Bio Final

Characteristics of all living organisms

1. Cellular organization

2. Ordered complexity

3. Sensitivity to environment

4. Growth, development, and reproduction

5. Energy utilization

6. Homeostasis

7. Evolutionary adaptation

Reductionism (in vitro)

To break a complex process down to its simpler parts

Systems biology (in vivo)

Focus on emergent properties that can’t be understood by looking at simpler parts

Ionic bond

Attraction of oppositely charged ions

Covalent bond

When atoms share 2 or more valence electrons

Nonpolar Covalent

Equal sharing of electrons

Polar Covalent

Unequal sharing of electrons

Properties of Water

High specific heat

High heat of vaporization

Solid is less dense than liquid

Good solvent

Dehydration synthesis

Formation of large molecules by the removal of water

Hydrolysis

Breakdown of large molecules by the addition of water

Lipids

They are insoluble in water

Fats, oils, waxes, terpenes, steroids, and even some vitamins

Saturated Fatty Acids

No double bonds between carbon atoms

Higher melting point

In animals

Unsaturated Fatty Acids

One or more double bonds

Lower melting point

In plants

Phospholipid Structure

Glycerol, Two fatty acids (nonpolar “tails”), A phosphate group (polar “head”)

Form all biological membranes

Cell Theory

1. All organisms are composed of cells

2. Cells are the smallest living things

3. Cells arise only from pre-existing cells

Basic Structural Similarities of Prokaryotes and Eukaryotes

1. Nucleoid or nucleus where DNA is located

2. Cytoplasm

3. Ribosomes

4. Plasma membrane

Prokaryotic Cells

Lacks membrane-bound organelles

Cell wall outside of the plasma membrane

Capsule (Gelatinous layer which aids in attachment and protection)

Bacterial Cell Walls

Peptidoglycan forms a rigid network.

• Maintains shape.

• Withstands hypotonic environments

Gram positive bacteria

Thick, complex network of peptidoglycan

Gram negative bacteria

Thin layer of peptidoglycan.

Resistant to many antibiotics

Bacteria Pili

Found in gram-negative bacteria.

Aid in attachment and conjugation.

Endomembrane System

Series of membranes throughout the cytoplasm

Divides the cell into compartments where different cellular functions occur

One of the fundamental distinctions between eukaryotes and prokaryotes

Golgi Apparatus

Flattened stacks of interconnected membranes (Golgi bodies)

Functions in packaging and distribution of molecules

Has cis and trans faces

Vesicles transport molecules to destination

Vacuoles

Membrane-bound structures typically found in plants

Storage, waste disposal, and structural support

Endosymbiosis Theory

Eukaryotic cells evolved by a symbiosis between two free-living cells

Prokaryote engulfed by and became part of another cell

Mitochondria and chloroplasts have similarities to prokaryotic cells

Evidence to support endosymbiosis theory

Organelles with their own DNA (i.e. mitochondrial DNA)

Double membrane

Have the own ribsomes

Microfilaments (actin filaments)

Two protein chains loosely twined together

Movements like contraction, crawling, and “pinching”

Microtubules

Largest of the cytoskeletal elements.

Dimers of α- and β-tubulin subunits.

Facilitate the movement of cells and materials within the cell.

Intermediate filaments

Between the size of actin filaments and microtubules.

Very stable – usually not broken down.

Centrosomes

Microtubule-organizing center

Animal cells

Adhesive junctions

Mechanically attaches cytoskeletons of neighboring cells or cells to the ECM (include adherens junctions, desmosomes, hemidesmosomes).

Septate, or tight, junctions

Connect the plasma membranes of adjacent cells in a sheet – no leakage.

Communicating junctions

Chemical or electrical signal passes directly from one cell to an adjacent one (gap junction, plasmodesmata)

Plasmodesmata

In plant cells

Specialized openings in their cell walls.

Cytoplasm of adjoining cells are connected.

Function similar to gap junctions in animal cells.

Channel Proteins

Allow the passage of ions through nonpolar interior of plasma membrane.

Gated channels – open or close in response to stimulus (chemical or electrical).

Carrier Proteins

Can help transport both ions and other solutes, such as some sugars and amino acids

Movement is via diffusion, requires a concentration difference across the membrane

Must bind to the molecule they transport

Peptide Bonds

Bond formed between the amino end and carboxyl end of two adjacent amino acids.

Motifs

Common elements of secondary structure seen in many polypeptides

Useful in determining the function of unknown proteins

Domains

Functional units within a larger structure

First Law of Thermodynamics

Energy cannot be created or destroyed

Energy can only change from one form to another

Total amount of energy in the universe remains constant

During each conversion, some energy is lost as heat

Second Law of Thermodynamics

Entropy (disorder; more accurately number of possible states) is continuously increasing

Feedback Inhibition

End-product of pathway increases in concentration as it is synthesized

More product increases probability that it binds to an allosteric site on an enzyme in the pathway and causes it to change so it cannot bind normal substrates

Shuts down pathway so raw materials and energy are not wasted

Final electron receptor in Aerobic Respiration

Oxygen

Final electron receptor in Fermentation

Organic Molecule

Substrate-level phosphorylation

Transfer phosphate group directly to ADP

Occurs during glycolysis

Oxidative phosphorylation

ATP synthase uses energy from a proton gradient

Oxidation of Glucose Stages

1. Glycolysis

2. Pyruvate oxidation

3. Citric acid cycle

4. Electron transport chain & chemiosmosis

Glycolysis

In cytoplasm

Converts 1 glucose (6 carbons) to 2 pyruvate (3 carbons)

Net production of 2 ATP molecules by substrate-level phosphorylation

2 NADH produced by the reduction of NAD+

When oxygen is present, pyruvate…

…is oxidized to acetyl coenzyme A (acetyl-CoA) which enters the citric acid cycle

Without oxygen, pyruvate…

…is reduced in order to oxidize NADH back to NAD+

Products of Pyruvate Oxidation

1 CO2

1 NADH

2 carbons from pyruvate attached to coenzyme A

Citric Acid Cycle

Oxidizes the acetyl group from pyruvate

1. Acetyl-CoA + oxaloacetate → citrate

2. Citrate rearrangement and decarboxylation

3. Regeneration of oxaloacetate

Citric Acid Cycle Yield

2CO2, 3 NADH, 1 FADH2, 1 ATP, regenerates oxalate

Electron Transport Chain

Electrons from NADH and FADH2 are transferred to complexes of the ETC

Chemiosmosis

Accumulation of protons in the intermembrane space drives protons into the matrix via diffusion

Uses energy of gradient to make ATP from ATP + P_i

Light-Dependent Reactions

1. Primary photo event

2. Charge separation

3. Electron transport

4. Chemiosmosis

Photosystem II and Photosystem I

Carry out a noncyclic transfer of electrons that is used to generate both ATP and NADPH

Photosystem I

Produces NADPH

Photosystem II

Oxidizes water to replace the electrons transferred to photosystem I

Calvin Cycle

In chloroplast stroma

Use inorganic carbon (CO2) to build organic molecules (glucose)

Three Phases of Calvin Cycle

Carbon fixation, reduction, regeneration of RuBP

Photorespiration

Oxidation of RuBP by the addition of O2.

Favored when stomata are closed in hot conditions.

Closed stomata create low-CO2 and high-O2

Used in CAM

Carboxylation

Addition of CO2 to RuBP

Autocrine

Respond to its own ligand

Juxtacrine Signaling

Direct contact

Paracrine signaling

Nearby cells

Endocrine signaling

Long distance

Cell-Surface Receptors

Chemically gated ion channels, Enzymatic receptors, G protein-coupled receptor

Chemically gated ion channels

Channel-linked receptors that open to let a specific ion pass in response to a ligand

Enzymatic receptors

Receptor is an enzyme that is activated by the ligand

G protein-coupled receptor

G-protein (bound to GTP) assists in transmitting the signal fromreceptor to enzyme (effector)

Steroid Hormone Receptors

Hormone (ligand)-binding domain, DNA-binding domain, Transactivation domain that interacts with coactivators to affect level of gene transcription

Receptor tyrosine kinases (RTK)

Influence cell cycle, cell migration, cell metabolism, and cell proliferation

Membrane receptor

A single transmembrane domain, Extracellular ligand-binding domain, Intracellular kinase domain

The Ras Proteins

Small GTP-binding protein (G protein)

Link between the RTK and the MAP kinase cascade

Active when bound to GTP, inactive when bound to GDP

Cohesin Proteins

Hold chromosomes together

Sister chromatids in 1 chromosome

2

G1 (gap phase 1)

Primary growth phase, longest phas

S (synthesis)

Replication of DNA, centrioles

G2 (gap phase 2)

Organelles replicate, microtubules organize

Kinetochore

Attachment site for microtubules

Cyclins

Proteins that are produced in synchrony with the cell cycle

Work with cyclin-dependent kinases (cdks) to regulate cell cycle checkpoints

Cyclin-Dependent Kinases (Cdks)

Enzymes that phosphorylate proteins

Primary mechanism of cell cycle control

Synapsis (UNIQUE TO MEIOSIS)

In Prophase 1

Homologous chromosomes become closely associated

Includes formation of synaptonemal complexes

Chiasmata

Site of crossing over

Nondisjunction

Failure of chromosomes to move to opposite poles during either meiotic division

Aneuploid gametes

Gametes with missing or extra chromosomes

Law of Segregation

Two alleles for a gene segregate during gamete formation (one from each parent) and are rejoined at random during fertilization

Phenotypic plasticity

Different phenotypes from same genotype due to environmental conditions

Genomic Imprinting

Phenotype depends on parental origin of allele

Recombination