Cell Biology Test 1

Front 1

Polymerization of macromolecules driven by covalent bond formation

Back 1

Big units need covalent bonds because they are stronger and will keep them stable. Ex) Phosphodiester bonds link nucleotides in DNA and RNA to form the ladder walls.

Front 2

Cellular molecules are formed and connected by covalent and non-covalent bonds.

Back 2

Smaller units can use either bonds depending on the need of the molecule. Covalent bonds are strong and don't break down easily. Non-covalent bonds are individually weak but strengthen in multiples.

Front 3

Order of Bonds by Strongest to Weakest

Back 3

Covalent : Peptide

Non-Covalent : Ionic, Hydrogen, Van der Waals, and thermal energy.

Front 4

Transient non-covalent bonds position substrates to enhance the formation of covalent bonds in cells

Back 4

Little weak bonds increase flexibility.

Ex) Hydrogen bonds between base pairs (rungs) position nucleotides for covalent phosphodiester bond (ladder) formation in transcription (mRNA).

Front 5

Van der Waals force is important for interactions between non polar molecules.

Back 5

Transient dipole moment creates transient partial charge that attracts other molecules. Extremely weak bond that doesn't require much energy to separate.

Front 6

Hydrophilic molecules establish aqueous parts of the cell.

Back 6

Hydrophillic = polar= charge= attracts polar water. Water us partially charged because the oxygen nucleus attracts electrons (more negative) than the hydrogen nuclei (more positive). Like dissolves like because they can form hydrogen bonds.

Front 7

Hydrophobic lipids do not readily dissolve in water.

Back 7

Hydrophobic=nonpolar=no charge= doesn't attract water. Nonpolar hydrophobic molecules do not have partial charges since electrons are equally shared in covalent bonds between carbon and hydrogen. Ex) oils, fats, sterols.

Front 8

First Law of Thermodynamics

Back 8

Energy is not created or destroyed, it only changes form. The cell absorbs energy and converts it into different forms. Ex) Chlamydomonas: light energy--> chemical energy--> mechanical energy

Front 9

Second Law of Thermodynamics

Back 9

Events proceed from higher free energy to lower free energy. The amount of disorder in the universe always increases (entropy). Cells need more energy to be organized. Measured with Gibb's equation.

Front 10

Gibb's free energy defines biochemical reactions.

Back 10

Negative G= breakdown of products= disorder=release of energy= EXERGONIC.

Positive G= Polymerzation of macromolecules= organization= requires energy= ENDERGONIC.

The change in free energy (G) equals the change in total energy (H) in the system/cell minus the energy unavailable to do work (entropy, T*S).

Front 11

Example of Gibbs

Back 11

ATP hydrolysis is the breaking of a covalent phosphor-anhydride bond between gamma and beta phosphate.

Front 12

Protein Primary Structure

Back 12

Successive peptide bonds (covalent) create primary structure, a sequence of amino acids.

Front 13

Amino acids are hydrophobic or hydrophilic

Back 13

Hydrophilic amino acids face polar environments and are dissolved by water.

Hydrophobic amino acids face nonpolar environments are not dissolved by water.

Front 14

Hydrophilic (Polar) amino acids

Back 14

Basic: Lysine (lys or K), Arginine (Arg or R), Histidine (His or H)

Acidic: Aspartate (Asp or D), Glutamate (Glu or E)

Polar AA with uncharged R groups: Serine (ser or S), Threonine (Thr or T), Asparagine (Asn or N), Glutamine (Gln or Q)

Front 15

Hydrophobic (non-polar) Amino Acids

Back 15

Alanine (Ala or A), Valine (Val or V), Isoleucine (Ile or I), Leucine (Leu or L), Methionine (Met or M), Phenylalanine (Phe or F), Tyrosine (Tyr or Y), Tryptophan (Trp or W)

Special AA: Cysteine (Cys or C), Glycine (Gly or G), Proline (Pro or P)

Front 16

Secondary Structure Alpha helix

Back 16

Alpha helix- twists as hydrogen bonds form between every fifth amino and carboxyl group in the linear strand (primary structure).

Structure- Elastic, stretching and reforming as weak hydrogen bonds are made and broken.

Found in dynamic parts of proteins that change conformation and in membrane spanning domains.

Front 17

Secondary Structure Beta Sheet

Back 17

Beta sheet- formed by hydrogen bonds between amine (N ends) and carboxy (C ends) groups of linear sequences of amino acids.

Structure- Stable, does not stretch

Found in stable parts of proteins, like binding sites, where structure must be consistent.

Front 18

Secondary Structure Beta Turns

Back 18

Beta Turns- Reverse the direction of a polypeptide with proline and glycine (special aa).

Proline bends because the side chain (R-group) is also bound to the amine (N-end) group.

Glycine is small because the side chain (R-group) is just hydrogen.

Front 19

Tertiary Structure

Back 19

Non-covalent bonds between side chains organize secondary structures into a thermodynamically stable arrangement. Proteins can be functional at this level. Spatially adjacent cysteines form covalent disulfide bridges that organize tertiary structure.

Ex) Hexokinase- stable beta sheets define binding site for glucose and ATP. Dynamic alpha helices define regions that change conformation. Beta turns link domains together.

Front 20

Quaternary Structure

Back 20

Multiple subunits linked together by non-covalent bonds. Each subunit has primary, secondary, and tertiary structure. Subunits can be also linked together with cysteine disulfide covalent bonds.

Front 21

Other protein motifs

Back 21

Coiled coil: Hydrophobic side chains interact to twist adjacent alpha helices.

Helix-loop-helix: Ca2+ binding site in the loop.

Zinc finger: DNA and RNA binding proteins.

Front 22

Enzymes are catalysts

Back 22

1) Required in small amounts

2) Not irreversibly altered so they can turnover and function again

3) Have no effect on thermodynamics.

Front 23

Substrates bind within the active site.

Back 23

This increases the probability that substrates (molecule) will interact. Amino acid side chains are important in the enzyme active site. Non-covalent bonds usually create enzyme-substrate complex.

Front 24

Enzyme Kinetics

Back 24

Enzymes bind to and stabilize the transition state, lowering the activation barrier.

Vmax- maximum rate that enzyme can turnover substrate to product.

Km- substrate concentration at 1/2 Vmax

Front 25

Competitive Inhibitors

Back 25

increase Km, and do not affect Vmax by competing with substrate for the same active binding site on the enzyme. (Consumes more substrate at the same fast pace)

Front 26

Noncompetitive Inhibition

Back 26

Decrease or increase Vmax but do not affect Km.

(Consumes the same amount of substrate at a slower or faster pace)

Front 27

Enzyme (and protein activity regulated by GTP/GDP binding

Back 27

GTP- Guanosine-5'-triphosphate is a purine nucleoside triphosphate.

Proteins are activated when GTP is attached through an exchange of GDP for GTP.

Proteins are inactivated by the hydrolysis of GTP to GDP.

Front 28

Membrane Organization and the Fluid Mosaic Model

Back 28

Membrane bilayer of lipids and proteins have two polar surfaces with a non-polar core.

Membrane lipids are amphipathic molecules, both polar and non-polar.

Hydrophobic tails of phospholipids associate to form the bilayer.

Glycolipids have carbohydrates for the polar head group.

Front 29

Different phospholipids affect packing density and membrane curvature

Back 29

Double bonds in hydrophobic fatty acid tails decrease the packing density of the bilayer.

Front 30

Functional Membranes Require Fluidity

Back 30

Carbon-carbon bonds in fatty acyl tails flex as they absorb thermal energy, converting membrane from gel to fluid.

Lateral shift of phospholipids within one side of the bilayer are common. Hydrophylic heads remain among hydrophilic heads remain among hydrophilic heads.

Uncatalyzed transvere shifts from cytosol to cell exterior (vice versa) are uncommon.

Front 31

Lipids are synthesized in the ER membrane

Back 31

Fatty acids elongate in cytoplasm.

Attached to glycerol phosphate and incorporated into cytoplasmic side of bilayer by acyl transferase enzymes in the ER membrane.

Head groups added by phosphotransferase enzymes

To maintain bilayer symmetry, about half the new phospholipids are flipped to the ER side of membrane by flippase

Front 32

Newly synthesized lipids move from ER to other membranes

Back 32

Three models:

Incorporated into vesicles (dominant mechanism)

Direct lipid transfer between bilayers

Cytoplasmic binding proteins remove specific lipids and insert into other membranes.

Front 33

Sterols in Membranes

Back 33

Amphipathic molecules that are synthesized at ER membrane and provide structural support to membranes. Influence fluidity by preventing close packing of phospholipids. Converted into important regulatory molecules.

Front 34

Integral membrane proteins

Back 34

connect across bilayer to create a mechanism of communication between two aqueous compartments. Membrane spanning alpha helices have non-polar amino acids (in the center between the plasma membrane). Aqueous parts (cytosol and exoplasm ends) of protein have more polar amino acids.

Front 35

Multiple alpha helices can form a transport channel

Back 35

Non-polar amino acids face the non-polar phospholipid fatty acid tails while polar amino acids face inside of the channel.

Front 36

Beta barrels can form large pore through membrane

Back 36

Beta sheets organize into a cylinder. Non-polar amino acids face the non-polar phospholipid fatty acid tails. Polar amino acids face inside of the channel.

Front 37

Lipid anchored proteins

Back 37

Covalent bonds connect directly to acid tails or to glycosylated lipid heads. Some move laterally within bilayer.

Function: cellular recognition, directing membrane fusion, signal transduction.

Ex) trimeric G protein

Front 38

Peripherally (on top) associated proteins

Back 38

Transient associations with membranes. Communication between protein complexes or different membranes. Form non-covalent bonds with polar phospholipid heads or integral membrane proteins.

Ex) Cytochrome C shuttle

Front 39

Diffusion

Back 39

movement down a concentration gradient directly through the membrane bilayer. (O2, CO2)

Front 40

Passive Transport-

Back 40

movement down a concentration gradient through protein channels. (Ions, glucose, H2O)

Front 41

Active Transport-

Back 41

Uses energy (ATP) to establish concentrated gradients of ions or other polar molecules. (Na+/K+, ATPase)

Front 42

Transport of polar molecules requires a transport protein ion channels

Back 42

Protein changes conformation to open gate. Usually due to binding of a secondary molecule. When the gated channel is open, ions rapidly flow down established concentration gradients. (K+, Na+, Cl-, H+, Ca2+, H2O).

Ex) Aquaporins-integral membrane proteins

Many ion channels are regulated by the binding of another molecule.

Ex) Trimeric G protein binds to the Potassium channel.

Front 43

Passive transport of Large molecules

Back 43

Open channels for large molecules (glucose, amino acids) would compromise the membrane integrity. Instead, facilitated transport proteins change conformation in sequential steps to shuttle large molecules (glucose, amino acids) down established concentration gradients. Transport has saturation kinetics, dependent on how fast protein changes conformation.

Front 44

Passive transport of Large Molecule Example

Back 44

Glut protein moves glucose from high to low conformation.

1) Transport protein open to high concentration side

2) glucose binds to protein

3) binding causes change in conformation

4) Protein closes to high side, opens to low concentration side

5) Glucose diffuses out of transport protein

6) In RBCs, transport is into cytoplasm (GLUT1)

Front 45

Active Transport

Back 45

ATP powered pumps make concentration gradients across membranes.

Calcium concentrated outside the cell or within ER lumen.

Protons concentrated outside the cell or within vacuoles and lysosomes

Sodium concentrated outside the cell while potassium concentrated in cytoplasm.

The speed of ion or molecular movement across the membrane is determined by how much the transport protein must change conformation.

Accomplished by different classes of pumps. Each class has a unique mechanism: P-class, V-Class, F-class, ABC superfamily

Front 46

Example of Active Transport

Back 46

Ca2+ ATPase uses phosphorylation and dephosphorylation to actively transport calcium ions from the cytoplasm and create a concentration gradient.

1) Ca2+ and ATP bind

2) ATP hydrolysis transfers phosphate to the protein

3) Phosphorylation causes the major conformational change

4) Ca2+ binding affinity reduced and Ca2+ released into ER lumen (or extracellular)

5) Phosphate is released and protein returns to original conformation

Front 47

The Sodium/Potassium ATPase

Back 47

ATP hydrolysis in the cytoplasm transports sodium and potassium across the plasma membrane, creating two concentration gradients.

The potential energy stored in concentration gradients is used by other membrane transport proteins to drive cellular metabolism.

Results: 3 sodium ions pumped from cytoplasm to extracellular and 2 potassium ions pumped from extracellular to cytoplasm.

Front 48

Established gradients are used to generate electric potentials

Back 48

K+ gradient established by Na/K ATPase.

Potassium gradient flows through gated K+ channel. This passive ion transport generates an electric potential across the plasma membrane.

Front 49

Established gradients are used to concentrate other molecules

Back 49

Sodium/Glucose Cotransport

Driven by established sodium gradient from Na+/K+ ATPase.

Two sodium and one glucose bind extracellular

Binding changes conformation of transporter, moving sodium and glucose into cytoplasm.

Glucose concentrated in cytoplasm.