Cell Biology: Chapter 2

Front 1

What term describes the chemical bond in which electron pairs are shared between two atoms?

Back 1

covalent bonds

Front 2

The formation of covalent bond is accompanied by the release of...

Back 2

energy, which must be reabsorbed at some later time if the bond is to be broken.

Front 3

The energy required to leave C-H, C-C, or C-O covalent bonds is quite large, typically between 80-100 kilocalories per mole of molecules, which makes these bonds...

Back 3

stable under most conditions

Front 4

Where are electrons present?

Back 4

around an atom's nucleus in "clouds" or orbitals that are roughly defined by their boundaries, which may be a spherical or dumbbell shape

Front 5

Each orbital contains a maximum of _________ electrons.

Back 5

two

Front 6

When two unlike atoms are covalently bonded, the positively charged nucleus of one atom exerts a greater attractive force on the outer electrons than the other. Consequently, the shared electrons tend to be located more closely to the atom the more ___________________ atom.

Back 6

electronegative

Front 7

Molecules, such as water, that have an asymmetric distribution of charge are referred to as ___________ molecules.

Back 7

polar

Front 8

Molecules that lack electronegative atoms and strongly polarized bonds, such as molecules that consist entirely of carbon and hydrogen atoms, are said to be _____________.

Back 8

nonpolar

Front 9

An atom with a net positive or negative charge because it has gained or lost one or more electrons during a reaction is called a(n) ___________.

Back 9

ion - results when strongly electronegative nuclei capture electrons

Front 10

What term describes the bonds that do not depend on shared electrons but rather on attractive forces between atoms having an opposite charge?

Back 10

noncovalent bonds - weaker than covalent bonds (broken and re-formed)

Front 11

What term describes the electrostatic attraction between a positively charged and negatively charged components?

Back 11

ionic bond

Front 12

The strength of ionic bonds in a cell is generally weak due to the presence of ___________.

Back 12

water

Front 13

The DNA molecule consists of two separate strands held together by __________________________.

Back 13

noncovalent hydrogen bonds

Front 14

Because of their inability to interact with water, polar molecules such as amino acids and sugars, are said to be ________________.

Back 14

hydrophilic or "water loving"

Front 15

What two things in cells are very closely related to the structure of molecules and atoms?

Back 15

structure and function

structure = function

Front 16

How many kilocalories are required to break a mole of covalent bonds?

Back 16

80-100 kilocalories

Front 17

What is the term used to describe unstable atoms or molecules with unpaired electrons?

Back 17

free radicals

They are formed during metabolism, are highly reactive and damage macromolecules such as DNA, and may play a role in aging.

Front 18

In what ways does the superoxide dismutase (SOD) enzyme destroy the superoxide radical (O2-)?

Back 18

SOD protects cells from damage due to the superoxide radical.

SOD extends the life span of laboratory animals that overproduce it.

Front 19

What kind of bonds determine the structure and properties of water?

Back 19

Hydrogen bonds

Front 20

What kind of bond occurs when nonpolar molecules associate and minimize their exposure to polar (water) molecules?

Back 20

hydrophobic interaction - water fearing (ex: oil in water)

Front 21

What occurs when two molecules with transitory dipoles are very close to one another and oriented in the appropriate manner?

Back 21

van der Waals force - weak forces

Front 22

The properties of water result from its _____________.

Back 22

structure

Front 23

Why is water such an important factor in a cell?

Back 23

It is able to form weak interactions with many different types of chemical groups.

Water molecules form hydrogen bonds with molecules that contain polar groups such as amino acids and sugars, which ensures their solubility within the cell.

Front 24

What is the term used to describe a molecule that is capable of releasing (donating) a hydrogen ion?

Back 24

acid

Front 25

What is the term used to describe a molecule that is capable of accepting a proton?

Back 25

base

Front 26

Why are most biological processes sensitive to pH?

Back 26

pH changes in hydrogen ion concentration affect the ionic state of biological molecules. Even slight pH changes can impede biological reactions.

Front 27

What is the term used to describe compounds that react with free hydrogen or hydroxyl ions, resisting changes in pH?

Back 27

buffers

Blood, for example, is buffered by carbonic acid and bicarbonate ions.

Front 28

Carbon forms _______ covalent bonds, with itself or other atoms.

Back 28

4

Front 29

What is the term used to describe carbon-containing molecules produced by living organisms?

Back 29

biochemicals

Front 30

Buffers do not maintain a pH of _____.

Back 30

7 (Our blood has a pH of 7.4)

Front 31

Which amphoteric molecules are often involved in buffering?

Back 31

bicarbonate, ammonium, and water

Front 32

What is the essential quality of carbon?

Back 32

the incredible number of molecules it can form (can bond with up to 4 other atoms)

Front 33

Many functional groups contain one or more electronegative atoms and make organic molecules more...

Back 33

more polar, more water soluble, and more reactive

Front 34

What is the term used to describe the highly-organized molecules that form the structure and carry out the activities of cells?

Back 34

macromolecules - proteins, nucleic acids, polysaccharides, and lipids

Front 35

What are the building blocks of macromolecules?

Back 35

sugars, amino acids, nucleotides, and fatty acids

Front 36

What is the term used to describe the RNA enzymes that play a catalytic role?

Back 36

ribozymes

Front 37

What is most of the energy being put to use at any given moment in any living organism called?

Back 37

adenine triphosphate (ATP)

Front 38

Which biological molecule includes simple sugars and sugar polymers?

Back 38

carbohydrates - serve as energy storage molecules

Front 39

Which biological molecules are polymers of amino acids that form a diverse group of macromolecules?

Back 39

proteins - exhibit a high degree of specifity

Front 40

What is the term used to describe the type of lipid that is made of glycerol linked by three ester bonds to three fatty acids?

Back 40

fat

Front 41

Which biological molecules are polymers of nucleotides that store and transmit genetic information?

Back 41

nucleotides - DNA and RNA

Front 42

Describe saturated fats.

Back 42

lack C=C double bonds and are solid at room temperature (butter)

straight chains that can stack (pencils)

Front 43

Describe unsaturated fats.

Back 43

have one or more C=C double bonds and are liquid at room temperature (most oils)

double bonds cause bends, no stacking (tree branching)

Front 44

What is the basic shared structure of steroids?

Back 44

four-ring skeleton

Front 45

In a set of enantiomers, the structure with the functional group on the left is which structure? Right?

Back 45

left - L
right - D

Front 46

Which sugars are produced by our bodies?

Back 46

D sugars

Front 47

Which sugars cannot be metabolized by our bodies?

Back 47

L sugars

Front 48

How does the orientation of the hydrogen on the carbonyl of a carbohydrate affect the structure?

Back 48

if the hydrogen is up = alpha

if the hydrogen is down = beta

Front 49

Sucrose and lactose are the two most common disaccharides (source of readily available energy). Sucrose is composed of glucose and fructose joined by a(n) ________________ linkage.

Back 49

1-->2 alpha

Front 50

Sucrose and lactose are the two most common disaccharides (source of readily available energy). Lactose is composed of glucose and galactose joined by a(n) _______________ linkage.

Back 50

1-->4 beta

Front 51

What is the structure of glycogen molecules?

Back 51

most highly branched

Front 52

What is the structure of starch molecules?

Back 52

helical

Front 53

What is the structure of cellulose molecules?

Back 53

unbranched and highly extended

Front 54

What are the components of an amino acid?

Back 54

carbon, amine group, a carboxyl group, and a variable R group

Amino acids differ in the R group attached to one of the bonds of the alpha-carbon.

Front 55

Which stereoisomer of amino acids appears in nature?

Back 55

L stereoisomer

Front 56

How are amino acids linked together to make a protein?

Back 56

by peptide bonds into a polypeptide chain

Peptide bonds form between an alpha carbonyl and the alpha amino.

Front 57

Where are the hydrophilic side chains in amino acids located?

Back 57

at the surface of the protein where they contact surrounding aqueous medium

Front 58

Where are the hydrophobic residues in amino acids located?

Back 58

within the center of the protein, particularly in the vicinity of the central heme group

Front 59

Name the amino acid that has a small R group, which makes the backbone flexible and able to move, making it useful in protein hinges.

Back 59

Glycine (Gly) - small R group allows 2 backbones (of same or different protein) to approach closely

Front 60

Name the amino acid that has an R group which forms a ring with amino group (imino group).

Back 60

Proline (Pro) - hydrophobic amino acid that does not readily fit into orderly secondary structure (alpha helix)

Front 61

Name the amino acid that has a reactive R group -SH.

Back 61

Cysteine (Cys) - forms disulfide (-S-S-) bridge with other cysteines often at some distance away in polypeptide backbone

Front 62

A protein's _____________ is critical to its function.

Back 62

structure - sequence of amino acids in the polymer

Front 63

In terms of secondary structure of proteins, which structure is most recognizable?

Back 63

alpha helix

Front 64

What shape is the alpha helix (proteins)?

Back 64

twisting spiral (coiled, cylindrical, coiled ribbon)

Front 65

What shape is the beta-pleated sheet (protein)?

Back 65

folded or pleated conformation (flat ribbon with arrows to show direction)

Front 66

The hydrogen bonds of an alpha helix are ______________ to the helix.

Back 66

parallel

Front 67

The hydrogen bonds of a beta sheet are _______________ to the helix.

Back 67

perpendicular

Front 68

Because beta strands are highly extended, the beta sheet...

Back 68

resists pulling forces (silk)

Front 69

Which structure describes the conformation of the entire protein?

Back 69

tertiary structure

Front 70

Whereas secondary structure is stabilized by hydrogen bonds, tertiary structure is stabilized by an array of _______________ bonds.

Back 70

non-covalent

Front 71

Which proteins have an elongated shape?

Back 71

fibrous proteins - most proteins that act as structural materials outside living cells

Front 72

Which proteins have a compact shape?

Back 72

globular proteins - most proteins within the cell

Front 73

Secondary structure is limited to a small number of conformations, but tertiary structure is...

Back 73

virtually unlimited.

Front 74

Which structure of polypeptides is the specific linear sequence of amino acids that constitutes the chain?

Back 74

primary structure

Front 75

What was the first protein to reflect the tertiary structure of a globular protein?

Back 75

myoglobin (1957) - John Kendrew

Myoglobin stores oxygen in muscle cells.

Front 76

What is the term used to describe a region within a protein (or RNA) that folds and functions in a semi-independent manner?

Back 76

domain

Most eukaryotic proteins are composed of two or more.

Front 77

Protein domains are often identified with a specific _____________.

Back 77

function

Front 78

What is the term used to describe predictable (nonrandom) movements within a protein that are triggered by the binding of a specific molecule?

Back 78

conformational changes

Front 79

Which structure of proteins is composed of subunits (more than one chain)?

Back 79

quaternary structure

Front 80

What is the term used to describe proteins that have multiple binding partners?

Back 80

hubs

Hub proteins are more likely to be essential than non-hub proteins because these are proteins that organisms cannot live without.

Front 81

How may proteins become denatured?

Back 81

detergents, organic solvents, radiation, heat, chemicals such as urea and guanidine chloride (all interfere with tertiary structure)

Front 82

The linear sequence of amino acids contains all of the information required for the formation of the polypeptide's 3D conformation. This means that..

Back 82

ribonuclease is able capable of self-assembly

Front 83

The tertiary structure is the lowest in energy, meaning that it is..

Back 83

the most thermodynamically stable structure that can be formed by that chain

Front 84

Creutzfield-Jakob Disease (CJD) results from ___________ proteins in the brain.

Back 84

misfolded

Healthy brains have a PrP^c protein, while CJD brains PrP^Sc, which is identical to the normal protein but is folded.

Mad cow disease, kuru, and scrapie are also caused by this misfolded protein.

Front 85

What is the term used to describe "helper proteins" that are used to prevent nonselective interactions during protein folding to achieve proper 3D conformation?

Back 85

molecular chaperones - bind to short stretches of hydrophobic amino acids that tend to be exposed in nonnative proteins but buried in proteins having native conformation

Front 86

Where are many molecular chaperones located?

Back 86

in the ER (endoplasmic reticulum) since the ER is also particularly involved in coordinating the efforts of assembling molecular structures

*Cells may use molecular chaperones to assemble molecular structures.

Front 87

Some proteins can self-assemble from purified subunits, while others (most) require ______________ for proper folding.

Back 87

molecular chaperones

Front 88

During heat shock response, what protects the protein structure?

Back 88

molecular chaperones

Front 89

What is the term used to describe the entire inventory of proteins produced by an organism?

Back 89

proteome - inventory of all proteins that are present in a particular tissue, cell, cellular organelle

Front 90

How does gel electrophoresis separate nucleic acids?

Back 90

by size