BIO311C Final Exam
Alpha Linkage
-the -OH group is below the plane of sugars
ICA 5 Pictures
#1,2
ICA 6 Pictures
#1,2,3
ICA 3 Pictures
#1,2,3,4,5
Hydrophobic Interactions
(water fearing) normally non polar, lipid-soluble molecules that are excluded from aqueous solutions by hydrogen bonding among polar molecules
Hydrophilic Interactions
(water loving) substances are normally polar, charged molecules, soluble in water
Carbonyl Group:
-C=O
Methyl Group:
-CH3
Carboxyl Group:
-COOH
Amino Group:
-NH2
Hydroxyl Group: formula, functional group of, polar or non polar, soluble?
-OH, alcohols and carbohydrates, polar, easily soluble in water
Phosphate Group:
-OPO3^(2-)
Sulfhydryl Group:
-SH
Proteins:
-amino acids are the building blocks of all proteins. -all amino acids contain an amino group and a carboxylic group combined with different side chains -perform many vital functions in living organisms
Peptide Bond: What is it? How is it formed?
-bond formed between two amino acids during protein synthesis by ribosomes -formed by condensation synthesis
Polysaccharides: What is it? 2 Types?
-carbohydrate polymers with more than 10 linked monosaccharide monomers -Storage Polysaccharides: 1. Starch: alpha-1,4 linked glucose, amylase, and amylopectin found in plants. They are major storage products in potato,rice, wheat, and corn. 2. Glycogen: alpha,4-linked stored in the liver and muscles of animals. Both starch and glycogen are easily digestible by humans. -Structural Polysaccharides: 1. Cellulose: beta-1,4-linked glucose molecules.They are major constituents of plant cell walls. 2. Callose: beta-1,4-linked glucose molecules. Formed at wounding sites in plants. Shorter than cellulose. 3. Chitin: beta-1,4-linked N-acetyl glucosamine. Major structural component of exoskeletons of insects and cell walls of fungi. Chitin in fungal cell walls can be degraded by the chitinase enzyme made by plants as a part of defense mechanisms against fungi.
Carotenoids: What are they? Example.
-color pigments used for photosynthesis in plants and for vitamin-A synthesis in animals -example: beta-carotene
Disaccharide: What is it? Example.
-formed by enzymes that combine two monosaccharides through glycosidic linkages -maltose, lactose, sucrose
Triglycerides or Fats: What is it? Saturated vs. Unsaturated?
-glycerol (a three-carbon alcohol) combined with fatty acids (a long hydrocarbon chain with a -COOH group) which may be in the form of mono-, di-, or triglycerides, depending on the number of fatty acids it contains -Saturated Fat: 1. Fatty acid carbon chain saturated with H 2. No double bonds or kinks bonds between Cs 3. Usually solid at room temperature 4. Closely packed to each other 5. Most animal fats and tropical oils. Example: coconut oil -Unsaturated Fat: 1. Not saturated with H 2. One or more double bonds 3. Liquid at room temperature 4. Not so close 5. Most plant fats especially temperate oils Example: canola oil -The greater the saturation level of the hydrocarbon, the higher the Tm (melting point) of the fat.
Phospholipids: What is it? Solubility? Function?
-glycerol + two fatty acids + a phosphate group +another chemical group -both hydrophilic and hydrophobic (amphipathic) -separate different parts of cells and maintain the compartments of membrane-bound structures
Steroids: What are they? Example.
-lipids with 4 fused C-rings -example: cholesterol, hormones such as testosterone, and estradiol
Monosaccharides: What is it? How many carbons?
-smallest carbohydrates (mono=one, saccharum=sugar) -contains three to seven carbon atoms
What is the biological hierarchy? Levels and examples.
1. Atoms = C,H,O 2. Molecule = amino acid, sugars 3. Macromolecules = proteins, lipids 4. Parts of cells = membrane, nuclei 5. Cell = bacteria, yeast, skin cell 6. Tissue = epithelial tissue, bone 7. Organ = brain, heart 8. Organ System = immune system 9. Organism = human 10. Population = all individuals of a single species 11.. Ecosystem = collection of populations 12. Biomes = desert, forest 13. Biosphere = Living crust of the earth
Protein Structure: Types of structures?
1. Primary Structure: amino acid sequence of a protein. Stabilized by peptide bonds. 2. Secondary Structure: the amino acid chain of a protein, rather than being stretched out in linear form, is folded into arrangements (alpha and beta) 3. Tertiary Structure: three-dimensional structure of a protein. 4. Quaternary Structure: interaction of two or more polypeptides or subunits of multimeric proteins
Proteins can form enzymes that can do multiple things but they cannot replicate. On the other hand, DNA can replicate but cannot act as enzymes to catalyze reactions. Based on the 3-D structure of proteins and DNA that you know so far, speculate as to why. List the reasons.
1. Proteins are made up of 20 amino acids with various functional groups resulting in diverse 3-‐‐D structures capable of functioning as enzymes. 2. Proteins cannot replicate from another proteins because there is no system to use a template to make a protein complement or copy. 3. DNA on the other hand forms a fixed double helix structure with complementary base pairing of A with T and G with C through H-‐‐bonding which is easily separable. 4. Since the freely accessible functional groups of DNA are limited in numbers and restricted in access, they cannot perform enzymatic function. 5. DNA can replicate due to complementary base pairing as the double helix separates and each strand can be used as a template to make a complementary copy by enzymes.
What will be the minimum length of a gene (in basepairs) that can encode a protein of 100 amino acids?
300
How much NaOH (MW = 40) is needed (in grams) to make a 200 ml of 0.5 M solution?
4 grams
How much volume (in ml) of 10% SDS is needed to make 500 ml of 1% SDS?
50 mL
As the temperature decreases, the saturated fatty acid side chains in the membrane lipids will relatively become ________________than unsaturated fatty acid side chains. A) more rigid B) more fluid C) shorter D) longer E) more liquid
A
Of the following compounds containing 12C, 1H and/or 16O, which one would have the greatest number of molecules in a sample of 2 grams each? A. CH4 B. CO2 C. CH3OH D. C2H5OH E. C6H12O6
A
The following DNA sequences were obtained from three DNA fragments of same DNA sample, which overlap each other in terms of their sequence. The 5' refers to start and the 3' refers to end of the DNA strand. 5'-AGATCGATT-3' 5'-TCCGGATCG-3" 5'-GATTGTCCGG-3" What will be the DNA sequence obtained by assembling these three overlapping sequences? A) 5'- AGATCGATTGTCCGGATCG -3' B) 5'-TTGTCCGGCCATGGAGTGG -3' C) 5'-CGATTGTCCGGCCATGGAGT-3' D) 5'-GATCGATTGTCC TTGTCCG-3' E) 5'-GATCGATTGTCCGGCCATGG-3
A
How will you make a 200 ml solution of 5 mM sucrose from a 100 mM sucrose solution? A. Mix 20 ml of the 100 mM sucrose and 180 ml of water. B. Mix 10 ml of the 100 mM sucrose and 190 ml of water. C. Mix 1 ml of the 100 mM sucrose and 199 ml of water. D.Mix 2 ml of the 100 mM sucrose and 198 ml of water. E. Mix 50 ml of the 100 mM sucrose and 150 ml of water.
B
As the unsaturation of fatty acid increases due to fatty acid desaturase activity, the melting temperature of such modified fatty acid________________ A) increases B) decreases C) stays same D) will increase first and then decrease E) will decrease first and then increase
B
Consider a starch consisting of 25 glucose molecules. The complete hydrolysis of this polysaccharide would result in the production of A) 24 water molecules. B) 25 glucose molecules. C) 24 glucose molecules. D) A and B only E) A and C only
B
Lactose when digested, it is hydrolyzed by lactase into its monomers, which are thenabsorbed by blood. Following are test results from a person done after 2 hours of drinking a lactose rich solution. The blood glucose levels were 80, 110, 140 and 160 mg / dL tested forevery 30 minutes. Based on this information does this person have lactose intolerance? A) Yes, because the glucose level is normally stable in a person with lactose intolerance. B) No, because the glucose level is normally stable in a person with lactose intolerance. C) Yes, because the glucose level normally increases in a person with lactose intolerance. D) No, because the glucose level significantly increases in a person with lactose intolerance. E) Yes, because the glucose level significantly increases in a person with lactose intolerance.(repeat of C à also incorrect)
B
The molecular mass of glucose is 180 g/mole. How will you make 0.25 M glucose solution? A) Dissolve 180 g of glucose in 4L of water. (The total volume will exceed 4 L due to 180 g glucose solid being added and hence the concentration will not be correct) B) Dissolve 18 g of glucose in a small volume of water, and then add more water up to 400 ml. (180 g/mole x Unknown mole/L x 400ml/1000ml x 1 L = 18 g à 18 g/180x 0.4 = 0.25 mole/L) C) Dissolve 180 g of glucose in a small volume of water, and then add more water up to 500 ml. D) Dissolve 45 g of glucose in a small volume of water, and then add more water up to 2 L. E) Dissolve 250 g of glucose in a small volume of water, and then add more water up to 500 ml.
B
When Magnesium and chlorines with two electrons and seven electrons respectively in their valence shells interact, they will form ___. A. covalent bonds B. ionic bonds C. H-bonds D. van der waals forces E. hydrophobic interactions
B
Which of the following, if changed significantly, would affect all the others? A) RNA B) DNA C) Proteins D) A and B E) A, B and C
B
Which part of the atom mainly determines how the atom behaves chemically? A. proton B. electron C. neutron D. meson E. gluon
B
24) Triglycerides are made of glycerol and fatty acid by the formation of a (an) A) peptide bond B) H-bond C) ester linkage D) phosphodiester bond E) glycosidic linkage
C
Carbonic acid and sodium bicarbonate act as buffers in the blood. When a small amount of acid is added to this blood, the H+ ions are used up as they combine with the bicarbonate ions. When this happens, the pH of the blood __________. A. becomes basic. B. becomes acidic. C. does not change much. D. is drastically changed E. will decrease significantly
C
Lysozyme is an enzyme made up of a single polypeptide with antibacterial activity and it is present in egg white, saliva and mucus. What is the highest level of 3-D structure found in lysozyme? A) Primary B) Secondary C) Tertiary. D) Quaternary. (Only complex proteins, i.e. more than one subunit would form this)
C
What will be the highest level of protein 3-D structure in a single protein such as lysozyme? A) Primary B) Secondary C) Tertiary D) Quaternary
C
When water freezes to form ice, the ___ connect the water molecules. A. covalent bonds B. ionic bonds C. H-bonds D. van der waals forces E. hydrophobic interactions
C
Which bonds will break when water evaporates? A. covalent bonds B. ionic bonds C. H-bonds D. van der waals forces E. hydrophobic interactions
C
Which of the following example correctly represents the biological hierarchy of organization? A) atoms - molecules - trunk - muscles -amino acids - proteins B) elephant - trunk - muscles - amino acids - proteins - atoms C) atoms - amino acids- proteins - cells - muscle - trunk - elephant D) muscle - amino acids- proteins - mitochondria- muscle - trunk E) atoms - muscles - mitochondria - proteins - elephant - trunk
C
Which of the following is not true of DNA double helix molecule? A) The bases are held together by hydrogen bonds. B) Nucleotides are attached through a phosphate in each strand. C) DNA contains ribose and deoxyribose in opposite strands. D) RNA contains uracil but DNA contains thymine instead. E) DNA double helix can be separated by changing pH
C
Which of the following molecule will be the most amphipathic (containing both polar and nonpolar groups) and a major component of biological membranes? A) Glucose B) Carotenoid C) Phospholipid D) Starch E) Triglyceride
C
Which of the following molecule will have the molecular formula C12H22O11? A) A polysaccharide B) A polypeptide C) A disaccharide D) A Monosaccharide E) An Amino Acid
C
Which of the following molecules is most polar? A. CO2 B. CH4 C. CH3OH D. C2H6 E. O2
C
Which of the following refers to the 5' and 3' of a DNA strand respectively? A) The 5th phosphate and third phosphate of the nucleotide B) The 5th carbon and third nitrogen respectively of the nucleoside C) The 5th carbon and third carbon of the deoxyribose D) The 5th carbon and third carbon of the ribose E) The 5th carbon and third phosphate of the deoxyribose
C
A solution contains 0.001 moles of hydroxide ions [OH-] per liter. Which of the following best describes this solution? A. Slightly acidic B. Slightly basic C. Strongly acidic D. Strongly basic E. Neutral in pH
D
Humans are unable to digest cellulose fibers but can digest starch because humans have enzymes that can digest only ____________. A) peptide bonds but not glycosidic bonds B) beta-1,4 glycosidic linkage but not alpha-1,4 glycosidic linkages. C) nonpolar covalent bonds but not polar covalent bonds D) alpha-1,4 glycosidic linkage but not beta-1,4 glycosidic linkages. E) ionic bonds but not covalent bonds
D
If 128 molecules of glucoses were covalently joined together, what would be the resulting molecule(s)? A) A polysaccharide B) A polypeptide C) 127 water molecules D) Both A and C E) Both B and C
D
Nitrogen and oxygen are much more electronegative than hydrogen. Which of the following statements is correct about the interactions between ammonia and water? The ammonia and water molecules will interact and form ____________________ between each molecule. A) polar covalent bonds B) non-polar covalent bonds C) ionic bonds D) hydrogen bonds E) hydrophobic interactions
D
What is the main difference between nucleoside and nucleotide? A) a nitrogenous base B) a pentose sugar C) an amino acid D) a phosphate group E) a nitrogenous base and a pentose sugar
D
What is the most common functional group present in all monosaccharides (in both linear and ring form) that makes simple sugars polar and easily soluble in water? A) Amine B) Carbonyl C) Carboxyl D) Hydroxyl E) Phosphate
D
What will the interaction between the side chains of leucine and isoleucine within a protein surrounded by aqueous solution? A) H-Bond B) Ionic bond C) Covalent bond D) Hydrophobic attraction E) Hydrophilic attraction
D
When the amino acid glycine with H in its side chain is placed in water it A) would function only as a base because of the amino group. B) is impossible to determine how it would function. C) would function as neither an acid nor a base. D) would function as both an acid and a base. (Because the -NH2 and -COOH groups are present in every amino acid) E) would function only as an acid.
D
When the water molecules evaporate to cool your body, which of the following bond/interaction is broken? A) hydrophobic interaction B) ionic bond C) nonpolar covalent bond D) hydrogen bond E) polar covalent bond
D
When you are scrambling an egg for breakfast, in which order you will be breaking the bonds in the protein and lipid molecules in the egg? Not all bonds and molecules may be included in the choices given below. A) Peptide/ester bonds first and then hydrogen bonds followed by hydrophobic interactions. B) Hydrogen bonds and then hydrophobic interactions followed by Van der Waals forces. C) Ionic bonds and then peptide/ester bonds and then hydrogen bonds. D) Van der Waals forces and then ionic bonds followed by peptide/ester bonds. E) Hydrophobic interactions and then peptide/ester bonds followed by hydrogen bonds.
D
Which bond connects the nucleotides in a single strand of RNA? A) peptide bond B) H-bond C) ester linkage D) phosphodiester bond E) glycosidic linkage
D
Which of the following best summarizes the relationship between condensation synthesis and hydrolysis? A) Condensation synthesis occurs only after hydrolysis. B) Hydrolysis creates monomers, and condensation synthesis break down polymers. C) Hydrolysis only occurs in the urinary system, and condensation synthesis only occurs in the digestive tract. D) Condensation synthesis assembles polymers, and hydrolysis breaks down polymers. E) Both A and C are correct.
D
Which of the following is the correct ranking of the three bonds and interactions in order from highest to lowest in terms of their bond strength between two side chains of a protein in their tertiary structure? I. Disulfide bond between two cystines II. Hydrophobic interactions between two leucines III ionic bonding between positive and negatively charged amino acids A) I, II, III B) II, III, I C) III, II, I D) I, III, II E) III, I, II
D
Which of the following molecules can form a monoglyceride through ester linkage by condensation synthesis? A) glucose and fructose B) cellulose and carotenoid C) fructose and saturated fats D) glycerol and an unsaturated fatty acid E) glycerol and cholesterol
D
Which of the following statements is (are) true about hydroxyl group? A) It is negatively charged. B) It has properties of an acid. C) it has properties of a base. D) it is hydrophilic. E) It is hydrophobic.
D
Which of the following structure is stabilized by H-bonds? A) Phosphodiester linkage of DNA B) α 1-4 linkage of the β glucose monomers C) Ester bond of triglyceride D) Complementary base pairing of RNA strand E) Amino acid sequence of a polypeptide
D
Which of the following will be an RNA strand that would be complementary to the DNAtemplate strand, 3'-ATCGGACGTAG-5'? A) 5'-ATCGGACGTAG-3' B) 5'-UACGGACGUAG-3' C) 3'-ATCGGACGTAG-5' D) 5'-UAGCCUGCAUC-3' E) 3'-UAGCCUGCAUC-5'
D
You are trying to label (attach a tag) to only proteins and not other molecules such as DNA, RNA or carbohydrates, in a bacterial cell. Which of the following radioactive compound you can add to the culture media to label only proteins? A) radioactive nitrogen B) radioactive uracil C) a radioactive hydrocarbon such as benzene D) a radioactive sulfur (S is not present in carbs, lipids or DNA) E) a radioactive hydrogen
D
Which of the following element will not label polysaccharide NAM-NAG in bacterial cell wall? A) Hydrogen B) Nitrogen C) Oxygen D) Carbon E) Sulfur
E
The side chain of leucine mainly contains -CH3 groups. In a folded protein, where would you expect to find leucine?A) In the interior of a cytoplasmic enzyme (-methyl being non-polar - hydrophobic) B) On the exterior of a membrane protein near phosphate groups C) On the interior of a membrane protein near fatty acid side chains (in a cell membrane) D) Both a and b are possible E) Both a and c are possible (Best and correct answer)
E
Which of the following list includes the components of the monomers used to make DNA and RNA? A) a nitrogenous base and a phosphate group B) a nitrogenous base and a pentose sugar C) a pentose sugar and a purine or pyrimidine D) a phosphate group and an adenine or uracil E) a nitrogenous base, a phosphate group, and a pentose sugar
E
Which of the following properties of water is the most essential to support life? A. Ability to maintain pH B. H-bonding property C. High specific temperature D. Good solvent for both polar and non-polar substances E. Medium and a reactant for biochemical reactions
E
Carbohydrates: Elements in carbohydrates and ratio, function, stored as in plant cells, stored as in animal cells
Elements: -carbon, hydrogen, oxygen (C:H2:O) Function: -major source of energy for cells Plant Cells: -Starch Animal Cells: -glycogen (The names of carbohydrates end in -ose.)
Nucleic Acids: Functions? Two Kinds? What are they made of?
Functions: -nucleotide ATP is the major form of cellular energy -nucleotides can accept and transport electrons -some nucleotides serve as signal molecules -hereditary Two Kinds: -Ribonucleic Acid (RNA) made of nucleotides = nitrogenous base + ribose + phosphate group -single stranded with a complex and variable secondary structure -A:U and G:C -Deoxyribonucleic Acid (DNA) made of deoxynucleotides = nitrogenous base + deoxyribose + phosphate group -double stranded with a consistent double helix structure -A:T and G:C
Lipids: Functions, polarity, solubility, three major types?
Functions: -storage of energy -insulation against heat loss and cushioning for vital organs -serve as vitamins, pigments, growth hormones, or regulators -structural component of the lipid bilayer of biological membranes Polarity: -non polar Solubility: -hydrophobic (do not mix with water) -soluble in organic solvents Three major types: -Triglycerides or Fats -Phospholipids -Others = Carotenoids and Steroids
when water evaporates which of the following bonds /interaction is broken
H bond
Which of the following is the correct ranking of the three bonds and interactions in order from highest to lowest in terms of their bond strength between two side chains of a protein in their tertiary structure? I. Disulfide bond between two cystines II. Hydrophobic interactions between two leucines III. H-bonding in water
I, III, II
Functional Groups
atoms or groups of atoms covalently bonded to the carbon skeleton
Ionic Bonds
bonding due to attraction of positive and negative charges (weaker than covalent bonds) (example: NaCl)
Hydrolysis
breaking down dimers, trimers or polymers into monomers by adding an -H and an -OH group derived from the splitting of a water molecule
What are the four major groups of biological molecules?
carbohydrates, lipids, proteins, and nucleic acids
mRNA (messenger)
carries information from DNA to be translated into protein
Condensation Synthesis
creates bonds between the monomers in carbohydrates, lipids, and proteins
H-Bonding
electrostatic attraction between polar molecules that occurs when a hydrogen (H) atom bound to a highly electronegative atom such as nitrogen (N), oxygen (O) or fluorine (F) experiences attraction to some other nearby highly electronegative atom (example: NH3)
tRNA (transfer)
involved in transferring amino acids during protein synthesis
rRNA (ribosomal)
major part of ribosomes involved in protein synthesis
Cellulose
one of the primary constituents of plant cell walls
vaccination against flu is advised to those who may be exposed to flu especially children and elderly people which of the following level of biological hierarchy the flu vaccination is done at an individual level
organism
Polypeptide:
protein containing many amino acids connected by peptide bonds
a solution contains .1o moles of hydrogen moles per liter which of the following best describes this solution
strongly acidic
several new medicines are tested to treat drug resistant TB some of the participants received drug abc or a sugar pill as a placebo which of the following is considered as a negative control
sugar pill or placebo
Beta Linkages
the -OH group is above the plane of sugars
Covalent Bonds (polar and non polar)
two atoms which share a pair of electrons polar = two atoms share electrons unequally (example: H2O) non polar = two atoms which share electrons equally (example: H2)
when you scramble eggs the bond and proteins will break in which of the following order
van der walls , h bonds, and ionic bonds
Van der Waals Interactions
weakest bond with temporary changes (example: lipids)
