Cells and genomes; Macromolecules

The building blocks of carbohydrates are called Monosaccharide

Glycine is an amino acid, not a carbohydrate.
The major job of the ribosome is to make proteins.
The chemical union of the basic units of carbohydrates, lipids, or proteins always produces the by-
product WATER, through the process known as a dehydration reaction.
DNA is a double-stranded compound that contains a five-carbon sugar and the bases adenine,
guanine, cytosine and thymine.
Protein does not belong to the group. Fats, oils, and steroids are lipids.
Glucose and fructose combine to form the disaccharide sucrose, the table sugar.
The Golgi apparatus functions to package and deliver proteins.
Centrioles are found in animal cells and are used in cell division; the spindle fibers attach to it.
Cell organelles are located within the cytoplasm of the cell.
Phospholipids have two hydrophobic tails and one hydrophilic head.
Unsaturated fatty acid has one or more double bonds.
Macromolecules (polymers) are formed from the individual subunits (monomers) through
DEHYDRATION REACTION.
CH2O is a generalized structure of a monosaccharide.

A polymer is a long molecule consisting of many similar building blocks.

These small building-block molecules are called monomers.
A dehydration reaction occurs when two monomers bond together through the loss of a water
molecule.
Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of
the dehydration reaction.
Proteins
A protein is a biologically functional molecule that consists of one or more polypeptides.
Polypeptides are unbranched polymers built from the same set of 20 amino acids.
Amino acids are organic molecules with carboxyl and amino groups.
Amino acids differ in their properties due to differing side chains, called R groups.

4 Levels of Protein Structure

The complete structure of a protein can be described at four different levels of complexity:  primary,
secondary, tertiary, and quaternary structure. A protein's primary structure is defined as the amino
acid sequence of its polypeptide chain; secondary structure is the local spatial arrangement of a
polypeptide's backbone (main chain) atoms; tertiary structure refers to the three-dimensional
structure of an entire polypeptide chain; and quaternary structure is the three-dimensional
arrangement of the subunits in a multisubunit protein.

Difference between α-helix and a β-pleated sheet

Alpha helix and beta plates are two different secondary structures of protein. Alpha helix is a right
handed-coiled or spiral conformation of polypeptide chains. In alpha helix, every backbone N-H
group donates a hydrogen bond to the backbone C=O group, which is placed in four residues prior.
Here, hydrogen bonds appear within a polypeptide chain in order to create a helical structure. Beta
sheets consist of beta strands connected laterally by at least two or three backbone hydrogen
bonds; they form a generally twisted, pleated sheet. In contrast to the alpha helix, hydrogen
bonds in beta sheets form in between N-H groups in the backbone of one strand and C=O
groups in the backbone of the adjacent strands.

α-helix
A rod-like structure
Helical backbone is held together by hydrogen bonds between the backbone amides of an n and n +
4 amino acids.
β-pleated sheet
Sheet-like arrangement
Side chains protrude from the sheet, alternating in an up-and-down direction

TERTIARY PROTEIN STRUCTURE (3o)

”whole molecule folding”
- interactions between distant amino acids
- hydrophobic interactions
- cytoplasm is water-based
- nonpolar amino acids cluster away from water
- H bonds & ionic bonds ¡ disulfide bridges
- covalent bonds between sulfurs in sulfhydryls (S–H)

QUATERNARY PROTEIN STRUCTURE (4o)

A quaternary structure is formed by the assembly of individual polypeptides into a larger functional
cluster.
FUNCTIONS OF PROTEINS
Enzymatic proteins
Function: Selective acceleration of chemical reactions
Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules.

Storage proteins
Function: Storage of amino acids
Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants
have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid
source for the developing embryo.

Hormonal proteins
Function: Coordination of an organism’s activities
Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration

Contractile and motor proteins

Function: Movement
Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin
proteins are responsible for the contraction of muscles.

Defensive proteins
Function: Protection against disease
Example: Antibodies inactivate and help destroy viruses and bacteria.

Transport proteins
Function: Transport of substances
Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the
lungs to other parts of the body. Other proteins transport molecules across cell membranes.

Receptor proteins
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by
other nerve cells.

Structural proteins
Function: Support
Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins
provide a fibrous framework in animal connective tissues.

Loss of structural integrity with accompanying loss of activity is called denaturation.

Proteins can be denatured by:
• heat or cold • chaotropic agents: urea and guanidinium
• pH extremes hydrochloride
• organic solvents
Membrane Structure

The presence of cholesterol in the plasma membranes of some animals: enables the membrane to
stay fluid more easily when cell temperature drops.
Cell membrane does not contain digestive enzymes.
CELL MEMBRANE - Gateway to the Cell

- Who proposed that the membranes are a phospholipid bilayer between two layers of hydrophilic
proteins? Davson and Daniellie
- Of the following functions, which is most important for the glycoproteins and glycolipids of animal
cell membranes? a cellʹs ability to distinguish one type of neighboring cell from another 
- When biological membranes are frozen and then fractured, they tend to break along the middle
of the bilayer. The best explanation for this is that: the hydrophobic interactions that hold the
membrane together are weakest at this point.
- According to the fluid mosaic model of cell membranes, which of the following is a true statement
about membrane phospholipids? They can move laterally along the plane of the membrane.
- Fluid mosaic model of the plasma membrane was proposed by: Singer and Nicolson
- When a membrane is freeze-fractured, the bilayer splits down the middle between the two layers
of phospholipids. In an electron micrograph of a freeze-fractured membrane, the bumps seen on
the fractured surface of the membrane are: integral proteins
- Cholesterol decreases fluidity at high temperatures and increases fluidity at low temperatures.

Sandwich Model (Danielli + Davson)

2 layers of globular proteins with phospholipid inside to make a layer and then join 2 layers together
to make a channel for molecules to pass

Unit Membrane Model (Robertson)

Outer layer of protein with phospholipid bilayer inside, believed all cells same composition, does not
explain how some molecules pass through or the use of proteins with nonpolar parts, used
transmission electron microscopy

Fluid Mosaic Model (Singer + Nicolson)

Phospholipid bilayer with proteins partially or fully imbedded, electron micrographs of freeze-
fractured membrane

Which membrane model is correct according to the electron micrograph? Fluid-Mosaic Model
The Plasma Membrane is composed of two layers of lipids.
- Having lipids in the plasma membrane means that at least a portion of the membrane repels the
water that constantly surrounds it. Allowing too much water inside the cell could cause the cell to
burst.
Fluid – the plasma membrane has the consistency of olive oil at body temperature, due to
unsaturated phospholipids.
Mosaic – membrane proteins form a collage that differs on either side of the membrane and from cell
to cell (greater than 50 types of proteins), proteins span the membrane with hydrophilic portions
facing out and hydrophobic portions facing in.

The phospholipids in the plasma membrane are arranged in two layers, called a phospholipid
bilayer, with a hydrophobic, or water-hating, interior and a hydrophilic, or water-loving,
exterior. Each phospholipid molecule has a head and two tails.

Phospholipid Bilayer
 Lipids
– Organic compounds
– Fats + Oils – Non-polar
– Insoluble in water (Not attracted to water)
 Phosphate Head
– Polar
– Water-soluble (Attracted to water)
Do you “love” or “fear” water?
 In water, phospholipids spontaneously form a stable two-layer sheet called a phospholipid bi-layer
QUESTION:
• Most cells have a watery internal and external environment. Given this information, how might you
expect the phospholipids to be arranged?

Amphipathic Lipids Spontaneously Form Micelles or Bilayers

•Shape of lipid determines packing of lipid molecules Micelle and Bilayer Formation is an Entropy-Driven
Process
Structure and Functions of the Plasma Membrane
• NOT just a barrier surrounding the cell.
– Selectivity
– Molecular recognition
– Export of wastes and cell products
– Import of nutrients
– Ability to change in response to environment
 The glycocalyx is formed by oligosaccharides of glycolipids and transmembrane glycoproteins.
 Selectins are cell adhesion molecules that recognize oligosaccharides exposed on the cell surface.
 The Outer Leaflet of the Membrane is Rich in Carbohydrates
 The carbohydrate-rich outermost face of the membrane is the glycocalyx
 Glycocalyx function is still poorly defined, but is believed to work in protecting cells, attaching cells
to the ECM and in cell recognition.
Membrane Movement and Cholesterol

 Most of the lipids and some proteins drift laterally on either side. Phospholipids do not switch from
one layer to the next.
 Cholesterol affects fluidity: at body temperature it lessens fluidity by restraining the movement of
phospholipids, at colder temperatures it adds fluidity by not allowing phospholipids to pack close
together.
Cholesterol in lipid bilayer

•The Planar Rings of Cholesterol Make the Membrane More Rigid, Less Permeable, and Resistant to Low
Temperature Crystallization

• Animal cells have cholesterol in the bilayer – Cholesterol is not found in plant membranes

The lipids and proteins in the cell membrane are not fixed in position but constantly moving.

• The proteins move laterally within the cell membrane – lateral diffusion

• While the lipids can move both laterally and rotate 360 degrees – flipflop diffusion

THE MEMBRANE PROTEINS

• Peripheral membrane proteins are proteins that dissociate from the membrane following treatments
with polar reagents that do not disrupt the phospholipid bilayer.

• Integral membrane proteins can be released only by treatments that disrupt the phospholipid bilayer.

• Transmembrane proteins span the lipid bilayer with portions exposed on both sides of the membrane.

Types of Membrane Proteins

1) Transport Proteins
Channel Proteins – channel for lipid insoluble molecules and ions to pass freely through
Carrier Proteins – bind to a substance and carry it across membrane, change shape in process
2) Receptor Proteins – Bind to chemical messengers (Ex. hormones) which sends a message into
the cell causing cellular reaction
3) Enzymatic Proteins – Carry out enzymatic reactions right at the membrane when a substrate
binds to the active site
4) Cell Recognition Proteins – Glycoproteins (and glycolipids) on extracellular surface serve as ID
tags (which species, type of cell, individual). Carbohydrates are short branched chains of less
than 15 sugars
5) Attachment Proteins - Attach to cytoskeleton (to maintain cell shape and stabilize proteins)
and/or the extracellular matrix (integrins connect to both).
 - Extracellular Matrix – protein fibers and carbohydrates secreted by cells and fills the spaces
between cells and supports cells in a tissue.
- Extracellular matrix can influence activity inside the cell and coordinate the behavior of all the
cells in a tissue.
6) Intercellular Junction Proteins
– Bind cells together
–Tight junctions
–Gap junctions

Types of Cell Junctions

Tight Junctions
• Transmembrane Proteins of opposite cells attach in a tight zipper-like fashion
• No leakage Ex. Intestine, Kidneys, Epithelium of skin
Desmosomes
• Cytoplasmic plaques of two cells bind with the aid of intermediate filaments of keratin
• Allows for stretching
• Ex. Stomach, Bladder, Heart
Gap Junctions
• Channel proteins of opposite cells join together providing channels for ions, sugars, amino acids, and
other small molecules to pass.
• Allows communication between cells.
• Ex. Heart muscle, animal embryos
Major Membrane Phospholipids
 Phosphatidyl-ethanolamine
 Phosphatidyl- serine
 Phosphatidyl- choline
 Sphingo – myelin
Structure of lipid rafts
 Phosphatidylcholine -- glycerol phospholipid with a head group formed from choline.
 Phosphatidylethanolamine -- glycerol phospholipid with a head group formed from
ethanolamine.
 Phosphatidylserine -- glycerol phospholipid with a head group formed from serine.
 Sphingomyelin -- phospholipid consisting of two hydrocarbon chains bound to a polar head
group containing serine.
 The fluid mosaic model of membrane structure is now generally accepted as the basic paradigm
for the organization of all biological membranes.
 Phosphatidylinositol is a phospholipid localized to the inner half of the plasma membrane,
which plays an important role in cell signaling.
 Glycolipids are lipids consisting of two hydrocarbon chains linked to a polar head group
containing carbohydrates.
 Cholesterol, a lipid consisting of four hydrocarbon rings, is a major membrane constituent of
animal cells.
A Scheme to Study a Membrane Protein – Solubilization, Purification, and Reconstitution in Liposomes
  Membrane Proteins Can Be Solubilized by Detergents That Disrupt the Membrane
 Solubilization typically is the first step in the purification or biochemical characterization of
membrane proteins.
 Because of this requirement, membrane proteins are notoriously difficult to work with.

Mobility of Membrane Proteins

 Lipid composition can perturb the free diffusion of membrane proteins.
 The basolateral domain is the surface region of a polarized epithelial cell that is in contact with
adjacent cells or the extracellular matrix.
 The apical domain is the exposed free surface of a polarized epithelial cell

Membrane function
Learning objectives:

 Identify the factors that influence the passage of substances across the plasma membrane
 Define the law of diffusion
 Explain passive transport
 Differentiate simple diffusion from facilitated diffusion
 Explain osmosis
 Discuss active transport

Permeability of the Plasma Membrane

 Differentially (selectively) Permeable

- Allows some materials to pass.
 Water, Oxygen, Carbon dioxide
- Prevents others from passing
 Proteins, carbohydrates
 Factors that determine how a substance may be transported across a plasma membrane:
- Size
- Polar or Nonpolar

Permeability of Phospholipid bilayer

 The internal composition of the cell is maintained because the plasma membrane is selectively
permeable to small molecules.
 Only small, relatively hydrophobic molecules are able to diffuse across a phospholipid bilayer at
significant rates by using passive diffusion.

Factors affecting permeability of cell membrane to a particular substance:

• molecular size of the substance: cell membrane generally is permeable to small molecules such as
water (H2O), carbon dioxide (CO2), glucose (C6H12O6) and amino acids
• electrical charge on the atom or molecule of the substance
• solubility of the substance in water
• solubility of the substance in lipid
Cell membrane is the boundary between inside & outside… – separates cell from its environment
Can it be an impenetrable boundary? No

• Gases (oxygen, carbon dioxide)

• Water molecules (rate slow due to polarity)
• Lipids (steroid hormones)
• Lipid soluble molecules (hydrocarbons, alcohols, some vitamins)
• Small noncharged molecules (NH3)

Facilitated Diffusion
• Diffusion through protein channels
– channels move specific molecules across cell membrane – no energy needed
• Cells obtain food for cell respiration
• Neurons communicate
• Small intestine cells transport food to bloodstream
• Muscle cells contract
– Osmosis is the diffusion of water across a differentially permeable membrane.
– Osmotic pressure is the pressure that develops in a system due to osmosis.
– Hypertonic - more solute, less water
– Hypotonic - less solute, more water
– Isotonic - equal solute, equal water
• Cell survival depends on balancing water uptake & loss
The Importance of Active Transport
• Bring in essential molecules: ions, amino acids, glucose, nucleotides
• Rid cell of unwanted molecules (Ex. sodium from urine in kidneys)
• Maintain internal conditions different from the environment

ACTIVE TRANSPORT
Active transport can be classed into 2 groups;
1. PRIMARY ACTIVE TRANSPORT
2. SECONDARY ACTIVE TRANSPORT

Vesicle Formation- moving things out.

Endocytosis - Vesicles form as a way to transport molecules into a cell
– Phagocytosis: Large,particulate matter (Bacteria, viruses, and aged or dead cells).
-- Pinocytosis: Liquids and small particles dissolved in liquid
– Receptor Mediated Endocytosis: Ligandreceptor complexes trigger infolding of a clathrin- coated pit
that forms a vesicle containing ligands ( low density lipoproteins (LDLs); some vitamins, certain
hormones, and antibodies.

-A patient has had a serious accident and lost a lot of blood. In an attempt to replenish body fluids,
distilled water, equal to the volume of blood lost, is transferred directly into one of his veins. What will
be the most probable result of this transfusion?

The patientʹs red blood cells will swell because the blood fluid is hypotonic compared to the cells.
-Which of the following would most likely move through the lipid bilayer of a plasma membrane more
rapidly? Carbon dioxide
-In receptor-mediated endocytosis, receptor molecules initially project to the outside of the cell. Where
do they end up after endocytosis? on the inside surface of the vesicle
-Which of the following statements is correct about simple diffusion? it is a passive process in which the
molecules move from an area of higher concentration to lower concentration
-Water quickly passes through the plasma membrane because: it moves through aquaporins in the cell
membrane
-Celery stalks that are immersed in fresh water for several hours become stiff and hard. Similar stalks left
in a salt solution become limp and soft. From this, we can deduce that the cells of the celery stalks are:
hypertonic to fresh water but hypotonic to the salt solution.
-Which transport mechanism is most probably functioning in the intestinal cells? facilitated diffusion
Several seriously epidemic viral diseases of earlier centuries were then incurable because they resulted
in severe dehydration due to vomiting and diarrhea. Today they are usually not fatal because we have
developed which of the following? hydrating drinks that include high concentrations of salts and glucose