Bio 1A03 Chapters 3-7

Front 1

Describe Stanley Miller’s spark-discharge experiment.

Back 1

- produced microcosm of ancient Earth
- tested for occurence of chemical evolution
- used water, methane, ammonia and hydrogen gas
- chemicals sealed in glass tubes and flasks connected in a loop (one flask containing water, one containing electrodes)
- water heated (evaporation)
- sparks from electrodes simulated lightning
- found complex carbon-containing compounds (HCN, H2CO, important for amino acids)

Front 2

Discuss the reasons why Miller’s results are significant to the understanding of chemical evolution.

Back 2

Conclusion: chemical evolution occurs readily if simple molecules with high free energy are exposed to a source of kinetic energy.

Front 3

What are some of the alternative hypotheses regarding chemical evolution?

Back 3

- macromolecules came from water (ex. hydrothermal vents)
- macromolecules came extraterrestrially (ex. meteorites)

Front 4

What did the analysis of the Murchison meteorite suggest with regards to chemical evolution?

Back 4

- components of macromolecules found on surface
- contamination?
- suggested origin of life may have come extraterrestrially instead of by chemical evolution

Front 5

Define monomer.

Back 5

- subunit or building block of a polymer

Front 6

Define polymer.

Back 6

- large molecules composed of several connected subunits, which are identical or similar

Front 7

In lectures, we reviewed that there are 20 major amino acids in living organisms.
List the three main categories of amino acids.

Back 7

- Nonpolar side chains (no charged or electronegative atoms to form H bonds; not soluble in water)
- Polar side chains (partial charges can form H bonds; soluble in water)
- electrically charged side chains (charged side chains form H bonds; highly soluble in water)

Front 8

What is the name of the reaction that joins two amino acids together?

Back 8

Condensation reaction/ dehydration synthesis

Front 9

What type of bond forms between two amino acids during a condensation reaction and where does the bond form?

Back 9

Peptide bond, between the carboxyl group of one and the the amino group on the other

Front 10

Describe the movement of the monomer and of water during a condensation reaction.

Back 10

monomer in, water out

Front 11

Describe the movement of the monomer and of water during hydrolysis.

Back 11

water in, monomer out

Front 12

What is a structural isomer? Give an example.

Back 12

Molecules with same chemical formula but have a different arrangement. Ethanol and dimethylether (C2H6O)

Front 13

What is a geometric isomer?

Back 13

Molecules with the same chemical formula, but have a different arrangement around the double bond (cis/trans). Ex. trans-2-butene and cis-2-butene (C4H8)

Front 14

What is an optical isomer?

Back 14

Mirror images of eachother, cannot be superimposed. Carbon is asymmetric. Ex. L- Dopa and D- Dopa

Front 15

Which form of Dopa is effective against Parkinson's?

Back 15

L- Dopa

Front 16

Describe primary structure.

Back 16

- unique sequence of amino acids in a protein.
- stabilized by peptide bonds

Front 17

Describe secondary structure.

Back 17

- stabilized by H bonding between groups along peptide-bonded backbone
- alpha helix and beta pleated sheet formation in a polypeptide

Front 18

Describe tertiary structure.

Back 18

- shape formed by side chain interactions: hydrogen bonds, van der Waals interactions due to hydrophobic side chains, disulfide bonds, ionic bonds

Front 19

Describe quaternary structure.

Back 19

- combo of polypeptides (tertiary structures)

Front 20

What is the difference between the normal condition and the sickle cell condition with regards to the primary
level of protein structure?

Back 20

Single change in amino acid sequence.

Front 21

Give an example of a quaternary structure.

Back 21

Hemoglobin.

Front 22

What is the function of chaperone proteins (or chaperonins)?

Back 22

Facilitate folding for renaturation (after cell experiences denaturation due to heat).

Front 23

What are prions and why are they significant? Give an example.

Back 23

- misfolded and infectious proteins
- can induce other proteins to change shape to the altered form
- ex. mad cow disease

Front 24

Discuss the significance of optical isomers with regards to the thalidomide tragedy. Relate this to cancer research.

Back 24

- thalidomide = combo of 2 optical isomers
- one isomer reduced morning sickness (sedative)
- the other cut off blood vessel development (causes babies to be born with missing limbs)
- may cut off blood supply to cancerous tumors, slowing growth

Front 25

What are the three parts of a nucleotide?

Back 25

- phosphate group
- 5-carbon sugar
- nitrogenous base

Front 26

What is the difference between pyrimidies and purines?

Back 26

Purines are double-ringed.

Front 27

What is a phosphodiester linkage?

Back 27

- result of a condensation rxn
- bond between phosphate grup of one nucleotide and the hydroxl group of the sugar component of another nucleotide

Front 28

Describe the structure of the double helix.

Back 28

- nitrogenous bases point to centre of double helix, sugar-phosphate backbone on outside
- A with T, G with C
- held together by H bonds

Front 29

What is gel electrophoresis?

Back 29

Technique used for the separation of DNA, RNA, or protein molecules using an electric field applied to a gel matrix.

Front 30

Why is gel electrophoresis useful to biologists?

Back 30

- diagnoses of genetic diseases
- genetic engineering (recombinant DNA)
- evolutionary relationship between plants and animals

Front 31

List some of the functions of carbohydrates.

Back 31

- energy source
- energy storage
- structural support
- transport of energy source
- cell surface signals

Front 32

What is a monosaccharide? Give some examples.

Back 32

- single/simple sugars
- Ex. RNA, DNA, glucose, galactose

Front 33

What is a disaccharide?

Back 33

- double sugars consisting of 2 monosaccharides which are joined by a condensation reaction

Front 34

Which disaccharide consists of 2 alpha glucose molecules?

Back 34

maltose (found in beer)

Front 35

Which disaccharide consists of 1 glucose and 1 fructose molecule?

Back 35

sucrose

Front 36

Which disaccharide consists of 1 beta glucose and one beta galactose molecule?

Back 36

lactose

Front 37

What is the difference between alpha and beta glucose?

Back 37

alpha - OH at carbon 1 is below plane of ring
beta - OH at carbon 1 is above plane of ring

Front 38

Explain a glycosidic linkage.

Back 38

Occurs when hydroxl groups on 2 monosaccharides (attached at carbon 1 and carbon 4) undergo a condensation reaction to form a bond.

Front 39

Which polysaccharides have alpha-1,4-glycosidic linkages?

Back 39

Starch and glycogen.

Front 40

Which polysaccharides have beta-1,4-glycosidic linkages?

Back 40

Cellulose, chitin and peptidoglycan.

Front 41

Give an example of where each of the following polysaccharides are found: starch, glycogen, cellulose, chitin, peptidoglycan.

Back 41

s - energy storage in potatoes
g - energy storage in liver and muscles
ce - structural support in algae
ch - structural support in external skeletons of insects
p - structural support in bacterial cell walls

Front 42

Explain lactose intolerance.

Back 42

- adults do not produce lactase (enzyme) which splits lactose into glucose and galactose
- can take lactaid pills containing lactase

Front 43

Explain galactosemia.

Back 43

- lack of enzyme that converts galactose into glucose
- can cause renal failure, enlarged liver, cataracts and brain damage

Front 44

Which polysaccharide has a structure consisting of highly branched helices?

Back 44

glycogen

Front 45

Which polysaccharide has a structure consisting of an unbranched helix (amylose) or branched helices (amylopectin)?

Back 45

starch

Front 46

Which polysaccharides have a structure consisting of parallel strands joined by H bonds?

Back 46

cellulose & chitin

Front 47

Which polysaccharide has a structure consisting of parallel strands joined by peptide bonds?

Back 47

peptidogylcan

Front 48

What are lipids?

Back 48

- Carbon-containing compounds that are non-polar and hydrophobic (do not readily dissolve in water) due to a hydrocarbon component.
- Defined by solubility instead of chemical structure

Front 49

Name the 4 major classes of lipids.

Back 49

Phospholipids, steroids, triglycerides, waxes

Front 50

What is the function of phospholipids (and glycolipids and some steroids)?

Back 50

membrane structure and function

Front 51

What is the function of steroids?

Back 51

hormones and regulators

Front 52

What is the function of triglycerides?

Back 52

food storage

Front 53

What is the function of waxes?

Back 53

protection against loss of water

Front 54

What is an amphipathic molecule?

Back 54

has a polar/hydrophilic region and a nonpolar/hydrophobic region

Front 55

Why are membranes important?

Back 55

- makes rxns more efficient
- endo & exocytosis
- regulate what comes in and out

Front 56

Why is membrane fluidity important?

Back 56

- allows permeability
- useful nutrients transported in, wastes transported out

Front 57

Membrane fluidity is related to: (4 things)

Back 57

- presence of unsat or sat fatty acids
- # of C atoms in fatty acid hydrocarbon tail
- absence or presence of cholesterol
- ambient temperature

Front 58

How does a shorter tail effect permeability?

Back 58

increases permeability

Front 59

How does cholesterol affect membrane fluidity at moderate temperatures? At low temperatures?

Back 59

- reduces membrane fluidity
- enhances membrane fluidity

Front 60

How does a high temperature affect fluidity?

Back 60

increases fluidity

Front 61

A fatty acid consists of a hydrocarbon chain bonded to ____________.

Back 61

A carboxyl (COOH) functional group.

Front 62

Fats are formed by which process? What is the name of the resulting covalent bond?

Back 62

Dehydration synthesis; ester linkage

Front 63

What kind of distinctive structure do all steroids have?

Back 63

four-ring structure

Front 64

Describe the structure of phospholipids.

Back 64

Glycerol linked to a phosphate group and to either 2 chains of isoprene or 2 fatty acids.

Front 65

List some of the functions of lipids.

Back 65

- storing chemical energy
- signals between cells
- pigments that respond to sunlight
- form waterproof coatings on leaves and skin
- act as vitamins
- necessary for membranes (lipid bilayer)

Front 66

What are micelles?

Back 66

Tiny droplets created when the hydrophilic heads of phospholipids face the water and the hydrophobic tails are forced together, away from the water.

Front 67

Explain selective permeability.

Back 67

Some substances cross a membrane more easily than others. (small, nonpolar molecules)

Front 68

Which 2 aspects of a hydrocarbon chain affect the way it behaves in a lipid bilayer?

Back 68

- # of double bonds
- length

Front 69

What is an unsaturated hydrocarbon chain?

Back 69

- contains at least one double bond which creates a kink in the tail

Front 70

How do unsaturated hydrocarbons affect permeability?

Back 70

Increase it due to spaces made between tails due to the kinks.

Front 71

How could you decrease a membrane's permeability to glycerol? Why would this work?

Back 71

Add cholesterol; cholesterol fills spaces in phospholipid bilayers

Front 72

What are the three components of a phospholipid's polar head?

Back 72

choline, phosphate, glycerol

Front 73

What does the nonpolar region of a steroid consist of?

Back 73

isoprene chain

Front 74

What does the polar region of a steroid consist of?

Back 74

4 steroid rings

Front 75

What does the nonpolar region of a phospholipid consist of?

Back 75

2 fatty acid tails

Front 76

What are the three types of transport across membranes?

Back 76

diffusion, facilitated diffusion, active transport

Front 77

What creates a concentration gradient?

Back 77

A difference in solute concentrations

Front 78

Explain diffusion.

Back 78

- net movement of a solute down a concentration gradient (from high to low concentration)
- passive & spontaneous

Front 79

Give 2 different definitions for osmosis.

Back 79

1) water diffuses from less concentrated solution (hypotonic) to a more concentrated solution (hypertonic)
2) water diffuses from a region of high concentration of free water molecules to a region of low concentration

Front 80

What is a hypotonic solution?

Back 80

solution with a lower solute concentration than inside the cell

Front 81

What is a hypertonic solution?

Back 81

solution with greater solute concentration than the inside of the cell

Front 82

What is an isotonic solution?

Back 82

solution with equal concentration compared to inside the cell

Front 83

Discuss the use of liposomal nanomedicines in cancer research.

Back 83

Drugs contained in liposomes (mycells) can be specifically targeted to kill only cancer cells. Therapeutic meds are protected from other agents in body and can accumulate in targeted location.

Front 84

Explain the Davson-Danielli sandwich model.

Back 84

- protein-lipid-lipid-protein sandwich
- incorrect

Front 85

How was the sandwich model disproved?

Back 85

- realization that membrane proteins could be amphipathic (nonpolar region stable in interior of bilayer which polar regions stable near polar heads and surrounding water)
- freeze-fracture and freeze-etch

Front 86

Explain freeze-fracture and freeze-etch.

Back 86

- membrane frozen, then fractured
-membrane split through hydrophobic region (least resistance) of phospholipid bilayer
- pits and mounds observed from membrane proteins

Front 87

What is the difference between integral and peripheral proteins?

Back 87

- integral: transmembrane proteins, embedded in membrane
- peripheral: non embedded in membrane, bind to hydrophilic ends of integral proteins

Front 88

What are integrins?

Back 88

- transmembrane proteins
- connect to fibronectins in ECM
- allow communication between inside and outside of cell

Front 89

Explain facilitated diffusion. Give 2 examples.

Back 89

- passive
- faster than simple diffusion due to transport proteins
- occurs down a concentration gradient
- Ex. oxygen through red blood cells, voltage gated sodium channels

Front 90

Explain active transport. Give an example.

Back 90

- requires ATP
- pumps molecules against concentration gradient
- Ex. sodium-potassium pump

Front 91

Explain cystic fibrosis.

Back 91

- Water stays within cells causing build up of mucus in lungs (palpitations help break it up)
- transport chloride ions not being moved properly due to abnormal CFTR membrane protein

Front 92

Name the 4 main differences between eukaryotic and prokaryotic cells.

Back 92

- location of DNA
- internal membranes and organelles
- cytoskeleton
- overall size

Front 93

Describe the membrane, components and function of the nucleus.

Back 93

M- double membrane (nuclear envelope) contains nuclear pores
C- chromosomes, nucleolus, nuclear lamina
F- genetic info, assembly of ribosomes, structural support

Front 94

What occurs in the nucleolus?

Back 94

- manufacturing of RNA molecules found in ribosomes
- assembly of ribosomal subunits

Front 95

What are the two key advantages of compartmentalization?

Back 95

- incompatible chem rxns can be separated
- efficiency of chem rxns is increased

Front 96

What is the function of the SER?

Back 96

- lipid synthesis

Front 97

What is the function of the RER?

Back 97

- protein synthesis and processing

Front 98

What is the function of the nuclear pores?

Back 98

- allow regulation
- rRNAs, ribosomal subunits, mRNA and tRNA exit nucleus
- enzymes associated with DNA replication enter nucleus

Front 99

Describe the molecules, which are involved in the importation and exportation of proteins through the nuclear pores.

Back 99

- proteins directed to nucleus posses an NLS which binds to importins
- exportins assist proteins leaving nucleus which posses an NES

Front 100

Describe the steps proposed by the Secretory Pathway Hypothesis.

Back 100

1) protein enters ER while being synthesized by ribosome
2) protein exits ER, travels to cis face of Golgi
3) protein enters Golgi and is processed as cisternum moves towards trans
4) protein exits Golgi at trans and moves to plasma membrane
5) protein secreted from cell

Front 101

Describe phagocytosis.

Back 101

1) plasma membrane surrounds a smaller cell or food cell and engulfs it
2) phagosome/food vacuole formed
3) gets digested by a lysosome
4) small mols from digested food particles released into cytosol

Front 102

Describe autophagy.

Back 102

1) damaged organelles are surrounded by a membrane
2) delivered to a lysosome to be digested and recycled
3) small mols recycled into cytosol

Front 103

Describe Receptor-Mediated Endocytosis.

Back 103

1) macromols outside cell bind to memb proteins that act as receptors
2) plasma memb forms vesicle called an early endosome
3) early endosome is processed (proton pumps activated which lower pH)
4) early endosome matures into late endosome that receieves digestive enzymes from Golgi
5) late endosome matures into lysosome

Front 104

What prevents bursting in a hypotonic solution?

Back 104

cell walls

Front 105

List the three main components of the cytoskeleton and the types of protein subunits from which they are made.

Back 105

- microfilaments: actin
- intermediate filaments: keratin
- microtubules: alpha and beta tubulin

Front 106

List the main functions of actin molecules and microtubules.

Back 106

cell motility, movement of chromosomes during mitosis (microtubules)/cell division during cytokinesis (microfilaments), maintenance of cell shape, organelle movement,

Front 107

Which technique allowed the isolation of kinesin (motor protein that generates vesicle movement) ?

Back 107

differential centrifugation

Front 108

List the three components in the structure of kinesin.

Back 108

- tail
- stalk
- two-pieced head (one binds to the microtubule and the other to ATP)

Front 109

Describe how a motor protein moves a vesicle along a microtubule.

Back 109

1) tail region binds to vesicle
2) conformational change occurs when the globular pieces bind and release ATP
3) 2 head regions switch between binding the microtubule and ATP
4) two globular head components work as feet and walk along microtuble
(every step requires ATP)

Front 110

Describe the structure of cilia and flagella.

Back 110

- 9 + 2 arrangement
- 9 pairs of microtubule doublets attached to dynein motor proteins
- 2 central microtubules
- joined by protein spokes and bridges
- surrounded by plasma membrane

Front 111

What is a basal body? Describe its structure (identical to centriole structure)

Back 111

- structure which attaches the axoneme to the cell
- 9 + 0 microtubule arrangement
- 9 triplets of microtubules, no central pair

Front 112

List and describe three examples of motility that depend upon microfilaments.

Back 112

- cell crawling: actin-myosin interactions push cytoplasm forward
- cell division in animals: actin-myosin interactions pinch membrane in two
- cytoplasmic streaming in plants: actin-myosin interactions move cytoplasm around cell

Front 113

Describe the experiment which helped researchers determine the location of the NLS (nuclear localization signal).

Back 113

- hypothesis: "send to nucleus" zipcode in tail or core of protein
- used protease to cleave tails off
- attached radioactive label
- injected labelled protein fragments into cytoplasm then waited
- conclusion: in tail region

Front 114

Explain the pulse-chase technique.

Back 114

- Palade and coworkers
- figured out order of secretory pathway hypothesis
- marked mols at specific intervals and examined position over time
- conclusion: proteins move from RER to Golgi to secretory vesicles to exterior of cell

Front 115

Describe rheumatoid arthritis in relation to lysosomes.

Back 115

Rheumatoid arthritis occurs where lysosomal enzymes leak into the joint fluid. So what happens in this condition is the (damaged) lysosomes leak hydrolytic enzymes, causing the break down of healthy things within the joints, leading to joint problems.

Front 116

What will happen to a cell when it is hypertonic relative to the outside environment (which is hypotonic).

Back 116

Water will rush in therefore cell will expand

Front 117

Why are trans fats bad for us?

Back 117

- saturated, therefore decrease cell fluidity
- bad cholesterol further decreases fluidity

Front 118

Describe a viscous state.

Back 118

the presence of saturated f.a. This is due to tight bonds between the phospholipids that result in lower permeability as lesser molecules are able to penetrate through.

Front 119

Describe a fluid state.

Back 119

presence of unsaturated f.a. The reason for the fluidity is due to the kinks caused from the double bonds. This provides space for molecules to penetrate through= higher permeability.