Biol 213 Cell Structure and Function

Instructor: Dr. Fondufe Email: gfondufe@gmu.edu

Course coordinator: Dr. Christensen Email: achriste@gmu.edu

iClicker Registration

Go to: www.iclicker.com/registration

Your student ID is your GMU email username (Example: gfondufe)

Chapter 2 The Chemical Context of Life

Hierarchy of biological organization

Atomic Molecular Organelle Cellular Tissue Organ Organ System Organism Higher Levels Carbon, hydrogen, oxygen DNA, proteins Nucleus, mitochondria, etc. Metabolism, cell signaling Smooth muscle, bone, etc. Heart, brain, liver, etc. Circulatory, digestive, etc. Mouse, human, maize Ecosystems, populations

Fig. 1.4 Exploring levels of Biological Organization

The biosphere Cells
10 m Organs and organ systems

Cell

Ecosystems Organelles Communities

1 m

Atoms

Tissues Populations Organisms

50 m

Molecules

Cell Biology
Cell

Smallest unit that can carry out all the activities required for the life of an organism

Cell Biology
Cell Properties / Organism Properties
Ability to reproduce Ability to grow Ability to process energy Ability to respond to the environment

Cell Biology
Organisms are composed of cells

Some are unicellular single cell

Some are multicellular multiple cells

Cell Biology
Multicellular Organism
Starts as a single cell (zygote)
Reproduces by division (mitosis)

Cells differentiate
Have different form and/or properties

Cell Biology

Cells may appear different, but they have many similarities

Cell Biology
In Cell Biology, we will be examining the many similarities (and some differences) of cells the similarities that make up the common STRUCTURAL and FUNCTIONAL properties of cells

Cell Biology
Biology - Study of life, living things
Biology is a multidisciplinary science Cell Biology - Study of cells To understand structure and function of cells, we need a basic understanding of Chemistry

Basic Chemistry for Cell Biologists

Matter
Composed Elements and Compounds Elements required by living organisms Atomic structure Chemical bonding Chemical reactions

Basic Chemistry -Matter

Matter
Anything which takes up space and has mass Composed of elements Exists in many forms Rock, wood, water, air, plastic, human, etc

Basic Chemistry - Matter

Element Substance which cannot be broken down into other substances by chemical means 92 natural elements + ~20 man-made

Has a symbol usually 1 or 2 letters of its name (may be derived from Latin or German)
H = Hydrogen He = Helium

Na = Sodium (Natrium) Fe = Iron (Ferrum)

Basic Chemistry - Matter

Compound
Substance consisting of two or more elements combined in a fixed ratio

Examples:
Water: H2O = 2 Hydrogen : 1 Oxygen

Table salt: NaCl = 1 Sodium : 1 Chlorine

Basic Chemistry - Matter

A compound has characteristics beyond those of its combined elements emergent properties Example:

Table salt: NaCl = 1 Sodium : 1 Chlorine

Sodium - very reactive (explosive) metal

Chlorine - poisonous gas

Combined = edible compound

Basic Chemistry for Cell Biologists

Matter
Elements and Compounds

Elements required by living organisms Atomic structure Chemical bonding Chemical reactions

Basic chemistry Elements Required for Life

Number required by living organisms
Only about 25 of 92 natural elements 96% of living matter composed of: Carbon, Hydrogen, Oxygen, Nitrogen Other 4% composed of:

Phosphorus, Sulfur, Calcium, Potassium, others

Table 2.1 Naturally Occurring Elements in the Human Body

Symbol Element % (by body weight) Elements that make up 96% of the human body O Oxygen 65 C Carbon 18.5 H Hydrogen 9.5 N Nitrogen 3.3

Elements that make up about 4% of the human body Ca Calcium 1.5 P Phosphorus 1.0 K Potassium 0.4 S Sulfur 0.3 Na Sodium 0.2 Cl Chlorine 0.2 Mg Magnesium 0.1
Copyright 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Basic Chemistry - Trace Elements

Trace Elements required only in very small quantities
Examples: Iron (Fe) hemoglobin, other proteins Iodine (I) thyroid hormone

Fig. 2.4b Goiter due to iodine deficiency

Iodine - thyroid hormone a daily intake of 0.15 mg of iodine is required for normal activity of the human thyroid gland

Basic Chemistry for Cell Biologists

Matter Elements and Compounds Elements required by living organisms Atomic structure Chemical bonding Chemical reactions

Basic Chemistry - Atomic Structure

Atomic structure determines behavior of element Atoms combine by chemical bonding to form molecules

Weak chemical bonds are important

Shape of molecule is related to function

Chemical reactions make and break bonds

Basic Chemistry - Atomic Structure

Atom Smallest unit of matter that still retains properties of an element

Basic Chemistry - Atomic Structure

Atom Composed of three types of particles Neutrons Protons Electrons - no electrical charge - positive electrical charge (+1) - negative electrical charge (-1)

Basic Chemistry - Atomic Structure

Atom Neutrons and Protons Packed together in dense core Atomic Nucleus Electrons Located in a cloud or shell around the nucleus Attracted to nucleus by positively charged protons

Basic Chemistry Atomic structure

Fig. 2.5 Models of a Helium (He) atom
Cloud of negative charge (2 electrons) Nucleus 2 protons 2 neutrons Electrons

(a)

(b)

Basic Chemistry - Atomic Structure

Nucleus Small in comparison to entire atom (5/1000) Electrons orbit at a distance from nucleus Accounts for nearly all of the weight Protons + neutrons (electron weight is negligible) Neutrons & protons - about the same mass ~1 dalton (~1.7 x 10-24g) After John Dalton, a British scientist

Basic Chemistry - Atomic Structure

Atomic Number Number of protons in an atom Unique for each element Written as a subscript to left of chemical symbol 2He, 8O, 16S, 26Fe

Number of protons and electrons are generally the same - no net charge

Basic Chemistry - Atomic Structure

Mass Number Number of protons and neutrons Written as a superscript to left of chemical symbol - 4He, 16O, 32S, 55Fe Atomic Weight approximately the mass number proton and neutron each 1 dalton

4He has a mass number of 4

estimated atomic weight of 4 daltons (4.003)

Basic Chemistry - Atomic Structure

Number of Neutrons No. of protons = Atomic Number No. of protons and neutrons = mass number

Mass number - Atomic Number = Number of neutrons

Basic Chemistry - Atomic Structure

Number of Neutrons
Can the number of neutrons vary in atoms of an element?

Basic Chemistry - Atomic Structure

Yes! Number of Neutrons may vary!
Isotopes - different numbers of neutrons Carbon - 12C - 6 protons + 6 neutrons
13C 14C

- 6 protons + 7 neutrons - 6 protons + 8 neutrons

Basic Chemistry - Atomic Structure

Isotopes Stability of an isotope Unstable (radioactive) breaks down (decays) and loses particles

12C and 13C are stable 14C is unstable (radioactive isotope)

Basic Chemistry - Atomic Structure

Radioactive Isotopes Useful in scientific research and medicine Tracing atoms through metabolic processes Diagnosing medical disorders Also useful in dating fossils Unfortunately, they pose a hazard to life Decay particles damage cellular molecules
From nuclear reactor accidents or a dirty bomb

Fig. 2.6 Using Radioactive Isotopes

Compounds including Incubators radioactive tracer 1 3 2 (bright blue) 20C 10C 15C Human cells
1 Human 4 25C 7 40C 5 30C 8 45C 6 35C 9 50C

cells are incubated with compounds used to make DNA. One compound is labeled with 3H.
2 The cells are

DNA (old and new)

placed in test tubes; their DNA is isolated; and unused labeled compounds are removed.

Fig. 2.6 Using Radioactive isotopes

3 The test tubes are placed in a scintillation counter.

Fig. 2.6 Using Radioactive Isotopes

Counts per minute ( 1,000)

30 20 10 0

Optimum temperature for DNA synthesis

10

20 30 40 50 Temperature (C)

Using Radioactive Isotopes

Cells containing radioactive DNA are exposed to a photographic emulsion. Then the emulsion is developed and viewed under a microscope.
Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2.7 PET (Positron Emission Tomography) SCAN

Radioactively-tagged nutrient is given and monitored Decay of isotope is detected and color indicates amount of isotope present Intensely colored areas indicate high metabolic rate - i.e., CANCER
Cancerous throat tissue

Basic Chemistry - Atomic Structure

Electrons Involved in chemical reactions between atoms Energy levels of electrons vary (potential energy) Discrete steps called electron shells

Low energy near nucleus

High energy further away

Fig. 2.8 Energy levels of an atoms electrons

(a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons

Third shell (highest energy level) Second shell (higher energy level) First shell (lowest energy level) Atomic nucleus Energy absorbed

Different amounts of potential energy are stepwise changes

Energy lost

(b)

Basic Chemistry - Atomic Structure

Electron configuration
Determines chemical properties of elements Depends upon the number of electrons in its outermost shell Termed valence shell and valence electrons The periodic table of elements shows the electron distribution of elements

Fig. 2-9 Electron distribution diagrams for the first 18 elements in the periodic table
Hydrogen 1H
First shell

Atomic mass

2 He 4.00

Atomic number Element symbol

Helium 2He

Electrondistribution diagram
Lithium 3Li Beryllium 4Be Boron 5B

Carbon 6C

Nitrogen 7N

Oxygen 8O

Fluorine 9F

Neon 10Ne

Second shell

Sodium Magnesium Aluminum 12Mg 11Na 13Al

Third shell

Silicon 14Si

Phosphorus 15P

Sulfur 16S

Chlorine 17Cl

Argon 18Ar

Basic Chemistry - Atomic Structure

Electron configuration
Valence shell and valence electrons Completed shell is unreactive chemically inert Helium, Neon, Argon Other atoms transfer or share electrons to complete valence shell Chemical bonds

Basic Chemistry - Atomic Structure

Electron shells or Orbitals
Once thought to be like planets orbiting the sun, but dont know exact path

An orbital is where electron is 90% of time

Only 2 electrons per orbital at any time

Basic Chemistry - Atomic Structure

Electron orbitals First energy shell - 2 electrons 1s orbital - 2 e Second energy shell - 8 electrons 2s orbital - 2 e Three 2p orbital - 6 e-

Fig. 2.10 Electron Orbitals

(a)
Electron-distribution diagram

Neon, with two filled shells (10 electrons)

First shell

Second shell

(b) Separate electron orbitals

x z y

1s orbital

2s orbital

Three 2p orbitals

(c) Superimposed electron orbitals 1s, 2s, and 2p orbitals

Basic Chemistry Atomic Structure

The presence of unpaired electrons in one or more orbitals of their valence shells accounts for the reactivity of an atom

Atoms interact with certain other atoms in order to complete their valance shells
Such interactions result in atoms staying close together, and held by attractions called chemical bonds

Basic Chemistry for Cell Biologists

Matter
Elements and Compounds Elements required by living organisms Atomic structure

Chemical bonding
Chemical reactions

Basic Chemistry for Cell Biologists

Chemical Bonds Covalent bonds Nonpolar

Polar
Ionic bonds

Hydrogen bonds
Van der Waals interactions

Covalent Chemical Bonds

Sharing of valence electrons Strongest of the chemical bonds

Covalent Bond
Sharing of a pair of valence electrons by two atoms
If unshared orbitals overlap, each atom can count both electrons toward its goal of filling the valence shell

Fig. 2.11 Formation of a

covalent bond
In each hydrogen atom, the single electron is held in its orbital by its attraction to the proton in the nucleus

Hydrogen atoms (2 H)

When two hydrogen atoms approach, the electron of each atom is also attracted to the proton in the other nucleus.

The two electrons become shared in a covalent bond, forming an H2 molecule Hydrogen molecule (H2)

Basic Chemistry - Molecules

Two or more atoms held together by covalent bonds constitute a molecule The molecular formula indicates the number and types of atoms present in a single molecule For molecular hydrogen: H2 Structural formula For molecular hydrogen: HH

Covalent Bonds
A single covalent bond, or single bond sharing of one pair of valence electrons A double covalent bond, or double bond sharing of two pairs of valence electrons

Covalent Bonds - Animation

Animation: Covalent Bonds

Copyright 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Covalent Bond - O2
Oxygen has 6 electrons in valence shell
Needs to add 2 e- to complete its valence shell

Two oxygen atoms can form a molecule by sharing two pairs of valence electrons
Forms a double covalent bond

Fig. 2.12 Covalent Bond - Oxygen

Name and Molecular Formula ElectronLewis Dot distribution Structure and Diagram Structural Formula Spacefilling Model

(b) Oxygen (O2)

Basic Chemistry - Valence

Every atom has a characteristic total number of covalent bonds that it can form - an atoms valence
The valence of hydrogen is 1

Oxygen is 2
Nitrogen is 3

Carbon is 4
Phosphorus has a valence of 5, forming 3 single covalent bonds and 1 double bond

Covalent Bonds
Can form between atoms of the same element or atoms of different elements. While both types are molecules, the latter are also compounds Water, H2O, is a compound in which two hydrogen atoms form single covalent bonds with an oxygen atom

Fig. 2.12 Covalent Bond - Hydrogen

Name and Molecular Formula

ElectronLewis Dot distribution Structure and Diagram Structural Formula

Spacefilling Model

(a) Hydrogen (H2)

Fig. 2.12 Covalent Bond - Water

Name and Molecular Formula Lewis Dot Electrondistribution Structure and Structural Diagram Formula Spacefilling Model

(c) Water (H2O)

Fig. 2-12 Covalent Bond - Methane

Name and Molecular Formula
ElectronLewis Dot distribution Structure and Diagram Structural Formula

Spacefilling Model

(d) Methane (CH4)

Covalent Bonds
Sharing of electrons between atoms

Equal - nonpolar covalent bond

Unequal - polar covalent bond

Some atoms have a greater attraction for an electron Electronegativity is a measure of the degree of attraction

Polar Covalent Bonds

Form between atoms with different electronegativity Water: Oxygen - high electronegativity Hydrogen - low electronegativity partial negative charge near the strongly electronegative atom partial positive charge near the weakly electronegative atom

Fig. 2.13 Polar covalent bonds in a water molecule

Oxygen is more electronegative than hydrogen
Partial negative

H H2O

+ Partial positive

Partial positive

Basic Chemistry for Cell Biologists

Chemical Bonds

Covalent bonds
Nonpolar

Polar
Ionic bonds

Hydrogen bonds
Van der Waals interactions

Basic Chemistry - Ionic Bonds

Transfer of electrons between atoms After such a transfer, both atoms have charges

A charged atom (or molecule) is called an ion

A cation a positively charged ion

An anion a negatively charged ion

An ionic bond is the attraction between an anion and a cation

Basic Chemistry - Ionic Bonds

Sodium and Chlorine Sodium has one electron in valence shell Chlorine has seven

Transfer one electron from sodium to chlorine

Sodium becomes positively charged - cation Chlorine becomes negatively charged - anion Both have complete valence shell

Fig. 2.14 Electron Transfer and Ionic Bonding

Na

Cl

Na

Cl

Na Sodium atom

Cl Chlorine atom

Na+ Sodium ion (a cation)

Cl Chloride ion (an anion)

Electron Transfer

Sodium chloride (NaCl)

Ionic Bonds - Animation

Animation: Ionic Bonds

Copyright 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Ionic Compounds
Compounds formed by ionic bonds

Formula indicates ratio of elements

NaCl - 1 atom of sodium: 1 atom of chlorine

MgCl2: 1 atom of Mg : 2 atoms of Cl

Strength of ionic bonds depends on environmental conditions dry conditions - salts are hard aqueous conditions - salts dissolve

Basic Chemistry for Cell Biologists

Chemical Bonds Covalent bonds Nonpolar Polar Ionic bonds Hydrogen bonds Van der Waals interactions

Basic Chemistry - Hydrogen Bonds

Weak type of bonding
Hydrogen atom covalently bonded to one atom (strongly electronegative) is attracted to another atom (also strongly electronegative) The partially positive charged hydrogen atom in a covalent bond is attracted to negatively charged (partial or full) molecules, atoms, or even regions of the same large molecule.

Fig. 2.16 A hydrogen bond between water and ammonia

Water (H2O) +

+ Hydrogen bond

Ammonia (NH3)
+ +

Basic Chemistry for Cell Biologists

Chemical Bonds

Covalent bonds
Nonpolar

Polar
Ionic bonds

Hydrogen bonds
Van der Waals interactions

Van der Waals Interactions

Because electrons are constantly in motion, there can be periods when partially positive and negative regions accumulate by chance in one area of a molecule This creates ever-changing regions of negative and positive charge within a molecule. Molecules or atoms in close proximity can be attracted by these fleeting charge differences, creating van der Waals interactions.

Van der Waals Interactions

Such bonds, collectively, can be strong as between molecules a geckos toe hairs and the surface of a wall

Function Relates to Shape

Shape of a molecule
determined by the arrangement of electron orbitals that are shared by the atoms involved in a bond A molecule with two atoms is always linear However, a molecule with more than two atoms has a more complex shape

Function relates to Shape

For atoms with electrons in both s and p orbitals, the formation of a covalent bond leads to hybridization of the orbitals to form four new orbitals in a tetrahedron shape
Fig. 2.17a Hybridization of orbitals s orbital
z x

Four hybrid orbitals Three p orbitals

(a)
y

Tetrahedron Hybridization of orbitals

Function Relates to Shape

In a water molecule the hybrid orbitals that oxygen shares with hydrogen atoms are spread in a V shape. In a methane molecule (CH4), all four hybrid orbitals are shared hydrogen nuclei are at the corners of the tetrahedron

Fig. 2.17b Molecular-shape models

Space-filling Model

Ball-and-stick Hybrid-orbital Model Model (with ball-and-stick model superimposed) Unbonded electron pair

104.5
Water (H2O)

Methane (CH4)

Function Relates to Shape

Molecules with similar shapes can interact in similar ways Opiate drugs (such as morphine) are similar to endorphins (the bodys natural pain killers) Both morphine and endorphins can bind to endorphin receptors on the surface of brain cells thereby relieving pain and producing euphoria

Fig 2.18 A molecular mimic

Key Natural endorphin Carbon Hydrogen Morphine Nitrogen Sulfur Oxygen

(a) Structures of endorphin and morphine Natural endorphin Morphine

Brain cell

Endorphin receptors

(b) Binding to endorphin receptors

Basic Chemistry for Cell Biologists

Matter
Elements and Compounds Elements required by living organisms Atomic structure

Chemical bonding
Chemical reactions

Basic Chemistry - Chemical Reactions

The making and breaking of chemical bonds

Chemical bonds are broken and reformed, leading to new arrangements of atoms
The molecules at the beginning of a chemical reaction are called reactants The molecules at the end of a chemical reaction are called products

Basic Chemistry Chemical reactions

All of the atoms in the reactants must be accounted

for in the products The reaction must be balanced

2 H2 Reactants

O2 Reaction

2 H2O Products

Basic Chemistry - Chemical Reactions

Reactants Products

In Photosynthesis (summarized reaction): 6 CO2 + 6 H2O C6H12O6 + 6 O2

This is not what happens chemically, but is a balanced equation of the summarized reaction

Basic Chemistry - Chemical Reactions

Reactants Products

Some reactions can go forward or reverse

3 H2 + N2

2 NH3

Reversible reactions indicated by the opposite headed arrows

Chemical Equilibrium
Rate at which products are made is the same as the rate at which products are being broken down At equilibrium The reactions are still going on, but there is no net change in the concentrations of reactants and products a dynamic equilibrium At equilibrium the concentrations of reactants and products are typically not equal, but their concentrations have stabilized