Cell Communication

cell junctions

[both animals and plants have cell junctions that allow muscles to pass readily between adjacent cells without crossing plasma membrane]

Explain the evolution of cell signaling!

Signaling in microbes has much in common with processes in multicellular mechanisms, suggesting an early origin of signaling mechanisms. Bacterial cells can sense the local density of bacterial cells by binding molecules secreted by other cells. In some cases, such signals lead to aggregation of these cells into biofilms.

What are three stages of cell signaling?

1. reception

2. transduction

3. response

What is apoptosis?

Apoptosis is a type of programmed cell death in which cell components are disposed of in an orderly fashion, without damage to neighboring cells.

Facts:

- In local signaling, animal cells may communicate by direct contact or by secreting local regulators, such as growth factors or neurotransmitters.

- The binding between signaling (ligand) and receptor is highly specific.

- Intracellular receptors are cytoplasmic or nuclear proteins.

- The behavior of testosterone is representative of steroid hormones.

- Most water-soluble molecules bind to specific sites on receptor proteins embedded in the cell’s plasma membrane.

Key terms:

Signal transduction pathway = series of steps when a signal on a cell’s surface is converted to a specific cellular response

Local regulators = influence cells in the vicinity

Hormones = chemicals for long-distance signaling

Ligand = a molecule that binds specifically to another molecule, usually a larger one

Cyclic AMP/ cAMP = cyclic adenosine monophosphate, a ring-shaped molecule made from ATP that is common intracellular signaling molecule (second messenger)

Receptor tyrosine kinase proteins = inactive monomers

Protein kinase = an enzyme that transfers phosphate groups from ATP to a protein

Adenylyl cyclase = an enzyme embedded in the plasma membrane; converts ATP to camp in response to extracellular signals

Scaffolding proteins = large relay proteins to which several other relay proteins are simultaneously attached

Apoptosis = a program of controlled cell suicide

Summary:

Signaling in microbes has much in common with processes in multicellular organisms, with processes in multicellular organisms, suggesting an early origin of signaling mechanisms. In local signaling, animal cells may communicate by direct contact or by secreting local regulators, such as growth factors or neurotransmitters. For signaling over long distances, both animals and plants use hormones. Earl Sutherland discovered how the hormone epinephrine acts on cells: the signal is transmitted by successive shape changes in the receptor and relay molecules.

The binding between a ligand and receptor is highly specific. The change of the receptor is often the initial transduction of the signal. A G protein-coupled receptor is a membrane receptor that works with the help of a cytoplasmic G protein. Ligand binding activates the receptor, which then activates a specific G protein, which activates another, propagating the signal along a signal transduction pathway. Another receptor in the plasma membrane is tryosine kinase. Specific signaling molecules cause ligand-gated ion channels in a membrane to open or close, regulating the flow of specific ions. Intracellular receptors are cytoplasmic or nuclear proteins.

Cascades of molecular interactions relay signals from receptors to target molecules in the cell.

Cell signaling leads to regulation of transcription or cytoplasmic activities.

Apoptosis is a type of programmed cell death in which cell components are disposed of in an orderly fashion, without damage to neighboring cells.

Extra:a real example of cell communication

(video!)

Photosynthesis

What is photosynthesis? Give the equation!

Photosynthesis is a a process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight.

photosynthesis equation

What is an autotroph?

Autotrophs are "self-feeders".

How does Ps relate to fall leaf colors?

Plants change their leaves color in the fall. Most leaves include the chlorophyll (green), xathophyll (yellow) and carotene (orange) pigments, but chlorophyll is much than the others. It covers other two. During fall, the strength of light is weaker and the temperature drops, too. Plants/leaves adopt to it by breaking down chlorophyll. N and Mg (building chlorophyll) are salvaged and moved into the stem for next year. Now other, accessory pigments are reflected the most and give leaves diverse “fall” colors.

Facts:

- Photosynthesis converts light energy to chemical energy of food!

- The light reactions convert solar energyto the chemical energy of ATP and NADPH.

- The Calvin Cycle uses ATP and NADPH to convert carbon dioxide to sugar.

- Alternative mechanisms of carbon fixation have evolved in hot, arid climates.

- All green parts of plants have chloroplasts.

Key terms:

Autotrophs – self feeders

Heterotrophs – obtain their organic material by the second major mode of nutrition, unable to make their own food

Chlorophyll – the green pigment within chloroplasts

Mesophyll – the tissue in the interior of the leaf

Stroma – the dense fluid within the chloroplasts

Thylakoids – interconnected membranous sacs

Grana – thylakoid coumn

Photophosphorylation – adition of a phosphate group to ADP

Carbon fixation – initial incorporation of carbon into organic compounds

Wavelength – the distance between the crest of electromagnetic waves

Summary:

Photosynthesis is a process in which light energy is converted to chemical energy and used to produce organic compounds. In plants, photosynthesis occurs within the chloroplasts. Photosynthesis consists of2 stages, the light and the dark reactions. The light reactions convert light into energy (ATP, NADPH) and the dark reactions use energy and carbon dioxide to produce sugar.

Extra: light dependant reaction of photosynthesis video!

Cellular Respiration [Harvesting Chemical Energy]

What is cellular respiration and its equation?

It is the process of releasing energy from food.

Equation: C₆H₁₂O₆ + 6O₂ --> 6CO₂ + 6 H₂O

(The energy is released from the bonds)

Name the 3 main stages of cell respiration and explain briefly

1) glycolysis

purpose: To split glucose and produce NADH and ATP

location: Cytoplasm (cytosol)

requirements: glucose, 2 ATP, 4 ADP, 2NAD+

products (net results): 2 pyruvic acids (3C acid), 2 ADP, 4 ATP, 2 NADH

a) Energy investment phase --> G3P (glycerolaldahyde, 3C sugar)

b) Energy harvest (payoff) phase --> pyruvate

krebs cycle (citric acid cycle)

--> doesn't require O2

purpose: oxidizing pyruvic acid to CO₂, production of NADH and FADH₂ (form of cell energy)

location: mitochondria matrix

requirements: pyruvic acid (3C acid), coenzyme A, 4 NAD^+, 1 ADP, 1 FAD (all double for each glucose)

products: 3 CO_2, acetyl CoA, 4 NADH, 1 ATP, 1 FADH₂

acetyl CoA --> acetyl coenzime A; the entry compound for the krebs cycle in celll respiration, formed from a fragment pyruvate attached to a coenzime

oxidative phosphorylation (electron transport chain)

purpose: converting NADH and FADH₂ into ATP

location: mitochondria cristae

ETC --> mitochondrial inner membrane (control of the energy transport)

requirements: NADH or FADH_2, ADP, O₂

products: NAD⁺ and FAD, ATP, H₂O (36-38 ATP --> total/ net result)

What is ATP synthase?

ATP synthase is a general term for an enzyme that can synthesize adenosine triphosphate (ATP) from adenosine diphosphate (ADP) and inorganic phosphate by using some form of energy. This energy is often in the form of protons moving down an electrochemical gradient, such as from the lumen into the stroma of chloroplasts or from the inter-membrane space into the matrix inmitochondria. The overall reaction sequence is:

ADP + P_i → ATP

5 facts:

- The energy stored in the organic molecules of food ultimately comes from the sun.

- To keep working, a cell must regenerate ATP.

- The electron transport chain is a collection of molecules embedded in the inner membrane of the mitochondria in eukaryotic cells.

- In prokaryotic cells, the krebs cycle occurs in the cytosol.

- At the end of electron transport chain, electrons are passed to oxygen, reducing it to water.

Key terms:

Aerobic respiration – the most relevant and efficient catabolic pathway

Anaerobic – no O₂

Cellular respiration – both aerobic and anaerobic processes

Oxidation – loss of electrons and energy

Oxidizing agent – the electron acceptor

Reduction – gain of electrons and energy

Reducing agent – the electron donor

NAD+ - electron carrier/acceptor, oxidizing agent in glycolisis

Chemiosmosis – energy-coupling mechanism

Fermentation – a way of harvesting chemical energy without using either oxygen or any ETC (no cell respiration)

Summary:

Cellular respiration allows organisms to use (release) energy stored in thechemical bonds of glucose. The energy in glucose is used to produce ATP. Cells use ATP to supply their energy needs. Cellular respiration is therefore a process in which the energy in glucose is transformed to ATP.

In respiration, glucose is oxidized and thus releases energy. Oxygen is reduced to form water. The carbon atoms of the sugar molecule are released as carbon dioxide.

The complete breakdown of glucose to carbon dioxide and water requires three major steps:

1)glycolysis; 2) krebs cycle; 3) oxidative phosphorylation

Glycolysis produces two ATP. Thirty-four more ATP are produced by aerobic pathways if oxygen is present.

Extra: Glucose Breakdown: RAP!

An Introduction to Metabolism

What is metabolism?

Metabolism is the collection of chemical reac

tions that occur in an organism.

What is energy and which are the forms of energy?

Energy is capacity to cause change.

Kinetic energy = Energy of action or motion

Potential energy = stored energy or capacity to do work

Energy of activation = Energy needed to convert potential energy into kinetic energy

How can regulation of enzyme help control metabolism?

Enzymes speed up metabolic reactions by lowe

ring energy barriers.

They are biological catalysts that cause the rate of a chemical reaction to increase.

Facts:

- Every chemical reaction between molecules involves both bond breaking and bond forming.

- The quantity of energy in the universe is constant, but quality is not.

- Energy released from ATP drives anabolic reactions.

- Energy from catabolic reactions "recharges" ATP.

- Each chemical reaction in the cell requires its own enzyme.

Key words:

Metabolism = the totality of an organism’s chemical reactions

Energy = the ability to do work

Kinetic energy = energy of motion / action

Potential energy = tored energy or capacity to do work

Energy of activation = Energy needed to convert potential energy into kinetic energy

Entropy = measure of disorder

Free energy = portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell

Exergonic reaction = release of free energy

Endergonic reaction = absorbs free energy

Energy coupling = a key feature in the way cells manage their energy resources to do work (chemical, transport, mechanical)

Phosphorylated = the recipient of the phosphate group

Summary:

Energy, the ability to do work can be kinetic, potential or activation energy. The laws of energy transformation say that it cannot be cr

eated or destroyed, only transfered and transformed. The second law states that spontaneous changes, those requiring no outside input of energy, increase the entropy (disorder) of the universe.

Free energy is the energy that can preform work when temperature and pressure are uniform throughout the system, as in a living cell. We can think of free energy as a measure of systems' instability - its tendency to change to a more stabile systems. The term that describes maximum stability is equilibrium.

Based on free energy changes, chemical reactions c

an be classified as either exergonic (energy released) or endergonic (energy absorbed).

ATP powers cellular work by coupling exergonic reactions to endergonic reactions.

Enzymes speed up metabolic reactions by lowering energy barriers. Their regulation helps control metabolism. An enzyme catalyzes a reaction by lowering the activation energy barrier, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures.

(diffusion, the relationship of free energy to work capacity, stability and spontaneous change)

Extra:

how ATP works (video)

Membrane Structure and Function

What is a plasma membrane and how is it composed?

It is membrane at the boundary of every cell, composed of a phospholipid bilayer and proteins.

What is meant by fluid-mosaic model of a membrane?

In 1972, S.J.Singer and G. Nicolson proposed that membrane proteins are dispersed, individually inserted into the phospholipid bilayer with their hydrophilic regions protruding. This molecular arrangement would maximixe contact of hydrophilic regions of proteins and phospholipis with water in the cytosol and extracellular fluid, while providing their hydrophobic parts with a nonaqueous environment. In this fluid-mosaic model, the membrane is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids.

What are protein functions in the membrane?

- Transport

- Enzymatic activity

- Receptor sites for signals

- Cell adhesion

- Cell-cell recognition

- Attachment to the cytoskeleton

Facts:

- A membrane is held together primarily by hydrophobic interactions (much weaker than covalent bonds).

- More than 50 kinds of proteins have been found so far in the plasma membrane of red blood cells.

- The Davson-Danielli sandwich model of the membrane has been replaced by the fluid mosaic model, in which amphipathic proteins are embedded in the phospholipid bilayer.

- Short chains of sugars are linked to proteins and lipids on the exteror side of the plasma membrane, where they interact with surface molecules of other cells

- One solute’s “downhill” diffusion drives the other’s “uphill“ transport

Key terms:

Integral proteins = transmembrane protein eith hydrophobic regions that extend into and often completely span the hydrophobic interior of the membrane and with hydrophilic regions in contact with the aqueous solution on either side of the membrane

Peripheral proteins = proteins loosely bounded to the surface of a membrane or to part of an integral protein and not embedded in the lipid bilayer

Glycolipids = molecules formed of membrane carbohydrates covalently bonded to lipids

Glycoproteins = membrane carbohydrates + proteins

Aquaporins = channel proteins (facilitate the passage of water molecules through the membrane)

Diffusion = the movement of molecules of any substance so they spread out evenly into the available space (passive transport)

Osmosis = the diffusion of water

Facilitated diffusion = the spontaneous passage of molecules or ions across a membrane with the assistance of specific transmembrane transport proteins

Passive transport = no energy required / invested

Active transport = energy required

Summary:

The Davison Danielli sandwich model of the cell membrane (1935) has been replaced by the fluid mosaic model, in which amphipathic proteins are embedded in the phospholipid bylayer. Proposed by Singer and Nicolson in 1972.

The plasma membrane controls the processes of the exchange of molecules and ions of the cell with its surrounding.

Besides enzymatic activity, receptor sites for signals, cell adhesion, cell-cell recognition and attachment to the cytoskeleton, the protein function in the membrane is transport, but the question is how do materials get across the cell membrane?! ... There are two ways of transport and these are passive and active. Passive (diffusion, osmosis, facilitated diffusion) does not require cellular energy. The way of movement of the atoms and ions is from higher to lower concentration until the equilibrium is reached. Active transport (Carrier-Mediated, endocytosis, exocytosis), unlike passive, requires cellular energy (ATP).

Extra:

osmosis (video)

A Tour of the Cell

What is a cell?

The cell is the fundamen

tal unit of life (for biology, as the atom is fundamental for chemistry). All organisms are made of cells --> basic units of structure and function. Each action of an organism begins at the cellular level.

What do biologists use to study cells?

To study cells, biologists use microscopes and the tools of biochemistry.

- light microscopes (LM) - uses visible light to illuminate the objects

- electron microscopes (EM) - uses beams of electrons instead of light

.. scanning electron microscope (EEM)- surface view

.. transmission electron microscope (TEM) - look inside

What is the difference bet

ween animal and plant cell?

- Plant cells have cell walls, a central vacuole, plasmodesmata and chloroplasts (animal cell x).

- Animal cells have Lysosomes, Centrosomes with centrioles and flagella (sometimes present in plan

t sperm)

Facts:

- The cell is fundamental to the living systems of biology as the atom is to chemistry.

- The light microscope offers

advantages in studying living cells (methods used in electron microscopy kill the cells).

- Larger organism do not generally have larger cells than smaller organisms - simply more cells.

- Improvements in microscopy that affect the parameters of magnification, resolution, and contrast have catalyzed progress in the study of cell structure.

- All cells are bounded by a plasma membrane.

Key terms:

cell = basic functional unit of all living things

lipid bilayer = double phospholipid membrane --> outer hydrophilic heads and hydrophobic tails pointing towards inside

organelles = bodies within the cytoplasm that serve to physically separate the various metabolic reactions that occur within the cells

nucleus = "brain" of the cell

ribosome = consisting of RNA

endoplasmic reticulum = stacks of flattened sacs involved in the production of various materials

golgi apparatus = group of flattened sacs arranged like a stack of bowls, functioning to modify and package proteins and lipids into vesicles

lyzosomes = vesicles from a golgi apparatus that contain digestive enzymes

mitochondria = organelles that carry out aerobic respiration

chloroplasts = organelles that carry out photosynthesis

flagella and cilia = structures that protrude from the cell membrane and make wavelike movements

Summary:

Although the cell is the smallest unit of life, it is by no means simple. The human body is made up of tens of trillions of cells, which have developed a highly synchronized set of components to carry out the processes that keep the organism alive, allow it to reproduce and adapt to changing environments.

Organelles are bodies within the cell cytoplasm that serve to physically separate the various metabolic reactions that occur within the cell. Some of them are : the nucleus, ribosomes, endoplasmic reticulum, golgu apparatus, lysosomes, peroxisomes, mitochondria, chloroplasts, microtubules, fagella and cilia, centrioles, cell walls, vacuoles and vesicles...

Extra:

animal cell (video)

The Structure and Function of Large Biological MoleculesWhat is a macromolecule?

What is a macromolecule?

Macromolecules are polymers- large molecules formed by joining many subunits together (monomers - "building blocks").

Four main macromolecules:

- carbohydrates (sugars)

- lipids (fats, oils)

- proteins (enzymatic, structural, storage etc. function)

- nucleic acids (DNA/RNA)

What are the levels of protein structure?

• PRIMARY - unique sequence of amino acids
• SECONDARY - alpha helix or beta pleated sheets
• TERTIARY - overall shape of a polypeptide resulting from
• QUATERNARY - overall protein structure

What is the difference between DNA and RNA?

DNA - deoxyribonucleic acid

- sugar: deoxyribose

- double helix

- nucleotides (nitrogenous bases): C (cytosine), G (guanine), A (adenine), T (thymine)

RNA - ribonucleic acid

- sugar: ribose

- single helix

- nucleotides: C, G, A,U (uracil)

Facts:

• Macromolecules are polymers, made of monomers
• Carbohydrates serve as fuel and building materials
• Triacylglicerols (fats or oils) are important energy source
• The two ends of phospholipids show different behavior toward water (hydrophilic / hydrophobic)
• A protein's specific structure determines how it works

Key terms:

Macromolecules (polymers) = Large molecules formed by joining many subunits together

Polymer = molecule that consists of a single unit (monomer) repeated many times

Monomer = A building block of a polymer

Dehydration/ Condensation synthesis = the chemical reaction that joins monomers into polymers. Covalent bonds are formed by the removal of a water molecule between the monomers

Hydrolisis = Reverse of

condensation synthesis. Breaks polymers into monomers by adding water.

Polypeptide = polymers of amino acids

Proteins = polypeptide chains of Amino Acids linked by peptide bonds

Fatty acid = a long carbon chain (12-18 C) with a -COOH (acid) on one end and a -CH₃ (fat) at the other.

Denaturation = pH shifts, high salt concentrations, heat

Nucleotide = monomer

of nucleic acid, consisting of a nitrogen base, deoxyribose (five-carbon sugar) and a phosphate group

Summary:

Organic molecules are those that have carbon atoms. In living systems, large organic molecules, called macromolecules, may consist of hundreds or thousands of atoms. Most macro

molecules are polymers, molecules that consist of a single unit (monomer) repeated many times.

Four important classes of organic molecules - carbohydrates, lipids, proteins and nucleic acids - are discussed below.

Carbohydrates - classified into 3 groups according to the number of sugar molecules present : monosaccharide, disaccharide, polysaccharide - and are all serving as fuel and building material.

Lipids are class of substances that are insoluble in water (and other polar solvents) but are soluble in no

npolar substances (ex. ether). There are 3 major groups of lipids: tryglicerides (fats, oils, waxes), phospholipids and steroids.

Proteins can be gr

ouped according to their functions: structural, storage, transport, defensive, enzymes.

Although the functions of proteins are diverse, their structures are similar (polymers of amino acids, covalently bonded).

Nucleic acids are divided into two groups: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). The genetic information of a cell is stored in molecules of DNA. The DNA, in turn, passes its genetic instructions to RNA for directing various metabolic activities of

the cell.

Extra:

Roger Kornberg --> Nobel Prize in Chemistry for using Xray crystallography to determine the 3D shape of polymerase II