Cell Biology Section 1 Review

Front 1

List the following levels of the biological hierarchy in order of increasing magnitude: molecules, particles, cells, atoms, organelles.

Back 1

Particles < Atoms < Molecules < Organelles < Cells

Front 2

What are the four elements that make up 96% of a living organism?

Back 2

Oxygen (65%)
Carbon (18.5%)
Hydrogen (9.5%)
Nitrogen (3.3%)

Front 3

What are four other relevant elements for this class?

Back 3

Phosphorus
Sulfur
Sodium
Chlorine

Front 4

Composition of an Atom

Back 4

Three types of particles:
-protons (positive, heavy, nucleus)
-neutrons (neutral, heavy, nucleus)
-electrons (negative, light, orbitals)

Overall positive charge in nucleus. Electrons (-) are attracted to nucleus.

Front 5

Shell Model

Back 5

-Electrons fill the innermost shell first.
-innermost shell can hold up to 2 electrons
-next shell can hold up to 8 electrons
-valence shell: whatever shell is the outermost shell (contains valence electrons)
-It takes E to move an electron from an inner shell to an outer shell.
-It releases E to move an electron from an outer shell to an inner shell.

Front 6

Atomic Number vs. Atomic Mass/Mass Number/Atomic Weight

Back 6

Atomic Number: number of protons in the nucleus
Atomic Mass/Mass Number/Atomic Weight: sum of protons and neutrons

Front 7

Ions

Back 7

-charged atoms
-result of gain/loss of an electron
-cause change in charge but not in atomic mass
-cation: overall pos. charge
-anion: overal neg. charge

Front 8

Isotopes

Back 8

-atoms with different numbers of neutrons
-result of extra neutron(s) being added to nucleus
-unstable, energy is released (radioactivity)
-affects atomic mass but not charge

Front 9

Molecules

Back 9

-2 or more atoms joined together
- two general ways that atoms interact = sharing of electrons and charge-based bonds

Front 10

Covalent Bonds

Back 10

-occur because of sharing of electrons between atoms
-When sharing of electrons between atoms is not equal (i.e. between atoms which have large differences in EN; atom with higher electronegativity more strongly attracts electrons), POLAR COVALENT BONDS form.
-When sharing of electrons is equal (i.e. EN difference is not that large), NONPOLAR COVALENT BONDS form.

Front 11

Types of Charge-Based Bonds

Back 11

Ionic Bonds
Hydrogen Bonds
van der Waals interactions

Front 12

Ionic Bonds

Back 12

-strongest type of charge-based bond
-occur as a result of interaction between ions
-e.g. NaCl

Front 13

Hydrogen Bonds

Back 13

-weaker than ionic bonds
-occur as a result of H atoms covalently bonding to highly EN elements (such as O)
-the resulting weak charge allows charge-based bonding b/t atoms/molecules
-inTERmolecular
-e.g. water

Front 14

van der Waals Interactions

Back 14

-weakest charge-based bond
-occur when electrons randomly cluster in regions of atom, resulting in local areas of slight neg. and slight pos. charge

Front 15

Properties of Water

Back 15

-dual charge makes water an important molecule
-interacts well with any charged atom/molecule
-is a great solvent (anything with a charge, i.e. polar, will dissolve in it)
-cohesion: attraction of water to other water molecules
-adhesion: attraction of water to other molecules/surfaces
-H and O are held together via a polar covalent bond, because O has a higher EN than H, and therefore it attracts Hydrogen's electrons. This results in a partial positive charge around the Hydrogens and a partial negative charge around the Oxygen.
-Water molecules interact via Hydrogen bonding.

Front 16

Acid/Base Scale

Back 16

-Pure water is neutral. [H+] = 10^-7 mol/L
-If [H+] > 10^-7 mol/L ACIDIC (0-6.9)
-If [H+] < 10^-7 mol/L BASIC (7.1-14)
-If [H+] = 10^-7 mol/L NEUTRAL (7)
-pH scale ranges from 0-14
-pH = -log[H+]

Front 17

Acid vs. Base

Back 17

Acid
-pH 0-6.9
-increases [H+] in a soln when added

Base
-pH 7.1-14
-decreases [H+] in a soln when added

Front 18

Back 18

Hydroxyl Functional Group
Charged due to polar covalent bond
Can act as a weak acid

Front 19

Back 19

Hydroxyl Functional Group
Charged due to polar covalent bond
Can act as a weak acid

Front 20

Back 20

Carboxyl Functional Group
Acts as an acid

Front 21

Back 21

Amine Functional Group
Acts as a base

Front 22

Back 22

Sulfhydryl Functional Group
Can form disulfide bonds with another SH

Front 23

Back 23

Phosphate Functional Group
Tends to be negative to to loss of H+

Front 24

Macromolecules

Back 24

-large molecules, bonds hold them together
-join monomers together to make polymers
-covalent linking by dehydration/condensation reaction
-breaking of macromolecule core bonds often involves hydrolysis reactions

Front 25

Four Classes of Macromolecules

Back 25

Carbohydrates (sugars, starch)
Lipids (fats, oils)
Proteins
Nucleic Acids (DNA, RNA)

Front 26

Condensation Reaction

Back 26

A-OH HO-B
(H and O bond to form water)
A-O-B + H2O

Front 27

Hydrolysis

Back 27

A-O-B + H2O
(water breaks bond)
A-OH HO-B

Front 28

Carbohydrates

Back 28

-energy source, cell identification, structurally important
-contain C, H, O
-simple forms usually in ratio: (CH2O)n (i.e. 1:2:1)
-monomers: monosaccharides
-vary by # of carbons (e.g. triose=C3H6O2, pentose=C5H10O5, hexose=C6H12O6)
-polymers: polysaccharides (2+ monosaccharides joined together; glycosidic bonds)
-names based on # of monomers joined together (e.g. disaccharides=2 monosaccharides, trisaccharides=3 monosaccharides)
-some important polysaccharides: starch (long glucose chains in plants, energy storage), glycogen (long glucose chains in animals, energy storage), cellulose (long glucose chains in plants, structural)

Front 29

Lipids

Back 29

-long CH chains/rings (covalently bonded)
-very hydrophobic due to nonpolarity
-how hydrophobic the molecule is is dependent on the length of the chain/size of ring
-functions: cell signaling, energy storage, membrane components
-components: fatty acids, triglycerides, phospholipids, steroids

Front 30

Fatty Acids

Back 30

-CH-rich chains with a -COOH at the end
-chains of FA can be saturated or unsaturated

Front 31

Triglycerides

Back 31

-3 FA chains linked onto glycerol
-type of lipid

Front 32

Phospholipids

Back 32

-2 FA chains + 1 Phosphate (-) group attached to glycerol backbone
-type of lipid
-amphipathic: hydrophobic on one side of molecule, hydrophilic on other side of molecule

Front 33

Steroids

Back 33

-very hydrophobic
-ringed
-CH-rich
-nonpolar covalent bonds
-functions: signals in cell (and b/t cells), cross membranes easily

Front 34

Saturated vs. Unsaturated

Back 34

Saturated: each C is bonded to the maximum # of Hs possible; no double bonds
Unsaturated: asymmetrical; double/triple bonds can exist

Front 35

Proteins

Back 35

-structural ("-in"), enzymatic ("-ase")
-monomer: amino acids (AAs)
-R groups determine the unique properties of different AAs
-If hydrophobic, R groups are CH-rich, nonpolar covalent bonds.
-If hydrophilic, R groups polar, ionic bonds.
-polymer: polypeptide (i.e. a protein) = 2+ covalently bonded AAs (hydrolysis occurs between two AAs, allowing AAs to bond to each other and form a polypeptide)
-peptide grows from N terminus --> C terminus
-N-terminus of new AA is added to (i.e. bonded) to C-terminus of growing polypeptide
-have four levels of structure; many are active at tertiary level, but not all

Front 36

Amino Acid

Back 36

-monomer of protein
-end with amine functional group is "N-terminus"
-end with carboxyl functional group is "C-terminus"

Front 37

Levels of Structure for Proteins

Back 37

*Primary:
-the chain of AAs in linear form; describes ordering of specific AAs
**Secondary:
-primary structure folds on itself due to H-bonding
-two main forms -- alpha helix and beta sheet
***Tertiary Structure:
-more folding of secondary structures to make a 3D structure
-ionic bonding, H-bonding, covalent bonding, van der Waals interactions
-many proteins are active at this level, but not all
****Quaternary Structure:
-2+ individual tertiary-level polypeptides that interact via all bond types

Front 38

Denaturation vs. Renaturation

Back 38

-Denaturation: unfolding of protein (b/c of heat breaking bonds)
-Renaturation: re-folding of denatured proteins

Front 39

Active Proteins

Back 39

-active once they have reached tertiary or quaternary structure
-can be structural ("-in") or enzymatic ("-ase")
-enzyme + substrate(s)
-Specific substrates fit into active sites of specific enzymes. The enzyme covalently bonds these substrates and releases them (or process can go in reverse direction).

Front 40

Nucleic Acids

Back 40

-hold genetic information
-monomers: nucleotides
-nucleotides contain a pentose sugar, a negatively
charged phosphate group, and a nitrogenous base
-polymer: DNA, RNA
-To make the polymer, nucleotides get added to 3' end of growing chain and covalent bonds form between 5' PO4(-) and 3'OH on adjacent nucleotides.
-nucleoside: sugar attached to base (no phosphate group)

Front 41

DNA Properties

Back 41

Sugar: DEOXYribose (H on 2' Carbon, NOT OH)
Phosphate (on 5' Carbon): PO4(-)
Nitrogenous Bases (on 1' Carbon): Adenine (purine, two-ring), Guanine (purine, two-ring), Cytosine (pyramidine, one-ring), Thymine (pyramidine, one-ring)

Front 42

RNA Properties

Back 42

sugar: ribose (OH on 2'C, NOT H on 2'C)
Phosphate (on 5' end): PO4(-)
Nitrogenous Bases (on 1'C): Adenine (purine, two-ring), Guanine (purine, two-ring), Cytosine (pyrimidine, one-ring), Uracil (pyrimidine, one-ring)

Front 43

Key macromolecule of cell membrane

Back 43

-Phospholipid
-phosphate group (neg. charge) attached to glycerol attached to two fatty acids (no charge)

Front 44

If you toss phospholipids into water, two things can happen...

Back 44

-form a micelle
-form a bilayer

Front 45

Micelle

Back 45

-one possibility when phospholipids encounter water
-polar/hydrophilic heads on outside, nonpolar/hydrophobic tails on inside

Front 46

Bilayer/Liposome

Back 46

-one possibility when phospholipids are thrown into water
-polar/hydrophilic heads on outside and inside of ring, nonpolar/hydrophobic tails meet between two layers of polar heads

Front 47

Phospholipid Bilayer Structure

Back 47

Front 48

Phospholipid Bilayer Details

Back 48

*Components:
-Phospholipids (2 layers)
-Proteins
-Integral: have a strongly hydrophobic region that makes protein sit IN membrane
-Peripheral: primarily hydrophilic
-Carbohydrates (used as cell markers)
-Glycoproteins: attached to proteins
-Glycolipids: attached to lipids
-Other Lipids
-Cholesterol: ringed, HC-rich, nonpolar; breaks up stacking of FAs, keeping membrane fluid

Front 49

What crosses the membrane easily vs. what doesn't

Back 49

DOES: gases, smaller uncharged molecules, water, steroids

DOESN'T: ions, big bulky molecules (sugars)

Front 50

Diffusion

Back 50

-molecules naturally want to flow from areas of high concentration to areas of low concentration
-requires no energy input to make this happen
-gradient: adjacent regions of high concentration and low concentration

Front 51

Facilitated Diffusion

Back 51

-Diffusion with the aid of a protein
-Proteins facilitate movement of ions (etc.) across the membrane.

Front 52

Osmosis

Back 52

-water movement across membrane

Front 53

Hypertonic Solution

Back 53

-concentration outside of cell is greater than inside cell
-water flows out, cell shrinks

Front 54

Isotonic Solution

Back 54

-concentrations are equal inside and out
-no net water flow

Front 55

Hypotonic Solution

Back 55

-concentration outside cell is less than concentration inside cell
-water flows in, cells swell