Chapter 3 Cell Bio Review

macromolecules of cell

• proteins

• nucleic acids

• polysaccharides

• lipids

proteins

• name comes from greek word preteios = “first place”

• extremely important in all organisms, occurring nearly everywhere in cell

nine major classes of proteins

• enzymes

• structural proteins

• motility proteins

• regulatory proteins

• transport proteins

• signaling proteins

• receptor proteins

• defensive proteins

• storage proteins

enzymes

communication b/w cells

structural proteins

catalysts, increasing rates of chemical reactions

motility proteins

cell contraction and movement

regulatory proteins

control and coordinate cell function

transport proteins

enable cells to respond to stimuli from environment

signaling proteins

move substances into and out of cells

receptor proteins

protect against disease

defensive proteins

physical support and shape

storage proteins

reservoirs of amino acids

20

only __ kinds of amino acids used in protein synthesis (number)

• some contain additional amino acids, usually result of modification

R group

every amino acid has same basic structure

• each has unique side chain called _______.

specific properties

R groups gives amino acid ____ ____.

asymmetric “a” carbon atom

almost all (except glycine have _______.

classes of R groups

• nonpolar amino acids (hydrophobic)

• polar, uncharged amino acids (hydrophilic)

• polar, charged amino acids (hydrophilic)

condensation

amino acids linked together stepwise into linear polymer by _______.

peptide bonds

amino acids linked together stepwise into linear polymer by condensation (dehydration) reactions, forming ___________.

asymmetry of peptide bonds

polypeptides have directionality due to _________.

N-terminus

polypeptide end with animo group called _____.

C-terminus

polypeptide end with carboxyl group _____.

protein synthesis

process of elongating chain of amino acids

polypeptide

immediate product of amino acid polymerization is a _________.

monomeric

proteins consist of single polypeptide

multimeric

proteins consist of two or more polypeptides

dimers, trimers, or tetramers

proteins consisting of two, three, or four polypeptides

covalent bonds and noncovalent interactions

_________ and _________ between amino acids residues (carboxyl, amino, and R groups) important for

• proteins to adopt its proper shape (or conformation)

• polypeptides to form multimeric proteins

noncovalent interactions

these are important for protein stability and folding

• hydrogen bonds

• ionic bonds

• van der waals interactions

• hydrophobic interactions

amino acid sequence and interactions

protein structure (shape) depends on ________ and _______.

primary, secondary, tertiary, and quaternary

four levels of organization that describes protein shape and structure

primary structure

• refers to amino acid sequence

  • by convention, amino acid sequences written from N-terminus to C-terminus

  • same direction with synthesis of polypeptide

secondary structure

• local regions of structure that result from hydrogen bonding between NH and CO groups along polypeptide backbone

• result in two major patterns

  • alpha helix

  • beta sheet

alpha helix

• spiral shape

• consists of peptide backbone, with R groups jutting out from spiral

• 3.6 amino acids per turn helix

• stabilized by hydrogen bonds between NH group of one amino acids and CO group of second amino acid one turn away

beta sheet

• extended sheetlike conformation

  • R groups just out on alternating sides of sheet

  • successive atoms of polypeptide chain located at “peaks” or “troughs”

    • also referred to as B-pleated sheet

motifs

• also called super secondary structures

  • combinations of short stretches of a helices and B sheets

    • B—a—B

    • hair loop

    • helix—turn—helix motifs

• do NOT predict biological functions

  • found in other proteins with dissimilar functions

tertiary structure

overall three-dimensional structure resulting from interactions of R groups

results in a 3-D structure (tertiary)

• hydrophobic residues avoiding water

• hydrophilic residues interacting with water

• repulsion of similarly charged residues

• attraction between oppositely charged residues

• stabilized by disulfide bonds

native conformation

• most stable possible three-dimensional structure of particular polypeptide

• proteins can be divided into two broad categories

  • fibrous proteins

  • globular proteins

fibrous proteins

• strand-like, water-insoluble, and stable

  • have extensive regions of secondary structure, either mainly a helix or mainly B sheet, with highly ordered repetitions

• provide mechanical support and tensile strength

examples of fibrous proteins

e.g., keratin, elastin, collagen, fibroin

globular proteins

• compact, spherical, water-soluble

  • can be mainly a helical, mainly B sheet, or mixture of both structures

• contain specific function regions (domains)

examples of globular proteins

e.g., antibodies, hormones, molecular chaperones, enzymes

protein domains

• discrete, locally folded unit of tertiary structure

  • typically 50-350 amino acids long, with regions of a helixes and B sheets packed together

  • usually with specific function

quaternary structure

• level of organization concerned with interaction and assembly of multiple folded subunits

• applies specifically to multimeric units

  • some proteins consist of multiple identical subunits

  • some contain two or more types of polypeptides

maintenance of quaternary structure

• bonds and forces

• process of subunit formation usually spontaneous

• molecular chaperones sometimes required to assist process

nucleic acids

• linear polymers of nucleotides

  • DNA (deoxyribonucleic acid)

  • RNA (ribonucleic acid)

store, transmit, and express genetic information

DNA role in cell

serves as repository of genetic information

RNA role in cell

• play several roles in expressing that information

four

_____ different types of nucleotides of DNA and RNA.

5-carbon sugar, phosphate group, N-containing aromatic base

Nucleotide each consists of __________ attached by _________ and_________.

Purine and pyrimidine

the two families of nitrogenous bases that make up DNA and RNA

adenine and guanine

nucleosides of purine

thymine, cytosine, and uracil (RNA)

nucleosides of pyrimidine

nucleosides

sugar-base complex without phosphate group

nucleoside monophosphates

has one phosphate group (e.g., adenosine monophosphate, AMP)

polynucleotide (DNA and RNA)

formed by this process has directionality

• 5’ phosphate group at one end and 3’ hydroxyl group at the other

• nucleotide sequences conventionally written in 5’ and 3’ direction

template

• preexisting molecule, used to ensure that new nucleotides (NTPs for RNA, dNTPs for DNA) added in correct order

complementary base pairing

• A forms two hydrogen bonds with T

• G forms three hydrogen bonds with C

5’ and 3’ direction

DNA and RNA synthesizes in a ___________.

RNA structure

• normally single stranded

• depends on base pairing

  • usually between bases in different areas of same molecule

  • less extensive than that of DNA

polysaccharides

long chain polymers of sugars and sugar derivatives

• consist of single kind of repeating unit or sometimes alternating pattern of two kinds

function of polysaccharides

serve primarily in structure and storage

• short polymers, oligosaccharides, sometimes attached to cell surface proteins

two types of monosaccharides

• aldehyde sugar (aldo sugar) with terminal carbonyl group

• ketone sugar (keto sugar) with internal carbonyl group)

carbon atoms

monosaccharides names generically based on how many _________ they contain

trioses

name of three carbons (classification of sugars)

tetroses

name of 4 carbons (classification of sugars)

pentoses

name of 5 carbons (classification of sugars)

hexoses

name of 6 carbons (classification of sugars)

heptoses

name of 7 carbons (classification of sugars)

aldohexose D-glucose

• C₆H₁₂O₆

• single most common monosaccharide in nature

• most stable form of glucose

  • many other stereoisomers possible

common formula for sugars

• C_nH_2nO_n

• leads to general term carbohydrate

  • one water molecule consumed for every molecule of CO₂ to incorporate into sugar

• carbons of glucose (and other organic molecules) number from more oxidized carbonyl end

linear & ring form

in cell D-glucose exists in dynamic equilibrium between_____ (fischer projection) and ______ (Haworth projection)

two alternative ring forms

• a—D—glucose (hydroxyl group downward)

• B—D—glucose (hydroxyl group upward)

hydroxyl group downward

a—D—glucose

hydroxyl group upward

B—D—glucose

glucose

_______ also exists in disaccharides

• two monosaccharide units covalently linked

common disaccharides with glucose

• maltose

• lactose

• sucrose

storage and structural

the polymers are ______ and _______ polysaccharides.

starch in plant cells

• storage polysaccharide

• unbranched amylose (10-30%) and branched amylopectin

• stored as starch grains within plastids

glycogen in animal cells and bacteria

• storage polysaccharide

• highly branches (every 8-10 glucose units)

• stored mainly in liver and muscle tissues

starch and glucogen

• both consist of a—D—glucose units

  • linked by “a” glycosidic bonds a (1→4) between carbons 1 and 4

• occasionally bonds a (1→6) between carbons 1 and 6 may form

  • formation of side chains (branching)

cellulose

• found in plant cell walls

  • best-know example of structural polysaccharides

  • composed of repeating monomers of B—D—glucose

  • most mammals cannot digest it

cellulose of fungal cell walls

• structural polysaccharide

• may contain either B (1→4) or B (1→3) linkages

bacterial cell walls

• structural polysaccharide

• contain two kinds of sugars derived from B—glucosamine

• linked alternatively by B(1→4) bonds

chitin

• structural polysaccharide

• found in insect exoskeletons, crustacean shells, and fungal cell walls

• GlcNAc (N-acetylglucosamine) joined by B (1→4) bonds

a and B glycosidic bonds

______ associated with marked structural differences.

a polysaccharides

starch and glycogen form loose helices that are NOT highly ordered because of side chains

B polysaccharides

• cellulose exists as rigid linear rods that aggregate into microfibril

• plant and fungal cell walls contain rigid microfibrils with other polysaccharide polymers or proteins

lipids

• not formed by linear polymerization that forms proteins, nucleic acids, and polysaccharides

  • regarded as macromolecules because of their high molecular weight

importance of lipids

• cellular structures, particularly membranes

• energy storage

• specific biological functions

fatty acids, triacylglycerols, phospholipids, glycolipids, steroids, terpenes

the main classes of lipids

fatty acids

• building blocks of several classes of lipids

• long amphipathic, unbranched hydrocarbon chain with carboxyl group at one end

polar carboxyl

“head” (hydrophilic) of hydrocarbon chain

nonpolar hydrocarbon

“tail” (hydrophobic) of hydrocarbon chain

saturated fatty acids

• each carbon atom in chain bonded to maximum number of hydrogens

• long straight chains that pack together well

Unsaturated fatty acids

Each have

• one or more double bonds

• Have bends in chains and less tightly packed

Trans fats

• unsaturated fatty acid with trans double bonds that causes less of bend in chains

• Relatively rare in nature & produced artificially in shortening and margarine

• Linked to increased risk of heart disease and elevated cholesterol levels

Triglycerides

• consist of one glycerol with three fatty acids attached to it

  • Monoacylglycerols contain one single fatty acid

  • Diacylglycerols have two fatty acids

• Three fatty acids may vary in length and degree of saturation

Fats (in animals)

• mostly saturated

• Usually solid or semisolid at room temperature