Unit 1: Biochemistry

Chapter 1: The Molecules of Life

Chapter 2: The Cell and its Components

Chapter 2: The Cell and Its Components Overview

Structures and functions of eukaryotic cells Organelles Cell membrane

The transport of substances across the cell membrane Diffusion Osmosis Active transport Membrane-assisted transport

Section 2.1: Structures and Functions of Eukaryotic Cells Animals, plants, fungi, and protists are

composed of eukaryotic cells All eukaryotic cells have these

characteristics: A membrane-bound nucleus that contains the

DNA A cell membrane composed of a phospholipid

bilayer The cell interior is filled with jelly-like cytoplasm,

which consists of everything outside the nucleus but within the cell membrane

The Nucleus The nucleus contains DNA, which replicates

the genetic information of the cell Each molecule of DNA in the nucleus

combines with an equal mass of protein to form a chromosome The number of chromosomes in the nucleus

varies from species to species Ex: Humans have 46 chromosome, while mosquitoes

have 6 Chromosomes are visible only in dividing cells In a non-dividing cell, chromatin represents the

unfolded state of chromosomes

The Endoplasmic Reticulum The nuclear envelope is connected to a

complex of membrane-bound tubules and sacs called the endoplasmic reticulum (ER)

The ER regions that synthesize proteins are studded with ribosomes, which are composed of proteins and RNA These regions are called rough endoplasmic reticulum

The rough ER ribosomes assemble proteins that become part of membranes or are exported from the cell Proteins that function in the cytosol, on the other hand,

are made by ribosomes that are freely suspended there.

The Endoplasmic Reticulum Regions of the ER that have no ribosomes

are called smooth endoplasmic reticulum The smooth ER synthesizes lipids and lipid-

containing molecules The smooth ER also performs other functions

depending on the type of cell Ex: In the liver, smooth ER helps detoxify drugs

and alcohol.

Ribosomes The ribosomes of eukaryotes have different

structures and mechanisms compared with those of prokaryotes

This is why antibiotics that kill bacteria cells do not harm the cells of the body Ex: Tetracycline is an antibiotic that inhibits

protein synthesis in prokaryotic ribosomes, but does not affect protein synthesis in human cells

The Endomembrane System: Protein Modification and Transport The endomembrane system acts to synthesize,

modify, and transport proteins and other cell products

It also compartmentalizes the cell so that particular functions are restricted to specific regions

This system consists of the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, and vesicles. The Golgi apparatus is a stack of curved membrane sacs

that packages, processes, sorts, and distributes proteins, lipids, and other substances within the cell

Vesicles are membrane-enclosed sacs used for transport and storage

Functions of the Endomembrane System The endomembrane system modifies and

transports proteins On the rough ER, polypeptides are produced

by bound ribosomes and are extruded into the lumen

The polypeptides travel through the lumen to the smooth ER, there they are stored and processed

When proteins are ready for transport, pieces of smooth ER pinch off to form vesicles containing the protein

Functions of the Endomembrane System Vesicles from the smooth ER travel across the cell

to the cis face (entry face) of the Golgi apparatus, where they merge with the membrane of the Golgi apparatus and release their contents into the interior

In the Golgi apparatus, some proteins are stored and others are modified further

When the modified proteins are ready for transport, pieces of the Golgi apparatus pinch off from the trans face (exit face) to form vesicles

These vesicles transport the proteins to the cell membrane, or to other destinations within the cell

Additional Functions of the Endomembrane System In animal cells, the Golgi apparatus also

produces lysosomes Membrane-enclosed sacs containing digestive

enzymes Lysosomes contain more than 40 enzymes that

catalyze hydrolysis reactions Break down macromolecules into smaller molecules Break down parts of the cell that are old or no longer

needed Break down bacteria and other foreign particles that

have been ingested by the cell The enzymes in lysosomes function best at the

acidic pH of around 5

Peroxisomes Peroxisomes are also membrane-enclosed

sacs containing enzymes, but they differ from lysosomes in two major ways: Lysosomes are produced by the Golgi apparatus,

while peroxisomes are produced by the endoplasmic reticulum.

Lysosome enzymes catalyze hydrolysis reactions, while peroxisome enzymes catalyze redox reactions (they are oxidases)

Peroxisomes Peroxisomes break down many biological

molecules and some toxic molecules Peroxisomes in some cells synthesize

molecules Many of the reactions that take place in

peroxisomes produce toxic hydrogen peroxide, H2O2

All peroxisomes contain the enzyme catalase, which breaks down hydrogen peroxide into water and oxygen gas.

Vesicle and Vacuoles “Vesicle” is used to

describe membrane-bound sacs used for the transport and storage of substances in the cell

Vesicles form by pinching off from cell membranes and organelle membranes

They can also fuse with cell membranes and organelle membranes to release their contents

Vesicles and Vacuoles Plant cells contain a

single large vesicle, called a vacuole

Stores water, ions, sugars, amino acids, and macromolecules

Also contains enzymes that break down macromolecules and cell wastes

Vesicles and Vacuoles The quantity of water in the vacuole

determines the turgor pressure, or internal pressure, of the plant cell

A full vacuole presses against the cell wall, making the cell rigid Source of rigidity in the flexible stems of

herbaceous plants. Without enough water, the vacuole will shrink

and pull away from the cell wall This is why unwatered plants wilt

Chloroplasts and Mitochondria Cells that perform photosynthesis contain one to

several hundred chloroplasts Chloroplasts contain the photosynthetic pigment

chlorophyll, which absorbs light energy as part of photosynthesis Photosynthesis converts carbon dioxide and water into

energy-rich organic molecules through redox reactions Chloroplasts are membrane-bound organelles

Filled with a thick liquid called stroma Stroma surrounds thylakoids, which contain chlorophyll

in their membranes A stack of thylakoids are called a granum (plural:

grana).

Chloroplasts and Mitochondria Mitochondria break down high-energy organic

molecules to convert stored energy into usable energy Provides the energy needed for all activities and

chemical reactions within the cell Mitochondria have a smooth outer membrane

and a folded inner membrane. The folds of the inner membrane are called cristae,

and the fluid-filled space in the inner membrane is called the matrix.

Both mitochondria and chloroplasts contain some of their own DNA, which encodes some of their own proteins

The Cell Wall and Cytoskeleton Cells of plants, fungi, and many types of protists

have a cell wall, which provides protection and support The composition varies with the type of cell, but it’s

usually a combination of polysaccharides, glycoproteins, or both

All cells contain an internal network of protein fibres called the cytoskeleton The fibres of the cytoskeleton extend throughout the

cytoplasm, providing structure and anchoring the cell membrane and organelles in place

Vesicles and organelles move along these fibres In some cells, cytoskeleton fibres form appendages

that enable the cell to propel itself

Cilia and Flagella Cilia and flagella are appendages that

develop on the outside of some eukaryotic cells

Composed of an internal shaft made of microtubules covered with an outer membrane that is a continuation of the cell membrane

Cilia and Flagella If there are just one or two longer

appendages, they are called flagella Flagella are like tails, and their whip-like

movement propels cells Ex: A human sperm cell has a single flagella

Cilia and Flagella If there are many shorter appendages,

they are called cilia In unicellular protists the wave-like motion of

cilia enable them to move In multicellular organisms, cells that line the

upper respiratory tract have cilia

The Cell Membrane All living cells exist in an aqueous medium

For a unicellular organism, this medium might be pond water

For the cells of a multicellular organism, the aqueous medium is the extracellular fluid that surrounds all cells

The contents of the cells are physically separated from the environment by the cell membrane Functions as a selective, dynamic cellular boundary Are incredibly thin If it fails to function properly, cellular processes fail

and the cell dies

The Cell Membrane Maintains the integrity of the cell by

regulating the passage of molecules and ions into and out of the cell

In the early 1900s researchers noticed that lipid-soluble molecules entered cells more rapidly than water-soluble molecules This led them to believe that lipids were a

component of cell membranes By 1925, chemical analysis had

demonstrated that phospholipids are a component of cell membranes and are arranged in a bilayer

The Cell Membrane The presence of lipids cannot account for all

properties of the cell membrane Ex: Some non-lipid molecules can pass through it

In the 1940s, researchers hypothesized that proteins are part of the membranes and proposed a model in which a phospholipid bilayer is sandwiched between two continuous layers of proteins This model was confirmed through electron

microscopy in the 1950s But a suitable model linking the structure and

properties of membranes to various functions remained elusive

The Cell Membrane In 1972, two American biologists, Jonathan

Singer and Garth Nicholson, proposed a model for membranes that remains in use today

They visualized proteins inserted into the phospholipid bilayer with their non-polar segments in contact with the non-polar interior of the bilayer and the polar portions protruding from the membrane surface

In this fluid mosaic model, an assortment of proteins and other molecules (in other words, “the mosaic”) floats in or on the fluid phospholipid bilayer

Features of the Fluid Mosaic Model According to the fluid mosaic model, each

layer of a membrane bilayer is composed of various macromolecules

Phospholipids act as the “scaffolding” in which proteins and other macromolecules are embedded

Membrane lipids are held together by weak intermolecular forces so the molecules in a membrane can move around freely If a puncture or tear occurs in a membrane,

molecules will quickly rearrange themselves to seal the rupture

Features of the Fluid Mosaic Model The lipid bilayer structure of membranes can

be explained based on chemical principles and the properties of phospholipids

A phospholipid molecule has a hydrophilic polar “head” and two hydrophobic non-polar “tails”.

When placed in water, phospholipids spontaneously form structures where the heads cluster together, facing the water molecules, while the tails are shielded from the water

Features of the Fluid Mosaic Model The heads interact with the water molecules

and each other using intermolecular interactions (ex: hydrogen bonding)

The tails are held together by hydrophobic interactions

The heads end up facing out and the tails face inward, away from the aqueous environment

The Fluidity of a Phospholipid Bilayer At room temperature, a phospholipid

bilayer has a viscosity similar to vegetable oil

This fluidity is an important property If it is too fluid, it permits too many

molecules to diffuse in and out of the cell If it is not fluid enough, it prevents too many

molecules from crossing

The Fluidity of a Phospholipid Bilayer The factors that affect fluidity include: Temperature

As temperature increases, the bilayer becomes increasingly fluid until it is unable to act as a barrier

As temperature decreases, the bilayer solidifies into a gel-like state

The Fluidity of a Phospholipid Bilayer Presence of double bonds in the fatty acid

“tails” Double bonds form “kinks” in a fatty acid tail that

cause fatty acids to be less tightly packed and more fluid

The Fluidity of a Phospholipid Bilayer Fatty acid “tail” length

Longer fatty acid tails have more intermolecular attractions and hold together more tightly, thus reducing fluidity

The most common tail length is 16-18 carbon atoms

The Fluidity of a Phospholipid Bilayer The presence of cholesterol

in cell membranes also affects fluidity

At room temperature and higher, cholesterol increases the intermolecular forces in the membrane and holds it more tightly together, thus reducing fluidity

At lower temperatures, cholesterol molecules break up the packing that occurs as phospholipids solidify into a gel, increasing fluidity

The Functions of Proteins in a Phospholipid Bilayer Two types of proteins are associated with

membranes: Integral proteins are embedded in the

membrane Peripheral proteins are more loosely and

temporarily attached to the outer regions of the membrane or to integral proteins

Peripheral proteins and some integral proteins help to stabilize membranes, and hold them in place by linking them with the cytoskeleton of the cell

The Functions of Proteins in a Phospholipid Bilayer Membrane proteins also determine the

function of the membrane by performing the following functions:

Transport Proteins play an essential role in transporting

substances across the cell membrane Reaction catalysis

Enzymes in cell membranes carry out chemical reactions

The Functions of Proteins in a Phospholipid Bilayer Cell recognition

The carbohydrate chains that protrude from glycoproteins on the outer layer of the cell membrane enable cells to “recognize” each other.

Signal reception and transduction Receptor proteins in cell membranes bind to signal

molecules and change shape as a result This initiates a cellular response to the signal,

enabling cells to receive and respond to signals from the brain and other organs

Section 2.2: The Transport of Substances Across a Cell Membrane The cell membrane can regulate the passage of

substances into and out of the cell, because it is semi-permeable

Processes that enable substances to move in and out of cells without an input of energy are referred to as passive transport

Some ions and molecules can move passively across the cell membrane easily because of a concentration gradient A difference between the concentration on the inside of

the membrane and the concentration on the outside of the membrane

Three types of passive transport are diffusion, osmosis, and facilitated diffusion

Passive Transport by Diffusion The net movement of ions and molecules

(i.e. solutes) from a region of higher concentration to a region of lower concentration is called diffusion

Net movement of the solutes will continue until the concentration is the same in all regions

Passive Transport by Diffusion In the context of cells, diffusion involves

differences in the concentration of solutes on either side of a cell membrane

The two factors that determine whether diffusion occurs across cell membranes are: Relative concentrations of the solutes inside and

outside the cell How readily a molecule or ion can cross the

membrane

Passive Transport by Diffusion The major barrier to crossing a biological

membrane is the hydrophobic interior that repels polar molecules (but not non-polar molecules)

If a concentration difference exists for a non-polar molecule, it will move across the membrane until the concentration is equal on both sides Movement in both directions still occurs, but

there is no net change in either direction

Passive Transport by Diffusion Factors that affect the rate of diffusion are: Molecule size

The larger the molecule, the more difficult it is for it to diffuse across a membrane

The rate of diffusion decreases as molecule size increases

Molecule polarity Small polar molecules diffuse across membranes more

slowly than non-polar molecules of the same size The rate of diffusion is lower for polar molecules

Molecule or ion charge Charged molecules and ions cannot diffuse across cell

membranes

Passive Transport by Diffusion Temperature and pressure can also affect

the rate of diffusion At higher temperatures, molecules have more

energy and can move faster, thus increasing the rate of diffusion

At higher pressures, molecules are forced across the membrane and the rate of diffusion increases

Passive Transport by Osmosis Movement of water molecules across biological

membranes is called osmosis Water molecules move because the membrane is

impermeable to the solute In order for osmosis to occur, solute

concentrations must differ on either side of the membrane

Water molecules move in or out of the cell, along the concentration gradient, until their concentrations on both sides of the membrane are equal At that time, water molecules continue to move in

and out, but there is no net movement of water.

Passive Transport by Osmosis The regulation of water entry is crucial to

cells The aqueous cytoplasm is a solvent for

cellular molecules and ions Cells must maintain enough water to enable

cellular processes Cells also interact with extracellular fluid,

the composition of which is constantly changing If too much water enters the cell, it swells If too much water leaves the cell, it shrinks Each response can affect the ability of a cell to

function

Passive Transport by Osmosis The concentration of all solutes in a

solutions determines its osmotic concentration

If two solutions have unequal osmotic concentrations: The solution with the higher solute

concentration is hypertonic (hyper = “more than”)

The solution with the lower solute concentration is hypotonic (hypo = “less than”)

When two solutions have the same osmotic concentration, they are isotonic (iso = “equal”)

Passive Transport by Facilitated Diffusion Many important molecules required by cells

cannot easily cross the plasma membrane These molecules can still enter the cell by

diffusion through specific channel proteins or carrier proteins embedded in the plasma membrane But there must be a higher concentration of the

molecule outside the cell than inside This process of diffusion that is mediated by a

membrane protein is called facilitated diffusion

Passive Transport by Facilitated Diffusion Channel proteins have a hydrophilic interior

that provides an aqueous channel through which polar molecules can pass when the channel is open

Carrier proteins, in contrast to channels, bind specifically to the molecule they assist, much like an enzyme binds to its substrate

Channel protein Carrier protein

Channel Proteins Channel proteins form highly specific channels

through the cell membrane The structure of a channel protein determines

which particles can travel through it. A channel protein has a tubular shape which is

composed of one or more helixes The exterior of a channel protein is usually

composed of amino acids with non-polar side chains that interact with the non-polar interior of the cell membrane, anchoring the protein in place

The shape and size of the hole through a channel protein determines the shape and size of particles that can pass through it

Channel Proteins Some channel proteins remain open all the

time Others have gates that the cell can open or

close to allow or prevent the passage of particles

Different types of gates open or close in response to a variety of signals, such as hormones, electric charge, pressure, or even light

In general, channel proteins permit the passage of ions or polar molecules

Carrier Proteins Carrier proteins bind to specific molecules,

transport them across the membrane, and then release them on the other side

Because they bind to the molecules they’re transporting, carrier proteins change shape while transporting molecules

Usually transport ions or small polar molecules, but can also transport larger molecules (ex: glucose)

They bind to only a few molecules at a time, so carrier proteins have lower rates of diffusion than channel proteins

Carrier Proteins The exterior of carrier proteins is usually

composed of non-polar amino acids that interact with the non-polar interior of the membrane

The interior of a carrier protein is lined with amino acids that can bind to the particle to be transported

Malfunctions in carrier proteins can cause a variety of diseases. Ex: Cystinurea is a hereditary disease caused by

the inability of carrier proteins to remove cystine and some other amino acids from urine

Active Transport: Movement Against a Concentration Gradient Diffusion, facilitated

diffusion, and osmosis are all passive transport processes that move substances down their concentration gradients

Cells can also actively move substances across a cell membrane against, or up, their concentration gradients

This process, called active transport, requires the expenditure of energy, usually from ATP

Active Transport: Movement Against a Concentration Gradient ATP (adenosine triphosphate) is the main

source of energy in the cell An ATP molecule is derived from an

adenosine nucleotide, but it has a triple phosphate group instead of a single phosphate group

Primary Active Transport Primary active transport uses ATP directly to

move molecules or ions from one side of a membrane to the other

Ion pumps are carrier proteins that use ATP to “pump” ions from one side of a membrane to the other, against a concentration gradient

One of the most well studied examples is the sodium-potassium pump This system transports sodium ions out of the cell

while transporting potassium ions into the cell Both processes occur against concentration

gradients, so this carrier protein requires ATP to function

Secondary Active Transport As an ion pump functions, a difference in charge (or

electric potential) builds up across the membrane. One side of the membrane gains a more positive or

negative charge compared to the other side, due to the accumulation of positive or negative ions

At the same time, a concentration gradient builds up across the membrane as the concentration of ions on one side increases compared to the other side

The combination of a concentration gradient and an electric potential across a membrane is called an electrochemical gradient This gradient stores potential energy that can be used

by the cell.

Secondary Active Transport Secondary active transport uses an

electrochemical gradient as a source of energy to transport molecules or ions across the cell membrane.

An example of secondary active transport is the hydrogen-sucrose pump

Membrane-Assisted Transport A cell can accumulate and excrete smaller

molecules and ions using membrane proteins Macromolecules, however, are too large to

cross the cell membrane through a channel or by means of a carrier protein

Instead, the cell forms vesicles to surround incoming or outgoing material and move it across the cell membrane through membrane-assisted transport This transport requires energy from the cell

The two forms are endocytosis and exocytosis

Endocytosis Endocytosis is the process by which a cell

engulfs material by folding the cell membrane around it and then pinching off to form a vesicle inside the cell

There are three methods of endocytosis: Phagocytosis Pinocytosis Receptor-mediated endocytosis

Endocytosis Phagocytosis occurs when the material the

cell takes in is made up of discrete particles, such as an organism or some other fragment of organic matter Phagocytosis literally means “cell-eating”

Pinocytosis occurs when the material the cell takes in is liquid Pinocytosis literally means “cell-drinking”

Virtually all eukaryotic cells constantly carry out these endocytotic processes, trapping particles and extracellular fluid in vesicles and ingesting them

Endocytosis Receptor-mediated endocytosis involves

the use of receptor proteins on a portion of a cell membrane that bind with specific molecules outside the cell

The area of the cell membrane containing receptor proteins is called a coated pit

The receptor proteins bind with molecules and the pit folds inward to form a vesicle

The contents of the vesicle may be used by the cell or digested by the cell, and the receptor proteins may be recycled by the cell membrane

Exocytosis Macromolecules and other

large particles can leave a cell by a process called exocytosis

In exocytosis, vesicles that contain cell products to be released, or waste material to be excreted, fuse with the cell membrane and empty their contents into the extracellular environment.

The vesicle itself becomes part of the cell membrane

Exocytosis In plant cells, exocytosis is an important

means of exporting through the cell membrane the materials needed to construct the cell wall

In animal cells, exocytosis provides a mechanism for secreting many hormones, neurotransmitters, digestive enzymes, and other substrates Ex: Specialized glands secrete sebum, which is

an oily substance that lubricates human skin, hair, and eyes

Ex: Cells in the intestines of animals secrete enzymes and acid to aid in the digestive process

Cellular Transport: A SummaryIs energy required for the mechanism to function?

Type of cellular transport mechanism

Primary direction of movement of substances

Essential related factor(s)

Examples of transported substances

No Diffusion Toward lower concentration

Concentration gradient

Lipid-soluble molecules, water, gases

No Facilitated diffusion

Toward lower concentration

Channel protein or carrier protein and concentration gradient

Some sugars and amino acids

Yes Active transport

Toward higher concentration

Carrier protein and energy

Sugars, amino acids, ions

Yes Endocytosis Toward interior of cell

Vesicle formation

Macromolecules

Yes Exocytosis Toward exterior of cell

Fusion of vesicle with cell membrane

Macromolecules