Module 2

Front 1

Amino Acids

Back 1

Building blocks of molecules. There are 20.

Front 2

Name the parts of an amino acid

Back 2

1) NH2 or amino functional 2) COOH or carboxyl 3) H or hydrogen 4) R group or group of atoms called a side chain. Amino acids vary because of the R groups.

Front 3

Dehydration/condensation reaction

Back 3

dehydration reactions = a water molecule lost when single sugars attach through condensation reactions

opposite = hydrolysis where water is added when sugars attach

Front 4

primary structure

Back 4

fundamental to its function.

Front 5

secondary structure

Back 5

created by hydrogen bonding between portions of the peptide-bonded backbone. They are distinctively shaped sections of proteins that are stabilized largely by hydrogen bonding that occurs between the carbonyl oxygen and one amino acid residue

Front 6

tertiary structure

Back 6

most of the overall shape resulting from interactions between R groups or R groups and the peptide backbone.

Front 7

Hydrogen Bonding side chain:

Back 7

hydrogen bonds form between hydrogen atoms and the carbonyl group come together in the backbone.

Front 8

Hydrophobic interactions side chain:

Back 8

hydrophilic side chains force hydrophobic side chains to come together

Front 9

Van der Waal interaction side chain:

Back 9

weak asymmetric charges that make molecules get extremely close to each other

Front 10

Covalent bonding side chain:

Back 10

sulfur comes together

Front 11

Ionic bonding side chain:

Back 11

groups that have fully opposing charges come together

Front 12

peptide bond for proteins

Back 12

peptide bond = when an amino acid polymerizes when a bond forms between the carboxyl group of one amino acid and the amino acid group of another.

Front 13

transition state

Back 13

transition state = a collision between reactants creating a combination of old and new bonds which is an intermediate condition called transition state/ transition between breaking old bonds and forming new ones

Front 14

activation energy

Back 14

activation energy = amount of energy required to reach the transition state

Front 15

polypeptide

Back 15

polypeptide = amino acids join together

Front 16

describe all of the levels of protein structure:

Back 16

primary structure = sequence of amino acidssecondary structure = bonds between atoms in the peptide-bonded backbone of the same polypeptide. These bonds produce structures such as a-helices and b-pleated sheetstertiary structure = overall shape of polypeptide. Most are a consequences of bonds or other interactions between R-groups or between R-groups and the peptide-bonded backbone.quaternary structure = multiple polypeptides interact to form a single protein

Front 17

what does an enzyme do?

Back 17

enzymes = effective catalyst because they bring reactant molecules called substrates together in a specific orientation so that the electrons involved in the reaction can interact/ not rigid and static but rather flexible and dynamic

Front 18

substrate

Back 18

substrates = a reactant that interacts with an enzyme in a chemical reaction

Front 19

active site

Back 19

active site = the location where substrates bind and react

Front 20

induced fit

Back 20

induced fit = many enzymes undergo a significant change in shape, or conformation when reactant molecules bind to the active site. This conformational change is the induced fit.

Front 21

prion

Back 21

prions = improperly folded proteins that act as infectious, disease-causing agents; they have the same amino acid sequence but their shapes are radically different; prion diseases are fatal

Front 22

cofactor

Back 22

cofactor = something that helps the enzyme act

Front 23

competitive inhibition

Back 23

competitive inhibition = when the molecule involved competes with the substrate for access to the enzymes active site

Front 24

components of a nucleotide

Back 24

1) phosphate group 2) a sugar 3) a nitrogenous base

Front 25

ribonucleotides

Back 25

ribonucleotides (form RNA) = nucleotide that is made of ribose sugar

Front 26

deoxyribonucleotides

Back 26

deoxyribonucleotides (form DNA) = nucleotide made of deoxyribose sugar

Front 27

purine

Back 27

purines = type of base that makes up DNA (A and G)

Front 28

pyrimidines

Back 28

pyrimidines = type of base that makes up DNA (C, T, and U)

Front 29

Chargaff’s Rule

Back 29

Amount of A = amount of T, Amount of C = amount of G, due to complimentary base pairing.

Front 30

DNA structure

Back 30

DNA = antiparallel, sugar on outside base on inside, must have purine-pyramidine pairs so hydrogen bonds can form, AT go together and CG go together

DNA contains Thymine and NOT Uracil. RNA has Uracil.

Front 31

template strand

Back 31

template strand = original strand of DNA, the base that gets original copy

Front 32

polymer

Back 32

large molecule with many parts

Front 33

polysaccharides

Back 33

polysaccharides = polymers that form when monosaccharides (one sugar) are linked together. Also known as complex carbohydrate. Can withstand pulling and pushing motion - stretchy.

Front 34

starch and glycogen

Back 34

starch = a carbohydrate in plants monosaccharides (one sugar) stored for later; a mixture of two polysaccharides amylose (no branch) and amylopectin (branch).

glycogen = a carbohydrate stored sugar in animals, much like starch in plants

Front 35

cellulose

Back 35

cellulose = a carbohydrate major component of cell wall in plants

Front 36

chitin

Back 36

Chitin = a carbohydrate in polysaccharide that stiffens the cell walls of fungi and animals

Front 37

Peptidoglycan

Back 37

Peptidoglycan = a carbohydrate that gives bacterial cell walls strength and firmness

Front 38

What is the difference between a monosaccharide, a disaccharide and a polysaccharide?

Back 38

A monosaccharide is a simple sugar whereas a polysaccharide consists of chains of monosaccharides or disaccharides bonded together. The difference is simply the number of monomers (sugar) in the molecule.

Front 39

glycosidic linkage

Back 39

glycosidic linkage = a covalent bond that occurs when simple sugars polymerize when a condensation reaction occurs between two hydroxyl groups

Front 40

phosphodiester linkage for nucleotides

Back 40

a chemical bond of the kind joining successive sugar molecules in a polynucleotide.

Front 41

peptide bond for proteins

Back 41

a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O).

Front 42

primary function of carbohydrates in cells?

Back 42

energy storage, cell identity, structure, building blocks for synthesis

Front 43

How can one quickly asses how much free energy an organic molecule has?

Back 43

Compare how many C-C and C-H (high free energy) bonds there are compared to C-O bonds (low free energy).

Front 44

monosaccharide

Back 44

simple sugar; presence of a carbonyl group and a few hydroxyl groups

Front 45

polysaccharide

Back 45

polymers that form when monosaccharides are linked together. Consists of two sugars called disaccharide.

Front 46

Glycosidic linkage for simple sugars

Back 46

They form between hydroxyl groups.

= a linkages are easy for enzymes to break

= B linkages are difficult for enzymes to break

They have differing amounts of carbon

Front 47

lipid

Back 47

lipids = carbon containing compound found in organisms that are non polar and hydrophobic (do not dissolve in water).

Front 48

fatty acid

Back 48

Fatty Acid = a hydrocarbon chain joined to a carboxyl functional group

Front 49

What are the two types of fatty acids?

Back 49

Two types of fatty acid = saturated and unsaturated

Front 50

saturated fatty acid

Back 50

saturated fatty acid = without double bond

single C—C bonds rather than double bonds; it contains all of the hydrogen atoms that it can (it’s filled, fatty)

Front 51

unsaturated fatty acid

Back 51

unsaturated fatty acid = with double bond

one or more of the C—C bonds are double and therefore they cannot connect to as many hydrogen atoms

Front 52

What are the three types of lipids?

Back 52

three main types of lipids = fats, steroids, phospholipids

Front 53

Difference between lipids and nucleotides

Back 53

Fats = three fatty acids and one glycerol molecule. The fatty acids are each joined separately to the glycerol and none touch each other. (Note: this is what makes lipids differ from nucleotides, monosaccharides, or amino acids - those ones are joined together whereas lipids remain separate only connected by the glycerol.)

Front 54

ester linkage

Back 54

Ester linkage = the hydration synthesis caused by the covalent bond between fatty acids and glycerol.

Front 55

Sterioids

Back 55

Steroids = family of lipids that contain four fused carbon rings. The variations of steroids stems from the type, number, and position of the functional groups

Front 56

cholesterol

Back 56

Cholesterol = has a hydrocarbon chain of isoprene subunits, which is referred to as its tail. Like all hydrocarbons, this tail is hydrophobic, whereas functional groups attached to other parts of the molecular structure may actually make that end of the molecule hydrophilic.

Front 57

amphipathic

Back 57

Amphipathic = molecules that have both hydrophilic and hydrophobic parts

Front 58

Phospholipids

Back 58

Phospholipids = two fatty acid chains linked to a glycerol that is attached to a phosphate that may also be linked to another small organic molecule.

Front 59

Why are phospholipids amphipathic?

Back 59

Phospholipids are amphipathic molecules; their “heads” (the glycerol/phosphate+ portion) are hydrophilic, while their “tails” (the two fatty acids or two isoprene chains) are hydrophobic.

Front 60

lipid bilayer

Back 60

Lipid Bilayer = when two sheets of phospholipid molecules align. (square formation) They usually have longer tails.

Front 61

What is the function of lipids?

Back 61

1. Store chemical energy

2. Become like messenger between body cells.

3. pigments which absorb light energy.

4. Waxes form waterproof coatings on things like leaves and our skin.

5. Vitamins that assist the activity of healthy enzymes.

6. Their part in the cell membrane, which allows the survival and well-being of organisms.

Front 62

Transmission electron microscopy

Back 62

Transmission electron microscopy (TEM) = forms an image from electrons passing through a specimen much like light microscopes form images from light rays that pass through a specimen

Front 63

How much can a TEM magnify?

Back 63

TEM magnifies up to = 250000x

Front 64

Scanning Electron Microscope

Back 64

Scanning Electron Microscopy (SEM) = coat their surfaces with a layer of metal atoms, microscope scans the surface with a narrow beam of electrons which reflect back from the surface in response to the beam then strike a detectors

Front 65

What can the SEM provide the researcher?

Back 65

SEM = records shadows and highlights, provides images with a 3D appearance

Front 66

Green Florescent Protein (GFP)

Back 66

Green Florescent Protein (GFP) = tags specific molecules under microscope and can track where they go

Front 67

confocal microscopy

Back 67

confocal microscopy = follows specific cell

Front 68

electron tomography

Back 68

electron tomography = trace an organelle

Front 69

x-ray crystallography

Back 69

x-ray crystallography = follow a molecules

Front 70

compound light microscope

Back 70

compound light microscope = used light to illuminate the specimen and two lenses to magnify it (compound because of two lenses)

Front 71

Who discovered the nucleus and what did he call it?

Back 71

Robert Brown; a "dark spot"

Front 72

What is the cell theory?

Back 72

cell theory = Cell Theory states that all living organisms are made of one or more cells, that the cell is the basic organizational unit of life, and that all cells come from other cells.

Front 73

cell membrane

Back 73

Cell membrane = boundaries of the cell, sort of like the skin on your body, control what goes in and what goes out of the cell

Front 74

homeostasis

Back 74

homeostasis = relatively stable conditions inside cells and organs

Front 75

electron micrograph

Back 75

electron micrographs = photographs taken with electron microscopes cannot look at live things, only light microscopes can do that

Front 76

What are the two types of phospholipids?

Back 76

micelles and lipid bilayers

Front 77

micelles

Back 77

Miscelles = tiny droplets created when the hydrophilic heads of them face the water, and the hydrophobic tails are forced together away from the water (circle formation) They usually have shorter tails.

Front 78

What does it mean when something is selectively permeable?

Back 78

Selective permeability = small non polar molecules move across bilayers quickly and large molecules and charged substances cross the membrane slowly, if at all.

Front 79

Liposome

Back 79

Liposomes = when lipid bilayers are agitated by shaking, the layers break + reform as small, spherical structures. Then the resulting vesicles have water on the inside as well as the outside because the hydrophilic heads of the lipids face outward on each side of the bilayer.

Front 80

How can you tell if a molecule will cross a membrane quickly or not?

Back 80

How quickly molecules move within and across membranes is a function of temperature and the structure of the hydrocarbon tails (or length of the tails) in the bilayer.

Front 81

Which lipids contain more saturated fatty acids - in plants or animals?

Back 81

lipids derived from animals = contain more saturated fatty acids

lipids derived from plants = contain more unsaturated fats/kinkier and more liquid

Front 82

When it's cold, is it easier or harder to cross the membrane?

Back 82

permeability of the membrane decreases as the temperature decreases - this is why people die of hypothermia because the cells die because they are solid and don't allow anything (even the positive things) to pass through the cell membrane.

Front 83

entropy

Back 83

entropy = a measure of the randomness or disorder in a system

Front 84

Diffusion

Back 84

Diffusion = movement of molecules and ions resulting from their kinetic energy. Move from high to low concentration gradient.

Front 85

concentration gradient

Back 85

Concentration gradient = difference in solute concentration

Front 86

key concept of diffusion

Back 86

Molecules and ions move randomly in all directions when a concentration gradient exists, but there is a net movement from regions of high concentration to regions of low concentration. Diffusion along a concentration gradient is a spontaneous process because it results in an increase in entropy.

Front 87

Osmosis

Back 87

Osmosis = the movement of water along the concentration gradient

Front 88

Hypertonic

Back 88

hypertonic = molecules in the cell want to get out of it, the cell shrinks (If the solution outside the membrane has a higher concentration of solutes that the interior has, the solutes are not able to pass through the lipid bilayer, then water will movie out of the vesicle into the solution outside). Hypertonic describes the solution outside the cell.

Front 89

Hypotonic [Think: hungry hungry hippos]

Back 89

hypotonic = molecules outside the cell want to get into it, the cell swells or even bursts from water entering it (If the solution outside the membrane has a lower concentration of solutes than the interior has, water will move into the vesicle via osmosis.) Hypotonic describes the inside solution.

Front 90

Isotonic

Back 90

isotonic = akin to equilibrium - the same amount of molecules want to get in and out of the cell, so the cell feels no change (If the solute concentrations are equal on either side of the membrane, the liposome will maintain its size because when the outside solution does not affect the membranes shape, that solution is equal toned).

Front 91

Does diffusion need energy?

Back 91

Diffusion is often referred to as a ‘passive process’ because it requires no energy

Front 92

amphipathic proteins

Back 92

amphipathic proteins (that have hydrophobic and hydrophilic parts) can insert themselves into lipid bilayers. Therefore proteins can have have both polar and non polar amino acids

Front 93

Fluid Mosaic Model

Back 93

Fluid Mosaic Model = singer and nicolson suggested that membranes are a mosaic of phospholipids and different types of proteins. The overall structures was proposed to be dynamic and fluid. (pg. 100)

Front 94

Freeze Fracture Technique. Describe it and what microscope does it use?

Back 94

Freeze Fracture Technique = developed to analyze plasma membranes, this technique freezes and fractures the membrane before analyzing it under a scanning electron microscope.

Front 95

Detergent

Back 95

Detergent = is a small amphipathic molecule.

When they are added to a solution surrounding a lipid bilayer, the hydrophobic tails of the detergent molecule interact with the hydrophobic tails of the lipids and with the hydrophobic portions of the transmembrane proteins. These interactions displace the membrane phospholipids and end up forming water-soluble, detergent-protein complexes.

Front 96

What are the three types of transport proteins?

Back 96

Three classes of transport proteins = channels, transporters, and pumps — each of these affect membrane permeability

Front 97

Ion channels

Back 97

Ion channels = in cells ions cross membranes through these specialized membrane proteins called ion channels.

Front 98

Electrochemical gradient

Back 98

Electrochemical gradient = ions move in response to a combined concentration and electrical gradient (102)

Front 99

Channel Proteins, and whats an example

Back 99

Channel Proteins = selective. Each channel protein has a structure that allows it to admit a particular type of ion or small molecule. Ex) aquaporins

Front 100

Gated Transport channels

Back 100

Gated transport channels = open or close in response to the binding of a particular molecule or to a change in the electrical charge on the outside of the membrane. Ex) CFTR

Front 101

Facilitated Diffusion

Back 101

Facilitated Diffusion = passive transport of substances that otherwise would not cross a membrane readily

Front 102

carrier proteins/transporters and an example

Back 102

carrier proteins/transporters = change shape and facilitate diffusion Ex) GLUT-1

Front 103

Active transport

Back 103

Active transport = import molecules or ions against their electrochemical gradient. Accomplishing this task requires energy, because the cell must counteract the entropy loss that occurs when molecules or ions are concentrated.

Front 104

pumps

Back 104

pumps = when pumps change shape membrane proteins can move against the electrochemical gradient. (105)

Front 105

Why can't lipids dissolve in water?

Back 105

Their inability to dissolve in water stems from the fact they are made up largely of hydrocarbons—smaller molecules made up solely of hydrogen and carbon.

Front 106

biologists write the sequence of amino acids in a polypeptide in which direction?

Back 106

amino to carboxy-terminus

Front 107

what two function groups are in every amino acid?

Back 107

an amino group and a carboxyl group

Front 108

Twenty different amino acids are found in the proteins of cells. What distinguishes these molecules?

Back 108

the composition of their side chains or R groups

Front 109

What determines the primary structure of a polypeptide?

Back 109

its sequence of amino acids

Front 110

In a polypeptide, what is the most responsible for the secondary structure called an a-helix?

Back 110

hydrogen bonds that form between carbonyl and amino groups on different residues

Front 111

What is a transition state?

Back 111

the complex formed as covalent bonds are being broken and re-formed during a reaction

Front 112

What type of bond allows sugars to polymerize?

Back 112

Glycosidic linkage

Front 113

What holds cellulose molecules together in bundles large enough to form fibres?

Back 113

Hydrogen bonds

Front 114

Why is it unlikely that carbohydrates played a large role in the origin of life?

Back 114

They do not polymerize without the aid of enzymes

Front 115

An isomer of a particular molecule is...?

Back 115

A molecule that has the same formula as the molecule in question, but a different shape

Front 116

Which of the following type of bonds is most important in determining the secondary structure of proteins?

Back 116

Hydrogen bonds

Front 117

A chain of amino acid residues is coiled into a helical form. This is a description of which of the following?

Back 117

The secondary structure of a protein

Front 118

Stanley Miller and Howard Urey Experiment according to them

Back 118

Stanley Miller and Harold Urey used inorganic compounds and energy to produce organic compounds. They demonstrated that water, in the presence of a reducing atmosphere, and electricity, can result in a variety of organic compounds. Their research has potential application to our understanding of the origin of life: life in the form of organic compounds might have originated from inorganic compounds in a reducing and warm environment.

Front 119

What do enzymes do in a cell?

Back 119

Enzymes act to catalyze or speed up reactions in the cells. All reactions depend on enzymes to achieve reaction speeds necessary for life to be sustained.

Front 120

What is responsible for holding the two strands together in the DNA double helix?

Back 120

Hydrogen bonds

Front 121

Which of the following best describes DNA’s secondary structure?

Back 121

Double antiparallel helical strands

Front 122

What is it about DNA’s structure that facilitates copying?

Back 122

the ability to have complimentary pairing between nucleotide bases.

Front 123

Which of the following choices best reflects the following relationship: monosaccharide versus polysaccharide

Back 123

Glucose vs. Glycogen

Front 124

Which of the following do starch and cellulose have in common?

Back 124

The size of their monosaccharide subunits

Front 125

If you were going to develop a new antibiotic you should probably become an expert on which of these carbohydrates?

Back 125

Peptidoglycan

Front 126

What type of covalent bond would you find between two monosaccharides?

Back 126

Glycosidic linkage

Front 127

How do the α and β forms of glucose differ?

Back 127

The hydroxyl group attached to carbon 1 lies in a different position relative to the plane of the ring in the two forms.

Front 128

Describe the four major functions of carbohydrates, and give an example of a specific carbohydrate that is specialized for each function.

Back 128

1. energy storage (glycogen), cell identity (starch tags proteins), structure (chitin), building blocks for synthesis (ribose)

Front 129

Early origin of life - what was here?

Back 129

Only monosaccharides may have played a role in early evolution of life as structural components of RNA. RNA is a more likely candidate because of its catalytic properties. Polysaccharides most likely did not play a major role in early chemical evolution despite their importance for many life processes. There still needs to be evidence shown for formation of glycoside linkages in monosaccharides and plausible mechanism for polymerization of monosaccharides.

Front 130

Phospholipid description

Back 130

A non-polar lipid molecule that is made amphipathic by the addition of a phosphate

Front 131

Which of the following do lipids have in common with proteins, nucleic acids, and carbohydrates?

Back 131

Their constituent parts are joined by dehydration synthesis reactions.

Front 132

Ribozyme

Back 132

A ribozyme is an RNA molecule that is capable of catalyzing a chemical reaction

Front 133

Ribonucleotide and deoxyribonucleotide

Back 133

The difference is the sugar. Ribose has an -OH group bonded to the 2' carbon. Deoxyribose has an H instead at the same location.

Front 134

Triose and pentose and hexose are all sugars that differ in the number of what?

Back 134

carbons

Front 135

Why do people use carbs in advertising?

Back 135

Carbohydrates are reduced molecules that have high-energy electrons.

Front 136

amylases

Back 136

the enzyme that breaks a-gycosidic linkages in starch

Front 137

phophorylase

Back 137

what catalyzes hydrolysis of a-glycosidic linkages