Concept Map 1

Chemical Bonds

Intramolecular Interactions

Dipole-Dipole

Ion-Dipole

Hydrogen Bonding

Van der Waals

Hydrophobic Interactions

Water Properties

Temperature Based

High Heat of vaporization

Expands when Freezing

Denser as a liquid

High Specific Heat

Structure Based

Universal Solvent

High Surface Tension

Hydrophobic/Hydrophilic Interactions

Intermolecular Forces

Covalent (electrons shared)

Electronegativity

>2.5

Polar

<2.5

nonpolar

Ionic (electrons transferred)

Eukaryotic/ Prokaryotic Cells

Domains of life

Archaea

Extremophiles

Extreme thermophiles

methanogens

Extreme Halophiles

Bacteria

Components

Nucleoid

Ribosomes

Plasma Membranes

Flagellum

Cell Wall

Fimbrae

Eukarya

Double Membrane Bounded

Animal Cells

Centrosome

region where microtubules are initiated

Flagellum

Lysosomes

Where macromolecules are hydrolized

Plant Cells

Chloroplast

converts energy of sunlight to chemical energy stored in sugar cells

Plasmodesmata

channels through cell walls that connects the cytoplasm of adjacent cells

Central Vacuole

used for storage, breaking down waste & hydrolysis of macromolecules

Cell Wall

maintains cell shape and protects cells from mechanical damage

Cells in plants and animals

Mitochondria

where cellular respiration occurs and ATP is generated

Plasma Membrane

Golgi Apparatus

responsible for the synthesis and secretion of a cells products

Cytoskeleton

microfilaments

microtubules

Endoplasmic Reticulum

Smooth ER

Rough ER

Nucleus

Nuclear Envelope

Nucleolus

Chromatin

Biomolecules

DNA/RNA

Polymer

Phosphodiester Linkage (5,3)

DNA= 2x strand
RNA= 1 strand

Monomer

Nucleic Acids

Pentane Sugar

Deoxyribose=DNA

Ribose=RNA

Nitrogenous Base

DNA

A,T,C,G

RNA

U

Phosphate Group

Proteins

Monomer

Amino Acids

Peptide Bonds

Structure

Primary

Secondary

Alpha + Beta Structures

H-Bonds

Tertiary

R group interactions

Disulfide Bonds

Quatenary

multiple tertiary protiens

Carbohydrates

Monosaccharides

Ketoses

Trioses (3C)

Pentoses (5C)

Hexoses (6C)

Aldoses

Disaccharides

Sucrose (glucose+fructose)

Lactose (glucose+galactose)

Maltose(glucose+glucose)

Polysaccharides

Storage

Starch (plants)

Amylose

Unbranched

a (1,4) glycosidic linkages

helical structure

Amylopectin

Branched

a (1,4), a (1,6) glycosidic linkages

helical structure

Glycogen (animals)

Extensively Branched

a (1,4), a (1,6) glycosidic linkages

helical structure

Structural

Cellulose

No branching

b (1,4) glycosidic linkages

linear structure

Lipids

Triglycerides (Fats)

Structure

Glycerol

fatty acids (3)

Saturated

No double bonds

solid at room temp.

Unsaturated

double bonds

liquid at room temp.

Phospholipids

Structure

glycogen

2 fatty acids

phosphate group

Function

forms phospholipid bilayers in cell membrane

amphipathic

Steroids

Structure

4 fused carbon rings

Cholesterol

High-Density Lipoprotein

helps remove excess cholesterol by taking it to the liver for excretion

Low-Density Lipoprotein

deposits extra cholesterol in blood cells which can lead to plaque buildup.

Hormones

Products: 2 pyruvate, 4 ATP, 2 NADH

Net Total: 2 pyruvate, 2 ATP, 2 NADH

Inputs: 2 Acetyl CoA

Products: 2 ATP, 6 NADH, 2 FADH

Step 6 + 7: The two G3P become 2 pyruvate and 4 ATP, 2 NADH are produced.

Concept Map 2

Membranes

Tonicity

Osmosis (H2O moves to areas with higher concentration)

ability to cause cell to gain/lose water

hypotonic sol.

relatively lower concentration
compared to the cell

Plants: turgid (ideal)
animal: lysed

Isotonic sol.

same concentration as the cells

Plant: Flaccid
animal: normal (ideal)

Hypertonic sol.

relatively higher concentration compared to the cell

Plant: Plasmolyzed
animal: shriveled

Transport

Passive

diffusion down a concentration gradient w/out using energy

Facilitated

uses proteins and other channels to aid passive diffusion

Channels

channel that allows water/solute to enter (no shape change)

Ion Channels

ungated

constantly openn

gated

stretch

opens/closes when deformed

ligand

opens/closes when ligand binds to a receptor

voltage

opens/ closes when membrane potential changes

Carrier proteins

changes shape to move solute

Bulk Transport

Use vesicles to transport large molecules. membrane stretches to engulf particles

endocytosis

phagocytosis

takes in "food" particles

pinocytosis

takes in fluids

receptor mediated

uses receptors and ligands to take in molecules

cell takes in substances

exocytosis

cell ejects substances

Active

Uses energy to transport solute against its concentration gradient

electrogenic pump

creates a charge gradience generating voltage across a membrane

Proton Pump

Na/K Pump

1. 3 Na in the cytoplasm bind to the pump

2. phosphorylation via kinase triggered (PO4 attaches to the pump)

3. Pump changes shape and releases Na+ out

4. 2 K+ outside the cell attach to the pump while removing PO4

5. pump returns to its original shape

6. K+ comes off the pump and the cycle repeats

2 K+ in
3 Na+ out

Cells are slightly - because there are fewer positive charges in the cell

Phases:

Resting State: na and k voltage gated pumps are closed

Depolartization: Na pump opens allowing Na to flow in making it less negative (if this hits a threshold it moves on to the rising phase)

Rising Phase: cell becomes positive while K pumps are still closed until action potential is reached

Falling Phase: Some k pumps open while na pumps close making the cell overall negative

Undershoot: the cell uses na/k pump to help return it to the resting phase.

Cotransport

when active transport indirectly transport of another

sucrose/H+: H+ drives sucrose in when H+ is pumped out of the cell and a gradient is created

Permeability (high to low)

small, nonpolar > small, uncharged polar > large, uncharged polar > ions

Structure

Fluidity

Temperature

high temp= fluid

lower temp= rigid

saturated fats

lower diffusion+ rigid

Unsaturated fats

higher diffusion+ fluid

Cholesterol

helps regulated fluidity when too rigid or too fluid

phospholipid bilayer

Cellular Respiration

Glycolysis

with O2

pyruvate oxidation

Citric Acid Cycle

Oxidative Phosphorelation

Inputs: 10 NADH, 2 FADH

Chemosmosis

ATP Synthase

Here, H+ in the intermembrane space, go back down their concentration gradient. This energy is used to add an inorganic phosphate to ADP to form ATP

Electron Transport Chain:

Complex III

Complex IV

O2 + H+ = H20

Outputs: H2O, about 26 - 28 ATP

Complex II

FADH2 transfers electrons to complex II

Complex I

NADH transfers electrons to complex I

Q

Cyt c

Inputs: Acetyl CoA

Step 1: Oxaloacitate goes to an enzyme and with Acetyl CoA becomes Citrate.

Step 2: Citrate becomes Isocitrate.

Step 3: Isocitrate becomes alpha ketogluta and NADH is released.

Other Steps: 2 NADH, ATP, FADH are formed.

Products: 1 ATP, 3 NADH, 1 FADH

Inputs: 2 pyruvate

Products: 2 Acetyl CoA, 2 Co2, 2 NADH

Inputs: 1 glucose, 2 ATP

Step 1: glucose binds to hexokinase and with ATP becomes G6P.

Step 2: G6P becomes F6P

Step 3: F6P binds to the phospho-fructo-kinase enzyme and with ATP becomes fructose 1,6 bi-phosphate

Step 4 + 5: That fructose 1,6 biphosphate becomes 2 G3P

Without O2

Alchohol Fermentation

Inputs: 2 Pyruvate,
NADH

Outputs: Ethanol
NAD+

Lactic Acid Fermentation

Inputs: 2 Pyruvate,
NADH

Outputs: Lactate,
NAD+

Enzymes

Inhibition

Competitive Inhibition

An inhibitor binds to the active site of an enzyme. This doesn't allow for the substrate to bind and it stops the enzyme for functioning.

Non-competitive Inhibition

An inhibitor binds to a site other than the allosteric site, and changes teh enzyme's shape. Even if the substrate binds the active site, the ezyme no longer works.

Allosteric Regulation

Allosteric inhibitor

A regulatory molecule binds to the allosteric site of an enzyme an locks it in its in-active form. Substrates can't bind.

Allosteric activator

A regulatory molecule binds to the allosteric site of an enzyme an locks it in its active form. Substrates can bind.

Cooperativity

The binding of one substrate molecule to the active site of one subunit locks all other subunits into the active shape.

Feedback Inhibition

The end product of a metabolic pathway shuts down the pathway by going back to the first enyme and binding to its allopsteric site.

Cell Signaling

G Protein signaling pathway

Signal binds to the GPCR which changes its shape and activates it

GCPR binds to G protein, bound by GTP, which activates the G protein

Activated G protein binds to the adenylyl cyclase. GTP hydrolyzes which activates adenylyl cyclase and changes its shape.

Adenylyl cyclase converts ATP to cAMP

cAMP activates pka which leads to cell response

Aldosterone Pathway

Signal moves through the membrane

Signal binds to the receptor, changes its shape and activates the receptor

Active Receptor travels into the nucleus and binds to DNA

Transcription occurs which produces mRNA

mRNA leaves the nucleus, ribosomes bind and translation occurs, producing a protein.

Metabolism

Anabolic

pathway that consumes energy to build larger complex molecules

Endergonic: energy is required, energy is absorbed

Spontaneous reaction: free energy is negative

Catabolic

pathway that releases energy by breaking down complex molecules to simple molecules

Subtopic

Photosynthesis

Light Reactions

Non-cyclic/ Linear flow

Photosystem II

Electron Transport Chain

Plastoquinone (Pq),

Cytochrome Complex

Plastocyanin (Pc)

ATP Synthase

ATP

Photosystem I

Light (photons) hit the chlorophyll in the light harvesting complex.

This excites the photons and then they return to ground state and the energy jumps between them until they reach the main chlorophyll a in the reaction center complex.

These main chlorophyll a get excited but instead of returning to ground state, these are captured by the primary electron acceptor.

These electrons are sent outside of photosystem I to Fd

ferredoxin (Fd)

NADP+ reductase

NADPH+

Light (photons) hit the chlorophyll in the light harvesting complex.

This excites the photons and then they return to ground state and the energy jumps between them until they reach the main chlorophyll a in the reaction center complex.

These main chlorophyll a get excited but instead of returning to ground state, these are captured by the primary electron acceptor.

These electrons get sent to the electron transport chain.

Calvin Cycle (C3)

3x CO2

3x Short-lived intermediate

6x 3-phosphoglycerate

6x 1,3 bisphosphoglycerate

6x Glyceraldehyde 3 Phosphate (G3P),

1 G3P

3x Ribulose bisphosphate

Rubisco

Concept Map 3

Transcription/ Processing

Initiation: RNA polymerase starts this process by binding to the promoter: no primers or helicases needed.

Eukaryotes: RNAP II,
transcription factors (proteins that help RNAP II to bind).

Pro: RNAP

Promoter: a sequence that allows RNAP to bind to the DNA strand

Elongation: the template strand is read from the 3' to 5' end and nucleotides are added to the 3' end of the RNA strand

Termination: a nucleotide sequence, AAUAA, is read by the RNAP which tells it when to cleave the RNA strand.

Prokaryotes

The process is done at this point RNA is made w/out processing

Eukaryotes

Pre-mRNA is formed: we get a poly-A tail which helps with the RNA's stability and we have a 5' cap which helps us with Translation later on.

Spliceosomes help remove introns leaving exons.

Alternate splicing: allows the expression of certain proteins over others.

introns: separate the coding nucleotides that will be expressed.

exons: the coding nucleotides that will be expressed (different ways of splicing = different proteins)

DNA Replication

Origin of replication (ORI): start point of replication in a strand of DNA, here two forks are formed creating the directions DNA are replicated

Initiation Enzyme/Protein

SSB: ensures that the single strands do not recombine

Topoisomerase: ensures that the DNA strand is not strained and knotted.

helicase: separates the two strands of DNA (breaks H bond)

Primase: creates RNA primers that attach to DNA

DNA Polymerase

adds bases to daughter strand in the 5' to 3' direction

DNA Polymerase III

adds nucleotides to the 3' end on the leading stand and the RNA primers on the lagging strand

DNA Polymerase I

kicks off primers from the RNA

Ligase: final step/ enzyme connects okazaki fragments (lagging strands)

Gene Expression (Eukaryotic)

Enhancer Sequence

DNA bending protein

General and Mediator transcription factors

RNA Polymerase II

RNA polymerase II binds the promoter and the gene has Increased Expression.

General transcription factors and mediator proteins bind the activators.

DNA bending protein brings the activators closer to the promoter and TATA box.

Activator Proteins bind to enhancer sequences (3 distal control elements)

DNA experiments/ Structure

Chargaffs Rule

A=T G=C
nucleotide bases come in proportionally equal amount

Hershey & Chase

labeled DNA with P32 and protein with S35 in bacteriophages, blended and centrifuged infected bacteria, and found DNA in the pellet

Discovered DNA carried genetic material

Griffith

Injected mice with pneumonia, S (deadly), R (safe), Heat killed S, heat killed S with R, and found that heat killed S with living R killed mice

Found that something (genetic material) was transferred from the dead S strain to the living R strain.

Messleson &Stahl

Cultivated DNA in N15 and mixed it with N14, allowed the DNA to replicate and observed the relative density of the solution created

Three models hypothesized: conservative (parental strands reassociate after replication), semi-conservative (strands separate and act as templates for complementary strands), Dispersive (part of the parent strand is mixed in the daughter strands)

Experiment found the solution had an intermediate strip and low density strip

confirmed semiconservative model.

Franklin, Watson, Crick

Discovered DNA was double stranded and helical

Translation

Initiation

Small ribosoman subunit binds to mRna. The initiator tRna binds to the start codon (AUG).

Prokaryotes amino acid is Formal Met

Eukaryotes amino acid is Met

Large ribosomal subunit binds with the help of tRna in the P site

Elongation

Ribosomes move along the mRna.

Codon recognition in the A site: anticodon of tRna pairs up with mRna in the A site

Peptide Bond Formation (P site): forms between the carboxyl end of polypeptide chain in P-site and the amino group of the A site. Pep bond catalyzed by peptidyl transferase

Translocation in the E site: the tRna in the P site is moved to the E site

Termination

The stop codon is found in the mRNA. Then a release factor binds to the A site of the ribosome complex

A release factor binds to the A site of the ribosome complex and the growing polypeptide chain is free

The traslation initiation complex in the ribosomes dissociates using GTP.

Gene Expression (prokaryotic)

Operon: genes that work together controlled by an on/off switch

Lac Operon

Lactose

Beta-Galactosidase: breaks down lactose to galactose and glucose

When lactose is present:

lactose repressor binds to it, which allows CAP activator to bind to it and facillitate transcription

When glucose is present

production of cAMP is blocked. The operon is off

Components: Regulatory gene Lac I, Strugtural genes lac z, lac y, lac A, promoters and an operator

Mutations

Frameshift

when inserting or deleting 1 or 2 nucleotides causes a shift in the reading frame

Missense

changes the amino acid

Nonsense

introduces a stop codon

Silent

no change in the amino acid

DNA structure (experiments)