Bio 311c Exam 1

Name at least three properties of water that emerge from its highly polar molecular structure.

Ability to hydrogen bond. Powerful solvent. Cohesion. adhesion, etc

What's an acid? What's a base? Give an example of each.

Acid < 7. Donates H+ to a solution. More H+ concentration, more acidic. Base > 7, accepts H+, dissociates into OH-. pH scale tells how acidic or basic. One magnitude (i.e. 7 -> 6) has a 10x concentration of H+. (7 -> 5 100x)

Tell how glucose bonds in amylose differ from bonds in cellulose.

Amylose is alpha glucose bonds and Cellulose is B glucose bonds

Explain why and which parts of molecules with polar covalent bonds can possibly form hydrogen bonds with other polar molecules and those with non-polar covalent bonds cannot.

Polarity causes a slight +/- force which leads to H bonds between slightly + H's and slightly - F,O,N. Nonpolar molecules do not experience this slight charge.

Describe and distinguish among four levels of structure in a protein.

Primary: order of amino acids Secondary: hydrogen bonds between amino and carboxyl groups make alpha helixes and beta pleated sheets Tertiary: Interactions between R groups- H bonds, VDW, hydrophobic, ionic, disulfide (between two -SH when H+ dissociates) groups, covalent. Most are weak except for covalent and disulfide (very strong) Quarternary: Two or more polypeptides bond together

What is the endosymbiosis hypothesis for the origin of eukaryotic cells? State three facts that support this hypothesis.

Prokaryotic cell began to have in foldings of the plasma membrane which lead to more compartmentalization. It engulfed an aerobic bacteria that would become mitochondria. It then engulfed a phtotosynthetic bacteria that became chloroplasts. 1) Mitochondria and chloroplasts have two membranes 2) They both have their own DNA 3) Divide in a prokaryotic fashion

Name two differences between prokaryotic cells and eukaryotic cells, one chromosomal and one cellular.

Prokaryotic: loop chromosome Eukaryotic: multiple, linear chromosomes Prokaryotic: no membrane bound organisms, small ribosomes, peptidoglycan in cell wall Eukaryotic: membrane bound organelles

Tell how presence of signal peptide gets a newly made protein into the ER lumen.

The signal peptide is made which then bonds to a signal receptor protein. SRP binds to a receptor protein in the ER membrane. Bounds ribosome. Forms a pore and has signal cleaving enzyme. SRP leaves and SCE cuts off signal.

Life story of a membrane protein. Birth, maturation, placement & function, death.

Born from a bound ribosome then taken into the lumen of the ER and folded. Vesicle pinches off to golgi where it is modified, vesicle pinches off and taken to membrane. Vericle fuses with membrane and protein is put in there. Could be used as transport or receptor or structural. Lysosome fuses with it and digests it into amino acids.

When table salt dissolves in water, what type of bonds are breaking/forming?

Breaking- ionic bonds, forming- h bonds. Water forms a hydration shell around the ions

Describe the relative bond strength in H bonds, ionic bonds in crystal form and in aqueous solution, hydrophobic interactions, van der Waals interactions. Give examples.

Covalent (H20 Molecule) > Ionic (crystal) (NaCl) > Ionic (aq) (Na+ and Cl-) > H bonds (between two water molecules) > Hydrophobic (phospholipid bilayer) > VDW (work with hydrophobic in oil coalescence)

Distinguish between microfilaments and microtubules in chemical make-up and means of contraction.

Microfilaments: Two intertwined strands of actin Use motor proteins to walk and get longer by adding actin. Microtubules: Hollow tubes made of tubulin. Elongate at one end and shorten at other end or motor proteins walk. Cillia/flagella. Work at periphery (pseudopodia) Intermediate filaments: overall shape of cell and hold nucleus

What is the structure of the nuclear envelope? What are nuclear pores? What is the nucleolus?

Nuclear envelope is a double membrane that surrounds the nucleus. Nuclear pores are small pores in the membrane lined with protein called pore complexes. These regulate the molecules that can get in and out of the nucleus. Nuclear lamina is what lines the nucleus. Nucleolus makes ribosomes.

What is the effect of membranes having more (a) unsaturated hydrocarbons and (b) cholesterol

a) Unsaturated hydrocarbons keep membrane more fluid because it cannot pack tightly like saturated CH chains will. b) As temperatures decrease, cholesterol keeps the layers from packing tightly.

Carbohydrate

n(CH2O) Monomer: Monosaccharide Polymer: Polysaccharide Linkage: Glycosidic Ex: glucose, sucrose, glycogen, amylose, starches

Methyl (-CH)

Nonpolar (Hydrophobic interaction) Hydrophobic No charge

What's the advantage of having compartments within cells? What forms the compartments?

Compartments allow for cell processes to occur that may damage the cells. Phospholipid bilayers line the compartments.

*Recognize the difference between (a) ring/chain glucose (b) alpha/beta glucose (c) glucose/galactose

(a) Ring and chain have the same molecular structure but different shapes (b) alpha glucose has OH in the #2 position while B glucose has OH in the #1 position. This creates a weird bond between B glucoses and results in cellulose. (c) Glucose and galactose are enantiomers because they are around an asymmetrical carbon

Which organelle is involved in the digestion of triglycerides?

(correct)Lysosome digests. Peroxisome- oxidation of hydrocarbon chains. Product is H2O2 but also neutralizes it.

Three characteristics of lipids

1) Nonpolar af 2) Hydrophobic 3) Used for longterm energy 4) Saturated or unsaturated

Complementary strand of 5'-TAGGCCT-3'

3'-ATCCGGA-5'

Explain how C and H atoms can share electrons to achieve stability. How many H's can bond covalently to one C?

4. Carbon has a valence of four and H has a valence of one. Bonding these together gives all atoms a stable outer shell.

Name three specific examples of steroids. Are steroids lipids?

Androgens, estrogens, progesterone. Steroids are lipids. Do not form by condensation reactions.

What is the function of chaperonin?

Chaperonin helps protein fold by creating a hydrophilic environment and shielding proteins from disruptive chemical conditions while folding.

Basic structure of a phospholipid? Is it polar or nonpolar?

Choline group bonded to a phosphate group bonded to glycerol and two fatty acid tails. It is amphipathic: both polar and nonpolar. Polar heads and nonpolars tails.

Explain how water's capacity for hydrogen bonding accounts for its physical properties. Give examples of how these physical properties and water's major role in cellular reactions help support life.

Cohesion/adhesion: water can get up to high parts of trees. Defy gravity. High specific heat/Heat capacity- keeps the earth temperate bc of high temp to break H bonds Powerful solvent- polar Liquid at room temperature: supports life Less dense as a solid: keeps oceans liquid.

In the early earth, there was very little O2. After a diversity of single-celled prokaryothes evolved, the evolution of what process led to changes known as the "oxygen revolution"? What were some of the evolutionary responses?

Cyanobacteria developed photosynthesis in which they gave off oxygen to the atmosphere. Bacteria at the time could have either died, hidden, tolerated, or used oxygen.

Compare DNA and RNA structure. What are their roles in the cell?

DNA is double stranded with a pentose sugar with no oxygen on the 2' portion. RNA is single stranded with a pentose sugar WITH oxygen in 2'. DNA holds genetic information. RNA is used to copy DNA and make proteins. rRNA is used to make ribosomes. mRNA transcribes DNA. tRNA is used to carry amino acids to ribosomes for protein synthesis.

Describe potential inter-molecular interactions: DNA-RNA, rRNA-protein, DNA-protein

DNA-RNA: H bonds (form during transcription so they have to be weak to separate) RNA-protein(depends on R group): H bonds, maybe ionic DNA-protein: ionic/H bonds

*Describe the IMFs that hold a transmembrane protein in place in the bilayer.

Definitely hydrogen bonds in the Polar regions. Hydrophobic interactions in the nonpolar regions.

Explain and distinguish processes of condensation and hydrolysis.

Dehydration synthesis occurs when a bond is formed between two monomers by removing an O and an OH -> H2O Hydrolysis occurs when a water molecule is added to break down a polymer into monomers.

*What bonds break up in protein denaturation? Digestion?

Denaturation: protein unravels/shape is altered. Broken down to primary structure but primary structure is unaffected. (H bonds, ionic, covalent, disulfide etc) Digestion: Hydrolytic enzymes break down proteins to their amino acids (monomers). These amino acids will then be used to make proteins that the body needs.

How do phsopholipids arrange themselves in water as a layer? What type of inter-molecular bonds hold them together?

Depends on how many there are. Sometimes will form a single layer circle with polar ends out and nonpolar ends in. If there are many, form a bilayer. Hydrogen/hydrophobic

Carboxyl ( -COOH)

Polar, negative charge, Acidic 1/2 of AA Ionic, H bonds

What makes a molecule hydrophillic or hydrophobic?

Hydrophillic- polar affinity for water, forms H-bonds with water (ex. cotton). Hydrophobic forms- nonpolar nonionic and nonpolar- coalesce to stay far away from H2O (oil)

What's the difference between a fat and a fatty acid?

Fat is composed of fatty acids. Fatty acids are the monomers of fats.

How did conditions int he early earth and atmosphere differ from those today?

First atmosphere had little oxygen but mostly water vapor, nitrogen, carbon dioxide, methane, and ammonia. Lots of lightning and volcanic eruptions and UV radiation. Miller and Urey tested Oparin and Haldane's hypothesis that the early environment was reducing. Found amino acids and other organic compounds were created.

What are the three building block molecules that react to dorm one triglyceride molecule?

Glycerol + 3 fatty acids joined by ester linkages

Draw out molecular structure common to all amino acids.

H | Amino group -C- Carboxyl group | R

*What's the difference between H bonds and hydrophobic interactions?

H bonds are IMFs between H and an electronegative atom. Hydrophobic interactions are formed to avoid H2O. H bonds are formed between water molecules, hydrophobic interactions are formed when oil is in water and coalesces to avoid it.

Tell how a water's properties make it an important- an ideal medium- for life on earth.

High specific heat- regulates temperature. Cohesion- organizes hydrophobic interactions. Less dense as a solid- oceans exist. Liquid at room temperature bc of h bonds. Involved in metabolic reactions.

What is a hydrogen bond? Explain where they would be in H2O and H2O and NH3.

Hydrogen bonds are weak intra molecular forces between a polar H and an electronegative atom (F,O,N). H bonds in water between H and O and H2O and NH3 are between the O and the N.

Explain how ions form. Give an example. What is an ionic bond?

Ions form when two elements bond ionically and one element takes the other element's electrons to give them (hopefully) a full outer shell. Ex. NaCl. Cl takes Na's valence electron and makes Na+ and Cl-. These two combine and form an ionic bond which ionizes in water.

What's the general role of a buffer in biological systems?

Keep the pH within range for the biological process to occur. For example, enzymes only work in a certain pH range so keeping he pH in that range allows the enzyme to function and that is done by buffers.

Explain differences between (a) light and electron microscopy (b) TEM and SEM (c) fluorescence and white light microscopy

Light: visible light is passed through specimen and through glass lenses which refracts the light and magnifies the specimen Electron: focuses beam of e- thru specimen SEM: 3D TEM: Internal structure. 1D. Show cross sections Fluorescence: fluorescent tags. Cell parts are different colors.

Macrophages engulf and digest bacteria and debris non-specifically, while lymphocytes secrete very specific antibodies. What organelles should be abundant in macrophages? In lymphocytes?

Macrophages should have many lysosomes to break up the bacteria. Lymphocytes should have a lot of rough ER to make surface proteins on the plasma membrane and highly specific surface receptor proteins.

Explain fluid mosaic membrane structure.

Made of phospholipid bilayer. It's fluid because the membrane is flexible and often the phospholipids move around in the membrane. It is mosaic because there are proteins scattered about in the membrane.

Draw structure of 2 isomers of C4H10

Make sure bonds break!

Compare and contrast membrane, DNA, and cell wall structures in the three domains of life.

Membrane: Archaea: membrane has unique branched hydrocarbons in phospholipids. Prokarya: peptidoglycan in cell walls (membrane similar to EU) Eukarya: phospholipid bilayer. Membrane around organelles DNA: Archaea: one loop Prokarya: one loop Eukarya: multiple and linear Cell Wall: Archaea: Present Prokarya: present + peptidoglycan Eukarya: plant cells have animal none

Tell the main function of mitochondria and chloroplasts. In what ways are these two similar in structure? What are their evolutionary ancestors?

Mitochondria: 2/3 of cell respiration does Krebs cycle and ETC Chloroplasts: photosynthesis (Light reactions and calvin cycle) Both have their own DNA, compartments, and double membranes. Both were prokaryotes at one point that were specialized to do respiration and photosynthesis.

What is the definition of Molarity (M)? How would you make 1 L of of a 1M solution of NaCl? 1 L of a .5M NaCl?

Molarity is the concentration of the solute in M/L. I mole NaCl (44g) plus 1000mL of water. .5 is 22g plus 1000mL of water.

Biological evolution began with origin of what molecule?

Molecule of heredity

Proteins

Monomer: Amino Acids Polymer: polypeptide Linkage: Polypeptide bonds Ex: anything that ends in -in

Lipids

Monomer: Glycerol and Fatty Acids Linkage: Esther linkages Ex: oil, steroids, cholesterol Steroids not made by condensation can't be digested!!

Nucleic Acids

Monomer: Nucleotide (sugar, phosphate group, nitrogenous base) Linkage: Phosphodiester bonds Ex: DNA/RNA

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?

Muscle cells would have a high concentration of microfilaments for flexibility and structure. An absorption cell would have villi for extra surface area, transport proteins, vacuoles.

When a cell must exchange substances with its surroundings, what factors determine the upper limit on cell size? Why can eukaryotes be successful with greater cell volumes than prokaryotes?

Must be able to import nutrients and export waste. Must have bigger surface area than volume. Eukaryotes have a greater cell volume because they have compartmentalization to do cell processes.

Rank these bonds from most polar to least polar

O-H, N-H, C-H, O-O

What bonds are not broken in denaturation? Why does a denatured protein not function properly?

Peptide bonds are not broken in denaturation. A denatured protein does not work properly because it's shape is altered so it cannot perform it's function. ie. an enzyme with a specific active site will not have the same shaped active site after denaturation.

What is the main function of peroxisomes? Are they formed from the endomembrane system?

Peroxisomes use oxidation to break down hydrocarbon chains of fatty acids. These are then transported to mitochondria to help with cellular respiration. Product is a oxidized CH and H2O2. Not formed from endomembrane system. Constructed from protein subunits (free ribosomes) unlike lysosomes.

What are three components of a nucleotide? Where are the bonds joining these three parts, and through what reaction are nucleotides joined to make polymers?

Phosphate group, pentose sugar, and nitrogenous base. Covalent bonding on all parts and H bonds between two nitrogenous bases. Nucleotides are joined using condensation reactions. On 3' end of pentose, -OH group, on 5' end, phosphate group.

Hydroxyl (-OH)

Polar (H bonds) Involved in dehydration and hydrolysis

Amino (-NH2)

Polar (H bonds, ionic) Basic 1/2 of amino acid Positively charged if it gains an H+

Phosphate (-H2PO4)

Polar (H/ionic), Negative Charge Acidic Links nucleotides in DNA/RNA Energy carrier for ATP

Distinguish between polar covalent bonds and non polar covalent bonds based on electronegativity.

Polar covalent bonds are created with atoms that have very different electronegativities (O-H, N-H). They do not share e- equally so it ends up being slightly charged. Nonpolar covalent bonds have atoms with similar electronegativities (C-H, O-O, C-C). These share e- more equally and have no charge.

What are ribosomes made out of and what is their function? What's the difference between ribosomes in prokaryotic and eukaryotic cells? When is a ribosome bound vs free?

Ribosomes are made out of protein and rRna. Ribosomes in prokaryotes are smaller than ribosomes in eukaryotes and unable to be bound. A ribosome is free when it is floating in the cytosol. It is bound when it is on the ER.

Describe how ribosomes, rough ER, golgi and transport vesicles are involved together in the synthesis, chemical modification, trafficking, and export (secretion) of a protein hormone.

Ribosomes synthesize proteins which have a signal sequence that binds a signal reception protein that takes it into the Lumen of the ER. Signal cleaving enzyme cuts off the SRP and then the protein is folded. The ER pinches off into a vesicle and taken to the golgi, where it is modified in compartments. A transport vesicle takes the protein to the outer membrane where it is secreted.

Sulfhydryl (-SH)

Slightly Polar (H bond, disulfide) 2 SH R groups react to form disulfide bridge

Which organelle is involved in the synthesis of triglycerides?

Smooth ER

How do smooth and rough ER differ in structure and function?

Smooth has no ribosomes. Synthesis of lipids, metabolism of carbs, detoxifications of drugs and poison. Many smooth ER in liver cells. Rough: bound ribosomes make secretory proteins. Makes membrane.

What are isomers? Distinguish among (a) structural (b) geometric (c) enantiomers

Structural: differ in covalent arrangements of atoms/double bonds Geometric (cis-trans): Covalent bonds- differ in structure around a double bond Enantiomers: Mirror images due to asymmetrical carbon

Why do sugars readily dissolve in water?

Sugar is slightly polar bc OH group which is very soluble in water.

What steps must have occurred in the early earth during "chemical evolution"? What types of weak bonding between molecules could cause proteins and lipids in water to form spontaneous proto-cells?

Synthesis of organic molecules from volcanic eruptions and lightning strikes, meteorites carried it to earth. Made chain of organic molecules. Protocells- have phospholipid bilayer that forms spontaneously in water due to hydrophobic interactions. Random macromolecules.

How could you use cell fractionation and centrifugation in order to study distribution of certain molecules carrying specific labels and tags inside different types of organelles?

Tag the specific molecules and then homogenize and centrifuge. You know that the nucleus is densest and will come off first, then the mitochondria, then other microsomes, and then ribosomes.

Which of the four levels of structure is held by bonds between R groups

Tertiary

A protein fits in 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 should be uncharged, hydrophobic, and nonpolar.

*Using the example of an antibody specific to binding flu virus, tell how the structure of a protein, its specific conformation and surface properties, can be adapted to its specific function.

The antibodies have very specific surface proteins that bind to the surface proteins on the virus. The surface of the protein will have properties like polarity and a charge. These can be changed depending on the amino acid sequence. Receptor protein and complementary shape. R groups

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 enzyme should have both a complementary charge and shape. The shape should be a spherical indentation and the charge should be negative so the particle is attracted to it.

Trans fat vs. cis fat

Trans: H atoms are opposite of each other: making it unsaturated (stacks bc more linear) Cis: H atoms are same side. This makes it unsaturated

How do unsaturated and saturated fats differ in bonds and shape?

Unsaturated fats have at least one double bond between two carbons giving it a kink. This makes it unable to solidify at room temperature. Saturated fats have no double bonds making it solid at room temperature.

Explain, "It's not the heat, it's the humidity."

When there is a lot of moisture in the air, evaporative cooling does not work as well. Evaporative cooling usually keeps you cool.