BIO 150 Final Key Terms

Covalent Bond

Covalent Bond

Pairs of electrons are shared between atoms

Molecules

2 or more covalently bonded atoms

Nonpolar Covalent Bond

Same atoms, share electronegativity

Polar Covalent Bond

Electrons are pulled closer to the more electronegative atom

Ion

Forms when an atom gains or loses an electron and becomes charged

Ionic Bond

Attraction between two oppositely charged ions

Hydrogen Bond

Attraction between a partial positive hydrogen atom and an electronegative atom with a partial negative charge

Hydrogen Bond Water

Water is a polar molecule

A hydrogen bond forms when a partially negatively charged region on the oxygen of one water molecule is attracted to the partially positively charged hydrogen of a water molecule

Isomers

Compounds that have the same molecular formula but different structures and therefore different properties

Three Types of Isomers

Structural

Cis-trans

Enantiomers

Macromolecules

Polymers, built from monomers

Polymers

Large carbohydrates (polysaccharides)

Proteins

Nucleic acids

Hydrolysis

Breaks bonds between two molecules by the addition of water

Can break down Polymers into Monomers

Dehydration Reaction

Two molecules become covalently bonded by the removal of water

Monomers → Larger Molecules

Disaccharides

Lactose

Sucrose

Carbon sources that can be converted to other molecules

Monosaccharides

Glucose

Fructose

Carbon sources that can be converted to other molecules

Polysaccharides

Cellulose (plants)

Starch (plants)

Glycogen (animals)

Chitin (animals and fungi

Triglycerol

Glycerol and three fatty acids

Important energy source

Fats or oils

Phospholipids

Glycerol

Hydrophilic phosphate group head

Hydrophobic two fatty acid tail

Lipid bilayer of membranes

Steroids

Four fused rings with attached chemical groups

Components of cell membranes (cholesterol)

Signaling molecules that travel through the body (hormones)

Nucleus

Surrounded by a nuclear envelope (double membrane) perforated by nuclear pores

Nuclear envelope is continuous with endoplasmic reticulum

Houses chromosomes (made of chromatin)

Contains nucleoli

Where ribosomal subunits are made

Pores regulate entry and exit of materials

Ribosome

Two subunits of ribosomal RNAs and proteins

Can be free in cytosol or bound to ER

Protein Synthesis

Endoplasmic Reticulum (ER)

Extensive network of membrane-bounded tubules and sacs

ER membrane separates the lumen from cytosol and is continuous with nuclear envelope

Smooth ER: synthesis of lipids, metabolism of carbohydrates, storage of calcium ions, detoxification of drugs and poisions

Rough ER: aids in synthesis of secretory and other proteins on bound ribosomes, adds carbohydrates to proteins to make glycoproteins, produces new membrane

Golgi Apparatus

Stacks of flattened membranous sacs

Has polarity (cis and trans faces)

Modification of proteins

Synthesis of many polysaccharides

Sorting of Golgi products, which are then released in vesicles

Lysosome

Membranous sac of hydrolytic enzymes (in animal cells)

Breakdown of ingested substances, cell macromolecules, and damaged organelles for recycling

Vacuole

Large membrane-bounded vesicle

Digestion

Storage

Waste disposal

Water balance

Cell growth

Protection

Mitochondrion

Bounded by double membrane

Inner membrane has infoldings

Cellular Respiration!!

Chloroplast

Typically two membranes around fluid stroma

Contains thylakoid stacked into grana

Photosynthesis!

Present in cells of photosynthetic eukaryotes, including plants

Peroxisome

Specialized metabolic compartment bounded by a single membrane

Contains enzyme that transfer H atoms from substrates to oxygen, producing hydrogen peroxide (H2O2) which is converted to H2O

Cytoskeleton

Functions in structural support for the cell

Motility

Signal Transmission

Microtubules

Shape the cell

Guide organelle movement

Separate chromosomes in dividing cells

Cilia and Flagella

Motile appendages continuing microtubules

Microfilaments

Thin rods

Muscle contraction

Amoeboid movement

Cytoplasmic streaming (speeds distribution of materials within cells)

Support of microvilli

Intermediate Filaments

Support cell shape

Fix organelles in place

Phospholipid Bilayer

Unsaturated hydrogen tails of some phospholipids keep membranes fluid at lower temperatures

Cholesterol helps membranes resist changes in fluidity caused by temperature changes

Membrane proteins function

Transport

Enzymatic activity

Signal transduction

Cell-cell recognition

Intercellular joining

Attachment to the cytoskeleton and extracellular matrix

Glycoproteins and Glycolipids

Synthesized in the ER and modified in the ER and Golgi apparatus

Hydrophobic substances

Soluble in lipids

Pass through membranes rapidly

Polar molecules and ions

Generally require specific transport proteins to pass through membranes

Diffusion

Spontaneous movement of a substance down its concentration gradient

Osmosis

Water moving in or out of a cell

Hypertonic

Solution has a higher solute concentration that outside

Hypotonic

Solution has a lower solute concentration outside

Facilitated Diffusion

A transport protein speeds water or solute movement down its concentration gradient across a membrane

Ion Channel

Facilitate the diffusion of ions across a membrane

Active Transport

Specific membrane proteins use energy (usually in the form of ATP) to do the work

Electrochemical Gradient

Combination of concentration (chemical) and voltage (electrical) gradients

Determine the net direction of ionic diffusion

Cotransport

Occurs when a membrane protein enables the “downhill” diffusion of one solute to drive the “uphill” transport of the other

Metabolism

Collection of chemical reactions that occur in an organism

Catabolic

Breaking down molecules, releasing energy

Anabolic

Building molecules, consuming energy

First law of thermodynamics

Energy cannot be created or destroyed

Second law of thermodynamics

Spontaneous processes increase the entropy of the universe

Free energy

Delta G

Enthalpy

Delta H

Amount of heat evolved or absorbed in a reaction

Entropy

Delta S

Molecular disorder

Exergonic Reaction

Spontaneous

Products have less free energy than the reactants

Negative delta G (free energy)

Endergonic

Nonspontaneous

Require an input of energy

Positive delta G (free energy)

Hydrolysis of ATP terminal phosphate

Yields ADP and phosphate group

Releases free energy (delta G)

Energy Coupling

Exergonic process of ATP hydrolysis drives endergonic reactions by transfer of a phosphate group to specific reactants

Forming a phosphorylated intermediate that is more reactive

ATP Hydrolysis

Causes change in the shape and binding affinities of transport and motor proteins

Activation energy

Energy necessary to break the bonds of the reactants in a chemical reaction

Enzymes

Lower activation energy barrier

Have a unique site that binds one or more substrates

Changes shape, binding the substrates more tightly (induced fit)

Active site can lower the activation energy

Has an optimal temperature and pH

Inhibitor

Reduces enzyme function

Competitive Inhibitor

Binds to the active site

Reduces enzyme function

Noncompetitive inhibitor

Binds to a different site on the enzyme

Reduces enzyme function

Allosteric Regulation

Regulatory molecules bind to specific regulatory sites affecting the shape and function of the enzyme

Cooperativity

Binding of one substrate molecule can stimulate binding or activity at other sites

Feedback inhibition

The end product of a metabolic pathway allosterically inhibits the enzyme for a previous step in the pathway

Fermentation

Process that results in the partial degradation of glucose without the use of oxygen

Electrons from NADH are passed to pyruvate, regenerating the NAD+ required to. ozidize more glucose

Cellular Respiration

A more complete breakdown of glucose

Aerobic Respiration

O2 is used as a reactant

Glucose is oxidized to CO2

O2 is reduced to H2O

Anaerobic Respiration

Other substances are used in place of O2 as a reactant

Occurs in 3 steps

1. glycolysis

2. pyruvate oxidation and the citric acid cycle

3. oxidative phosphorylation

   1. electron transport chain and chemiosmosis

Redox Reaction

One substance partially or totally shifts electrons to another

Oxidation

Loss of electrons

Reduction

Addition of electrons

Electron Transport Chain

Conducts the electrons to O2 in energy-releasing steps

Energy is used to make ATP

Glycolysis

Harvests chemical energy by oxidizing (losing electrons) glucose to pyruvate

Splitting of sugars

Inputs: Glucose

Outputs: 2 Pyruvate, 2 ATP, 2 NADH

Pyruvate Oxidation and the Citric Acid Cycle

After pyruvate is oxidized, the citric acid cycle completes the energy-yielding oxidation of organic molecules

Pyruvate enters the mitochondrion and is oxidized into acetyl CoA which is further oxidized in the CAC

Inputs: 2 Pyruvate, 2 Acetyl CoA, 2 Oxaloacetate

Outputs: 2 ATP, 6 CO2, 8 NADH, 2 FADH2

Oxidative Phosphorylation

Chemiosmosis couples electron transport to ATP synthesis

NADH and FADH2 transfer electrons to the ETC

Creation of a proton-motive force (hydrogen ion gradient)

Phosphorylation of ADP to ATP (chemiosmosis)

Output: maximum 32 ATP

Under Anaerobic (no oxygen) conditions

Anaerobic respiration or fermentation can occur

Both use glycolysis to oxidize glucose

Respiration: ETC, makes more ATP

Fermentation: no final electron acceptor

Aerobic respiration (with O2 as the final electron acceptor) yields 16 times as much ATP

Photosynthesis

6CO2 + 12H2O + Light Energy = C6H12O6 + 6 O2

Redox process

H2O is oxidized

CO2 is reduced

Chloroplasts

Light reactions in thylakoid membranes split water releasing oxygen, producing ATP, forming NADPH

incorporating the electrons of hydrogen and oxygen

Calvin cycle in the stroma forms sugar from CO2, using ATP for energy and NADPH for reducing power

Pigment

Absorbs light of specific wavelengths

Goes from a ground state to an excited state when a photon of light boosts one of the pigments electrons to a higher energy orbital (excited=unstable)

Photosystem

Composed of a rection-center complex

Surrounded by light harvesting complexes that funnel the energy of photons to the reaction center complex

Cyclic Electron Flow

Employs only one photosystem, producing ATP but no NADPH or O2

Chemiosmosis in Mitochondria and Chloroplasts

ETC generate a hydrogen ion gradient across a membrane

ATP synthase uses this proton motive force to make ATP

Calvin Cycle

Uses chemical energy of ATP and NADPH to reduce CO2 to sugar

Occurs in the stroma

Uses electrons from NADPH and energy from AP

CO2 is reduced, H2O is oxidized

3 Stage Cell Signaling Pathway

1. signal reception

2. signal transduction

   1. relay molecules

3. activation of cellular response

Signal Transduction

A signaling molecule (ligand) binds to a receptor causing it to change shape

A specific shape change in a receptor is often the initial transduction of a signal

3 Major Types of Cell-Surface Transmembrane

1. G protein coupled receptors (GPCRs)

2. Receptor tyrosine kinases (RTKs)

3. Ligand gated ion channels

G Protein-Coupled Receptors (GPCRs)

Work with cytoplasmic G proteins

Ligand binding activates the receptor, which then activates a specific G protein, thus propagating the signal

Receptor Tyrosine Kinases (RTKs)

React to the binding of signaling molecules by forming dimers and then adding phosphate groups to tyrosines on the cytoplasmic part of the other monomer making up the dimer and then adding phosphate groups to tyrosines on the cytoplasmic part of the other monomer making up the dimer

Relay proteins in the cell can then be activated by binding to different phosphorylated tyrosines, allowing this receptor to trigger several pathways at once

Ligand Gated Ion Channels

Open or close in response to binding by specific signaling molecules

Regulating the flow of specific ions across the community

Phosphorylation Cascades

A series of protein kinases each add a phosphate group to the next one in line, activating it

Second Messengers

cAMP (made from ATP, can be used by G proteins to activate adenylyl cyclase) (usually directly activates protein kinase a)

Ca2+ ion in GPCR and RTK pathways

Diffuse readily through the cytosol and this help broadcast signals quickly

Cell Division

Interphase

G1

S

G2

Mitotic (M) Phase

Prophase

Prometaphase

Metaphase

Anaphase

Telophase and Cytokinesis

Mitotic Spindle

Made up of microtubules (kinetochore and nonkinetochore) and centrosome

Controls chromosome movement during mitosis

Interphase

Duplication of chromosomes

Production of new mitochondria

Growth of the cell

Production of the ER

Protein Production

DNA is replicated in the S phase

Prophase

Beginning of the formation of a spindle apparatus

Chromosomes pair up