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Composition of the cell Flashcards

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Biology 101 flashcards
1
Q

92 naturally occurring elements

A

Living organisms made of only small selection of elements.

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2
Q

Carbon,

Hydrogen

Nitrogen

and Oxygen

A

make up 96.5% if an organism’s weight

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3
Q

Properties of materials from which living cells are made depend on which atoms they contain and the way these atoms are linked together to form molecules.

Atoms are held together in molecules by ________ _______?

Two types. ______ ,______

A

chemical bonds

covalent

non- covalent

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4
Q

chemical bonds:

Covalent-

A

* involve sharing of electrons between atoms

* strong bonds

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5
Q

chemical bonds:

Non- covalent

A

*attractions between atoms that do not involve sharing of electrons

*Weak bonds

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6
Q

Covalent Bonds:

Two atoms share a pair of electrons

A

*when one atom forms covalent bonds with several others -multiple bonds have definite orientations in space relative to one another.

* Specific bond angles, lengths, and energies depend on atoms involved in molecule formation

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7
Q

single and double covalent bonds

Single-

A
  • sharing of 2 electrons ( 1 from each atom)
  • allows the rotation of one part of the molecule relative to another around the bond axis
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8
Q

Double -

A
  • sharing of more than 2 electrons
  • shorter and stronger than single
  • no rotation, more rigid than single - it influences the 3-D shape of molecules
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9
Q

single and double covalent bonds-

A
  • the pair of electrons is often shared unequally
  • One atom attracts the shared electrons more than other —> polar covalent bond—> positive change concentrated toward one end of the molecule ( positive pole) and negative towards the other end ( negative pole)
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10
Q

Polar bonds

A
  • allow molecules to interact through electrical forces—> extremely important in cell biology
  • Large molecules with multiple polar groups have a pattern of partial (+) and (-) charges on their surface—> attraction of molecule with a complementary set of charges—> surfaces will stick to each other.
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11
Q

Ionic Bond-

A

caused by attraction between positively and negatively charged atoms ( (ions) formed by giving electrons to -or accepting electrons from -another atom

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12
Q

cation-

A

positively charged atom or molecule

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13
Q

anion-

A

Negatively charged atom or molecule

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14
Q

Hydrogen Bond-

A

caused typically by attraction between a positively charged hydrogen atom held in one molecule by a polar covalent bond and another atom ( typically N or O) that is partially negatively charged in another polar molecule

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15
Q

Hydrogen Bond-

Water-

A

each molecule forms hydrogen bonds with 2 other water molecule—> Network—–> responsible for surface tension

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16
Q

Hydrogen Bond-

can also occur between different parts of a single large molecule-

A

-special shapes (molecule folding)

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17
Q

Van der Waals Attraction

A

attraction between atoms caused by fluctuating electrical charges.

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18
Q

Hydrophobic Interactions:

A

attraction between non-polar atoms and molecules in aqueous solution caused by their inability to form hydrogen bonds with water molecules.

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19
Q

Hydrophobic molecules-

A

are insoluble in water and tend to self- associate to minimize the disruption of hydrogen bonds among water molecules ( minimum energy state)

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20
Q

Bond strength

A

measured by the amount of energy needed to break a bond

  • Average thermal motion of atoms-0.8 kcal/mol
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21
Q

Single non-covalent bond is not strong enough to hold two atoms together for very long-

A

but they are important in situations where molecules have to associate and dissociate readily to carry out their functions in the cell.

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22
Q

Because non-covalent bonds are weak -

A

it takes a large number of bonds to achieve a stable molecular association.

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23
Q

Because non-covalent bonds act over short distances-

A

the number of bonds formed depends on the degree to which two molecules or different parts of the same molecule fit together (“goodness of fit”)

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24
Q

Life evolved in an aqueous environment and cells are made up predominately of water.

A

Therefore, the properties of water are very important in determining the chemistry of cells.

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25
Q

Properties of Water

A

* water molecules are polar

*Electrons spend more time associated with oxygen atom, making it slightly negative and less time associated with the hydrogen atoms, making them relatively positive.

* Water molecules are transiently attracted to one another by hydrogen bonds—> water molecules are very cohesive

-cohesiveness of water responsible for

—high surface tension

—solubility properties of other molecules

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26
Q

-The ability of other molecules to dissolve in aqueous solution is determined by how they interact with ______ __________?

A

water molecules

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27
Q

Solubility in Aqueous Solution:

Molecules that attract water molecules through ______ _____ effects are soluble in water?

A

electrical charge

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28
Q

Solubility in Aqueous Solution:

Molecules that disrupt hydrogen bonding between water molecules are ______?

A

insoluble

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29
Q

Soluble Molecules-

A

hydrophilic “water loving”

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30
Q

Solubility in Aqueous Solution:

soluble molecules-

Ionic substances-

A

-attract the polar end of water molecules with the opposite charge and surround themselves with a shell of water molecules

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31
Q

Solubility in Aqueous Solution:

soluble molecules-

Polar substances-

A

-form hydrogen bonds with water molecules and surround themselves with a shell of water molecules.

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32
Q

Solubility in Aqueous Solution:

Insoluble molecules-

A

-hydrophobic “water fearing”

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33
Q

Insoluble molecules

Hydrocarbons and other nonpolar molecules-

A
  • break hydrogen bonds between water molecules ( it requires energy)
  • tend to self- associate to reduce the degree of disruption of hydrogen bonding—-> lowest energy state.
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34
Q

Small Biological Molecules

molecule

A

-cluster of atoms held together by covalent bonds

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35
Q

Small Biological Molecules

Cell Molecules-

A

organic -carbon compounds

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36
Q

Small Biological Molecules

Four major families of small organic molecules in cells:

A

sugars

fatty acids

Amino Acids

Nucleotides

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37
Q

Small Biological Molecules

Sugars (carbohydrates)

A
  • Cell’s energy source and building blocks of
  • monosaccharides ( single sugar molecule)
  • Disaccharides ( two sugar molecules)
  • Oligosaccharides ( several sugar molecules)
  • Polysaccharides ( large number of sugar molecules)
  • Glycoproteins ( sugar + protein)
  • Glycolipids ( sugar + lipid)
38
Q

Small Biological Molecules-

Monosaccharides-

A

the general formula

(CH2O)n

Also called carbohydrates ( because of this formula

39
Q

Small Biological Molecules-

Types of Monosaccharides-

A

triose-3 carbons

-tetrose-4 carbons

pentose-5 carbons

hexose-6 carbons

heptose-7 carbons

40
Q

Small Biological Molecules-

Three-dimensional Structure of Pentoses and Hexoses-

A
  • 5 and 6 carbon sugars form rings in aqueous solution
  • hexoses-6 atom rings ( 5C’s + 1 O)
  • pentoses-5 atom rings ( 4 C’s + 1 O)
41
Q

Small Biological Molecules-

Isomers-

A
  • Monosaccharides that differ only in the spatial arrangement of atoms ( have the same chemical formula)
  • Minor change in the chemical properties - recognized by other molecules ( e.g. enzymes) - can have important biological effect.
42
Q

Small Biological Molecules-

Isomers-

A
  • Monosaccharides that differ only in the spatial arrangement of atoms ( have the same chemical formula)
  • Minor change in the chemical properties -recognized by other molecules (e.g. enzymes) -can have important biological effect.
43
Q

Small Biological Molecules-

Glycosidic Bond-

A

-Monosaccharides can be covalently linked to each other via a glycosidic bond to form chains:

* disaccharide- two monosaccharides (e.g. sucrose)

* trisaccharide- three monosaccharides oligosaccharide- short chain (e.g., blood group)

* polysaccharide- long chain (e.g, glycogen, starch)

44
Q

Small Biological Molecules -

Glycosidic Bond Formation-

A

-Can form between the Oxygen associated with the 1 carbon and any carbon carrying a hydroxyl (-OH) group

45
Q

Small Biological Molecules

Glycosidic Bond Formation-

Condensation-

A

-dehydration reaction- loss of water

46
Q

Small Biological Molecuales

Glycosidic Bond Formation-

Glycosidic bond can be broken by the reverse reaction- _____?

A

hydrolysis

47
Q

Small Biological Molecules

Alpha and Beta Links-

A

the hydroxyl group on the 1- carbon can change from one position to another:

*alpha position-hydroxyl below the plane of the ring

* beta position- hydroxyl above the plane of the ring

48
Q

Small Biological Molecules

When a glycosidic bond forms, the hydroxyl is fixed in either the ____ or ____ position forming an _____ or _______ _________ ______?

A

alpha

beta

alpha

beta

glycosidic link

49
Q

Small Biological Molecules

Complexity of Sugars-

A
  • A small number of monosaccharides can form an extremely large number of chemically distinct molecules.
  • Basis of chemical recognition e.g. blood groups.
50
Q

Small Biological Molecules:

Sources of Complexity-

A

*isomerization

*multiple ways to link monosaccharides

*branching

*formation of chemical derivatives

51
Q

Small Biological Molecules:

Multiple Linkage Patterns:

A
  • Because each monosaccharide has several free hydroxyl groups, two identical monosaccharides can be linked in 11 different ways to form 11 chemically distinct disaccharides.
  • Three identical monosaccharides can be linked to form about 110 chemically distinct disaccharides.
52
Q

Small Biological Molecules

Branching

A

-A monosaccharide can form more that one glycosidic bond, to produce a branched chain.

53
Q

Small Biological Molecules:

Chemical Derivatives of Sugars:

A

-Various chemical groups can be attached to sugars by dehydration reactions involving hydroxyl groups:

+ carboxylic acid group—> sugar acids

+amino groups—-> amino sugar

+ N-acetyl group —-> N-acetyl sugar

54
Q

Lipids

A

Lipids are a family of hydrophobic molecules based on hydrocarbon chains.

55
Q

Lipids-

lipids are a family of hydrophobic molecules based on hydrocarbon chains.

Fatty acids-

A

-energy storage and building blocks of other lipids

56
Q

Lipids-

lipids are a family of hydrophobic molecules based on hydrocarbon chains.

-Triacylglycerols-

A

energy storage and building blocks of other lipids

57
Q

Lipids-

lipids are a family of hydrophobic molecules based on hydrocarbon chains.

Phospholipids-

A

biological membranes

58
Q

Lipids-

lipids are a family of hydrophobic molecules based on hydrocarbon chains.

Steroids-

A

cell signaling

59
Q

Lipids-

lipids are a family of hydrophobic molecules based on hydrocarbon chains.

Polyisoprenoids-

A

membrane synthesis

60
Q

Lipids-

lipids are a family of hydrophobic molecules based on hydrocarbon chains.

Glycolipids (lipid + oligosaccharide)-

A

cell signaling

61
Q

Lipids:

Fatty Acids-

A
  • unbranched hydrocarbon chains terminating in a carboxylic acid (~COOH) group.
  • Serve as building blocks for other lipids
62
Q

Lipids:

Fatty Acids:

two types

A

-* Saturated- no double bonds, straight chain

*unsaturated- one or more c=c double bonds, kinked chain.

63
Q

Lipids:

Triacylglycerols/Triglycerides

A
  • storage form of fatty acids
  • Serve as building blocks for phospholipids
64
Q

Lipids:

Triacylglycerols/Triglycerides

*structure

A

Glycerol + 3 fatty acids + phosphate group + hydrophilic compound ( e.g. choline)

65
Q

Lipids:

Phospholipids

A

-Major consituents of cell membranes

66
Q

Lipids:

Phospholipids

*structure

A
  • glycerol + two fatty acids + phosphate group + hydrophilic compound (e.g. choline)
  • the hydrophilic head group and phosphate group are soluble in aqueous solution—> hydrophilic head
  • The fatty acid tail is insoluble in aqueous solution—> hydrophobic tail
67
Q

Lipids:

Phospholipids-

*phospholipid Aggregates-

A

in aqueous solution, phospholipids aggregate to form structures that remove the hydrophobic tails from contact with water

68
Q

Lipids

Pospholipids:

*Phospholipid Aggregates

-three forms of Aggregates:

A
  1. Micells
  2. Lipid monolayers
  3. Lipid bilayers
69
Q

Lipids:

Phospholipid Aggregates-

Micelles-

A
  • form in aqueous solution when the concentration of lipid is relatively low
  • speres with hydrophobic tails in the center and hydrophilic heads on the surface.
70
Q

Lipids

Phospholipid Aggregates-

Lipid monolayers-

A
  • form at the air- surface of an aqueous solution
  • spheres with hydrophobic tails in the center and hydrophilic heads in the solution
71
Q

Lipids:

Phospholipid Aggregates

Lipid bilayers-

A
  • form in solution at higher concentrations of lipids
  • membrane composed of two layers of lipid molecules with the hydrophobic tails in the center and the hydrophilic heads on the two surfaces.
72
Q

Amino Acids

A
  • building blocks of proteins
  • The same 20 amino acids make up the proteins of all life forms
73
Q

Amino Acids

General Structure-

A
  • central carbon atom-ALpha
  • Amino group
  • Carboxylic acid group
  • Side group (R)
  • Hydrogen
  • Chemical variety comes from the side chains
74
Q

Amino Acids-

Ionization-

A
  • Amino Acids can become charged
  • The carboxyl end can become negatively charged
  • Both ends can be chaged at the same time
  • Charge is a function of the pH of the solution
75
Q

Amino Acids

Ionization-

in cell-

A
  • PH close to 7- free amino acids exist in ionized form
76
Q

Amino Acids

Amino Acid Side Chains-

A

The structure and function of polypeptides is determined by the nature of the amino acid side chains.

77
Q

Amino Acids-

Four families of amino acid side chains:

A

* acidic (2)

  • can become negatively charged

* basic (3)

  • can become positively charged

* uncharged polar (5)

  • neutral
  • soluble in water (hydrophilic)

*nonpolar (10)

  • neutral
  • some (5) are insoluble in water ( hydrophobic)
  • two cysteines can form disulfide (-S-S-) bonds
78
Q

Amino Acids

Peptide Bonds-

A
  • two amino acids can be joined together via a condensation ( dehydration) reaction to form a covalent peptide bond.
  • Links the carboxyl end of one amino acid to the amino end of another —> C-N bond
  • The portions of the molecule on either side of the bond are relatively free to rotate about the axis of the bond.
79
Q

Amino Acids

Polypeptides-

A
  • chain of amino acids linked by peptide bonds
  • Very flexible chain
  • No branching
  • Polarized molecule
  • Amino terminus ( N-terminus) -NH2 group
  • either or both ends and one more side groups may be charged (ionized)
80
Q

Amino Acids-

Naming of Amino Acid Chains:

A

* small peptides

  • Dipeptide
  • Tripeptide
  • Tetrapeptide
  • ect… ( using greek numbers)

* medium sized= oligopeptides

* Large = polypeptides

-Amino acids ( except glycine) exist in D- and L- forms ( optical isomers) – only L forms and only the same 20 out of many amino acids are found in proteins.

81
Q

Nucleotides-

A

-Molecules consisting of one or more nitrogen -containing rings ( bases) covalently linked to a pentose sugar, and one e or more phosphate groups attached to sugar.

82
Q

Nucleotides-

Functions:

A

* Building blocks of nucleic acids

-DNA and RNA information storage

* High energy compounds ( high energy phosphoanhydride bonds between 3 phosphate groups)

-ATP and GTP

* Coenzymes

-coenzyme A

* Intercellular and intracellular signaling

-cyclic AMP

83
Q

Nucleotides-

Structure:

Three components-

A

1- Pentose Sugar

  • beta- ribose
  • beta-2-deoxyribose
    2) Nitrogen Bose
  • cytosine, thymine, uracil, adenine, guanine
    3) Phosphate
  • Monophosphate, diphosphate, triphosphate
84
Q

Nucleotides-

Nomenclature

A
  • Base + Sugar= Nucleoside
  • Nucleoside + phosphate = Nucleotide
85
Q

Nucleotides-

Nucleic Acids-

A
  • Polymers of nucleotides linked by phosphodiester bonds
  • Very flexible unless stabilized by complementary base pairing, do not branch
86
Q

Nucleotides-

Phosphodiester Bond-

A
  • Between the phosphate group attached to the sugar of one nucleotide and a hydroxyl group on the sugar of the next nucleotide.
  • Linkage: -C-O-P-O-C- between the 5’ -carbon of one nucleotide and the 3’ -carbon of a second nucleotide—> “3’-5’ phosphodiester bond”
  • Creates a sugar- phosphate-sugar backbone with the nucleotide bases sticking out-Condensation ( dehydration) reaction
87
Q

Nucleic Acids

A
  • polymers of nucleotides linked by phosphodiester bonds
  • Very flexible unless stabilized by complementary base pairing, do not branch
88
Q

Nucleic Acids-

Polarity-

A

nucleic acids are polarized molecules ( i.e. have two chemically distinct ends)

  • 3’-end ( usally bearing an -OH group)
  • 5’- end ( usally bearing a phosphate group)
89
Q

Nucleic Acids

two types-

A

Differ by a type of sugar in their sugar - phosphate backbone

*Ribose -ribonucleic acids- RNA- contain AGCU

*Deoxyribose- deoxyribonucleic acid- DNA- contain AGCT

  • RNA- single-stranded chain
  • DNA- double-stranded ( double helix- two polynucleotide chains running antiparallel, held together by hydrogen bonds between bases of two chains)
  • encode genetic information.
90
Q

Macromolecules

A
  • polymers of small organic molecules linked by covalent bonds
  • building blocks of cell components
  • Abundant in cells
91
Q

Macromolecules

A
  • polymer grows by addition of a monomer to the end of a growing polymer chain via condensation reaction ( stepwise polymerization of monomers)
  • Catalyzed by specific enzymes
  • Subunits added in particular order (sequences)—> biological function of proteins, nucleic acids and polysaccharides depend on the sequence of subunits in the chain—> variation in the sequence of subunits—> enormous diversity in the polymeric molecules that can be produced

–e.g. for a very small protein chain 1- amino acids long made of 20 amino acids–> 2010 possible combinations

  • Macromolecules bind together into multiunit complexes ( sue to noncovalent bonds and close fit between their surfaces)
  • Complexes of macromolecules form cell machineries that perform complex tasks

cell Bio (14 decks)

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