fundamental building blocks: chemistry, water, and ph

Copyright © 2009 Pearson Education, Inc., publishing as Pearson Benjamin Cummings.

BIOLOGYA GUIDE TO THE NATURAL WORLD

FOURTH EDITION

DAVID KROGH

Fundamental Building Blocks:Chemistry, Water, and pH

Chapter 2

Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.

Chemistry’s Building Block: The Atom

• All objects in the universe are made of matter (= anything that occupies space and has mass).

• The fundamental unit of matter is the atom.

• The three basic parts of an atom are:

1.protons (p+)

2.neutrons

3.electrons (e-)


Protons, Neutrons, and Electrons

• Protons have a positive (+) electrical charge, neutrons have no charge, and electrons have a negative (-) charge.

• Protons and neutrons exist in the atom’s nucleus, while electrons move around the nucleus.

Copyright © 2009 Pearson Education, Inc., publishing as Pearson Benjamin Cummings.Figure 2.2

electronshell

electron(negative charge)

proton(positive charge)

neutron(no charge)

nucleus

Hydrogen (H) Helium (He)


The Element

• An element is any substance that cannot be reduced to any simpler set of substances through chemical means.

• Each elem. is defined by the number of protons in its nucleus.

• An elem. has its own unique chemical properties.

• An atom is the smallest unit that retains the properties of a particular elem.


Matter is Transformed Through Chemical Bonding

• Atoms can link to one another through chemical bonding.

• When two or more atoms are linked together, it forms a molecule.

• Covalent bonds form when atoms share one or more pairs of e-’s.

• Ionic bonds can form when atoms gain or lose e-’s.


Formation of a Molecule

Figure 2.8

hydrogen (H)atom

hydrogen (H)atom

oxygen (O)atom

hydrogen (H)atom

hydrogen (H)atom

oxygen (O)atom

(b) One water molecule(a) Two hydrogen atoms and one oxygen atom


Covalent Bond

• Atoms of different elements differ in their power to attract e-’s.

• If the attraction of two atoms is similar, they can share e-’s equally, resulting in a nonpolar covalent bond

• The elec. charge is spread equally across the mol.


Polar Bonding

• If atoms attract e-’s differently, they can form a polar covalent bond

• The e-’s are not shared equally and “prefer” one atom over the other

• The mol. is polar (= one end is slightly pos. while another end is slightly neg.)


Ions

• An atom with equal numbers of p+’s and e-’s is neutral (= has no net charge because the pos. charges perfectly cancel out the neg. charges).

• But atoms can gain or lose one or more e-’s and become ions (the number of p+’s remains the same).

• Positive ions have lost e-’s and negative ions have gained e-’s.


Ions


Ionic Bonding

• The charge differences between pos. and neg. ions can link the ions together into a molecule.

• This type of attraction is an ionic bond.


Hydrogen Bonding

• H-bonds are not true chemical bonds because they do not form molecules

• Instead they help shape a mol. or attract 2 mol.’s together

• Hydrogen bonds form between a partially pos. hydrogen atom and a second partially neg. atom.

• H-bonds are very weak by themselves but, in large numbers, can be very strong.


Hydrogen Bonding

Figure 2.11

hydrogen bond


Water and Life

• Water is a polar mol. and has several qualities that strongly affect life on Earth.

1.Water is a powerful solvent, with the ability to dissolve polar and ionic substances in greater amounts than any other liquid.

• A solution is a uniform mixture of two or more kinds of molecules, atoms, or ions.

• The mol. dissolved in solution is the solute; whatever is doing the dissolving is the solvent.


Water’s Structure Gives It Many Unusual Properties

2. Because ice is less dense than liquid water, bodies of water do not freeze solid in winter.

• Allows life to flourish under the ice.

3. Water has a great capacity to absorb and retain heat.

• Because of this, the oceans act as heat buffers for the Earth, thus stabilizing Earth’s temperature, and the water in your cells does the same for your body.


Hydrophobic and Hydrophilic

• Non-polar molecules do not interact well with water and are called hydrophobic.

• Water cannot break down hydrophobic molecules (which is why oil and water don’t mix).

• Molecules that are polar or carry an electric charge will interact with water and are called hydrophilic.


Acids and Bases Are Important to Life

• Water (H2O) can dissociate (fall apart) into a hydrogen ion (H+) and a hydroxide ion (OH-)

• The pH scale measures the concentration of H+’s that a given solution has and determines how basic or acidic that solution is.

• This scale runs from 0 to 14, with 0 most acidic,14 the most basic (or alkaline), and 7 neutral.


Acids and Bases Are Important to Life

• An acid is any substance that yields H+ when put in a liquid solution.

• A base is any substance that accepts H+’s in solution.

• The pH of a solution (or cell or body) is very important, affecting the chemical reactions that can occur.


REMINDER

• Health/Safety regulations prohibit food and drink in lab classrooms, so please NO FOOD OR DRINK IN CLASS



FOURTH EDITION

DAVID KROGH

Life’s Components:Biological Molecules

Chapter 3


Molecules of Life

• Living cells produce several categories of biologically important molecules:

1.Carbohydrates

2.Lipids

3.Proteins

4.Nucleic acids


Why is Carbon Central to Life?

• Biol. import. mol.’s usually are organic (consisting primarily of carbon and hydrogen atoms) – water (H2O) is an exception (it’s import. but not organic).

• The carbon atoms bond covalently with up to four other atoms, often in long chains or rings called the carbon backbone of the mol.

• Attached to the backbone are a variety of functional groups (clusters of atoms that provide special properties to the mol.)


Functional Groups

Table 3.1


Structure and Function

• The three-dimensional shape of a molecule is important as it determines its function.

• If the shape of the mol. is altered/destroyed, so is its function.


Building Organic Molecules

• Complex organic mol.’s are often very large and are called macromolecules.

• Usually they are built by joining multiple sub-units, or monomers, into larger polymers.

1. Joining monosaccharides produces carbohydrates

2. Joining amino acids produces proteins

3. Joining nucleotides produces nucleic acids


Monomers vs. Polymers


Carbohydrates

• Functions:

1. Source of quick energy

2. Transportable/storable forms of energy

3. Structural components

• Simple sugars are monosaccharides used for a particular purpose

• Complex carbs, or polysaccharides, are polymers of monosacc.’s


Complex Carbohydrates

• Four polysaccharides are critical in the living world:

1.starch – stores energy in plants

2.glycogen – stores energy in animals

3.cellulose – used to build plant and algal cells

4.chitin – used to build fungi and some animal cells


Four Complex Carbohydrates

Figure 3.6

Starch Glycogen Cellulose Chitin

(a) (b) (c) (d)Potato Liver Algae Tick


Lipids• Lipids do not readily dissolve in water (= are

non-polar and hydrophobic).

• Functions include:

1. Store more energy than other types of molecules

2. Structural components

3. Used to build cell membranes

• Lipids are not built of monomers like other biological molecules.


Lipids

• Triglycerides have three fatty acid chains and comprise most of the fat in our diets

• Steroids have a core of four carbon rings and include cholesterol, testosterone, and estrogen

• Phospholipids have two fatty acid chains and a phosphate group; these form the outer membrane of cells

• Waxes are composed of a single fatty acid linked to a long-chain alcohol and are widely used as waterproofing and lubrication


The Triglyceride Tristearin

Figure 3.9

glycerolfatty acids


Steroids

Figure 3.12

testosterone

estrogen cholesterol

(a)

(b)

Four-ring steroid structure

Side chains make each steroid unique


Phospholipids

Figure 3.14

(a) Phospholipid structure

(b) Phospholipid orientation

variablegroup

phosphategroup

polar head nonpolar tails

phospholipids

oil (nonpolar)

water (polar)

“like attracts like”

polar hydrophilicheads exposed to water

nonpolar hydrophobictails (fatty acids) exposed to oil

—


Waxes

Figure 3.15


Proteins

• Proteins are an extremely diverse group of molecules composed of around 20 different amino acids.

• Sequences of amino acids are strung together to produce polypeptide chains, which then fold up into working proteins.

• Proteins are used in transportation, communication, and defense in the body and as structural units and enzymes.


Types of Protein

Table 3.3


Four Levels of Protein Structure• The primary structure is the order in which

amino acids join to form a polypeptide chain.

• The secondary struct. is formed by folding the prim. struct.

• The tertiary struct. forms by packing the sec. struct. more tightly.

• The quaternary struct. results from two or more tert. struct.’s joining together.

• The sec., tert., and quat. struct.’s are held by H – bonds.


Beginnings of a Protein

Figure 3.18

ala

ala

gln

gln

ile

ile

. . . produces a polypeptide chain like this:

A typical protein wouldconsist of hundreds ofamino acids

The linkage of several amino acids . . .


Levels of Protein Structure

Figure 3.20

Primary structure

Secondary structure

Tertiary structure

(a)

(b)

(c)

(d) Quaternary structure

amino acid sequence

beta pleated sheet

alpha helix

random coil

folded polypeptidechain

two or morepolypeptide chains

Four Levels of Structure In Proteins

The primary structure of any protein is simply its sequence of amino acids. This sequence determines everything else about the protein’s final shape.

Structural motifs, such as the corkscrew-like alpha helix, beta pleated sheets, and the less organized “random coils” are parts of many polypeptide chains, forming their secondary structure.

These motifs may persist through a set of larger-scale turns that make up the tertiary structure of the molecule

Several polypeptide chains may be linked together in a given protein, in this case hemoglobin, with their configuration forming its quaternary structure.


Why is Protein Structure So Important?

• Protein structure determines function.

• A single amino acid substitution can cause a serious change in function (e.g. sickle cell anemia).

• A protein can denature, or unfold and lose its 3-dimensional shape, altering/destroying its function.

• Denaturation can be caused by changes in pH or temperature and by exposure to certain chemicals (e.g. detergents).


Nucleic Acids

• Nucleic acids are polymers composed of nucleotides.

• DNA is a double – stranded molecule which encodes the genetic information of all living things.

• The information in the DNA molecule is converted into a second type of nucleic acid called RNA (which are single – stranded).

• Various types of RNA convert this information into proteins.


Nucleotide Functions

• Nucleotides can have other functions – some function in metabolism and others as chemical messengers.

• Perhaps the most important is ATP – a nucleotide with three attached phosphate groups.

• ATP is used as the “energy currency” in a cell.

• When a phosphate group is removed, it releases energy that the cell can use.


ATP as an Energy Source


Biological Molecules

Table 3.4



FOURTH EDITION

DAVID KROGH

Life’s Home:The Cell

Chapter 4


Cells are the Fundamental Units of Life

• The cell theory states:

1. The cell is the smallest unit that retains the properties of life.

2. Every form of life on Earth consists of one or more cells.

3. Cells only arise through the growth and division of pre-existing cells.


What is a Cell?

• All cells have a plasma membrane (PM), cytosol, DNA, and ribosomes.


What is a Cell?

• The PM is the boundary layer separating the inside of the cell from the outside environment.

• The cytosol is a jelly-like fluid filling the interior of the cell.

• DNA codes for the genetic info.

• Ribosomes are structures that produce proteins.


Plasma Membrane Structure (Ch. 5)

• The PM is composed of phospholipids, membrane proteins, and other molecules.

• Phospholipids have two fatty acid “tails” attached to a glycerol and phosphate “head”.

• The tails are hydrophobic (non-polar) but the head is hydrophilic (polar).


Plasma Membrane Structure (Ch. 5)

• The ph-lipids are arranged as a bilayer (two layers of ph-lipids with the heads facing away from each other).

• This is required because there is water both inside and outside of the cell.

• This ph-lipid bilayer portion of the PM controls what substances enter or leave the cell.


Plasma Membrane Structure


Membrane Proteins (Ch. 5)

• Structural prot.’s lie on the inner surface and give support to the cell’s components.

• Recognition prot.’s identify cells as “self” or “non-self”.

• Communication prot.’s allow signals to be sent between cells.

• Transport prot.’s help specific molecules cross the PM.

• Receptor prot.’s bind to specific mol.’s, which cause a response in the cell.


Plasma Membrane Structure


Prokaryotic Cells• All cells are classified as either prokaryotic or

eukaryotic.

• Prok. cells are the smallest and simplest cells.

• They lack organelles (internal structures made of membrane the divide the cell into smaller compartments).

• The DNA is floating in the cytosol, in an area called the nucleoid region.

• Prok. cells are found in single-celled organisms called bacteria and archaea.


Eukaryotic Cells

• Most types of living things (plants, animals, fungi, and protists) have euk. cells.

• Euk. cells are larger and more complicated than prok. cells.

• Most euk. organisms are multi-celled.

• Euk. cells contain organelles which allow different sets of chemical reactions to be isolated from one another.

• One of these organelles, the nucleus, contains the DNA.


Prokaryotic vs. Eukaryotic Cells

Figure 4.2

Prokaryotic cells Eukaryotic cells

DNA

Size

Organization

Organelles

in “nucleoid” regionwithin membrane-bound

nucleus

much smaller much larger

always single-celled often multicellular

no organelles many types of organelles


The Eukaryotic Cell

• There are five principal components to the euk. cell:

1. the cytosol

2. the PM

3. the nucleus

4. other organelles

5. the cytoskeleton


The Eukaryotic Cell

Figure 4.4

nuclear envelope

nuclear poresDNA

nucleolus

nucleussmooth endoplasmic

reticulum

free ribosomes

cytosol

mitochondria

lysosomes

Golgi complex

plasma membrane

transport vesicle

rough endoplasmic

reticulum

cytoskeleton


The Nucleus

• The nucleus is formed by two layers of membrane (= two ph-lipid bilayers), called the nuclear envelope.

• Information for the construction of proteins is contained in the DNA and passes out through small openings (nuclear pores) into the cytosol.

• The nucleus controls the functions of the rest of the cell.


The Nuclear Envelope


The Rough ER

• Proteins are produced by ribosomes, some of which lie in the cytosol while others are attached to the rough endoplasmic reticulum (ER).

• The rough ER takes the “raw” polypeptide chains from the ribosomes and begins to edit them into proteins.

• Once the rough ER has finished, the proteins leave in small sacs of membrane called vesicles.


The Rough ER


The Golgi Complex• Once protein processing is finished in the

rough ER, vesicles move the proteins to the Golgi complex.

• Here, they are processed further and marked for shipment to other locations.

• Together, the rough ER, vesicles, and Golgi complex make up the endomembrane system, a series of membrane-bound structures used in transport.

• In addition to transporting substances, vesicles can also be used for storage.


The Golgi Complex

Figure 4.8

cisternalspace

cisternae

Transport vesicle fromRER fuses with Golgi

Protein undergoesmore processingin Golgi

Proteins aresorted and shipped…

to cytosol

for exportout of cell

Side chains are edited (sugars may be trimmed, phosphate groups added). to plasma

membrane

vesicle

Golgi complex

1.

2.

3.


Smooth ER

• In addition to the rough ER, a cell has smooth ER which does not have attached ribosomes and so is not involved with protein production.

• The smooth ER is a network of membranes that synthesize lipids and help detoxify potentially harmful substances.


Mitochondria

• Mitochondria are the “powerhouses” of the cell.

• They extract energy from organic compounds (= food) through the process of cellular respiration.

• This energy is then transformed into a chemical form the cell can use (= ATP).


Mitochondria

Figure 4.10

Mitochondrion

foodoxygen

watercarbon dioxideATP

outermembrane

innermembrane


Chloroplasts

• Plants and some protists have an organelle not found in other euk. cells: the chloroplast.

• Chloroplasts are used to capture the energy from the sun through the process of photosynthesis.

• This solar energy is used to build complex carbohydrates which serve as a food supply for the cell.


Chloroplasts

Figure 4.18

sugar (food) oxygen

outer membrane

inner membrane

watercarbon dioxide

minerals


The Cytoskeleton

• The cytoskeleton is a network of protein filaments stretching throughout the cytosol.

• It functions in:

1. cell structure

2. cell movement

3. the transport of materials within the cell.


The Cell Wall

• All plant cells and most fungi, prokaryote, and protist cells (but NOT animal cells) have a cell wall.

• This is much thicker layer of material outside of the PM.

• The cell wall gives the cell structural strength and helps regulate the intake and retention of water.


Structures in Plant and Animal Cells

Table 4.1


The Animal Cell

Figure 4.2


The Plant Cell

Figure 4.16

nuclear envelopenuclear pores

nucleolus

nucleus

plasma membrane

cytoskeleton

smooth endoplasmic reticulum

rough endoplasmic reticulum

free ribosomes

cytosol

chloroplast

mitochondrion

cell wall

centralvacuole

DNA

Golgi complex

Plant cells have a cell wall, chloroplasts, and a central vacuole, while animal cells do not.

fundamental building blocks: chemistry, water, and ph

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