Chapter 2 Cell bio review

Carbon atom

Most important atom in biological molecules

Five principles important to cell biology

• characteristics of carbon

• Characteristics of water

• Selectively permeable membranes

• Synthesis by polymerization of small molecules

• Self-assembly

bonding properties of carbon

• has valence of 4

• Forms four chemical bonds

Covalent bond

Sharing of pair of electrons b/w two atoms

Single bond

Sharing one pair electrons

Double bonds

Sharing two pairs of electrons

Triple bonds

Sharing three pairs of electrons

Stability

Bond energy expresses

Carbon-containing molecules

Are stable

More covalent bonds

Higher bond energy, harder to break

Visible light

Cannot break bonds of organic molecules

Higher-energy ultraviolet light

More hazardous

Hydrocarbons

• chains or rings composed only of C and H

• NOT soluble in water

• Economically important, but less important in biology

Biological compounds

• Contain C, H, O, N, P, or S

• Functional groups confer specific chemical properties

Bond polarity

• describes sharing of electrons between atoms

• Nonpolar bonds

• Polar bonds

Nonpolar bonds

• (e.g. C—C or C—H)

• electrons shared equally b/w two atoms

polar bonds

• (e.g. C—O and C—S)

• electrons not shared equally

• result from high electronegativity (affinity for electrons) of oxygen and sulfur compared to carbon and hydrogen

carbon—containing molecules can…

form stereoisomers

structure of a carbon atom

tetrahedral

Stereoisomers

isomeric molecules exist when four atoms bonded to four corners of tetrahedron

asymmetric carbon atoms

carbon atoms attached to four different types of atoms or groups of atoms

two

____ stereoisomers are possible for each asymmetric carbon atom

n,2ⁿ

one compound with __ asymmetric carbons will have __ possible stereoisomers

Water

• universal solvent in biological systems

• single most abundant component in cells and organisms

polarity of water

• due to unequal distribution of electrons

• allows water to have

  • cohesiveness

  • temperature—stabilizing capacity

  • solvent properties

cohesiveness

• water molecules attracted to each other via hydrogen bonds

• extensive network of hydrogen bonded molecules

  • formed by electrostatic attraction b/w oxygen and hydrogens

  • ~ 1/10 as strong as covalent bonds =

temperature—stabilizing capacity

• extensive hydrogen bonds also make water high in

  • specific heat

  • heat of vaporization

specific heat

amount of heat a substance absorbs to raise its temperature 1 C

solvent properties

• many molecules in cells (e.g. NaCl) take part in electrostatic interaction with water molecules

  • polar water molecules form spheres of hydration around ions

  • lowers chances of anions and cations to reassociate

hydrophilic

• water loving

• sugars, organic acids, and some animo acids

hydrophobic

• water fearing

• lipids and some proteins

importance of selectively permeable membranes

• cells need physical barrier b/w their contents and outside environment

• impermeable to much of cell contents, permeable to some materials

insoluble in water (hydrophobic)

• phospholipids

• glycolipids

• sterols (cholesterol in animals, ergosterol in fungi, phytosterol)

Membrane lipids

• amphipathic (both hydrophobic and hydrophilic)

• form lipid bilayer

amphipathic

• both hydrophobic and hydrophilic

lipid bilayers

• hydrophobic interior

• permeable to non-polar molecules

  • very small uncharged polar molecules can diffuse

• impermeable to most polar molecules

ions, sugars, and amino acids

these 3 things are transported by protein channels and carriers

macromolecules

most cellular structures made of ordered arrays of linear polymers

carbohydrates

includes polysaccharides—> contain disaccharides —→ composed of two monosaccharides

lipids

include

• triglycerides—> composed of fatty acids and glycerol

proteins

composed of 10 amino acids

• peptides → composed of amino acids

nucleic acids

include

• RNA & DNA → composed of nucleotides

DNA and RNA considered as “informational macromolecules”

small organic molecules, macromolecules, supramolecular structures, organelles, cell

cellular hierarchy

general principle of biological chemistry

• macromolecules responsible for most living systems generated by polymerization of small organic molecules

monomer

a small, simple molecule that can chemically bond with other similar or identical molecules to form a larger, complex structure called a polymer

sequence of amino acids

determines structure and thus function of protein

protein functions

• structure

• defense

• transport

• catalysis and signaling

polysaccharides

• consists of single repeating subunits or two alternating subunits

  • cellulose and chitin (structure)

  • starch and glycogen (storage)

structure

function of cellulose and chitin

storage

function of starch and glycogen

order of nucleotide monomers

contain information that specifies precise amino acid sequences of proteins

monomer activation

monomers with available H and OH groups are activated by coupling them to the appropriate carrier molecule, using energy from ATP or a similar high energy compound

monomer condensation

the first step in polymer synthesis involves the condensation of two activated monomers, with the release of one of the carrier molecules

polymerization

the nth step will add the next activated monomer to a polymer that already has n monomeric units

three phosphate groups, ribose, and adenine

ATP consists

carrier molecules

molecules used for different kind of polymers

• sugars- activated by linking ADP (adenosine diphosphate), or UDP (uridine diphosphate)

• amino acids- linked to transfer RNA (tRNA)

• nucleotides- DO NOT need carrier molecules

  • often high energy molecules (ATP, GTP)

condensation

elongates polymer in sequential stepwise process by forming covalent bond between H and OH

hydrolysis

degrades polymer by breaking bond between monomers and adding one H and one OH

self-assembly

process by which macromolecules adopt defined arrangement without guidance or management from outside source

noncovalent bonds and interactions

• important in the folding of macromolecules

• many cellular structures are held together by these two things

ionic bonds

strong noncovalent electrostatic interactions between two oppositely charged ions

Van der waals interactions

• weak attractions between two atoms

• occur only if atoms close to one another and oriented appropriately

hydrophobic interactions

• tendency of nonpolar groups associates with each other and minimizes contact with water

protein conformation

• once polypeptide folds into a correct structure

alteration factors of protein conformation

• changing conditions (pH or temperature)

• treating with certain chemical agents

denaturation

• unfolding of polypeptides

• loss of biological activity (function)

renaturation

• refolding into correct conformation

• may happen when original conditions returned

• may restore protein function

molecular chaperones

• needed to prevent incorrect folding of proteins

  • bind to exposed regions in early stages of assembly

  • inhibit unproductive assembly pathways that would lead to incorrect structures

  • not components of completed structures

examples of self—assembly

• ribosomes

• membranes

• lipid bilayers

limit of self—assembly

some assembly systems depend additionally on information provided by pre-existing structure

• e.g., membranes and cell walls

chemical simplicity

• relatively few subunits used for wide variety of structures

efficiency of assembly

• small number of condensation reactions needed

quality control

• defective components discarded prior to incorporation into higher level structure

• reduced waste of energy and materials