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