Cell Structure & Function

Physiology - science that describes how organisms FUNCTION and survive in continually changing environments
 

Levels of Organization:

CHEMICAL LEVEL - includes all chemical substances necessary for life (see, for example, a small portion - a heme group - of a hemoglobin molecule); together form the next higher level

CELLULAR LEVEL - cells are the basic structural and functional units of the human body & there are many different types of cells (e.g., muscle, nerve, blood, and so on)

TISSUE LEVEL - a tissue is a group of cells that perform a specific function and the basic types of tissues in the human body include epithelial, muscle, nervous, and connective tissues

ORGAN LEVEL - an organ consists of 2 or more tissues that perform a particular function (e.g., heart, liver, stomach, and so on)

SYSTEM LEVEL - an association of organs that have a common function; the major systems in the human body include digestive, nervous, endocrine, circulatory, respiratory, urinary, and reproductive.

There are two types of cells that make up all living things on earth: prokaryotic and eukaryotic. Prokaryotic cells, like bacteria, have no 'nucleus', while eukaryotic cells, like those of the human body, do. So, a human cell is enclosed by a cell, or plasma, membrane. Enclosed by that membrane is the cytoplasm (with associated organelles) plus a nucleus.

Cell, or Plasma, membrane - encloses every human cell

• Structure - 2 primary building blocks include protein (about 60% of the membrane) and lipid, or fat (about 40% of the membrane). The primary lipid is called phospholipid, and molecules of phospholipid form a 'phospholipid bilayer' (two layers of phospholipid molecules). This bilayer forms because the two 'ends' of phospholipid molecules have very different characteristics: one end is polar (or hydrophilic) and one (the hydrocarbon tails below) is non-polar (or hydrophobic):

• Functions include:
• supporting and retaining the cytoplasm
• being a selective barrier
• The cell is separated from its environment and needs to get nutrients in and waste products out. Some molecules can cross the membrane without assistance, most cannot. Water, non-polar molecules and some small polar molecules can cross. Non-polar molecules penetrate by actually dissolving into the lipid bilayer. Most polar compounds such as amino acids, organic acids and inorganic salts are not allowed entry, but instead must be specifically transported across the membrane by proteins.
• transport
• Many of the proteins in the membrane function to help carry out selective transport. These proteins typically span the whole membrane, making contact with the outside environment and the cytoplasm. They often require the expenditure of energy to help compounds move across the membrane
• communication (via receptors)

Source: http://bio.winona.msus.edu/berg/ANIMTNS/Recep.htm

• recognition

Source: http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html

Cells, cytoplasm, and organelles:

• Cytoplasm consists of a gelatinous solution and contains microtubules (which serve as a cell's cytoskeleton) and organelles (literally 'little organs')

• Cells also contain a nucleus within which is found DNA (deoxyribonucleic acid) in the form of chromosomes plus nucleoli (within which ribosomes are formed)

• Organelles include:
• Endoplasmic reticulum -
• comes in 2 forms: smooth and rough; the surface of rough ER is coated with ribosomes; the surface of smooth ER is not
• functions include: mechanical support, synthesis (especially proteins by rough ER), and transport
• Golgi complex -
• consists of a series of flattened sacs (or cisternae)
• functions include: synthesis (of substances likes phospholipids), packaging of materials for transport (in vesicles), and production of lysosomes
• Lysosomes -
• membrane-enclosed spheres that contain powerful digestive enzymes
• functions include destruction of damaged cells (which is why they are sometimes called 'suicide bags') & digestion of phagocytosed materials (such as bacteria)

• Mitochondria -
• have a double-membrane: outer membrane & highly convoluted inner membrane

• inner membrane has folds or shelf-like structures called cristae that contain elementary particles; these particles contain enzymes important in ATP production
• primary function is production of adenosine triphosphate (ATP)
• Ribosomes-
• composed of rRNA (ribosomal RNA) & protein
• may be dispersed randomly throughout the cytoplasm or attached to surface of rough endoplasmic reticulum
• often linked together in chains called polyribosomes or polysomes
• primary function is to produce proteins
• Centrioles -
• paired cylindrical structures located near the nucleas
• play an important role in cell division
• Flagella & cilia - hair-like projections from some human cells
• cilia are relatively short & numerous (e.g., those lining trachea)
• a flagellum is relatively long and there's typically just one (e.g., sperm)

• Villi - projections of cell membrane that serve to increase surface area of a cell (which is important, for example, for cells that line the intestine)

DNA (Deoxyribonucleic acid) - controls cell function via transcription and translation (in other words, by controlling protein synthesis in a cell)

Transcription - DNA is used to produce mRNA

Translation - mRNA then moves from the nucleus into the cytoplasm & is used to produce a protein

• requires mRNA, tRNA (transfer RNA), amino acids, & a ribosome

tRNA molecule

Used with permission of John Kimball

• sequence of amino acids in a protein is determined by sequence of codons (mRNA). Codons are 'read' by anticodons of tRNAs & tRNAs then 'deliver' their amino acid.
• Amino acids are linked together by peptide bonds (see diagram to the right)
• As mRNA slides through ribosome, codons are exposed in sequence & appropriate amino acids are delivered by tRNAs. The protein (or polypeptide) thus grows in length as more amino acids are delivered.
• The polypeptide chain then 'folds' in various ways to form a complex three-dimensional protein molecule that will serve either as a structural protein or an enzyme.

COMPONENTS OF THE CELLULAR ENVIRONMENT

Water:

• comprises 60 - 90% of most living organisms (and cells)
• important because it serves as an excellent solvent & enters into many metabolic reactions

• found in both intra- & extracellular fluid
• examples of important ions include sodium, potassium, calcium, and chloride

• about 3% of the dry mass of a typical cell
• composed of carbon, hydrogen, & oxygen atoms (e.g., glucose is C6H12O6)
• an important source of energy for cells
• types include:
• monosaccharides (e.g., glucose) - most contain 5 or 6 carbon atoms
• disaccharides
• 2 monosaccharides linked together
• Examples include sucrose (a common plant disaccharide is composed of the monosaccharides glucose and fructose) & lactose (or milk sugar; a disaccharide composed of glucose and the monosaccharide galactose)
• polysaccharides
• several monosaccharides linked together
• Examples include starch (a common plant polysaccharide made up of many glucose molecules) and glycogen (commonly stored in the liver)

• about 40% of the dry mass of a typical cell
• composed largely of carbon & hydrogen
• generally insoluble in water
• involved mainly with long-term energy storage; other functions are as structural components (as in the case of phospholipids that are the major building block in cell membranes) and as "messengers" (hormones) that play roles in communications within and between cells
• Subclasses include:
• triglycerides - consist of one glycerol molecule + 3 fatty acids (e.g., stearic acid in the diagram below). Fatty acids typically consist of chains of 16 or 18 carbons (plus lots of hydrogens).

• phospholipids - a phosphate group (-PO4) substitutes for one fatty acid & these lipids are an important component of cell membranes
• steroids - include testosterone, estrogen, & cholesterol

• about 50 - 60% of the dry mass of a typical cell
• subunit is the amino acid & amino acids are linked by peptide bonds
• 2 functional categories = structural (proteins part of the structure of a cell like those in the cell membrane) & enzymes
• Enzymes are catalysts. Enzymes bind temporarily to one or more of the reactants of the reaction they catalyze. In doing so, they lower the amount of activation energy needed and thus speed up the reaction.

Used by permission of John W. Kimball

Nucleic Acids:

• DNA
• RNA (including mRNA, tRNA, & rRNA)

Movement Across Membranes

1 - Passive processes - require no expenditure of energy by a cell:

• Simple diffusion = net movement of a substance from an area of high concentration to an area of low concentration. The rate of diffusion is influenced by:
• concentration gradient
• cross-sectional area through which diffusion occurs
• temperature
• molecular weight of a substance
• distance through which diffusion occurs
• Osmosis = diffusion of water across a semipermeable membrane (like a cell membrane) from an area of low solute concentration to an area of high solute concentration (check rbl.cvmbs.colostate.edu/hbooks/cmb/cells/pmemb/osmosis.html for more information about osmosis)

• Facilitated diffusion = movement of a substance across a cell membrane from an area of high concentration to an area of low concentration. This process requires the use of 'carriers' (membrane proteins). In the example below, a ligand molecule (e.g., acetylcholine) binds to the membrane protein. This causes a conformational change or, in other words, an 'opening' in the protein through which a substance (e.g., sodium ions) can pass.

• Active transport = movement of a substance across a cell membrane from an area of low concentration to an area of high concentration using a carrier molecule

Active Transport: The Sodium-Potassium Pump
Used with permission of Gary Kaiser

• Endo- & exocytosis - moving material into (endo-) or out of (exo-) cell in bulk form

Used with permission of Gary Kaiser

Shown here is one way that active transport can occur. Initially, the membrane transport protein (also called a carrier) is in its closed configuration which does not allow substrates or other molecules to enter or leave the cell. Next, the substance being transported (small red spots) binds to the carrier at the active site (or binding site). Then, on the inside of the cell, ATP (Adenosine TriPhosphate) binds to another site on the carrier and phosphorylates (adds one of its phospate groups, or -PO4, to) one of the amino acids that is part of the carrier molecule. This attachment of a phosphate group to the carrier molecule causes a conformational change in (or a change in the shape of ) the protein so that a channel opens between the inside and outside of the cell membrane. Then, the substrate can enter the cell. As one molecule of substrate enters, the phosphate group comes off the carrier and the carrier again 'closes' so that no other molecules can pass through the channel. Now the transport protein, or carrier, is ready to start the cycle again. Note that as materials are transported into the cell, ATP is used up and ADP and -PO4 accumulate. More ATP must be made by glycolysis and the Kreb's cycle.

Characteristics of Facilitated Diffusion & Active Transport - both require the use of carriers that are specific to particular substances (that is, each type of carrier can 'carry' one type of substance) and both can exhibit saturation (movement across a membrane is limited by number of carriers & the speed with which they move materials; see graph below).

CELLULAR METABOLISM:

Cells require energy for active transport, synthesis, impulse conduction (nerve cells), contraction (muscle cells), and so on. Cells must be able to 'capture' and store energy & release that energy in appropriate amounts when needed. An important source of energy for cells is glucose (C6 H12O6):

However, this reaction releases huge amounts of energy (for a cell). So, cells gradually break down glucose in a whole series of reactions & use the smaller amounts of energy released in these reactions to produce ATP (Adenosine Triphosphate) from ADP (Adenosine Diphosphate). Then, cells can break down ATP (as in this reaction):

The energy released in this reaction is used by cells for active transport, synthesis, contraction, and so on. Cells need large amounts of ATP &, of course, must constantly make more. But, making ATP requires energy. The breakdown of glucose does release energy. But, how, specifically, is the energy released in the breakdown of glucose used to make ATP.

A primary source of ENERGY is OXIDATION. Specifically, cells use a type of oxidation called HYDROGEN TRANSFER to generate energy:

These hydrogen transfer reactions are so-named because pairs of hydrogens are 'transferred' from one substance (XH2 in the above reaction) to another (YH2 in the above reaction). Because the reactants (XH2 + Y) represent more energy than the products (X + YH2), this reaction releases energy.

In a cell, hydrogen transfer reactions occur in MITOCHONDRIA. Pairs of hydrogens are successively passed from one substance to another, and these substances are called HYDROGEN CARRIERS.

These hydrogen transfer reactions release energy that is used to make ATP from ADP (in other words, to add a third phosphate to adenosine diphosphate in a reaction called phosphorylation). So, what occurs in mitochondria involves hydrogen transfer (a type of oxidation) + phosphorylation, or, in other words, OXIDATIVE PHOSPHORYLATION. Oxidative phosphorylation produces lots of energy but requires hydrogen. Where do the hydrogens come from?

Sources of hydrogen include GLYCOLYSIS and the KREB'S CYCLE.

Glycolysis involves the breakdown of glucose. Cells obtain glucose from the blood. Blood glucose levels are maintained by the interaction of two processes: glycogenesis and glycogenolysis. Glycogenesis is the production of glycogen from  glucose and occurs (primarily in the liver and skeletal muscles) when blood glucose levels are too high (for example, after a meal).

Glycogenolysis is the reverse process - the breakdown of glycogen to release individual molecules of glucose. This occurs when blood glucose levels begin to decline (for example, several hours after a meal). The interaction of these two processes tends to keep blood glucose levels relatively constant.

Glucose taken up by cells from the blood is used to generate energy in a process called glycolysis.

In the first few steps of glycolysis, glucose is converted into fructose-1,6-diphosphate. These reactions, like all chemical reactions, involve making and breaking bonds between atoms, and this sometimes requires energy. Even though glycolysis, overall, releases energy, some energy must be added initially to break the necessary bonds and get the energy-producing reactions started. This energy is called activation energy. In the above diagram, energy (i.e., a molecule of ATP) is needed at steps 1 & 3. So, before the energy-producing reactions of glycolysis begin, a cell must actually use two molecules of ATP.

Overall, glycolysis can be summarized as:

So, glycolysis produces 2 direct ATP (ATP produced directly from the reactions that occur during glycolysis) and 6 indirect ATP (the 4 hydrogens produced in glycolysis will subsequently go through oxidative phosphorylation and produce 3 ATP per pair, i.e., 4 hydrogens equals 2 pair and 2 pair times 3 ATP equals 6 ATP). Thus, glycolysis produces a total of 8 ATP.

Next comes an intermediate step (called oxidative decarboxylation):

the 2 Pyruvic Acid are converted into 2 Acetyl CoA & this reaction produces 4 hydrogens (2 NADH₂). Those hydrogens (i.e., 2 pair of hydrogens) go through oxidative phosphorylation and produce 6 more ATP (2 pair @ 3 ATP per pair).

Finally, comes the Kreb's Cycle:

2 Acetyl CoA go through this cycle of reactions and produce 2 ATP (= GTP in the above diagram) + 16 hydrogens (6 NADH₂ + 2 FADH₂) plus the waste products carbon dioxide + water. The 16 hydrogens go through oxidative phosphorylation and produce 22 ATP [22 because 12 of these hydrogens (6 NADH₂) go completely through the reactions of oxidative phosphorylation and produce 18 ATP (6 pair @ 3 ATP per pair), while 4 of these hydrogens (2 FADH₂) go through only some of the reactions and produce 4 ATP (2 pair @ 2 ATP per pair).

Overall, therefore, the Kreb's cycle produces 24 ATP (2 direct & 22 indirect).

OVERALL ATP PRODUCTION from glucose = 8 (from glycolysis) + 6 (from the hydrogens produced when the 2 pyruvic acid are converted into 2 acetyl CoA) + 24 (from the Kreb's cycle) for a GRAND TOTAL OF 38:
 

Glucose (carbohydrates) are not the only source of energy for cells. Fats (or lipids), like triglycerides, are also metabolized to produce energy.

Triglycerides ----> Glycerol + Fatty Acids:

• Glycerol ----> Glyceraldehyde ----> Pyruvic Acid ----> Acetyl CoA ----> Kreb's Cycle
• Fatty Acids are converted into molecules of Acetyl CoA in a process called BETA OXIDATION.

This reaction not only produces lots of Acetyl CoA (or acetate) but lots of hydrogens. The Acetyl CoA goes through the Kreb's Cycle, while the hydrogens go through Oxidative Phosphorylation.
 

Proteins are also used as a source of energy.

Proteins are first broken down into amino acids. The nitrogen component of amino acids is then removed (in a reaction called DEAMINATION), and these deaminated amino acids are then converted into Acetyl CoA which passes through the Kreb's Cycle to make more ATP.

Related (and Useful) Links:

Cell Biology Topics

Cell Organelles

DNA Workshop: You Try It

What are cell organelles?

Macromolecules

Membrane Transport Mechanisms

Protein Synthesis

Cellular Organization

Tutorial: Cellular Respiration

Back to the BIO 301 syllabus
 

Lecture Notes 2 - Neurons & the Nervous System I

Lecture Notes 2b - Neurons & the Nervous System II

Lecture Notes 3 - Muscle

Lecture Notes 4 - Blood & Body Defenses I

Lecture Notes 4b - Blood & Body Defenses II

Lecture Notes 5 - Cardiovascular System

Lecture Notes 6 - Respiratory System