are not broken in denaturation? Why does a denatured protein not function properly?
Bonds in the backbone or in the primary structure are not broken. A denatured protein does not function due to the loss of shape which is directly related to its function
Certain proteins contain amino acid sequences in them that act as localization signals. Look at Fig. 17.22 & tell how the presence of a "signal peptide" gets a newly made protein into the ER lumen.
The signal peptides of proteins bind with a recognition particle that guides the ribosomes to the receptors present in the rough ER; this binding allows proteins to be absorbed into the lumen
Explain and distinguish the processes of condensation (=dehydration synthesis) and hydrolysis.
Condensation is when bonds are formed between monomers by taking out two hydrogen atoms and an oxygen atom to form a water molecule. Hydrolysis is breaking bonds in polymers by adding water to form the separate monomers.
Look at the chart of the four groups of organic compounds on Handout 2. How does the lipid group differ from the other three with respect to monomer and polymer structures?
There are no simple monomers for lipids. Triglycerides are made from glycerol (a carbon alcohol) and three fatty acids.
How do phospholipids arrange themselves in water as a layer? What types of weak intermolecular bonds hold them together?
They arrange themselves into a phospholipid bilayer. They hold themselves together by: Hydrophobic interactions between fatty acid tails, and polar/ionic bonds between phosphate heads.
What are general characteristics of lipids? Name 3 examples of types of lipids.
They have no true polymers, and mix poorly with water (hydrophobic). Three types include fats, phospholipids, and steroids.
If one strand of a DNA ends in a sugar (deoxyribose), what is at the other end of that strand? Looking ahead- Amino Acid structure (applying your knowledge of functional groups)
a phosphate
Be able to recognize and label the 5 functional groups named below (locate it on part of a large molecular structure): hydroxyl, carboxyl, amino, phosphate, methyl. [We'll also be mentioning sulfhydryl SH and carbonyl C=O groups, see Figure 4.9] For each, tell (a) whether it is polar or nonpolar (b) whether it's often charged in cell solutions or always electrically neutral.
a) All functional groups are polar except for methyl. b) see diagram
How did conditions in the early earth and atmosphere differ from those today?
"It was hot, wet, and there was lightning." -Gareth The idea of the large amount of energy around made it possible for organic molecules to form from inorganic molecules. There were no cells, no enzymes, no aerobic respiration or photosynthesis, or free oxygen. There was a lot of water vapor and ammonia in the atmosphere, as well as UV radiation, and high temperatures.
extra stuff
...ose- normally indicates sugar Sugars have many hydroxyl groups ...ase- normally indicates enzymes ...in- normally indicates protein Plasma membrane - normally refers to one of the phospholipid membranes associated with a cell
What is a hydrogen bond? Using a dotted line to represent a hydrogen bond, draw the position of a hydrogen bond (dipole-dipole) between two H2O molecules and one between H2O and NH3 molecules
A hydrogen bond is the weak attraction between a hydrogen and an electronegative atom. The hydrogen atom has a partial positive charge that allows it to be attracted to a different electronegative atom. (typically fluorine, oxygen or nitrogen).
Name and distinguish the four major groups of cell biomolecules; answer to 1-21 on back.
Carbohydrates Monomer: monosaccharides Polymer: polysaccharides Monosaccharides consist of a string of carbons (either linear or a ring form) being saturated by Hydrogen and Hydroxyl groups Monomers are connected by glycosidic linkages to form polysaccharides Lipids Lipids are not true polymers, because they are not made of chains of similar molecules. Some lipids, like Fats and Phospholipids, are constructed of combinations of glycerol and fatty acids, but these cannot be chained together into arbitrarily long molecules. Rather, only a few can be connected together via condensation reactions. Steroids are not made of sub-parts, and are complete molecules in themselves. Look at pictures of lipids for additional clarification. Phospholipid Bilayer consists of polar head and nonpolar hydrocarbon tail Proteins Monomer: Amino Acids Polymer: Polypeptides Amino Acids consists of an asymmetric carbon, surrounded by an amino group, a carboxyl group, a hydrogen atom, and an R group (which differs from amino acid to amino acid) Monomers are connected by peptide bonds to form polypeptide chains Nucleic Acids Monomer: nucleotide Polymer: polynucleotides (nucleic acids) Nucleotides consist of a phosphate group, a 5 carbon sugar, and a nitrogenous base Monomers are connected by phosphodiester linkages to form polynucleotides
Explain how carbon (C) and hydrogen (H) atoms can share electrons to achieve stable, full outer electron shells in both. Up to how many hydrogen atoms can covalently bond to one carbon atom?
Carbon and hydrogen interact with each other by each sharing one valence electron, resulting in a pair of shared electrons that creates a covalent bond. By sharing their electrons they can complete their outer shells. Carbon needs 4 electrons to fill its outer shell, so 4 hydrogens can covalently bond to one carbon.
What two functional groups are in every amino acid?
Carboxyl and amino groups
Steroids are lipids. Name three specific examples of steroids
Cholesterol, estrogen, testosterone
What makes a molecule "hydrophilic" or "hydrophobic"? Give examples of each.
Hydrophilic molecules consist of polar regions that are able to interact with water molecules whereas, hydrophobic molecules consist of mostly nonpolar regions that do not easily interact with water. Monosaccharides are hydrophilic and fatty acid tails are hydrophobic.
What is the endosymbiosis hypothesis for the origin of mitochondria and chloroplasts? State three facts about cells that support this hypothesis
Endosymbiosis hypothesis states that mitochondria and chloroplasts were originally individual prokaryotic cells that were engulfed by a larger prokaryotic cell. Mitochondria and chloroplasts have their own DNA, their DNA is a single loop, and have two membranes. They replicate by fission, inner membranes of both organelles have transport systems similar to bacteria, and they have cellular machinery needed to transcribe and translate their DNA into proteins.
Name two differences between prokaryotic cells and eukaryotic cells, one chromosomal and one cellular.
Eukaryotic cells generally have membrane bound organelles and linear DNA, while prokaryotes do not have membranes and their DNA is looped. Eukaryotic cells have nuclear envelope and larger ribosomes than prokaryotic.
What's the structure of a fatty acid? What's the difference between a fat and a fatty acid?
Fatty acids have long hydrocarbon skeletons, usually 16-18 carbons in length. The carbon at one end of the group is part of a carboxyl group, which gives it acidic traits. Fatty acids are relatively non-polar and therefore make the fats hydrophobic. A fat is constructed from glycerol and fatty acids.
What steps must have occurred in the early earth during what we call "chemical evolution"? What types of weak intermolecular bonding could cause proteins and lipids in water to spontaneously form cell-like aggregations - "proto-cells"?
First, organic molecules formed from inorganic molecules. After the formation of organic molecules, energy traps such as heated gas inside of bubbles and the heat of sediment allowed monomers to form. The contact of amino acids or nucleotides onto hot surfaces like rocks in early earth circumstances could have spurred the polymers which would lead to more complex organic molecules. Covalent bonds or hydrogen bonds between the R-groups of proteins could have created these cell-like aggregations. Proto-cells are the complex molecular structures that occured before true cells occurred.
Hydrogen bonding and hydrophobic interactions are both very weak bonds. How do they differ from each other? Give examples of substances that form each of these types of weak bond.
Hydrophobic interactions = two nonpolar interactions (Ex: oil clusters in H2O) Hydrogen bonding = two polar interactions (Ex: H2O & H2O)
How could you use cell fractionation and centrifugation in order to study the distribution of certain molecules carrying specific labels/tags (radioactive, fluorescence) inside different types of organelles?
Fractionation: breaking the cell up into its smaller pieces. Centrifugation: separates the remaining pieces by density (slower spinning = things with large density differences will separate. Faster spinning = things with smaller density differences will separate
What are the building block molecules that react to form one triglyceride molecule(technically called "triacylglycerol")?
Glycerol (3-Carbon) & 3 fatty acids joined by an ester linkage, a bond formed by the condensation between hydroxyl and carbonyl (carboxyl?) group.
How do saturated & unsaturated fats differ in bonds & shape? What are "hydrogenated" oils?
If there are no double bonds between carbon atoms in the hydrocarbon chains of fatty acids, then the structure is said to be saturated. When the hydrocarbon chains have one or more double bonds between carbon atoms, the fatty acid is considered unsaturated. "Hydrogenated" means that unsaturated fats have been synthetically converted to saturated fats by adding hydrogen, allowing them to solidify
What are some types of bonds that are broken in protein denaturation? What breaks in digestion?
In denaturation, the bonds at the secondary level (hydrogen bonds between the amino groups and carboxyl groups on the amino acids) and tertiary/quaternary structure, which include hydrogen, disulfide, and ionic bonds are broken. In digestion, the primary structure of polypeptides (peptide bonds) are broken down (digested) through hydrolysis.
When salt crystals (Na+Cl-) dissolve in water, what types of bonds are being broken and forming?
Ionic bonds are broken due to the hydration shell and ion-dipole interactions (hydrogen bonds) are formed.
Explain how ions form. Give an example. What is an ionic bond? What's an ion-dipole interaction?
Ions form when the electronegativity of an atom is able to strip electrons from another atom with a lower electronegativity. For example, the difference between the electronegativities of chlorine and sodium enables chlorine to take the valence electron from sodium. Chlorine would have a -1 charge (an anion) and sodium would have a +1 charge (a cation). An ionic bond is the electrostatic attraction between two ions, not the transfer of an electron itself. Compounds formed by ionic bonds are called ionic compounds, or salts. An ion-dipole interaction occurs between an ion and a molecule that has a dipole (two oppositely charged regions). For example, positively charged sodium ions in solution will attract the partially negative oxygen ends of water molecules.
Distinguish between microfilaments and microtubules in chemical make-up & means of contraction
Microfilaments are composed of Actin proteins (which don't contract themselves) that are contracted by other motor proteins. Microtubules are made of Tubulin protein that can either a) be shortened on one end and enlarged on one end or b) they serve as a "track" for motor proteins.
What are isomers? Distinguish among these types of isomers; that is, for each type define how two isomers differ: (a) structural; (b) geometric isomers; (c) enantiomers ( = stereoisomers).
Isomers are molecules that have the same exact number atoms with different locations of bonds. Structural Isomers differ in the sequence that their atoms are linked Geometric Isomers differ in the arrangement of atoms around a double bonded Carbon atom Enantiomers are "mirror images" of one another (think your hands) Isomers are pairs of molecules that have identical atoms but different structures. (a) not involving asymmetry around atoms; spontaneous changes unlike geometric (b) every geometric isomer involves two carbon atoms double bonded (c) mirror images of one another Enantiomers differ in their spatial arrangement of atoms around an asymmetric carbon that creates "mirror images". Atoms are bonded in the same order but differ in configuration of atoms around these bonds
Which type of organelle is involved in the digestion (hydrolysis) of triglycerides (fats and oils)?
Lysosomes - carry specific hydrolytic enzymes used for intracellular digestion
Macrophages engulf and digest bacteria & debris non-specifically, while lymphocytes secrete very specific antibodies. What organelles should be very abundant in macrophages? In B-cell lymphocytes?
Macrophages : Lots of lysosomes for digesting bacteria and debris. Also golgi apparatus because it makes lysosomes. B-cell lymphocytes (produces antibodies): Rough ER/Golgi for protein synthesis and specialization of proteins. Abundant Vesicles to secrete antibodies.
What's an advantage of having membrane compartments within cells?
Membrane compartments provide different environments within the cell to perform specific metabolic functions. This allows processes that are typically not compatible to occur simultaneously in the same cell without disturbing or being disturbed by other process
What is the definition of molarity (M)? How would you prepare 1 liter of a 1 M solution of NaCl? [note: 1 mole of NaCl is about 58 grams]. How would you prepare 1 liter of a 0.5 M NaCl solution?
Molarity is the number of moles of solute per liter of solution.To prepare 1 liter of a 1 M solution of NaCl, you would weigh out about 58g (molar mass) then add water to bring the volume of the solution to 1 liter. To prepare for 1 liter of a 0.5 M NaCl solution, you would weigh out about 29 grams then add water to bring the volume of the solution up to 1 L.
The molecular formula of every monosaccharide is a multiple of what set of atoms? Sugars (monosaccharides and disaccharides) readily dissolve in water - Why?
Monosaccharides follow multiples of n(CH₂O). They readily dissolve in water because they have hydroxyl groups, which are regions that can form hydrogen bonds with the water.
Briefly explain the Miller-Urey experiment; tell how it tested hypotheses about the origin of life.
Non-organic compounds were placed in conditions similar to the early earth, and after around a week, simple organic compounds were found such as amino acids. This showed that it was possible for organic molecules to form from non organic molecules. The organic molecules would then evolve into more complex living cells, starting the first step towards the origin of life. The amino acid was produced through this experiment. [What are the implications of this for the origin of life on earth?][GG]
Biological evolution, instead of just chemical evolution, began with the origin of what molecules?
Nucleic (amino) acids, which lead to RNA, a necessity for reproduction. This eventually evolved into DNA, a more advanced and efficient form of gene safekeeping. Some RNA were self replicating and had sequences that allowed them to replicate faster and without errors. This allowed them to outcompete other RNA. "RNA world"- RNA self replicated in protocells that carried them. (how did RNA become DNA?)
Rank these covalent bond examples from most polar to least polar: N-H, O-O, C-H, O-H
O-H > N-H > C-H = O-O (C-H and O-O are non polar)
What is the main function of peroxisomes? Are peroxisomes formed in the endomembrane system?
Peroxisomes are responsible for the oxidative breakdown of long-chain fatty acids in energy metabolism pathways (removes H atoms and transfers to O, creates hydrogen peroxide) Peroxisomes are NOT part of the endomembrane system.
Distinguish between polar covalent bonds and nonpolar covalent bonds in terms of differences in electronegativity values of the two bonded atoms.
Polar covalent bonds occur when a covalently bonded molecule has an unequal sharing of electrons resulting from a difference in electronegativities. Nonpolar covalent bonds occur on a molecule where electrons are equally shared, meaning their electronegativities are nearly identical. These are both intramolecular attractions.
Describe how ribosomes, rough ER, Golgi and transport vesicles (endomembrane system) are involved together in the synthesis, chemical modification, trafficking, and secretion of a protein hormone.
Ribosomes are bound to rough ER where they are responsible for synthesizing proteins (forming its tertiary and possibly quaternary structure); the proteins are then sent to the golgi via vesicles where they are further processed (chemically altered and packaged) and secreted in new transport vesicles. The vesicle becomes a part of the cell membrane and the protein is released outside of the cell. (The below diagram corresponds with this question
Ribosomes are composed of what two types of biomolecules? What's the difference between ribosomes in prokaryotic and eukaryotic cells? When is a eukaryotic ribosome "bound" versus "free"?
Ribosomes are composed of rRNA and protein. Bound ribosomes are attached to the ER, through the endomembrane system. Free ribosomes are suspended into the cytosol. Eukaryotic Ribosomes are significantly larger than Prokaryotic Ribosomes. In Eukaryotic cells ribosomes are free and bound, whereas, in prokaryotic cells, they're only in free form.
How do smooth ER and rough ER differ in structure and in function
Rough ER is lined with ribosomes, protein synthesis. Smooth ER, lipid, steroid, hormone synthesis, detoxification.
As cells mature and differentiate, they specialize structurally (shape, organelles present, etc) for specific functions. How would a muscle cell differ from a cell specialized for absorption of nutrients?
Since a muscle cell needs more energy, they would have an abundance of cytoskeletal structure and mitochondria. A cell that was specialized for an absorption of nutrients would have an abundance of lysosomes.
Which organelle is mainly involved in the synthesis (condensation) of triglycerides (fats and oils)?
Smooth ER - functions in synthesis of lipids
Name at least three properties of water that emerge from its highly polar molecular structure.
Temperature moderation, ice expands when solid (insulates the water under it and allows life under layer of ice), cohesion (water move up the tree),high specific heat and high heat of vaporization. Temperature moderation: this is due to water's relatively high specific heat, and will change its temperature less than other substances when it absorbs or loses a given amount of heat. It can store large amount of heat of hot days, and gradually cooling water can warm the air. Expansion upon freezing: the molecules expand upon freezing, making ice less dense and allowing it to float on water. The ice prevents the water beneath it from freezing in the winter, and provides a habitat for many creatures on its surface. Cohesion: contributes to the transport of water and dissolved nutrients against gravity in plants, adhesion of water to the molecules of cell walls helps counter gravity, surface tensions is a measure of how difficult it is to break the surface of a liquid Versatility as a solvent: due to the polarity of the water molecule, dissolves other polar molecules by forming a hydration shell
Which of the four levels of structure are held by bonds between R groups?
Tertiary and Quaternary structures
A certain small, compact protein functions entirely within the non-polar middle of a phospholipid bilayer. The R groups on the surface of that protein are expected to have what properties?
The R groups on the surface of the protein are expected to have nonpolar/hydrophobic properties.
In the early earth, there was very little O2. After a diversity of single-celled prokaryotes evolved, the evolution of what process was followed by changes known as the "oxygen revolution"? What were some of the subsequent evolutionary responses of organis
The evolution of photosynthetic prokaryotes lead to the oxygen revolution as oxygen is a product of photosynthesis. Some of the subsequent responses included becoming accustomed to an aerobic environment, which is how cellular respiration evolved, while others either stayed in anaerobic environments or simply died out.
Tell the main function of mitochondria and that of chloroplasts. In what ways are these two organelles similar in structure? What is the evolutionary ancestor of mitochondria? (review L.O.1-51)
The main function both of these structures is to change energy from one form to another (energy transformation). Mitochondria are sites for cellular respiration where ATP is produced, and chloroplasts are the sites for photosynthesis and the production of glucose. Mitochondria evolved from a prokaryotic ancestor that had been engulfed by an ancestor eukaryotic cell (endosymbiotic theory). (Mitochondria ancestor- non photosynthetic prokaryote, Chloroplast ancestor- photosynthetic prokaryote
When you are provided information about the very specific function of a protein, be able to predict its specific shape (conformation), surface R group properties and structure. Examples antibody protein (defense), trans-membrane ion channel protein(trans
This would mean an understanding of the relationship between the structure (shape, polarity, charge) of a protein and its function. Ex. trans-membrane protein would need hydrophobic surface r groups at the region of the protein embedded within the hydrophobic tails of the phospholipid bilayer
What's the difference between a "trans fat" and a "cis fat"? Which occurs in nature? Cis and Trans hydrocarbon chains are examples of which type of isomers?
Trans fat: hydrogenated unsaturated fats with double bonds, no kink Cis fat: naturally occuring fatty acids, with kink Cis and trans hydrocarbon chains are examples of geometric isomers.
Why does it feel hotter outside on humid days? What about evaporation can explain that?
Water evaporates from skin in an attempt to cool off but another water molecule from the air replaces it, reducing the effects of evaporative cooling. High concentration of water vapor in the air inhibits the evaporation of sweat from the body. The molecules with the most kinetic energy are most likely to leave as a gas.. We sweat to cool down→ when we sweat, evaporation occurs, which effectively cools us down since evaporation requires heat from your skin, therefore more evaporation=more cooling; evaporation is more effective when is it dry as opposed to humid. Evaporation= breaking hydrogen bonds which absorbs heat
Tell how water's properties make it important - an ideal medium - for life on earth.
Water molecules stay close to each other as a result of hydrogen bonding; collectively, the hydrogen bonds hold the substance together, a phenomenon called cohesion: makes water more structured than other liquids. Water has the ability to moderate air temperature by absorbing heat from air that is warmer and releasing the stored heat to air that is cooler. Because of its polarity, it is able to dissolve ions in our body and transport them from one part to another.
Look at the R group of the amino acids in the figure below and also of valine, phenylalanine, glutamic acid, serine, lysine in Figure 5.14. For each tell whether the tip of the R group is polar or nonpolar, electrically charged or neutral. Tell a type of bond each R group could form with another R group to contribute to the tertiary structure.
You do not have to memorize the specific R side chains, but if given a picture, you should be able to predict their properties [polar, nonpolar, negative/positive charge, etc
. Explain differences between the two members of each pair: (a) light & electron microscop (b) TEM (transmission) & SEM(scanning) electron microscopy (c) fluorescence & white light microscopy.
a)Light: visible light is passed through the specimen and then through glass lenses that refract (bend) the light so the image of the specimen is magnified as it is projected into the eye or into a camera Electron: beams electrons through a specimen; better resolution b)TEM: cell sliced into thin slices; allows you to see individual organelles/components of the cell SEM: Cell is coated in a metal, and electrons are beamed onto the cell. The electrons bounce off and create a 3D image of the surface of the cell c)Fluorescence allows for the location of specific molecules as a result of dyes while white light provides little contrast
What two functional groups are in every amino acid?
carboxyl and amino
Explain the weak intermolecular forces and interactions that hold the "fluid mosaic" model of membrane structure.
hydrophobic interactions that hold the mosaic together. Hydrophilic reactions hold the heads of the phospholipids together as well.
Describe the intermolecular interactions that hold a transmembrane protein in place in the phospholipid bilayer
ydrophobic interactions between non-polar R-groups and a transmembrane protein and adjacent non-polar phospholipid tails