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UH / Biology / BIOL 1361 / Why do most polar covalent bonds involve nitrogen or oxygen?

Why do most polar covalent bonds involve nitrogen or oxygen?

Why do most polar covalent bonds involve nitrogen or oxygen?

Description

BIOL 1361 Fall 2018


Why do most polar covalent bonds involve nitrogen or oxygen?



Exam 1 Preparation

Exam 1 covers Chapters 1 – 4, 6, 7, 41

Concepts

Chapter 1, end of chapter: Q2

What does it mean to say that experimental conditions are controlled? It means that all physical conditions except for one are identical for all groups tested. Chapter 2, blue text in Fig. 2.7

Why do most polar covalent bonds involve nitrogen or oxygen? Oxygen and  nitrogen have high electronegativities. They hold shared electrons more tightly  than C, H, and many other atoms, resulting in polar bonds.

Chapter 2, section 2.3 Check Your Understanding Q2

CH4 + 2O2  CO2 + 2H2O


What type of bond is directly involved in the formation of an alpha-helix?



Determine if the reaction above is spontaneous or not, addressing both potential  energy and entropy.

The reactants have higher chemical energy than the products. The entropy,  however is not increased or decreased based only on the number of molecules  involved. The heat given off from this reaction would lead to increased entropy in the environment. Overall, the reaction would be spontaneous based on the  change in potential energy. If you want to learn more check out What is the painting bronzino's venus, cupid, folly, and time mannerism, about 1546, all about?
We also discuss several other topics like How is the consumer price index (cpi) calculated?

Chapter 2, blue text in Fig. 2.20

Which parts of the apparatus mimic the ocean, atmosphere, rain, and lightning? The water-filled flask is the ocean; the gas-filled flask is the atmosphere; the  condensed water droplets are rain; the electrical sparks are lighting. Chapter 3, blue text in Fig. 3.2


What determines the primary structure of a dna molecule?



Based on the relative electronegatives of O, N, C, S, and H, explain why the R groups highlighted in green are nonpolar and why R-groups highlighted in pink  are polar.

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BIOL 1361 Fall 2018

The R-groups shaded in green contain mostly C and H, which have roughly equal  electronegativities. Electrons are evenly shared in C-H bonds and C-S bonds, so  the groups are nonpolar. All of the R-groups shaded in pink have a highly  electronegative oxygen atom with a partial negative charge, making them polar.

Chapter 3, section 3.1 Check Your Understanding blue text Draw the structural formula for two glycine residues (glycine’s R-group is an H)  linked by a peptide bond and label the amino and carboxy terminus. We also discuss several other topics like What are the cell junctions?

Chapter 3, section 3.2 Check Your Understanding Q2

Predict where amino acid residues with nonpolar R-groups would be found within the overall structure of a protein such as chymotrypsin, shown in Figure 3.8d.  Nonpolar amino acid residues would be found in the interior of a globular protein  like trypsin, grouped with other nonpolar residues due to hydrophobic  interactions.

Chapter 3, end of chapter  

Question 1  

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What two functional groups are bonded to the central carbon of every free amino  acid monomer? An amino group and a carboxyl group.

Question 2 We also discuss several other topics like He believed that psychology needed to become a verifiable science; who is he?

What type of bond is directly involved in the formation of an alpha-helix? Hydrogen  bonds between amino acid residues.

Question 7

Why are proteins not considered to be a good candidate for the first living  molecule? They cannot serve as a template for replication.

Chapter 4, section 4.1 Check Your Understanding Q1

Draw a simplified diagram of the phosphodiester linkage between two nucleotides,  indicate the 5’ to 3’ polarity, and mark where the next nucleotide would be  added to the growing chain.

Chapter 4, end of chapter  

Question 2

What determines the primary structure of a DNA molecule? Deoxyribonucleotide  sequence. If you want to learn more check out The brain is made up of how many cells?

Question 4

Single strands of nucleic acids are directional, meaning that there are two different  ends. What functional groups define the two different ends of a strand? One end  has a free phosphate group on the 5’ carbon and the other end has a free  hydroxyl group bonded to the 3’ carbon.

Question 7

What would be the sequence of the strand of DNA that is made from the following  template: 5’ -GATATCGAT-3’? How would the sequence be different if RNA were  made from this DNA template? The DNA sequence of the new strand would be  5’-ATCGATATC-3’. The RNA sequence would be the same, except each T would be

replaced by a U.

Chapter 6, section 6.1 Check Your Understanding Q2

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Compare and contrast the structure of a steroid, a fat, and a phospholipid. Steroids  have a distinctive four-ring structure with variable side groups attached; fats  consist of three fatty acids linked to glycerol; many phospholipids also have a  

glycerol linked to fatty acids, but instead of three fatty acids, they have two plus  a hydrophilic, phosphate – containing “head” region.

Chapter 6, end of chapter

Question 2

If a solution surrounding a cell is hypertonic relative to the inside of the cell, how will water move? It will move out of the cell via osmosis. Don't forget about the age old question of What will be used for the sampling frame?

Question 3

What two conditions must be present for osmosis to occur? For osmosis to occur, a  concentration gradient and a membrane that allows water to pass, but not the  solute, must be present.

Question 4

Integral membrane proteins are anchored in lipid bilayers. Which of the following  groups of amino acid residues would likely be found in the portion that crosses  the lipid bilayers? nonpolar.

Question 8

Suppose a cell is placed in a solution with a high concentration of potassium and no  sodium. How would the cellular sodium-potassium pump function in this  environment? It would continue using ATP to pump sodium out of the cell and  potassium into the cell.

Question 9

In an experiment, you want to create two groups of liposomes in a solution  containing 0.1 NaCl – one made from red blood cell membranes and the other  from frog egg cell membranes. When the liposomes are placed in water, those  with red blood cell membranes burst more rapidly than those made from egg  membranes. Evaluate each of the following statements and identify those that  could explain these results.

T/F The red blood cell liposomes are more hypertonic relative to water than the frog  egg liposomes.

T/F The red blood cell liposomes are more hypotonic relative to water than the frog  egg liposomes.

T/F The red blood cell liposomes contain more aquaporins than the frog egg  liposomes.

T/F The frog egg liposomes contain ion channels, which are not present in the red  blood cell liposomes.

The first two response are false because the interior solution in both sets of  liposomes is the same. The third response is true because aquaporins allow for  an increased rate of water transport. The fourth response is true because if the  Na or Cl ions can cross the membrane in frog eggs, then osmosis may be  reduced or even be prevented from occurring.

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Themes in Biology & the Scientific method (Ch 1 & ant case)

∙ List characteristics shared by all living things

o Cells: organisms are made up of membrane-bound organelles o Energy: to stay alive & reproduce, organism acquire or use energy o Information: organism process hereditary or genetic information encoded  

in their genes, respond to information from environment & adjust to  maintain homeostasis

o Replication: can reproduce

o Evolution: organisms are product of evolution; population continue to  evolve

∙ Explain the difference between a hypothesis and prediction

o A prediction is more of a guess, concerning a particular outcome, based  off of observations.

o A hypothesis includes a possible explanation for what is being  seen/observed, or something else that could be tested in addition through  further experiments.

Digestion & Absorption (Ch 41)

∙ Distinguish regions of the alimentary canal and accessory glands by function:  digestion, secretion, or absorption

1. Alimentary canal: Begins at the mouth and ends at the anus

2. Digestion: The breakdown of food

3. Absorption: The uptake of specific ions and molecules across the epithelium  that lines the digestive tract.

4. Salivary glands: Contains amylase, helps with the breakdown of starch in food  in the mouth; Saliva is intended to moisten, digest, and cleanse. 5. Pancreas: Secretes enzymes to aid in digestion; Proteases help digest the  proteins, amylase digests the sugars/carbohydrates, and the lipases helps digest the fat.

6. Liver: Intended to process nutrients absorbed from small intestine; bile from  liver is secreted into small intestine, also helping to digest fat.

7. Gallbladder: Holds bile that is produced in liver until it is needed for digesting  fatty foods in the duodenum of the small intestine.

∙ Name the digestive secretions released into the mouth, stomach, duodenum o Mouth:

o salivary amylase – breaks down food chemically

o mucus – lubrication of mouth, pharynx, and esophagus

 o Hormone Gastrin: stimulated by food; secreted by stomach; increases HCl, pepsin and mucus

 o Hormone Secretin: stimulated by acids; secreted by Duodenum; targets  stomach and pancreas; increases HCO3 – in pancreases and decreases  gastric juices (stomach)

 o Hormone Cholecystokinin: stimulated by amino acids and fats; secreted by duodenum; increases enzymes (pancreas), increase bile (gallbladder),  decreases gastric juices and pyloric openings (stomach)

∙ Name the source of each digestive secretion and state its function 5

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∙ Identify types of biomolecules in particular foods

o carbohydrates

o nucleic acids

o proteins  

o lipids

∙ List types of biomolecules digested in each digestive compartment: mouth,  stomach, duodenum

o Mouth:

o starches (carbohydrates) due to salivary amylase

o Stomach:  

o protein

o Duodenum:

o peptides, lipids, sugars and nucleic acids

∙ List what is absorbed in each compartment, explain how absorption occurs for  different molecules: water, glucose, amino acids, fats

o Small intestine  

o glucose, amino acids and fats

 jejunum and ileum absorb

 monosaccharides, fatty acids, monoglycerides, amino acids,  and water

 Monosaccharides (single sugar): fructose, glucose

 fatty acids part of fats

 monoglycerides (one glyceride): fats

o Large intestine

o water and (vitamins)

 home to bacterial community (gut microbes) that produce  

vitamin K, biotin, and folic acid

∙ Relate structure of gastrovascular cavities and alimentary canals to variables in  Fick’s Law of Diffusion

o Gastrovascular cavities: serves the dual purpose of digestion and nutrient  transport and is the only opening for two major animal phyla: Cnidaria  (jellyfish), and Platyhelminthes (flatworms). Here the body wall, that  surrounds the central cavity; is only two cells thick, which is relatively thin, allowing for a higher rate of diffusion.

o Alimentary canal/Digestive tract: The pathway food takes from the mouth  to the anus. Material exchange, generally through diffusion, takes place at the small intestine of our body. Digested material is transported in blood  vessels through the walls of small intestine by diffusion. Small intestines  have very large surface area. Not only are these several folds, there are  also very many villi and microvilli, allowing for an increased rate of  diffusion.

∙ Describe the structure of the intestinal lining

o villus (shag carpet structure) are finger-like projection of intestinal lining. o made of epithelial cells, connective tissue, capillaries, and lymph  duct (transports fats)

o Microvillus points towards intestinal lumen; sticks into food in intestine. 6

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o Are tiny finger-like projection of apical membrane of intestinal  epithelial cells, containing many transport proteins (part of a single  cell)

∙ Explain how structure of the intestinal lining enhances surface area o Microvilli [wavy cell membrane] helps to increase surface area ∙ Trace digestion and absorption of each component of a meal through the human  digestive tract

o Ingestion, mouth, pharynx, salivary glands, epiglottis, trachea, esophagus, esophageal sphincters, diaphragm, stomach, pyloric sphincter, liver,  gallbladder, bile duct, appendix, small intestine, ileocecal valve  (sphincter) pancreas, pancreatic duct, large intestine, rectum, and anus  

∙ Explain the function of epithelia in each digestive compartment o absorbs nutrients and water

o Duodenum:

o Some enzymes made by intestinal epithelium:

 HCO3- (bicarbonate) neutralizes stomach acid  

 Pancreatic enzymes: proteases (digest proteins), lipases  

(digests fats and lipids), carbohydrases (digest  

carbohydrates)

 Liver secretions: Biles (emulsifies fats)

∙ Explain the function of tight junctions in epithelia in relation to digestion and  absorption

o Plasma membranes of neighboring epithelial cells bound together by  proteins

o Form a continuous seal around the cells

o Separate the outside fluids from inside body

∙ Predict the effect of an increase or decrease in each variable in Fick’s Law of  Diffusion on nutrient and water absorption in the small intestine o Fick’s Law of Diffusion:

o Qs = DA ([C2-C1]/X) t

 Qs = Quantity of Substance

 D = Diffusion of Coefficient (depending on permeability and  

temperature)

 *not always same; differs on temperature and material

of membrane*

 A = Area of Surface

 C2 – C1 = Concentration Gradient (Absolute value; one side – other side)

 X = Surface thickness

 t = time

- As A increases, the larger surface area would increase diffusion rate. - As distance over which diffusion occurs, D, decreases, the diffusion rate would  increase.

- As the pressure difference between the two sides increases, so does the diffusion  rate.

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∙ Trace transfer of biomolecules from intestine into blood or lymph and into organs o The capillaries and veins that carry nutrient rich blood away from the villi  converge into hepatic portal vein, a blood vessel that leads directly to the  liver. From the liver, blood vessels travel to the heart and then to the other tissues and organs.

o Ex: Sugar fructose moves by facilitated diffusion down to its concentration gradient from the lumen into the epithelial cells. From there, fructose exits the basal surface and is absorbed into microscopic vessels or capillaries at the core of each villus.

Lipids & Cell Membranes (Ch 6)

∙ Identify the type of lipid based on a structural diagram: fat, phospholipid, or  steroid

o Steroids:

o 4 ring carbon structure

 Three 6 carbon rings, one 5 carbon ring (“Three hexagons and a  house”)

o Animal cell membranes contain cholesterol

 Same as anabolic steroids

o Fatty acids

o Carboxyl group (COOH) linked to a hydrocarbon chain

o Saturated:

 All C atoms linked by single covalent bonds

 All C are bonded to maximum number of H (= “saturated”)

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 solid or semi-solid at room temperature

 ex: butter and margarine

 Happens because structure CAN fit tightly together

o Unsaturated:  

 Have bent tail (due to double bond of Carbon)

 Some C atoms linked by double bonds

 Can have more than one double bond in fatty acids

 C skeleton is not saturated with H

 Liquid at room temperature

 Coconut oil will be solid when cooler, liquid when warmer

o Fats:

o Glycerol linked to 3 fatty acids (wax is fat)

o energy storage in plants and animals

o Phospholipids:

o Glycerol + 2 fatty acids + phosphate & choline

∙ Know the function of fats, phospholipids, and steroids

o Fats:

o Protection, insulation, and is an energy source

 Triglycerides constitute 95% of fats in human body, consisting of two different types of building blocks: one glycerol and three  

fatty acids

o Phospholipids:

o Important structural component of cell membranes

o Steroids:

o physiology regulators and components of cell membranes

∙ Draw a saturated and an unsaturated hydrocarbon

∙ Distinguish between saturated and unsaturated fatty acids

SATURATED

Unsaturated

∙ ALL CARBON ATOMS ARE  

LINKED BY SINGLE COVALENT

∙ Some carbon atoms are linked by  DOUBLE bonds

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BONDS

∙ ALL CARBONS ARE BONDED TO A MAXIMUM NUMBER OF  

HYDROGENS

∙ SOLID/ SEMI-SOLID AT ROOM  TEMPERATURE

∙ MORE LONG SATURATED FATTY ACIDS = LESS FLUID/  

PERMEABLE

∙ Carbon skeleton is NOT saturated  with Hydrogen as C-H bond is  

removed to form a C=C double  

bond

∙ Has a KINK

∙ Liquid at room temperature

∙ More short unsaturated fatty acids = more fluid/ permeable

∙ Define monomer and polymer

o monomer: A small molecule that can covalently bind to other similar  molecules to form a larger macromolecule

o polymer: Any large molecule composed of small repeating units  (monomers) bonded together

 The main biological polymers are proteins, nucleic acids, and  

polysaccharides

∙ Explain why lipids are not polymers

o Polymers are several smaller, similar units (monomers) that together in a  chain create a larger molecule with new properties

o Macromolecules are giant molecules that are produced by the bonding of  smaller molecules

 Carbs, lipids, proteins, and nucleic acids are considered to be  

macromolecules

o However, lipids are not considered to be polymers, because lipids do not  contain monomers and polymers are made up out of monomers

 Moreover, basic units of lipids are fatty acids and glycerol  

molecules, which do not form repetitive chains (thus lipids contain  non-similar units)

o A property of monomers is also that bonds dissolve in water.

 This is the case for proteins and carbohydrates, but not for lipids  (which does not dissolve in water).

∙ Explain the fluid mosaic model of cell membrane structure

o Bilayer Formation:

 Phospholipids spontaneously form a bilayer in aqueous solution  Will face water in aqueous solution (water will be at  

hydrophilic head)

 Hydrophobic tails associate with each other

 Hydrophilic heads interact with aqueous solution

∙ Define selective permeability

o some substances can cross the bilayer

 There are pores that allow substances to cross

o Depending on size, polarity, and charge of substance

 polar molecules: have two atoms that have plentiful  

electronegativity; tug of war between electron atoms

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 partial positive and partial negative charges

 hydrophilic (dissolves well in water)

 some ions can be 2+ or 2-  

 non-polar molecule: covalent bond where electrons are shared  equally among atoms

 no positive or negative charges

 hydrophobic (dissolves well in lipid)

∙ Define active transport

o The movement of ions or molecules across a membrane in a single  direction, often against a gradient

 Requires energy (e.g., from hydrolysis of ATP) and assistance of a  transport protein (e.g., pump).

∙ Explain how Na+-K+ ATPase creates an ion gradient across the cell membrane 1. 3 Na+ binds to intracellular side of protein

2. Na+ - K+ ATPase removes phosphate group from ATP

 catalyzes removal of Na+ 

3. ATP-ase changes shape and ADP is released into cytosol

 Shaking look = changing shape

4. 3 Na+ are transferred outside cell

 Exposes potassium sites

5. 2 K+ enter open extracellular gate

6. 2 K+ bind to ATPase

7. PO4 (Phosphate) group is released from ATPase; extracellular gate closes,  intracellular gate opens

8. 2 K+ enter cell

 Affinity of sodium-potassium ATPase is only for sodium and  

potassium, not for any other molecules

∙ Define diffusion & osmosis

o Diffusion: Random movement of molecules

o Osmosis: Diffusion of water across a membrane that is permeable to  water, but impermeable to most solutes

 Water molecules move toward area of high solute concentration  toward “dehydrated” or “thirstier” solution

∙ Compare diffusion and osmosis, giving examples of substances that cross the  membrane by each process

Diffusion

Osmosis

∙ Solutes on one side can move to  other side spontaneously

∙ Diffusion down concentration  gradient/ away from higher  

concentration = spontaneous  

because increase in entropy

∙ At equilibrium molecules continue  to move back & forth across the

∙ Unbounded water molecules can  move across permeable  

membrane

∙ Flow to the higher concentration ∙ Movement of water is  

spontaneous as it is driven by the  increase of entropy

∙ Hypotonic: solution inside

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membrane at equal rates

membrane has lower  

concentration of solutes than  

exterior; water moves out of the  vesicle and into solution outside  vesicle shrinks

∙ Hypertonic: solution inside  

membrane has higher  

concentration of solutes than  

exterior, water moves into vesicle   swells

∙ Isotonic: solute concentration is  equal on both sides

∙ Define passive transport

o Diffusion of a substance across a membrane

o When this event occurs with the assistance of membrane proteins,  it is called facilitated diffusion

∙ Define facilitated diffusion

o Hydrophilic substances cross cell membrane from high to low  concentration by passing through channel or transport proteins

∙ Explain how water crosses the cell membrane

o hypertonic solution: Water moves from inside to outside

 Water moves towards the higher solute concentration, which is  outside

 Leads to cell shriveling

 Pressure decreases, volume decreases

o hypotonic solution: Water moves from outside the cell to inside the cell  higher solute concentration is inside the cell; water moves towards  it

 leads to cell swelling, leading to cell lysing (bursting of cell)

 pressure increases, volume increases, vesicle bursts

o isotonic solution: Water equally diffuses from outside of cell to inside  and inside to outside

 equal amounts of solute concentration both on outside and inside of cells (no net change of solute)

 Cell retains normal shape

 Pressure inside stays the same

∙ Explain why co-transport is a type of active transport

o One of the solutes moved by the cotransporter is actively transported  against its concentration gradient

 The energy for this transport comes from the concentration  

gradient of the other solute, which was established by an  

electrogenic pump (proton pump) that used energy to transport the  other solute across the membrane

∙ Compare transport by a carrier protein vs transport by a channel protein 12

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Carrier Proteins

Channel Proteins

∙ Facilitated diffusion – specialized  membrane proteins that change  shape during the transport  

process

∙ Polar molecule attaches to one  side of protein  protein changes  shape, moves substance across  

cell membrane

∙ Ion channels from pores or  

openings in a membrane, ions  

move through these pores in a  

predictable direction: from regions of high concentration to regions of low concentration and from areas  of like charge to area of unlike  

charge

∙ Channel proteins are selective –  Each channel protein has a  

structure that permits only a  

particular type of ion or small  

molecule to pass through it

∙ EX: aquaporins allow water to  cross faster

∙ Gated channels: they open/close  in response to a signal

∙ Enable ions/polar molecules to  move across bilayer in response to existing gradient = responsible for FACILITATED diffusion = no energy

∙ Predict changes in intracellular solute concentrations and cellular volume if the  cell adds or removes certain types of transport proteins to or from the  membrane (some examples below)

GLUT1 (see fig. 6.24 and section 6.4); aquaporin (fig. 6.22); passive K+  channel (not gated)

∙ Glucose binds to GLUT-1, it changes shape of protein in a way that  moves the sugar through the hydrophobic region of membrane and  releases it to the other side

o Diffusion powers that movement

o GLUT-1 facilitates diffusion by allowing glucose to enter the carrier  from either side of membrane

o Glucose will pass through carrier in the direction dictated by  

concentration gradient

∙ Aquaporins have pore that is lined with polar functional groups =  carbonyl groups that interact with water

o Channel’s pore = hydrophilic relative to the hydrophobic  

residues facing the phospholipid tails of membrane

o Key side chains in interior of pore function as a molecular filter o Distance between these groups across the channel allows only  those substances capable of interacting with all of them to pass  

through other side

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∙ Carbohydrates

o Location of carbonyl group

o Number of carbon atoms present

o Spatial arrangement of atoms – relative position of (-OH) groups ∙ Reactions

o tightly = more electronegativity = low potential energy

∙ (+) and polar = hydrophilic = dissolve in water

∙ (-) and nonpolar = hydrophobic – maintains shape and bond with one  another  

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Biomolecules (Ch 2, 3, 4)

Note: “Identify” means correctly name or label the item, given a drawing of it.  ∙ Draw the general structural formula (letter to represent atoms, lines to represent bonds) of the 3 types of carbon skeletons

∙ Identify each of the 6 functional groups within a biomolecule, given a structural  diagram  

∙ Name the properties of each functional group: polar, non-polar, acid, base,  negative charge

o Amino Group

 Tend to attract

 Base

 Participate in Hydrogen bonding

o Carboxyl Group

 Acid

 Lose protons

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 Participate in Hydrogen bonding

o Carbonyl Group

 Found on aldehyde & ketone molecule (ex: formaldehyde/ acetone)  Site of reactions that link these molecules into larger, more complex compounds

o Hydroxyl Group

 Weak acids – drops proton

 Protons involved in acid-base reactions come from this group   Polar

 Molecules containing this group will form hydrogen bond -soluble o Phosphate Group

 Carry 2 (-) negative charges

 Phosphates that are bonded together store chemical energy  reactions

o Sulfhydryl Group

 Sulfur atom bonded to hydrogen

 Linked to another sulfhydryl group via disulfide bonds

 Contribute to protein structure

∙ Draw the general structure of an amino acid, designating the side chain as R,  label the amino group and the carboxyl group

o Amino acids have amino & carboxyl groups

 Linked by covalent bonds

o Amino group = base in water; acts as protons to NH3

o Carboxyl = acidic because of oxygen electronegativity – pulls electrons  away from H atom  lose proton

o Nonpolar side chains lack charged or highly electronegative atoms  capable of forming hydrogen bonds with water. Instead of dissolving,  hydrophobic side chains tend to coalesce in aqueous solution.

o Polar or charged side chains interact readily with water and are  hydrophilic. Hydrophilic side chains dissolve in water easily.

o (-) side chain = loses a proton – acidic

o (+) side chain = gains a proton – base

o Uncharged = does it have an oxygen atom  result in polar covalent bond  – uncharged polar

o If no to the above 3, then it is a nonpolar amino acid

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∙ Identify an amino acid based on its structural formula

∙ Define primary, secondary, tertiary, and quaternary protein structure

Primary

∙ Unique sequence of amino acids in a protein ∙ R – groups affect properties/ functions ∙ Protein folding is directed by sequence of  amino acids

∙ Stabilized by peptide bonds

∙ Individual polypeptides

Secondary

∙ created in part by hydrogen bonding between groups of peptide-bonded backbone

∙ Hydrogen bonding occurs between the  oxygen on the C=O group of one amino acid  residue and the hydrogen on the N-H groups  of another

∙ H-bonds form and the 2 groups align when  backbones form either: an a-helix (alpha helix), in which the polypeptide’s backbone is coiled; or a B-pleated sheet (beta-pleated  sheet), in which segments of peptide chain  bend 180° and then fold in the same plane

∙ These shapes depend on the primary  structure – geometry and properties of amino acid in the sequence

∙ Stable due to the many H-bonds the helix and pleated sheet

∙ Shape of protein is defined

∙ Individual polypeptides

Tertiary

∙ Overall shape of protein due to interaction  between R groups or between R groups and  backbone

∙ Side chains are now involved with bonds  rather than just H-bonds between the  

backbones

∙ H-bonds: between polar R groups and  opposite partial charges in either the peptide  backbone or other R groups

∙ Hydrophobic interactions

∙ Van der Waals Interaction: hydrophobic side  chains are stabilized by these electrical  

attractions – weak

∙ Covalent bonding: form between side chains  of sulfhydryl groups

∙ Ionic bonding: between groups that have a

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full and opposing charges

∙ Each contact between R groups causes  peptide-bonded backbones to bend and fold  3D shape

∙ Individual polypeptides

Quaternary

∙ Combination of polypeptides

∙ Held together by same types of bonds as in  tertiary

∙ Explain how each level of protein structure affects its function

∙ Identify a nucleotide based on its structural formula

o Phosphate group

o Five-carbon sugar

o Nitrogenous base

∙ Draw ribose and deoxyribose

∙ Identify the structural difference between ribose and deoxyribose

Ribose

Deoxyribose

∙ Sugar = -OH group bonded to the  2’ carbon

∙ Sugar = has an H+ bonded to the  2’ carbon

∙ Draw a nucleotide, labeling the pentose sugar, phosphate group, and  

nitrogenous base

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BIOL 1361 Fall 2018 ∙ Define primary, secondary, and tertiary structure of RNA and DNA polymers

DNA

RNA

Primary

∙ Sequence of A, G,  

C, T nucleotides

∙ as template for the  synthesis of a  

complementary  

strand, DNA  

contains the  

information  

required for a copy  

of itself to be made

∙ Sequence of A, G,  

C, U nucleotides

∙ OH- on 2’ carbon  

makes it more  

reactive than DNA

Secondary

∙ 2 anti-parallel  

strands linked by H

bonds

∙ Twisted into double  helix because of  

hydrophobic  

interactions

∙ Single strand can  

fold onto itself –  

hairpin structure

∙ H-bonds from  

between  

complementary  

Nitrogenous bases

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BIOL 1361 Fall 2018

(nitrogenous base  

inside & sugar

phosphate  

backbone outside)

∙ Van der Waals  

interaction between

the stacking of the  

bases

∙ Directed by  

hydrophobic  

interactions

Tertiary

∙ NONE - supercoiling

∙ Can fold into  

complex shape

∙ Explain how RNA structure facilitates catalytic activity, but DNA structure does  not

o Ribosome catalyzes both the hydrolysis and the condensation of  phosphodiester linkages in RNA

o 3D nature = ribosomes have an active site

∙ Compare potential energy stored in glucose, protein (example in fig. 3.6), and a  triglyceride (example in fig. 6.4)

o Glucose: chemical energy stored in the C-H and C-C bonds of  

carbohydrate is transferred to a new bond linking a third phosphate group  to ADP to form ATP

Cells (Chapter 7)

∙ Compare structure of prokaryotic & eukaryotic cells

Eukaryotic Cell

Prokaryotic Cell

Nucleus

Present

Absent

Number of chromosomes

More than one

One – but not true

Plasmids

Cell Type

Usually multicellular

Usually unicellular (some  cyanobacteria may be  multicellular)

True Membrane bound  Nucleus

Present

Absent

Example

Animal and Plants

Bacteria and Archaea

Genetic Recombination

Meiosis and fusion of  

gametes

Partial, undirectional  

transfers DNA

Lysosomes and  

peroxisomes

Present

Absent

Microtubules

Present

Absent or rare

Endoplasmic reticulum

Present

Absent

Mitochondria

Present

Absent

Cytoskeleton

Present

May be present

DNA wrapping on proteins

Eukaryotic wrap their DNA around proteins called  histones.

Multiple proteins act  

together to fold and  

condense prokaryotic

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BIOL 1361 Fall 2018

DNA. Folded DNA is then  organized into a variety of conformations that are  supercoiled and wound  around tetramers of the  HU protein.

Ribosomes

Larger

Smaller

Vesicles

Present

Present

Golgi apparatus

Present

Absent

Chloroplasts

Present (in plants)

Absent; chlorophyll  

scattered in the cytoplasm

Flagella

Microscopic in size;  

membrane bound; usually  arranged as nine doublets  surrounding two singlets

Submicroscopic in size,  composed of only one  fiber

Permeability of Nuclear  Membrane

Selective

Not present

Plasma membrane with  steroid

Yes

Usually no

Cell wall

Only in plant cells and  fungi (chemically simpler)

Usually chemically  

complexed

Vacuoles

Present

present

Cell size

10-100um

1-10um

∙ List the 4 characteristics shared by all cells

o cell membrane, DNA, ribosome, and cytoplast

∙ Describe the function of each eukaryotic organelle: nucleus, smooth  endoplasmic reticulum, rough endoplasmic reticulum, lysosome, Golgi  apparatus, mitochondria, chloroplasts

1. Nucleus

o Usually found at the center of the cell

o Has a nuclear membrane which contains nuclear pores

o Contain cell’s DNA in one of 2 forms

o chromatin – DNA bound to protein (non-dividing cell)

o chromosomes – condensed structures seen in dividing cell

o Also contains an organelle called nucleolus – which makes the cell’s  ribosomes

2. Mitochondria

o Energy center or “powerhouse” of the cell. Turns food into useable energy  (ATP)

3. Golgi Apparatus

o Processing, packages and secretes proteins; proteins are transported in  vesicles

4. Lysosome

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BIOL 1361 Fall 2018

o Contains digestive enzymes that can break things down, also called a  “suicide sac” because the rupturing of the lysosome will cause the cell to  destroy itself

5. Endoplasmic Reticulum

o Transport, “intracellular highway”. Ribosomes are positioned along the  rough ER, protein made by the ribosomes enter the ER for transport. o Smooth ER – no ribosomes

o Rough ER – contains ribosomes

6. Chloroplasts

o Uses sunlight to create food, photosynthesis (only found in plant cells),  contains green pigment chlorophyll

∙ Describe how secreted proteins are transported through the endomembrane  system and out of the cell by exocytosis

o begins on ribosomes in cytoplast, move ribosome and growing protein to  ER, vesicles containing protein move to Golgi apparatus, then go out ∙ Draw a double phospholipid bilayer, such as that surrounding the nucleus,  mitochondrion, & chloroplast

∙ Explain why there is an inter-membrane space when there is a double membrane o It is a space presented in two organelles- Mitochondria and Chloroplast. o It is a site for oxidative phosphorylation and exchange of molecules  between cytoplasm and inner region of these organelles. It acts as a  

secondary barrier between the inner matrix and outer cytoplasm. o If there was no inter-membrane space, the molecules could easily enter  the mitochondrial or chloroplast matrix and this could cause disturbance  in the inside environment. Also there would be a separate site as well as  mechanism for ATP formation. This is because presence of inter membrane space provides chemical as well as electrical gradient for the  ATP synthesis.

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BIOL 1361 Fall 2018

Draw. The last question is always a diagram or graph. Possible topics for  this question are listed below. PRACTICE!

∙ a saturated and an unsaturated hydrocarbon

∙ an amino acid, designating the side chain as R, label the amino group and the  carboxyl group

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BIOL 1361 Fall 2018 ∙ a nucleotide, labeling the pentose sugar, phosphate group, and nitrogenous base

24

BIOL 1361 Fall 2018 ∙ Epithelium: label apical membrane, basolateral membrane, tight junctions

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BIOL 1361 Fall 2018 ∙ Given the variables in an experiment, identify the independent and  

dependent variables and graph the relationship between the two. o Example experiment description: A research group tested whether  camouflage protected mice from predators. Light colored mice were  released one at a time into an arena. Then an owl was released and  allowed to hunt for 5 minutes. Ten light colored mice were released  into an arena with light colored sand and ten light colored mice were  released into an arena with dark soil. In the sand arena, 2 light colored mice were eaten. In the dark soil arena, 9 mice were eaten.

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BIOL 1361 Fall 2018

Independent variable: the presence of moonlight and the soil color Dependent variable: the number of mice caught by the owls

 

Vocabulary

Adaptation: Any heritable trait that  increases fitness of an individual with  the trait, compared with individuals  without the trait, in a particular  environment

alimentary canal: A chamber or tube  where digestion takes place

o aka gastrointestinal (GI) tractor  digestive tract

apical membrane: Toward the top;  Side of epithelial layer that faces  environment and not other body  tissue; direction villi face

basolateral membrane: towards the  bottom and sides; side of epithelial  layer facing other body tissues and not the environment

cholecystokinin (CCK): A peptide  hormone secreted by cells in lining of  small intestine

o Stimulates secretion of  

digestive enzymes from  

pancreas and release of bile by  gallbladder

co-transport: is the name of a process  in which two substances are  

simultaneously transported across a  membrane by one protein, or protein  complex which does not have ATPase  activity.

diffusion: spontaneous movement of a  substance from one region to another,  often with a net movement from a  region of high concentration to one of  low concentration (i.e., down a  concentration gradient).

digestion: The physical and chemical  breakdown of food into molecules that can be absorbed into the body of an  animal

duodenum: Upper part of intestine,  which functions in digesting peptides,  lipids, sugars, and nucleic acids  (digests all 4 macromolecules) epithelium: (plural: epithelia) An  animal tissue consisting of sheet-like  layers of tightly packed cells that line  

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BIOL 1361 Fall 2018

an organ, a gland, a duct, or a body  surface.

o Also known as epithelial tissue facilitated diffusion: passive  

movement (diffusion) of a substance  across a membrane with the  

assistance of transmembrane carrier  proteins or channel proteins.

gastrin: A hormone produced by cells  in the stomach lining in response to  the arrival of food or to a neutral  signal from the brain.

o Stimulates other stomach cells  to release hydrochloric acid

gastrovascular cavity: Digestive  compartment with one opening o food in, waste out in the same  opening

o Digestive secretions enter  cavity

o prey is digested

o Nutrients are absorbed by body  cells

Helicobacter pylori: a type of bacteria  that can enter the body and live in  digestive tract.

o After many years, can cause  sores (aka ulcers) in lining of  stomach or in duodenum of  

small intestine, which if  

infected, lead to stomach  

cancer

hydrolysis: A chemical reaction in  which a molecule is split into smaller  molecules by reacting with water.

o In biology, most hydrolysis  reactions involve splitting of  

polymers into monomers

hyperosmotic: Referring to solution  that has greater solute concentration,  and therefore a lower water  

concentration, than another solution hypoosmotic: Referring to a solution  that has lower solute concentration,  and therefore a higher water  

concentration than another solution ileum: Third portion of the small  intestine (between jejunum and  cecum)

o absorbs vitamin B12 and bile salts and whatever else was not absorbed by the jejunum

ingestion: the act of bringing food into  the digestive tract

integral/transmembrane protein: any  membrane protein that spans the  entire lipid bilayer which is also called  transmembrane protein.

isosmotic: referring to a solution that  has the same solute concentration and water concentration as one another jejunum: Second part of small  intestines; lies between duodenum  and ileum (middle gut or middle  intestine)

o Focuses on absorption of small  nutrient particles which have  been previously digested by  

enzymes in the duodenum, and  once absorbed, nutrients (minus fats which go to lymph) pass  

from enterocytes into  

enterohepatic circulation and  enter the liver via hepatic portal vein, where blood is processed

o also involved in magnesium  absorption

lipid: Any organic substance that does  not dissolve in water, but dissolves  well in nonpolar organic solvents

o Include fatty acids, fats, oils,  waxes, steroids, and  

phospholipids

microvilli: (singular: microvillus) Tiny  protrusions from the surface of an  epithelial cell that increase surface  area for absorption of substances osmosis: diffusion of water across a  selectively permeable membrane from a region of low solute concentration  (high water concentration) to a region  of high solute concentration (low  water concentration).

o For osmosis to occur, the solute  would not be able to pass  

through the membrane

pepsin: A protein-digesting enzyme  secreted in inactive form (as  

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BIOL 1361 Fall 2018

pepsinogen) by chief cells in stomach  lining

peristalsis: Rhythmic waves of  muscular contraction

o In digestive tract, pushed food  along

phagocytosis: Uptake by a cell of small particles or cells by invagination and  pinching off of the plasma membrane  to form small, membrane-bound  vesicles

saturated fatty acid: Referring to lipids in which all the carbon-carbon bonds  are single bonds. Such compounds  have relatively high melting points. secretin: A peptide hormone secreted  by cells in the small intestine in  response to the arrival of food from  the stomach.

o Stimulates secretion of  

bicarbonate (HCO3-) by pancreas selective permeability: the property of  a membrane that allows some  substances to diffuse across it much  more readily than other substances. tight junction: A type of cell-cell  attachment structure that links plasma membranes of adjacent animal cells,  forming a barrier that restricts  movement of substances in space  between cells

o Most abundant in epithelia (e.g., intestinal lining)

unsaturated fatty acid: Referring to  lipids in which at least one carbon carbon bond is a double bond. Double  bonds produce kinks in hydrocarbon  chains and decrease the compound’s  melting point. (ex: oil (polyunsaturated fat that is liquid at room temperature) villi: (Singular: villus) Small, fingerlike  projections

channel protein: A transmembrane  protein that forms a pore in a cell  membrane, which may open or close  in response to a signal

o The structure of most channels  allows them to admit just one or a few types of ions or molecules

carrier protein: a transmembrane  protein that facilitates diffusion of a  small molecule (e.g., glucose) across a membrane by a process involving a  reversible change in the shape of the  protein.

o aka carrier or transporter

cholesterol: is a waxy type of a lipid, a  substance that is insoluble in water,  like oil or fat.

dehydration: aka condensation  reaction; a chemical reaction in which  two molecules are joined covalently  with the removal of an -OH from one  and an -H from another to form water.

o In biology, mo9st condensation  reactions involve the joining of  monomers into polymers

ester linkage: the covalent bond  formed by a condensation reaction  between a carboxyl group and a  hydroxyl group.

o Ester linkages join fatty acids to  glycerol to form a fat or  

phospholipid.

osmolarity: The concentration of  dissolved substances in a solution,  measured in osmoles per liter phospholipid: A class of lipid having a  hydrophilic head (including a  phosphate group) and a hydrophobic  tail (consisting of two hydrocarbon  chains)

o Major components of plasma  membrane and organelle  

membranes

prokaryote: (adjective: prokaryotic) A  member of the domain Bacteria or  Archaea; a unicellular organism  lacking a nucleus and containing  relatively few organelles or  

cytoskeletal components

eukaryote: (adjective: eukaryotic) A  member of the domain Eukarya; an  organism whose cells contain a  nucleus, numerous membrane-bound  organelles, and an extensive  

cytoskeleton.

o May be unicellular or  

multicellular

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BIOL 1361 Fall 2018

plasmid: A small, usually circular,  supercoiled DNA molecule  

independent of the cell’s main  chromosome(s) in prokaryotes and  some eukaryotes

endocytosis: General term for any  pinching off of the plasma membrane  that results in the uptake of material  from outside the cell.

o Includes phagocytosis,  

pinocytosis, and receptor

mediated endocytosis

peptide bond: the covalent bond  formed by a condensation reaction  between two amino acids; links the  residues in peptides and proteins.

o between the carboxyl group of  one amino acid and the amino  group of another.

o C-N COVALENT bond that results from this condensation reaction o water molecule is removed in  the condensation reaction, the  carboxyl group is converted to a carbonyl functional group (C=O) in the resulting polymer, and  the amino group is reduced to  an N-H.

o Peptide bonds are stable  

compared to linkages in other  types of macromolecule  

because of a pair of valence  

electrons on the nitrogen is  

partially shared in the C-N bond  primary structure: The sequence of  amino acid residues in a protein; also  the sequence of nucleotides in a  nucleic acid

secondary structure: In proteins,  localized folding of a polypeptide chain into register structures (i.e., alpha helix and beta-pleated sheet)  stabilized by hydrogen bonding  between atoms of peptide backbone

o In nucleic acids, elements of  structure (e.g., helices and  

hairpins) stabilized by hydrogen bonding and hydrophobic  

interactions between  

complementary bases

tertiary structure: The overall 3D  shape of single polypeptide chain,  resulting from multiple interactions  among amino acid side chains on  peptide backbone

o In single-stranded nucleic acids, 3D shape is formed by  

hydrogen bonding and  

hydrophobic interactions  

between complementary bases nucleotide: a molecule consisting of a  five-carbon sugar (ribose or  

deoxyribose), a phosphate group, and  one of several nitrogen-containing  bases.

o Equivalent to a nucleotide plus  one or more phosphate group. phosphodiester bond: Chemical  linkage between adjacent nucleotide  residues in DNA and RNA.

o Forms when phosphate group of one nucleotide condenses with  hydroxyl group on sugar of  

another nucleotide

o aka phosphodiester linkage microfilaments: aka actin filament; a  long fiber, about 7 nm in diameter,  composed of two intertwined strands  of polymerized actin protein; one of  three types of cytoskeleton fibers

o involved in cell movement microtubules: A long, tubular fiber,  about 25 nm in diameter, formed by  polymerization of tubulin protein  dimers; one of three types of  cytoskeletal fibers

o Involved in cell movement and  transport of materials within cell intermediate filaments: A long fiber,  about 10 nm in diameter, composed of one of various proteins (e.g., keratins,  lamins); one of three types of  cytoskeletal fibers

o Used to form networks that help maintain cell shape and hold  nucleus in place

lysosomes: A small, acidified organelle in an animal cell containing enzymes  that catalyze hydrolysis reactions and  can digest large molecules

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golgi apparatus: A eukaryotic  organelle, consisting of stacks of  flattened membranous sacs  

(cisternae), that functions in  

processing and sorting proteins and  lipids destined to be secreted or  directed to other organelles

o Also called Golgi complex

endoplasmic reticulum: A network of  interconnected membranous sacs and  tubules found inside eukaryotic cells  that functions in synthesis of lipids  and proteins that reside in endo  membrane system, plasma  

membrane, or are secreted from the  cell

o Rough ER: portion of ER that is  dotted with ribosomes

o involved in synthesis of  

plasma membrane  

proteins, secreted  

proteins, and proteins  

localized to the ER, Golgi  

apparatus, and  

lysosomes

o Smooth ER: The portion of ER  that lacks attached ribosomes o involved in synthesis and  

secretion of lipids

exocytosis: Secretion of intracellular  molecules (e.g., hormones, collagen),  contained within membrane-bound  vesicles, to the outside of the cell by  fusion of vesicles to the plasma  membrane

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