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Smartbook Chapter 1 Sections 1, 3, 4
Organism: Living things that maintain internal order that is separate from environment
Atom: smallest unit of element that has chemical properties of elements - all matter composed of atoms
Molecules of macromolecules: atoms bond together to form of molecules; many molecules bonded together is macromolecules
Cells: simplest unit of life; surrounded by membrane and contains variety of molecules and macromolecules
Tissues: a group of cells that have a similar structure and function
Organ: composed of 2+ tissues that carry out a particular function or set of functions
Organ Systems: In multicellular species, organs are typically a part of a larger, interacting system. In animals, such as birds and mammals, the heart is a part of the circulatory system
Population: A group of organisms of the same species that occupy the same environment
Species:
Community: A biological community is an assemblage of populations of different species. The types of species found in a community are determined by the environment and by the interactions of the species with each other
Ecosystem: Formed by the interactions of a community of organisms with their physical environment
Biospheres: Includes all of the places on Earth where living organisms exist. Life is found in the air, in bodies of water, on the land, and in the soil
Species: A group of collected organisms that share distinctive attributes in nature and for sexually reproducing, with one capable of inter breeding
Biological evolution: A heritage change in a population of organisms from one generation to the next
Smartbook Chapter 1 Sections 2, 5, 6
1.2: Core Concepts of Biology
A key proposal of Vision and Change was to relate biology education to the five core concepts of biology
Evolution: The diversity of life evolved over time by processes of mutation, natural selection, and genetic exchange
Structure and function: Basic units of structure define the function of all living things
Information flow, exchange, and storage: The growth and behavior of organisms are activated through the expression of genetic information
Pathways and transformations of energy and matter: Biological systems grow and change via processes that are based on chemical transformation pathways and are governed by the laws of thermodynamics
Systems: Living systems are interconnected and interacting. The interactions of living systems result in emergent properties, which are properties that manifest themselves as the result of various system components working together, not as a property of any individual component.
1.5: Biology as a Scientific Discipline:
In biology, science is defined as the observation, identification, experimental investigation, and theoretical explanation of natural phenomena.
Model Organisms: Organisms studied by many different researchers so they can compare their results and determine scientific principles that apply more broadly to other species
Not all discoveries are made by following the scientific method, some discoveries are made simply by gathering new information
Ecology: The study of organisms in their natural environments, which considers populations, communities, and ecosystems
Anatomy: The study of the structures of living things
Physiology: The study of the functions of living things
Cell biology: the study of cells and their interactions
Molecular biology: A field of study made possible by genetic technology that allows researchers to study the structure and function of the molecules of life
Reductionism: Reducing complex systems to simpler components as a way to understand how the system works. In biology, reductionists study the parts of a cell or organism as individual units.
Biologists use the term system biology to describe research aimed at understanding how emergent properties arise. This term is often applied to the study of cells.
System biology: Involve the investigation of groups of genes that code proteins with a common purpose.
Hypothesis: A proposed explanation for a natural phenomenon; it’s a proposition based on previous observations or experimental studies. A hypothesis is meant to be testable—the hypothesis can be shown to be consistent or inconsistent with data that are obtained via experimentation
Predictions: expected outcomes that can be shown to be correct or incorrect
Theory: A broad explanation of some aspect of the natural world that is substantiated by a large body of evidence.
Discovery-based science or discovery science: The collection and analysis of data without the need for a preconceived hypothesis; also called discovery science.
Hypothesis Testing:
Observations are made regarding natural phenomena
These observations lead to a hypothesis that tries to explain the phenomena. A useful hypothesis is one that is testable because it makes specific predictions
Experimentation is conducted to determine if the predictions are correct.
The data from the experiment are analyzed
The hypothesis is considered to be consistent with the data, or it is rejected
The Scientific method is intended to be an objective way to gather knowledge.
One set of experiments is done on the control group whereas another set is conducted on the experimental group.
The result of experimentation is a set of data from which a biologist tries to draw conclusions
When experimentation involves control and experimental groups, a common form of analysis is to determine if the data collected from the two groups are truly different.
A hallmark of science is that valid experiments are repeatable—similar results are obtained when an experiment is conducted on multiple occasions.
After performing observations and experiments, biologists communicate their results in various ways.
Following a submission, a paper usually undergoes a peer-review process in which other scientists, who are experts in the area, evaluate the paper and make comments regarding its quality.
Another social aspect of research is that biologists often attend meetings where they report their most recent work to the scientific community.
1.6: Core Skills of Biology:
Structural models: The physical structures of components that make up living organisms.
Mechanistic models aka physiological model: Describes the workings of the individual parts of a complex system, and the manner in which they interact.
There are two proposed models, symplastic and apoplastic transport, which describe two possible pathways by which minerals are taken into root of a plant
Mathematical models: A description of a process or a system using mathematical concepts, symbols, and diagrams. Many are presented as one or more equations
Temporal Models: depicts a biological process as it occurs over a short or long period of time. In cell biology, some processes occur very quickly
Hierarchical Models: Organisms, parts of organisms, or observations fall into nested levels. For example, the field of taxonomy organizes species into progressively smaller groups, such as kingdom, family, and genus (plural, genera). ONe or more genera are found within a family, and many different families are found within a kingdom.
Model-based learning: An educational approach in which students evaluate or generate models as a way to enhance their understanding of scientific concepts and improve their critical-thinking skills.
Cultivating Biological Literacy: A Framework for Undergraduate Biology Education
Executive Summary
The rapid acceleration of biological discovery necessitates a fundamental shift in undergraduate biology education. The Vision and Change initiative, led by the American Association for the Advancement of Science (AAAS) and other stakeholders, argues that the traditional model—focused on packed syllabi and rote memorization—is no longer sufficient. To prepare a diverse student population for the "New Biology" of the 21st century, the curriculum must transition toward a framework built upon five core concepts and six core competencies.
This framework is designed to be adaptable across diverse academic institutions and emphasizes that biological literacy is essential not only for future scientists but for all citizens, including educators, policymakers, and the general public. The goal is to move from "covering" biology to "doing" biology, ensuring students understand the interconnectedness of living systems and possess the quantitative, communicative, and interdisciplinary skills required for modern scientific practice.
The Mandate for Curricular Reform
The "Vision and Change" report identifies a critical tension in modern education: the need to keep classrooms current without overwhelming students. The current pace of discovery requires a shift in focus from broad, superficial coverage to a deep conceptual understanding.
Drivers of Change
Scientific Advancement: The extraordinary pace of discovery makes historical lecture-based models counterproductive.
Student Diversity: Curricula must meet the needs of an increasingly diverse student population.
Broad Societal Impact: Biology education serves a wide array of future professionals. As Alan Leshner of the AAAS noted, the classroom includes "future biologists, doctors, chemists, and poets... US presidents and members of Congress."
The "New Biology": A focus on multidisciplinary, systems-level inquiry rather than isolated sub-disciplines.
Core Concepts for Biological Literacy
The framework proposes five organizing themes that define the lines of inquiry in modern biology. These concepts provide a roadmap for students to organize the multitude of facts encountered in their studies.
Key Applications of Concepts
Evolution: Provides the basis for understanding drug resistance in microbes and the diversity of domesticated species.
Structure and Function: Informs rational drug design (e.g., HIV protease inhibitors) and biomechanics.
Information Flow: Applied through bioinformatics to understand signal transduction and gene expression networks.
Energy and Matter: Essential for bioengineering plants and microorganisms for remediation or industrial production.
Systems: Utilizes mathematical and computational tools to construct predictive models of complex biological processes.
Core Competencies and Disciplinary Practice
To practice biology effectively, students must develop specific skills that allow them to generate and communicate knowledge. The report identifies six essential competencies.
1. Ability to Apply the Process of Science
Biology is evidence-based. Students must learn to "do" science by:
Posing problems and generating hypotheses.
Designing experiments and observing nature.
Interpreting and evaluating data.
Engaging in authentic research experiences (course-based or independent).
2. Ability to Use Quantitative Reasoning
Modern biology relies on the analysis of dynamic systems and mathematical modeling. Students must be able to:
Apply statistics to biological problems.
Interpret quantitative data from diverse sources.
Understand nonlinear dynamics, such as those found in immune system development or population ecology.
3. Ability to Use Modeling and Simulation
Computational tools are now standard in biology. Students should be able to:
Use mathematical and computational tools to describe complex, interactive systems.
Identify the advantages and limitations of reductionist versus systems approaches.
Implement computational algorithms to test ideas about spatiotemporal complexity.
4. Ability to Tap Into the Interdisciplinary Nature of Science
The most exciting areas of study often emerge between traditional disciplines. Students can achieve this through:
Developing expertise in biology and a related field (e.g., computer science or social science).
Gaining fluency in related disciplines while maintaining deep expertise in one.
Collaborating as a biological specialist on multidisciplinary teams.
5. Ability to Communicate and Collaborate
Scientific research is increasingly global and team-based. Essential skills include:
Communicating concepts through written, visual, and oral methods.
Engaging in peer mentoring to solidify comprehension.
Collaborating with diverse working communities to leverage multiple perspectives.
6. Ability to Understand the Relationship Between Science and Society
Biology exists within a societal context. Practitioners must:
Evaluate the impact of scientific discoveries on human society.
Address the ethical implications of biological research.
Advocate for the value of science in addressing global problems like health and environmental sustainability.
Conclusion: A Flexible Foundation
The Vision and Change framework is not a "one-size-fits-all" directive but a consensus-driven resource. It emphasizes that introductory courses, which often serve as the only science exposure for non-majors, must provide a solid foundation in these concepts and competencies. By prioritizing the ability to think like a scientist over the simple acquisition of facts, undergraduate biology education can better prepare all students—from future researchers to policymakers—to address the complex challenges of the 21st century.
Smartbook #3: Chapter 2 sections 2.1 and 2.2
Section 2.1
All life-forms are composed of matter which is defined as anything that has mass and occupies space
There are 3 different states matter may exist in for living organisms, these include: solid, liquid, or gas
All matter is composed of atoms and they can’t be further broken down into other substances by ordinary chemicals or physical means.
Molecules is defined as two or more atoms bonded together
When atoms and molecules are studied in the context of a living organism, the science of biochemistry emerges
The simplest atom, hydrogen, is approximately 0.1 nanometer in diameter, roughly one-millionth the diameter of a human hair
Each type of atom is called an element which is defined as a pure substance made up of only one kind of atom
There are three subatomic particles that can be found within atoms: protons (a positively charged particle found in the nucleus of an atom), neutrons (an uncharged particle found in the nucleus of an atom), and electrons (a negatively charged particle found in orbitals around an atomic nucleus).
The number of protons in an atom is called the atomic number and defines each type of element
The atomic number of an element is equal to the number of protons it contains and its atomic mass includes the number of protons and the number of neutrons.
The protons and neutrons are confined at the center of an atom or the atomic nucleus—the center of an atom; contains protons and neutrons
In most atoms, the number of protons and electrons are identical, but the number of neutrons may vary
The three subatomic particles all have a difference electric charge: Protons have 1 unit of positive charge, electrons have 1 unit of negative charge, and neutrons are electrically neutral
Within an atom, particles with nearly equal mass are protons and neutrons, while electrons have a much smaller mass
When there is a like charge, they repel each other, and opposite charges attract each other. The positive charges in the nucleus attract the negatively charged electrons
The nucleus has a net positive charge equal to the number of protons it contains. The entire atom has no net electric charge, however, because the number of negatively charged electrons around the nucleus is = to the number of positively charged protons in the nucleus
Rutherford Determined the Modern Model of the Atom:
In the early 1900s, many scientists, including Chemist Ernest Rutherford, hypothesized that the positive charge and the mass of an atom were evenly dispersed throughout the atom
Rutherford’s hypothesis was basically that atoms in gold foil are composed of diffuse, evenly distributed positive charges that should usually cause a particles to be slightly deflected as they pass through
He ended up using a thin sheet of gold foil, a particle emitter, and zinc sulfide detection screen
He would emit a beam of a particles, pass the beam through gold foil, and then detect a particles on zinc sulfide screens after they pass through foil or bounce back. He would then record the number of a particles detected on zinc sulfide screens and their locations
After the experiment concluded, the hypothesis was rejected, as most of the volume of an atom is empty space, with the positive charges concentrated in a small volume.
Rutherford realized that 98% of the a particles passed right through the foil as though it wasn’t there, leading to him concluding that most of the volume of an atom was empty space
The existence of the small dense region of highly concentrated positive charge explains how some a particles could be so strongly deflected by the gold foil (the 2%).
Today we know that more than 99.99% of an atom’s volume is outside the nucleus
A central nucleus is surrounded by cloudlike orbitals containing electrons
Electrons Occupy Orbitals Around an Atom’s Nucleus
Since it’s impossible to predict the precise location of an electron, scientists are only able to describe the region of space surrounding the atomic nucleus in which there is a high probability of finding that electron, which is known as orbital.
Some orbitals are spherical (s orbitals), some are described as a propeller or dumbbell (p orbitals)
An orbital can contain a maximum of 2 electrons; any atom with more than 2 electrons must contain more than 1 orbital
Electron shells: A region around an atom’s nucleus where electrons reside; larger atoms have more electron shells than smaller atoms. They’re numbered with shell 1 being closest to the nucleus
Energy: The capacity to do work or cause a change
Electrons have kinetic energy
Different electron shells may contain 1+ orbitals, each orbital holding up to 2 electrons.
The innermost electron shell of all atoms has room for only 2 electrons, which spin in opposite directions within a spherical orbital
The 2nd electron shell is composed of 1 spherical orbital and 3 dumbbell-shaped orbitals, meaning the 2nd shell can hold up to 4 pairs of electrons
The shell closest to the nucleus fills up with the lowest energy electrons first, and then each subsequent shell fills with higher and higher energy electrons, one shell at a time
In the second shell, the s orbital has lower energy, whereas the 3 p orbitals have slightly higher and roughly equal energies.
A nitrogen atom has 7 protons and 7 electrons, with 2 electrons filling the 1st shell, and 5 electrons are in the 2nd shell. The remaining 3 electrons in the 2nd shell are found singly in each of the 3 p orbitals
Atoms that have unfilled electron shells tend to share, release, or obtain electrons to fill their outer shell
Valence electron: An electron in the outermost shell of an atom that is available to share with other atoms. Such electrons allow atoms to form chemical bonds with each other.
Each Element Has a Unique Number of Protons
The number of protons in an atom is its atomic number and is used to distinguish it from other elements.
With the exception of ions, the number of protons and electrons in a given atom are identical, meaning the atomic number is also = to the number of electrons in the atom, resulting in a net electric charge of 0
An atom’s atomic number is the same number of protons it contains. In an atom that isn’t an ion, this number also equals the number of electrons
In a periodic table, the rows (known as periods) indicate the number of electron shells (H = 1, Li = 2, Na = 3). The columns (known as groups) indicate the numbers of electrons in the outer shell (Left to right: Li = 1, Be = 2, B = 3).
One electron in the outer shell ←→ left-most column in periodic table
Only one electron is required to fill the outer shell ←→ Column second from the right in the period table
Several electrons needed to fill the outer shell ←→ Middle section of the periodic table
Outer shell filled ←→ Noble gases in the right-most column in periodic table
The similarities of elements within a group occur because those elements have the same number of valence electrons, resulting in them having a similar chemical bonding property
Elements have increasingly full orbitals as you look from left to right on the periodic table
Atoms Have a Small but Measurable Mass
Protons and neutrons are nearly equal in mass, and each has more than 1800 times the mass of an electron, because the size, the mass of the electrons in an atom is ignored in calculations of atomic mass
Atomic mass indicates an atom’s mass relative to the masses of other atoms
By mass, the most abundant element in living organisms is oxygen
The most common type of carbon atom, which has 6 protons and 6 neutrons, is assigned an atomic mass of exactly 12
Carbon shares the most similar bonding properties with silicon because they have the same number of valence electrons
Weight is derived from the gravitational pull on a given mass.
Atomic mass is measured in units called daltons, after chemist John Dalton, who postulated that matter is composed of tiny indivisible units and referred to them as atoms, thereby laying the groundwork for atomic theory
1 dalton (Da) or the atomic mass unit, equal 1/12 the mass of a carbon atom, or about the mass of a proton or a hydrogen atom.
A mole: the amount of any substance that contains the same number of particles as there are atoms in exactly 12 g of carbon
Isotopes Vary in Their Number of Neutrons
Isotopes: A form of an element that contains a different number of neutrons from the element’s other isotopes
Isotopes of an atom have similar chemical properties but may have very different physical properties
Radioisotope: An isotope found in nature that is inherently unstable and usually does not exist for long periods of time. Such isotopes decay and emit energy in the form of radiation
The Mass of All Living Organisms Is Largely Composed of Four Elements
Oxygen, carbon, hydrogen, and nitrogen account for the vast majority of atoms in living organisms and typically make up about 95% of the mass of living organisms
Much of the oxygen and hydrogen occur in the form of water, which accounts for 60% of the mass of most animals and up to 95% or more in some plants.
Mineral elements: A chemical element other than oxygen, hydrogen, carbon, and nitrogen that is required for life and present in significant amounts in living organisms.
Trace elements: An element that is essential for normal growth and function of living organisms but is required in extremely small quantities
Section 2.2
2+ atoms bonded together make up a molecule or a compound ie. 2 oxygen atoms can combine to form 1 oxygen molecule 02
Molecular formula: A representation of a molecule that consists of the chemical symbols for all of the atoms present and subscripts that indicate how many of those atoms are present
Compound: A substance composed of 2+ different elements
One of the most important features of compounds is their emergent properties. This means that the properties of a compound differ greatly from those of its elements.
Covalent Bonds Are Formed When Atoms Share Electrons to Fill Their Outer Shells
A covalent bond is a chemical bond in which 2 atoms share a pair of electrons and can occur between atoms whose outer shells are not full
Example: Nitrogen has 3 unpaired electrons in its outer shell. What is the maximum number of covalent bonds that a nitrogen atom can form with other atoms while still remaining uncharged? 3
Atoms tend to be most stable when their outer shells are filled with electrons
Example of this principle:
The outer shell of a hydrogen atom is full when it contains 2 electrons, though a hydrogen atom has only 1 electron
The outer shell of a fluorine atom in full when it contains 8 electrons, though a fluorine atom has only 7 electrons in its outer shell
In the Hydrogen Fluoride molecule, the 2 atoms share a pair of electrons, which spend time in the outer shells of both atoms. This allows both of the outer shells to be full
Covalent bonds are strong chemical bonds, because the shared electrons behave as if they belong to each atom
Structural formula: A type of chemical formula for molecules in which each covalent bond is represented by a line indicating a pair of shared electrons. Example: (HF) = H—F
Each atom forms a characteristic number of covalent bonds, which depends on the number of electrons required to fill the outer shell.
Octet rule: The observation that many atoms are most stable when their outermost shell is full, with 8 electrons
The octet rule applies to most atoms found in living organisms, including oxygen, nitrogen, carbon, phosphorus, and sulfur. These atoms form a characteristic number of covalent bonds to make an octet in their outermost shell. (It doesn’t always apply)
Double bonds occur when atoms share two pairs of electrons (four electrons) rather than 1 pair.
A common example is when 2 carbon atoms form bonds in compounds and share 1 pair of electrons (single bond) or 2 pairs (double bond), depending on how many other covalent bonds each carbon forms with other atoms
Ex: A new element found on earth has 4 unpaired electrons in its outer shell. Predict the maximum number of bonds in which the new element can participate. Answer: 4
Atoms that have partially filled energy shells tend to share, lose, or gain electrons and can form compounds
Due to Electronegativity, Covalent Bonds May Be Nonpolar or Polar
Some atoms attract shared electrons more strongly that other atoms
The electronegativity of an atom is a measure of an atom’s ability to attract electrons in a bond with another atom.
H = 2.20
C = 2.55
N = 3.04
O = 3.44
Na = 0.93
Cl = 3.16
Atoms with higher values attract electrons more strongly than those with lower values
Covalent bonds between atoms with similar electronegativities are called nonpolar covalent bonds
Examples include: Carbon and Hydrogen, Oxygen & Oxygen, and Hydrogen & Hydrogen
Atoms that form nonpolar covalent bonds differ in electronegativity by less than 0.4
When 2 atoms with an electronegativity difference from 0.4 to 1.8 form a covalent bond, the shared electrons are more likely to be closer to the nucleus of the atom of higher electronegativity than to the nucleus of the atom of lower electronegativity also known as polar covalent bonds because the distribution of the shared electrons around the nuclei creates a polarity, or difference in electric charge, across the molecule
Examples include: Nitrogen & Hydrogen and Oxygen & Hydrogen
Polar molecules usually have 1+ polar covalent bonds, whereas nonpolar molecules tend to have bonds that are mostly nonpolar covalent
Hydrogen Bonds and van der Waals Dispersion Forces Promote Interactions Between and Within Molecules
An important effect of a certain polar covalent bonds is the ability of one molecule to loosely associate with another molecule through a weak interaction called a hydrogen bond
A hydrogen bond forms when a hydrogen atom in one polar molecule becomes electrically attracted to an electronegative atom, such as an oxygen or a nitrogen atom, in another polar molecule
In other words: A hydrogen bond forms when a hydrogen atom with a partial positive charge becomes electrically attracted to an electronegative atom with a partial negative charge
Ex: The hydrogen bonds connecting water molecules form between an oxygen atom on one molecule and a hydrogen atom on another molecule
Ex: When 2 water molecules are near each other, a hydrogen bond will form between the more positive hydrogen and the more negative oxygen atoms of neighboring water molecules
Collectively many hydrogen bonds provide a strong force that helps maintain the 3D structure of a molecule. This is true in deoxyribonucleic acid (DNA) — the molecule that makes up the genetic material of living organisms
The 2 strands of genetic material are held together along their length by hydrogen bonds between different portions of the molecule.
When an interaction between 2 molecules involves relatively few hydrogen bonds, such an interaction tends to be weak and readily disrupted
Enzymes are molecules that catalyze many biologically important chemical reactions. The small molecules are later released, after the enzymes have changed their structure
Van der Waals dispersion forces: Attractive forces between molecules in close proximity to each other, caused by the variations in the distribution of electron density around individual atoms
At any moment, the electrons in the outer shells of the atoms in a nonpolar molecule may be evenly distributed or unevenly distributed
A fleeting electrical attraction to other nearby molecules may arise
Ionic Bonds Involve an Attraction Between Positive and Negative Ions
Atoms are electrically neutral because they contain equal numbers of negative electrons and positive protons. If an atom or molecule gains or loses one or more electrons, it acquires a net electric charge and becomes an ion
Ions that have a net positive charge are called cations
Ions with a net negative charge are called anions
An ionic bond occurs when a cation binds to an anion
An ionic bond may occur between atoms that differ greatly in their electronegativities
Substances such as NaCl, in which the atoms are held together by ionic bonds, are called ionic compounds. By comparison, a molecule such as O2, in which the atoms are held together by covalent bonds, is considered to be a molecule
Molecules May Change Their Shapes
The covalent bonds between the atoms form particular angles with one another, giving the groups of atoms very specific shapes
A single molecule may assume different 3D shapes without breaking any of the covalent bonds between its atoms
For a six-carbon molecule, hydrogen atoms above the blue plane are shown in white; those below the blue plane are blue
2 molecules are shown schematically as having complementary shapes that permit them to interact
During the interaction, the flexible nature of the molecules causes molecule 2 to twist sufficiently to assume a new shape
Free Radicals Are a Special Class of Highly Reactive Molecules
An atom or an ion is most stable when each of its orbitals is occupied by a full complement of electrons
Free radical: A molecule containing an atom with a single, unpaired electron in its outer shell
Free radicals can interact with other molecules to “steal” an electron from one of their atoms, thereby filling the orbital in the free radical
In the process, a new free radical may be created from the donor molecule, setting off a chain reaction
Free radicals can be formed by exposure of cells to radiation and toxins
Examples of biologically important free radicals are superoxide anion (·O₂-), hydroxyl radical (·OH), and nitric oxide (NO·)
Free radicals can be either charged or neutral
Free radicals can cause a cell to rupture or damage the genetic material
Most free radicals that arise in an organism need to be inactivated so they don’t harm healthy cells
Antioxidant: A molecule that can donate electrons to a free radical without becoming highly reactive itself.
Examples include vitamins C and E, which are found in fruits and vegetables, and the numerous plant compounds known as flavonoids
Chemical Reactions Change the Properties of Atoms or Molecules and Create New Molecules
Chemical Reaction: A process in which one or more substances are changed into other substances by the making or breaking of bonds.
This can happen when 2+ elements or compounds combine to form a new compound, when one compound breaks down into 2+ molecules, or when electrons are added to or removed from an atom
Most chemical reactions in living organisms occur in aqueous solutions
Chemical reactions share similar properties
They all require a source of energy so that atoms and molecules can move and encounter each other. The energy required for atoms and molecules to interact is provided partly by heat, or thermal energy
Heat causes them to vibrate and move (brownian motion) and without heat, atoms and molecules would be totally stationary and unable to interact
Chemical reactions that occur in living organisms often require more than just Brownian motion…a catalyst is an agent that speeds up the rate of a chemical reaction.
Enzymes are proteins that are found in all cells and catalyze most chemical reactions
Chemical reactions tend to proceed in a particular direction but eventually reach a state of equilibrium
When a single molecule of methane reacts with 2 molecules of oxygen, one molecule of carbon dioxide and 2 molecules of water are produced
Reactant: A substance that participates in a chemical reaction and becomes changed by that reaction
In living organisms, most chemical reactions involve reactants and products that are dissolved in water
In the conversion of methane and oxygen to carbon dioxide and water, oxygen reacts
Products: The end result of a chemical reaction
Example: In the conversion of methane and oxygen to carbon dioxide and water, carbon dioxide is a product because in the conversion process, carbon dioxide is created
If the products aren’t converted to other molecules, chemical reactions eventually reach chemical equilibrium, in which the rate of formation of products equals the rate of formation of reactants
The concentrations of products and reactants don’t change
In a chemical reaction, if there is no longer a change in the concentration of reactants and products, then equilibrium has been reached
A final feature common to chemical reactions in living organisms is that most reactions occur in watery environments
Such chemical reactions involve reactants and products that are dissolved in water
Smartbook #4 Chapter 2 Sections 2.3 & 2.4
Section 2.3
People can survive for a month or more without food but usually die in less than a week without water
The bodies of all organisms are composed largely of water; most of the cells in an organism’s body are not only filled with water but also surrounded by it
Up to 95% of the weight of certain plants come from water
In humans, typically 60-70% of body weight is due to water
The brain is roughly 70% water, blood is about 80% water, and the lungs are nearly 90% water
Even our bones are about 20% water
Most of the chemical reactions that occur in nature involve molecules that are dissolved in water, including those reactions that happen inside the cells of living organisms and in the spaces that surround the cells
Ions and Polar Molecules Readily Dissolve in Water
Substances dissolved in a liquid are known as solutes, and the liquid in which they are dissolved is the solvent
Solutes dissolve in a solvent to form a solution
Solutions made with water are called aqueous solutions
The covalent bonds linking the 2 hydrogen atoms to the oxygen atom in a water molecule are polar.
The oxygen in water has a slight negative charge, and each hydrogen has a slight positive charge
To dissolve in water, a substance must be electrically attracted to water molecules
Example: Table salt (NaCl) is a solid crystalline substance because of the strong ionic bonds between positive sodium ions (Na+) and negative chloride ions (Cl-)
When a crystal of sodium chloride is placed in water, the partially negatively charged oxygens of water molecules are attracted to Na+, and the partially positively charged hydrogens are attracted to Cl-
Clusters of water molecules surround the ions, allowing Na+ and Cl- to separate from each other and enter the water–that is, to dissolve
Molecules or compounds that contain ionic and/or polar covalent bonds dissolve in water
Such molecules are called polar or hydrophilic, which translates to water loving
Molecules composed predominantly of carbon and hydrogen are relatively insoluble in water, because carbon-carbon and carbon-hydrogen bonds are nonpolar
These molecules have few or no partial positive and negative charges and, therefore, are not attracted to water molecules
Nonpolar or hydrophobic, meaning water-fearing
Oils are a familiar example of substances that are composed of hydrophobic molecules
Some Molecules Have Both Hydrophilic and Hydrophobic Regions
Molecules that have both hydrophilic regions at one or more sites and hydrophobic regions at other sites are called amphipathic (or amphiphilic, from the Greek for “both loves”) —refers to molecules containing a hydrophobic region and a hydrophilic region.
When mixed with water, long amphipathic molecules may aggregate into spheres called micelles (a sphere formed from the aggregation of long amphipathic molecules when they are mixed with water), with their polar regions at the surface of each micelle
Such an arrangement minimizes the interaction between water molecules and the nonpolar ends of the amphipathic molecules, which face inward
Familiar examples of amphipathic molecules are those in detergents, which can form micelles that help to dissolve the oils and nonpolar molecules found in dirt
Amphipathic molecules may form structures consisting of double layers of molecules called bilayers
Bilayers have 2 hydrophilic surfaces facing outside, in contact with water, and a hydrophobic interior facing away from water
Bilayers play a key role in cell membrane structure
The Amount of a Dissolved Solute per Unit Volume of Liquid Is Its Concentration
Solute concentration is defined as the amount of a solute dissolved in a unit volume of solution
If 1 gram of glucose was dissolved in enough water to make 1 liter of solution, we would say that the solute concentration is 1 g/L
A comparison of the concentrations of 2 different substances on the basis of the number of grams per liter of solution does not directly indicate how many molecules of each substances are present
Let’s compare 10 g each of glucose (C6H12)6) and sucrose (612H22O11) Because the individual molecules of glucose have less mass than sucrose, 10 g of glucose contains more molecules than 10 g of sucrose
Another way to describe solute concentration is according to the moles of dissolved solute per volume of solution. To make this calculation, we must know three things: the amount of dissolved solute, the mass of the dissolved solute, and the volume of the solution
The molecular mass of a molecule is equal to the sum of the atomic masses of all the atoms in the molecule
Glucose (C6H12O6) has a molecular mass of 280 (6 x 12 + 12 x 1 + 6 x 16 = 180
1 mole of a substance is the amount of the substance in grams equal to its atomic or molecular mass
The molarity of a solution is defined as the number of moles of a solute dissolved in 1 L of solution
A solution containing 180 g of glucose 1 mol dissolved in enough water to make 1 L is a 1 molar (a term used to describe a solution’s molarity; a 1 molar solution contains 1 mole of a solute dissolved in enough water to make 1 L of solution) solution of glucose
Smartbook Questions & Answers:
A solution in which water is the solvent is called an aqueous solution
To dissolve in water, a substance must be electrically attracted to water
Which of the following molecules are predicted to easily dissolve in water:
Carbohydrates that contain negatively-charged -OH groups
Ions that carry fully electric charges
Oils that contain uncharged C-H groups
Chemical reactions involving molecules that are dissolved in water are vital for a cell, but only if they occur within the cytoplasm. True or False? False
Which of the following statements describe hydrophilic molecules?
They are soluble in water
They contain many nonpolar covalent bonds
They are smaller than hydrophobic molecules
They are uncharged
Answer: They are soluble in water
Substances dissolved in liquid are called:
Solutes
Solutions
Micelles
Solvents
Answer: Solutes
What type of bonds are most likely to be found in a hydrophobic molecule?
Polar Covalent
Nonpolar covalent
Hydrogen
Weak
Ionic
Answer: Non polar covalent
An aqueous solution is one in which the solvent is _______.
An oil
Water
Hydrophobic
Answer: Water
Amphipathic molecules have both hydrophilic regions and hydrophobic regions
When NaCl dissolved in water, Na+ becomes surrounded by the partially negatively charged oxygen atoms of water molecules and Cl- becomes surrounded by the partially positively charged hydrogen atoms of water molecules
In a micelle, which portion of the amphipathic molecules are oriented toward the surface of the sphere?
The polar region
The nonpolar region
The hydrophobic region
Answer: The polar region
Molecules are likely to dissolve easily in water if they contain what type of bonds?
Polar Covalent Bonds
Nonpolar covalent bonds
Ionic bonds
Answer: Polar covalent bonds & Ionic bonds
The polar groups of a micelle are oriented toward the outside, while its nonpolar groups are oriented toward the inside
Which of the following describe molecules that only have hydrophobic regions?
Contain many nonpolar covalent bonds
Form micelles when placed in water
Have atoms with partial positive and partial negative charges
Dissolve well in nonpolar solvents
Are relatively insoluble in water
Answer: Contain many nonpolar covalent bonds, dissolve well in nonpolar solvents, & are relatively insoluble in water
Ice floats on water. This is because the H2O molecules in ice have greater intermolecular distances between them, causing ice to be less dense than water
Hydrophobic molecules tend to contain many nonpolar covalent bonds, such as the bond between 2 carbon atoms or the bond between carbon and hydrogen
Why does ice float in liquid water?
Ice is less dense than liquid water
Liquid water is less electronegative in ice
Water molecules form few hydrogen bonds with each other in ice
Ice solidifies around a hollow core
Answer: Ice is less dense than liquid water
What are the characteristics of an amphipathic molecule?
Has polar regions
Dissolves completely in water
Has non-polar regions
Is electrically neutral
Answer: Has nonpolar and polar regions
Which state of water is the most dense?
Liquid
Solid
Gas
Answer: Liquid
What part of an amphipathic molecule would be oriented toward the center of a micelle? The nonpolar region because this region is hydrophilic. Thus, it will be at the surface of the micelle, where it is attracted to the surrounding water molecules
Which of the following changes in the physical state of water require the input of energy? Changing from liquid to gas & changing from solid to liquid
When mixed with water, amphipathic molecules may aggregate into spheres called micelles
Hydrolysis reactions break apart molecules via water
Put the physical states of water in order based on the intermolecular distances between water molecules. The top position should be the state in which the molecules are the farthest apart: The gaseous state, the solid state, the liquid state
The Chemical Basis of Life II: Organic Molecules
Of the countless possible molecules that can be produced from the known elements in nature, certain types contain carbon and are found in all forms of life. These carbon-containing molecules are collectively referred to as organic molecules, so named because they were first discovered in living organisms.
Organic molecules include lipids and large, complex compounds called macromolecules, which can be proteins, nucleic acids, and some carbohydrates.
The science of carbon-containing molecules is known as organic chemistry
Vitalism held that organic molecules were created by, and therefore imparted with, a vital life force that was contained within a plant or an animal’s body
Vitalism was disproved by Friedrich Wöhler, a physician and chemist interested in the properties of inorganic and organic compounds
An important application of organic chemistry is the wide use of organic molecules to benefit humans
Many drugs for treating human diseases are organic molecules
Understanding the structures of organic molecules may lead to the ability to synthesize them in large enough amounts to treat many people
In 1935, chemist Percy Lavon Julian first synthesized the drug physostigmine
This led to the treatment of glaucoma, an eye disorder
A key property of the carbon atom is its ability to form four covalent bonds with other atoms, including other carbon atoms
This occurs because carbon has 4 electrons in its outer shell, and it requires a total of eight electrons, or four additional electrons, to fill this shell
In living organisms, carbon atoms most commonly form covalent bonds with other carbon atoms and with hydrogen, oxygen, nitrogen, and sulfur atoms
Carbon can form single or double bonds with other carbon atoms and with oxygen and nitrogen
Triple bonds can be formed between two carbon atoms and between carbon and nitrogen
Carbon and hydrogen have similar electronegativities, therefore, carbon-carbon and carbon-hydrogen bonds are nonpolar
Molecules with a high proportion of hydrogen-carbon bonds, called hydrocarbons, are hydrophobic and poorly soluble in water
In contrast, when carbon forms polar covalent bonds with more electronegative atoms, such as oxygen or nitrogen, the resulting molecule has regions of partial negative and partial positive charges
Such a molecule is typically hydrophilic and soluble in water because of its electrical attraction to polar water molecules
The ability of carbon to form both polar and nonpolar bonds contributes to its ability to serve as the backbone for an astonishing variety of biologically important molecules
Another feature of carbon that is important to living organisms is that carbon bonds are stable within the large range of temperatures associated with life
This property arises in part because the carbon atom is small relative to most other atoms
The distance between carbon atoms forming a carbon-carbon bond is quite short
Shorter bonds tend to be stronger and more stable than longer bonds, which form between 2 large atoms. For this reason, carbon bonds are compatible with what we observe about life-forms today; namely, living organisms can inhabit environments with a range of temperatures, from Earth’s frigid icy poles to the superheated water of deep-sea vents
Most organic molecules and macromolecules contain functional groups—groups of atoms with characteristic chemical structures and properties
Each type of functional groups exhibits the same chemical properties in all molecules in which it occurs
There are 6 functional groups: hydroxyl, carboxyl, amino, sulfhydryl, phosphate, methyl
The amino group acts like a base. In the pH range found in living organisms, an amino group readily binds H+ to become NH3+, thereby removing H+ from an aqueous solution and raising the pH
Amino groups are found in proteins and also in other types of organic molecules
Two or more molecules with the same chemical formula but different structures and characteristics are called isomers
This depicts 3 ways in which isomers may occur
Structural isomers contain the same atoms but in different bonding relationships
Urea and ammonium cyanate fall into this category
Stereoisomers have identical bonding relationships, but the spatial positioning of their atoms differ
2 types of stereoisomers are cis-transisomers and enantiomers
In cis-trans isomers are the two hydrogen atoms linked to the 2 carbons of a C==C double bond may be on the same side of the carbons, in which case the C==C bond is called a cis double bond
If the hydrogens are on opposite sides, it is a trans double bond
Cis-trans isomers may have very different chemical properties from each other, most notably their stability and sensitivity to heat and light
The light-sensitive region of your eye contains a molecule called retinal, which exists in either a cis or trans form
In darkness, the cis-retinal form predominates
The energy of sunlight, however, causes the retina to isomerize to the trans form. The trans-retinal activates the light-capturing cells in the eye
A second type of stereoisomer, called an enantiomer, exists as one of a pair of molecules that are mirror images
4 different atoms can bind to a single carbon atom in 2 possible ways, designated as a left-handed and a right-handed structure
Many of these are relatively small molecules, however some organic molecules are extremely large macromolecules composed of thousands or even millions of atoms
Such large molecules are formed by linking together many smaller molecules called monomers (meaning one part) and are known as polymers (meaning many parts)
During a condensation reaction, 2 molecules form a covalent bond, usually with the loss of a small molecule. When the small molecule that is lost is water, the condensation reaction is also called a dehydration reaction
The mechanism of dehydration reaction is when the length of a polymer is extended with each dehydration reaction. Some polymers reach great lengths by this mechanism
During the synthesis of DNA, dehydration reactions produce linear strands of DNA that contain millions of monomers called nucleotides
The formation and breakdown of polymers:
Monomers combine to form polymers in living organisms by dehydration reactions, in which a molecule of water is removed each time a new monomer is added to the growing polymer.
Polymers can be broken down into their constituent monomers by hydrolysis reactions, in which a molecule of water is added each time a monomer is released
The process by which a polymer is broken down into monomers is called a hydrolysis reaction, because a molecule of water is added back each time a monomer is released
By analyzing the cells of many different species, researchers have determined that all forms of life have organic molecules and macromolecules that fall into four broad categories, based on their chemical and biological properties: carbohydrates, lipids, proteins, and nucleic acids
Carbohydrates: Simple carbohydrates are metabolized to make ATP which is used as a source of energy. Larger carbohydrates called polysaccharides store energy or may play a structural role, as in plant cell walls. Some carbohydrates function as molecular tags allowing recognition of specific cells and molecules
By breaking its bonds, cells extract ATP or energy from glucose
Examples include simple sugars, such as glucose; larger polysaccharides, such as glycogen, starch, and cellulose
Lipids: Lipids are nonpolar molecules that are primarily composed of carbon and hydrogen, with some oxygen.
lipids are a key part of cell membranes and also function as hormones and an energy storage; in animals, they act as insulators and shock absorbers
examples include phospholipids, estrogen, testosterone, and triglycerides
Proteins: a polypeptide is a structural unit composed of a linear sequence of amino acids. A protein is a functional unit composed of one or more polypeptides
proteins play a key role in cell structure and carry out a diverse array of cellular functions; for example, there are proteins involved with gene expression and regulation, motor proteins, defense proteins, cell signaling proteins, metabolic enzymes, structural proteins, and transporters
Nucleic Acids: a nucleic acid is a linear sequence of nucleotides; DNA is a double-stranded; RNA a single-stranded, but may have double stranded regions
DNA stores genetic information and units called genes. RNA is made from DNA and provides access to the information
Molecules that contain carbon and that are found in all forms of life are called organic molecules
Organic chemistry is defined as the study of Carbon-containing compounds
match these properties of carbon bonding with the resulting effect on the formation of organic molecules:
carbon has four electrons in its outer shell: Carbon can form four covalent bonds with other atoms
the length of a carbon- carbon bond is short: molecules with carbon bonds can function across a broad range of temperatures
carbon atoms can form polar and nonpolar bonds: carbon serves as the backbone for a variety of biologically important organic molecules
The number of covalent bonds a carbon atom can form with other atoms is 4
Covalent bonds that form between molecules of similar electronegativities are nonpolar, while those that are formed between molecules of different electronegativities are polar
What element is found in all organic molecules? Carbon
Which of the following atoms form nonpolar covalent bonds with carbon? Hydrogen and carbon
The science of carbon containing molecules is known as: Organic chemistry
In the chemical structure in this diagram which numbered bond is a polar covalent bond? Bond 3
The chemical structure of propionic acid is shown here. Which of the following numbered bonds is/are nonpolar covalent bonds? Bond 1 because the C-H bonds are nonpolar and Bond 2 because the C-C bonds are nonpolar
What are the three main properties of carbon that are important in forming organic molecules? Carbon can form multiple covalent bonds with other atom, carbon can form both polar and nonpolar bonds, carbon bonds are stable across a broad range of temperatures
How many shells of electrons does carbon have? 2 electrons shells
What are functional groups? Groups of atoms with characteristic chemical features and properties
What determines whether a covalent bond is polar or nonpolar? The difference in the electronegativities of the two atoms
Which of the following functional groups are polar? Hydroxyl group, carbonyl group, amino group
Carbon can form polar covalent bonds with which atoms? Nitrogen and oxygen
Match each chemical formula shown on the left with the correct name of the functional group:
-CO: Carbonyl
-COOH: Carboxyl
-CH3: Methyl
-OH: Hydroxyl
Isomers are molecules that have the same chemical formula but different structures and characteristics
Groups of atoms with characteristic chemical features and properties are called functional groups
Which type of isomers have the same atoms in different bonding relationships? Structural isomers
Which functional group is acidic? The carboxyl group
Considered two molecules that have identical bonding relationships, but defer in the spatial arrangement of their atoms. These types of isomers are referred to as stereoisomers
Which of the following atoms form nonpolar covalent bonds with carbon? Carbon and hydrogen
What are macromolecules? Large molecules that are formed by joining smaller molecules together
Lesson 3.4 carbohydrates
Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen atoms in or close to the proportions represented by the general formula Cn ( H2O)n
Most of the carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl function group. However, other functional groups, such as amino and sulfate groups, are also found in certain carbohydrates
Sugars are small carbohydrates that usually taste sweet. The simplest sugars are monomers known as monosaccharides (from the Greek meaning single sugars).
The most common types of monosaccharides contain either five carbons or six carbons
Important pentosis are ribose and the closely related deoxyribose which are part of RNA and DNA molecules
The most common hexose is glucose. Like other monosaccharides, glucose is very water soluble and circulates in the blood or fluids of animals, where it can be transported across cell membranes
Once inside a cell, enzymes can metabolize glucose into smaller molecules, thereby releasing energy. This energy is then used to produce another molecule, called adenosine triphosphate or ATP, which, in turn, powers a variety of cellular processes, making sugar the source of energy by living organisms
The chemical energy stored in glucose molecules can be harnessed by living organisms. This energy is used to perform numerous functions that support life, including the synthesis of new molecules, growth, digestion, locomotion, and many others
D glucose is the isomer of glucose that is commonly found in living cells. It is recognized by enzymes that can use it as a monomer to synthesize polymers, such as starch. By comparison, l-glucose is rarely found in living cells, and it binds poorly to enzymes that recognize d glucose
other types of isomers are formed by changing the relative position of the hydrogens and hydroxyl groups attached to carbons in the sugar ring
Glucose exists in two interconvertible forms, with the hydroxyl group attached to the number one carbon atom lying either above, or below, the plane of the ring
If the hydroxyl group on carbon atom number four of glucose is above the plane of the ring instead of below it, the sugar is called galactose
Monosaccharides can be linked together by dehydration reactions to form larger carbohydrates. Carbohydrate monomers are also known as monosaccharides
The covalent bond formed between 2 monosaccharides by a dehydration reaction is called a glycosidic bond linkage
Disaccharides which means two sugars are carbohydrates composed of two monosaccharides
A familiar disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose
The linking together of most monosaccharides involves the removal of a hydroxyl group from one amount of saccharide and a hydrogen atom from the other, releasing a molecule of water and covalently bonding the two sugars together through an oxygen atom
The bond formed between two sugar molecules by such a dehydration reaction is called a glycosidic bond
Maltose is a-glucose linked to a-glucose, and lactose is b-galactose linked to b-glucose
When many monosaccharides are linked together to form long polymers, the products are polysaccharides meaning many sugars
Carbohydrate polymers are also called polysaccharides
Starch found in plant cells, and glycogen, found in animal cells, are examples of polysaccharides
The high degree of branching and glycogen contributes to its solubility and animal tissues, such as muscle tissue, because the extensive branching creates a more open structure in which many hydrophilic hydroxide groups that have access to water and can hydrogen bond with it
Some polysaccharides such as starch and glycogen store energy in cells
They can be hydrolyzed to yield monosaccharides, which are metabolized to produce ATP, a common energy source for cells
Other polysaccharides play structural role, rather than storing energy
Cellulose is a major constituent of plant cell walls
Cellulose is a polymer of b-d glucose, with a linear arrangement of carbon- carbon bonds and no branching
Each glucose monomer and cellulose has an opposite orientation from its adjacent monomers
linear chains of cellulose conform hydrogen bonds with each other and thereby arrange themselves in a parallel pattern
The enzymes that break the bonds between monomers of alpha D glucose in starch do not recognize the shape of the cellulose polymer, which is due to the bonds between BD glucose monomers.
Therefore, plant cells can break down starch without breaking down cellulose. In this way, cellulose can be used for other functions, notably in the formation of the rigid cell walls characteristic of plants
Unlike most animals and plants, some organisms do not have enzyme capable of breaking down cellulose
For example, certain bacteria present in the gastrointestinal tracts of grass and wood eaters, such as cows and termites, respectively, can digest cellulose until usable monosaccharides because they contain an enzyme that can hydrolyze the bonds between BD glucose monomers
Other polysaccharides also play structural roles. Chitin, a tough, structural polysaccharide, forms the external skeleton of insects and crustaceans as well as the cell walls of fungi
Glycosaminoglycans are large polysaccharides that play a structural role in animals. They are abundantly found in cartilage, the tough, fibrous material found in joints and other animal structures
Glycosaminoglycans are also abundant in the extracellular matrix that provides the structural framework surrounding many of the cells in an animal's body
Peptidoglycan is the major structural polymer in most bacterial cell walls. It consist of polysaccharides that are cross length via peptide side chains
Lesson 3.5 Lipids
Lipids are hydrophobic molecules composed mainly of hydrogen and carbon atoms, and some oxygen. The defining feature of lipids is that they are nonpolar and therefore insoluble in water. Lipids account for about 40% of the organic matter in the average human body and include fats, phospholipids, steroids, and waxes
They are not considered to be macromolecules because they are not composed of many monomers that are covalently connected. However, lipids may associate with each other non-covalently to form complex structures such as those found in membranes
Triglycerides ( often called fats) are formed when glycerol bonds to three fatty acids. Glycerol is a three carbon molecule with one hydroxyl group bonded to each carbon
Each of the hydroxyl groups in glycerol is linked to the carboxyl group of a fatty acid by the removal of the molecule of water via a dehydration reaction
The formation of a triglyceride occurs via three dehydration reactions in which fatty acids are bonded to glycerol
The fatty acids found in fats and other lipids differ with regard to their lengths and the presence of double bonds. Most fatty acids in nature have an even number of carbon atoms, with 16 and 18 carbon fatty acids being the most common in the cells of plants and animals
Fatty acids are hydrocarbon chains that have a carboxyl functional group at one end and contain either no double bonds between carbons or one or more double bonds
Stearic acid, for example, is an abundant saturated fatty acid in animals, whereas linoleic acid is an unsaturated fatty acid found in plants
The presence of two C==C double bonds introduces 2 kinks into the chain structure of linoleic acid. As a consequence, unsaturated fatty acids are not able to pack together as tightly as saturated fatty acids
Fatty acids also differ with regard to the presence of double bonds. When all of the carbons in a fatty acid are linked by single covalent bonds, the fatty acid is said to be a saturated fatty acid, because all carbons are saturated with covalently bonded hydrogens. The term saturated indicates that each carbon has a maximal number of attached hydrogens.
Unsaturated fatty acids are fatty acids that contains one or more C=C double bonds
Phospholipids, another class of lipids, are similar in structure to triglycerides but with one important difference. In a phospholipid, the third hydroxyl group of glycerol is linked to a phosphate group instead of a fatty acid. In most phospholipids, a small polar or charged nitrogen-containing molecule is attached to this phosphate
The glycerol backbone, phosphate group, and a charged molecule constitute a polar head at one end of the phospholipid, whereas the fatty acid chains form nonpolar tails at the opposite end.
Amphipathic: refers to molecules containing a hydrophobic region and a hydrophilic region
Within human cells, lipids are stored in structures called lipid droplets. The surface of such a droplet has a monolayer of phospholipids and the interior is composed of neutral lipids, such as triglycerides. Some proteins are also attached to the polar head groups of the phospholipids
In water, phospholipids become organized into bilayers, with their polar heads interacting with the water molecules and their nonpolar tails facing the interior of the bilayer, where they’re shielded from water
The bilayer arrangement of phospholipids is critical for determining the structure of cellular membranes
Phospholipids arrange into bilayers because the hydrophilic ends attract water while the hydrophobic ends exclude water and the bilayer is the most energetically favorable arrangement in aqueous solution
The parts that make up the polar hydrophilic region of a phospholipid molecule is the glycerol backbone, phosphate group, and charged nitrogen-containing region
Steroids have a distinctly different chemical structure from the other types of lipid molecules discussed. 4 fused rings of carbon atoms form the general structure of all steroids. 1+ polar hydroxyl groups are attached to the fused ring structure, but they’re not numerous enough to make a steroid highly water-soluble.
Steroids with one hydroxyl group are known as sterols—one of the most well-known being cholesterol
The minor structural differences between estrogen and testosterone dramatically affect their biological functions. The differences between female and male cardinals are one example from the animal world of sex-dependent differences in form and function that are due to these two hormones
In steroids, minor differences in chemical structure result in profoundly different biological properties.
All steroid hormones are derived from cholesterol and share similarities in structure, but with some important differences.
Estrogen is a steroid hormone found in high amounts in female vertebrates. Estrogen differs from testosterone, a steroid hormone found in higher amounts in males, by having one less methyl group, a hydroxyl group instead of a ketone group, and additional double bonds in one of its rings.
Many plants and animals produce lipids called waxes that are secreted onto their surfaces, such as the leaves of plants and the cuticles of insects.
Although any wax may contain hundreds of different compounds, all waxes contain one or more hydrocarbons and long structures that resemble a fatty acid attached by its carboxyl group to another long hydrocarbon chain.
Waxes are very nonpolar and therefore exclude water, providing a barrier to water loss. Some waxes are also used as structural elements–as in the honeycomb in a bee hive, which is made of beeswax
Overall the major classes of lipids are: Steroids, waxes, fats, phospholipids
Lesson 3.6 Proteins
Proteins play critical roles in nearly all life processes. The word protein comes from the greek proteios (meaning of the first rank), which aptly describes their importance. Proteins account for about 50% of the organic material in a typical animal’s body
Major Categories and Functions of Proteins
The monomers of proteins are amino acids
Compounds with a structure in which a carbon atom, called the a-carbon, is linked to an amino group and a carboxyl group. The a-carbon also is linked to a hydrogen atom and a side chain, designated with the letter R. Proteins are polymers of amino acids
When an amino acid is dissolved in water at neutral pH, the amino group accepts a hydrogen ion and is positively charged, whereas the carboxyl group loses a hydrogen ion and is negatively charged. Such molecules are called amino acids because they have an amino group and also a carboxyl group that acts as an acid
All amino acids except glycine exist in more than one isomeric form, called the d and l forms, which are enantiomers. An exception is in the cell walls of certain bacteria, where d-amino acids may play a protective role against molecules secreted by the host organism in which the bacteria live
The 20 amino acids in proteins are distinguished by their side chains
The amino acids are categorized by whether their side chains are nonpolar, polar and uncharged, or polar and charged
The structures of the side chains are critical features of protein structure and function
Amino acids are joined together by a chemical reaction that covalently links the carboxyl group of one amino acid to the amino group of another
To link these two amino acids together to form a dipeptide, the carbon in the carboxyl group of the first 2 amino acids together to form a dipeptide, the carbon in the carboxyl group of the first amino acid forms a covalent bond with the nitrogen in the amino group of the second amino acid. This type of bond is called a peptide bond
The first amino acid has been detached from its tRNA. In the dipeptide containing the two amino acids, the other tRNA remains attached to the second amino acids. This process can be repeated many times to create a polypeptide composed of many amino acids
When two or more amino acids are linked together, one end of the resulting polypeptide has a free amino group. This end is the amino end, also called the N-terminus, because it has a nitrogen atom. The other end of the polypeptide is called the carboxyl end, or C-terminus, because it has a carbon atom; the C-terminus has a free carboxyl group
mRNA provides the information for the synthesis of a polypeptide with a defined amino acid sequence. This information gives the polypeptide directionality: The first amino acid that is specified by the mRNA is at the N-terminus and the last amino acid specified is at the C-terminus.
Polypeptides are polymers of amino acids. They’re formed by linking amino acids via peptide bonds. This process is called translation. Each amino acid that is added to the polypeptide is initially attached to a tRNA molecule, which looks like a cloverleaf.
When translation is completed, the last tRNA is removed. Every polypeptide has an amino end, or N-terminus, and a carboxyl end, or C-terminus
How many peptide bonds would be produced during the formation of a polypeptide that is 72 amino acids long? The process would produce 71 peptide bonds, one less than the number of amino acids in the polypeptide
A protein is a functional unit composed of one or more polypeptides that have folded and twisted into a precise 3D shape
Scientists describe protein structure at 4 progressive levels: primary, secondary, tertiary, and quaternary. Each higher level of structure depends on the preceding levels.
Changing the primary structure may affect the secondary, tertiary, and quaternary structures
The primary structure of a protein is the amino acid sequence of its polypeptides. The primary structure of proteins is determined by genes.
The protein Ribonuclease functions as an enzyme to degrade ribonucleic acid molecules after they are no longer required by a cell
Ribonuclease is composed of a relatively short polypeptide consisting of 124 amino acids. Considering that most polypeptides contain between 50 and 2,000 amino acids
Human B-globin, which is composed of 146 amino acids, is a polypeptide that is a component of the protein called hemoglobin, which carries oxygen throughout the body
Mutations within genes can alter the amino acid sequence of a polypeptide and thereby affect protein function. Remarkably, a mutation in the b-globin gene that changes a single amino acid in the b-globin polypeptide has a profound effect on human health.
Changing the 6th amino acids from a glutamic acid to a valine causes sickle cell disease.
Amino acid sequence of a polypeptide causes the polypeptide to fold into a more compact structure.
Amino acids can rotate around bonds within a polypeptide. Consequently, these chains are flexible and can fold into a number of shapes, just as a string of beads can be twisted into many configurations.
Folding can be irregular, or certain regions can have a repeating folding pattern called secondary structure. The 2 basic types of secondary structure are the a helix and the b pleated sheet
The hydrogen linked to a nitrogen atom forms a hydrogen bond with an oxygen atom that is double-bonded to a carbon atom. These hydrogen bonds occur at regular intervals along the polypeptide backbone and cause the backbone to twist into a helix
In a b pleated sheet, regions of the polypeptide backbone lie parallel to each other. Hydrogen bonds between a hydrogen linked to a nitrogen atom and a double-bonded oxygen form between these adjacent, parallel regions.
When this occurs, the polypeptide backbone adopts a repeating zigzag, or pleated, shape
The a helices and b pleated sheets are key determinants of a protein’s characteristics.
a-helices in certain proteins are composed primarily of nonpolar amino acids. Proteins containing stretches of nonpolar amino acids tend to anchor themselves into a lipid-rich environment, such as a cell’s plasma membrane
A protein whose function is required in a specific location such as a plasma membrane can be retained there.
Secondary structure also contributes to the great strength of certain proteins, including the keratins found in hair and hooves, the proteins that make up the silk webs of spiders, and collagen, the chief component of cartilage in vertebrate animals.
As the secondary structure of a polypeptide becomes established due to the particular primary structure, side chains of amino acids interact with each other.
The polypeptide folds and refolds upon itself to assume a 3D shape—its tertiary structure. The tertiary structure is the 3D shape of a single polypeptide. Tertiary structure includes all secondary structures plus any interactions involving amino acid side chains.
Most proteins are composed of 2+ polypeptides that each adopt a tertiary structure and then assemble with each other. The individual polypeptides are called protein subunits.
Subunits may be identical polypeptides, or they may be different. When proteins consist of more than one polypeptide, they are said to have quaternary structure.
The five factors are critical for protein folding and stability:
1. Hydrogen bonds. The large number of weak hydrogen bonds within a polypeptide and between polypeptides collectively produces a strong force that promotes protein folding and stability. As mentioned, hydrogen bonding is a critical determinant of protein secondary structure and also is important in tertiary and quaternary structure
2. Ionic bonds and other polar interactions. Some amino acid side chains are positively or negatively charged. Positively charged side chains may bind to negatively charged side chains via ionic bonds. Similarly, uncharged polar side chains in a protein may bind to ionic amino acids. Ionic bonds and polar interactions are particularly important in tertiary and quaternary structure.
3. Hydrophobic effect. Some amino acid side chains are nonpolar. As a protein folds, the nonpolar amino acids are likely to be found in the center of the protein, minimizing their contact with water. Some proteins have stretches of nonpolar amino acids that anchor the proteins in the hydrophobic portion of membranes. The hydrophobic effect plays a major role in tertiary and quaternary structures.
4. Van der Waals dispersion forces. Atoms within molecules have temporary weak attractions for each other if they are an optimal distance apart. These weak attractions are termed van der Waals dispersion forces. If 2 atoms are too close together, their electron clouds will repel each other. If they are far apart, the van der Waals dispersion forces will diminish. The van der Waals dispersion forces contribute to tertiary structure and quaternary structure.
5. Disulfide bridges. The side chain of the amino acid cysteine contains a sulfhydryl group, which can react with a sulfhydryl group in another cysteine side chain and form a covalent bond. The result is a disulfide bridge, or disulfide bond, which links the two amino acid side chains together. Disulfide bridges can occur within a polypeptide or between different polypeptides. Though other forces are usually more important in protein folding, the covalent nature of disulfide bridges can help to stabilize the structure of a protein.
Ribonuclease was exposed to a chemical called b-mercaptoethanol, which breaks S–S bonds, and to urea, which disrupts hydrogen and ionic bonds. This treatment caused ribonuclease to be denatured, that is, to become unfolded.
The hypothesis that Anfinsen was testing was that the information necessary for determining the three dimensional shape of a protein is contained within the protein itself. In other words, the chemical characteristics of the amino acids that make up a protein determine the protein’s 3D shape
The urea and b-mercaptoethanol were used in the experiment because the urea disrupts hydrogen and ionic bonds that are necessary for protein folding. The b-mercaptoethanol breaks the S—S bonds that form between certain amino acids of the same polypeptide. Both substances cause the polypeptide to unfold, disrupting the 3D shape
The result that was crucial to the discovery that the tertiary structure of ribonuclease may depend entirely on the primary structure. Anfinsen removed the urea and b-mercaptoethanol from the ribonuclease by size-exclusion chromatography. After removing these substances, Anfinsen discovered that the protein refolded into its proper 3D shape and became functional again. This was important because the solution at that point contained only the protein and lacked any other cellular material that could possibly assist in protein folding. This demonstrated that the protein could refold itself into the functional conformation.
Lesson 3.7 Nucleic Acids
Nucleic acids are organic macromolecules that account for about 2% of the weight of animals like humans, yet these molecules are extremely important because they are responsible for the storage, expression, and transmission of genetic information. The expression of genetic information in the form of specific proteins determines whether an organism is a human, a frog, an onion, or a bacterium.
The two classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
DNA molecules store genetic information coded in the sequence of their building blocks. RNA molecules are involved in decoding this information into instructions for linking a specific sequence of amino acids to form a polypeptide
The monomers in DNA must be arranged in a precise way so that the correct code can be read
Like other macromolecules, DNA and RNA are polymers consisting of linear sequences of repeating monomers. Each monomer, known as a nucleotide, has 3 components:
1: A phosphate group, 2: a pentose (five-carbon) sugar (either ribose or deoxyribose), and 3: a single or a double ring of carbon and nitrogen atoms known as a base
A nucleotide of DNA is called a deoxyribonucleotide; one of RNA is a ribonucleotide. The nucleotides in DNA contain the 5-carbon sugar deoxyribose.
4 different nucleotides are present in DNA, corresponding to the 4 different bases that can be linked to deoxyribose. The purine bases, adenine and guanine, have a fused double ring of carbon and nitrogen atoms, and the pyrimidine bases, cytosine and thymine, have a single-ring structure
A DNA molecule consists of 2 strands of nucleotides coiled around each other to form a double helix. The two strands are held together by hydrogen bonds between a purine base in one strand and a pyrimidine base in the opposite strand.
Nucleotides are covalently linked together to form strands of DNA. The phosphates and sugar molecules form the backbone of a DNA strand, with the bases projecting from the backbone
If the sequence of bases in one strand of a DNA double helix is known, the base sequence of the opposite strand can be predicted because it has to be complementary to the first strand, because A must be paired with T, and G with C. For instance, if a portion of the first strand has the sequence AATGCA, the opposite strand for that portion will be TTACGT
In a DNA molecule, A on one strand pairs with T on the opposite strand, and G pairs with C.
Such a rare event can result in a mutation that alters the sequence of bases in the DNA.
If we know the amount of one type of base in a DNA molecule, we can predict the relative amounts of each of the other 3 bases.
If a DNA molecule is composed of 20% A, it must also have 20% of T. That leaves 60% of the bases that must be G and C combined. Because the amounts of G and C must be equal, this particular DNA molecule must contain 30% each of G and C. This specificity provides the mechanism for duplicating and transferring genetic information
RNA structure differs in only a few respects from DNA structure. Like DNA, RNA consists of nucleotides covalently linked together. RNA usually consists of a single strand of nucleotides. In RNA, the sugar in each nucleotide is ribose instead of deoxyribose. Also, the pyrimidine base thymine found in DNA is replaced in RNA with the pyrimidine base uracil. The other three bases found in DNA–adenine, guanine, and cytosine–are also found in RNA
27 concepts based on chapters 4.1, 4.2, and 4.3:
Cell theory:
Identify the three parts of the cell theory:
Cells are the smallest units of life
All living organisms are composed of one or more cells
New cells come only from pre-existing cells by cell division
Which of these statements is not a part of the cell theory? All cells are replaced
New cells come only from pre-existing cells by cell division
All cells are replaced
All living organisms are composed of one or more cells
Cells are the smallest units of life
4.3 Overview of Cell Structure and Function:
Which of the following factors determine cell structure? Matter, energy, organization, and information
What is the term used for the complete set of genetic material present in a cell or organism? Genome
What are the two types of life forms? Prokaryotes and eukaryotes
Prokaryotes differ from eukaryotes because they lack a membrane-enclosed nucleus or nuclei, which houses the DNA
The structure and function of cells are determined by three factors: matter, energy, and organization. True or false? False
The entire complement of the genetic material of a species is its genome
Based on cell structure, all life forms can be placed into 2 categories called prokaryotes and eukaryotes
What is the phospholipid bilayer barrier between the cell and its external environment called? Plasma membrane
In a bacterial cell, the region of the cell contained within the plasma membrane is called the cytoplasm
Where is the DNA housed in a bacterial cell? Nucleoid region
What structure functions in polypeptide synthesis? Ribosome
What is the term used for the complete set of genetic material present in a cell or organism? Genome
4.1 - Origin of Living Cells on Earth:
The interaction of which of the following macromolecules plays an important role in the formation of living cells? DNA, RNA, and Proteins
DNA
RNA
Carbohydrates
Proteins
Lipids
Stage 3: Cell-like Structures May Have Originated When Polymers Were Enclosed by a Boundary:
It’s during the third stage in the origin of life that an outer boundary formed to separate the internal polymers from the environment.
In protobionts, a boundary such as a lipid bilayer separates internal polymers from the environment.
Stage 2: Organic Polymers May Have Formed on the Surface of Clay:
The origin of life was likely preceded by a period in which small organic molecules accumulated on what surface? Clay
Which macromolecule forms the foundation for the structure and activities of living cells? Protein
During the second stage in the origin of life, small organic molecules polymerized to form which of the following on the surface of clay?
Macromolecules because organic molecules cannot polymerize to form microorganisms, which are made of cells. Under the correct conditions, they can polymerize to form larger molecules called macromolecules.
Stage 4: Cellular Characteristics May Have Evolved via Chemical Selection, Beginning with an RNA World:
Which of the following are crucial functions of RNA?
1. RNA has the ability to store information in its nucleotide base sequence
2. Due to base pairing, its nucleotide sequence has the capacity for self-replication
3. RNA can perform a variety of catalytic functions. The results of many experiments have shown that some RNA molecules can function as ribozymes—RNA molecules that catalyze chemical reactions
The three key functions of RNA are its ability to store information in its nucleotide sequence, its capacity for self-replication, and its ability to perform a variety of catalytic functions.
The RNA World Was Superseded by the Modern DNA/RNA/Protein World:
The different chemical properties of amino acids have given proteins greater catalytic ability than RNA molecules.
How would early cells benefit from DNA replacing RNA as the information storage molecule? Information would be stored in a more stable molecule and RNA would have more flexibility in its catalytic function
4.2 Microscopy:
A magnification tool that enables researchers to study the structure and function of cells is the microscope
Microscopes can be divided into two main categories based on the source of illumination
Which of these is an optical instrument that allows researchers to view and study very small objects, such as cellular structures? Microscope
What is the main difference between a light and electron microscope? The source of illumination
A light microscope utilizes light for illumination, whereas an electron microscope uses a beam of electrons
When did life begin?
Origin of simple organic molecules
Reducing atmosphere hypothesis: Organic molecules formed in reducing atmosphere and slowly accumulated.
Extraterrestrial hypothesis: Meteorites brought organic molecules to Earth
Deep-sea vent hypothesis: H2S + Fe —> FeS2 + H2; Provides energy
Origin of polymers
Monomers (amino acids, nucleotides) turn to polymers (proteins, RNA, and DNA)
Solid surface from clay helping concentration of polymers increase
Could have also happened in evaporating tidal pools
Formation of boundaries
Protobiont: Aggregate of prebiotically produced molecules and macromolecules.
Has acquired a boundary allowing it to maintain distinct internal chemical environment
Beginning of RNA World
3 key RNA functions: Ability to store information, capacity for self-replication, enzymatic function (ribozymes)
DNA and proteins cannot do all 3 functions
Majority of scientists favor RNA as the first macromolecule of protobionts
Smartbook Assignment #8: Sections 4.4-4.8
4.4: The Cytosol
We will start with the cytosol: The region of a eukaryotic cell that is inside the plasma membrane and outside the organelles
Although many steps of metabolism also occur in cell organelles, the cytosol is a central coordinating region for many metabolic activities of eukaryotic cells
Some metabolic pathways involve the breakdown of a molecule into smaller components, a process termed catabolism
The metabolic reactions that break down larger molecules into smaller components are referred to as catabolism or catabolic
Anabolism is when a metabolic pathway that results in the synthesis of cellular molecules and macromolecules; requires an input of energy
The cytoskeleton is a network of three different types of protein filaments: microtubules, intermediate filaments, and actin filaments
Microtubules: a type of hollow protein filament composed of tubulin proteins that is part of the cytoskeleton and is important for cell shape, organization, and movement.
Intermediate filament: A type of protein filament of the cytoskeleton of animal cells that helps maintain cell shape and rigidity
Actin filaments: A thin type of protein filament that is composed of actin proteins, forms part of the cytoskeleton, and supports the plasma membrane; plays a key role in cell strength, shape, and movement
Types of Cytoskeletal Filaments Found in Eukaryotic Cells:
Dynamic instability: The oscillation of a single microtubule between growing and shortening phases; important in many cellular activities, including the sorting of chromosomes during cell division
Microtubule-organizing center (MTOC): A site in eukaryotic cell from which microtubules grow
Centrosome: A single structure often near the nucleus of a eukaryotic cell that forms a nucleating site for the growth of microtubules; also called a microtubule-organizing center
Centrioles: A pair of structures within the centrosome of animal cells. Most plant cells and many protists lack centrioles
Microfilaments: Actin filaments; they’re long, thin fibers approximately 7nm in diameter
Pseudopodia: Temporary, finger-like projections of the plasma membrane that are used for cell movement and for engulfing particles
Motor proteins: A type of cellular protein that uses ATP as a source of energy to promote movement; consists of three domains called the head, hinge, and tail
The head is the site where ATP binds and is hydrolyzed to adenosine diphosphate (ADP) and inorganic phosphate (Pi)
Motor proteins can cause three kinds of movements: movement of cargo via the motor protein, movement of the filament, or bending of the filament.
Movement of cargo: The filament is fixed in place. The tail region of a motor protein called kinesin is attached to a cargo, and the motor protein moves the cargo from one location to another
Movement of the filament: A motor protein called myosin can remain in place and cause the filament to move. This occurs during muscle contraction
Bending of the filament: A third possibility is that both the motor protein and the filament are restricted in their movement due to the presence of linking proteins. In this case, when motor proteins called dynein attempt to walk toward the minus end, they exert a force that causes the microtubules to bend
In certain kinds of cells, microtubules and motor proteins facilitate movement involving cell appendages called flagella and cilia (singular, flagellum and cilium
The difference between the two is that flagella are usually longer than cilia and are typically found singly or in pairs
Flagella: Relatively long cell appendages that facilitate cellular movement or the movement of extracellular fluids
Cilia (singular, cilium): Cell appendages that have the same internal structure as flagella and function like flagella to facilitate cell movement; cilia are shorter and more numerous than are flagella
Axoneme: An internal structure of eukaryotic flagella and cilia that contains microtubules, the motor protein dynein, and linking proteins
Basal bodies: A site at the base of flagella or cilia from which microtubules grow. Basal bodies are anchored on the cytosolic side of the plasma membrane
4.5: The Nucleus and Endomembrane System
Nucleus (plural, nuclei):
In cell biology, an organelle is found in eukaryotic cells that contains most of the cell’s genetic material.
In chemistry, the region of an atom that contains protons and neutrons
In neurobiology, a group of neuronal cell bodies in the CNS that are involved in a particular function
The major functions of the nucleus are gene regulation and protecting the genome
Endomembrane system: A network of membranes that includes the nuclear envelope, the endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, peroxisomes, and plasma membrane
The nucleus is the compartment that is enclosed by a double-membrane structure termed the nuclear envelope and houses the genetic material
Nuclear pores: A passageway for the movement of molecules and macromolecules into and out of the nucleus; formed where the inner and outer nuclear membranes make contact with each other
Although cell biologists view the nuclear envelope as part of the endomembrane system, the materials within the nucleus are not
Chromosome: A discrete unit of genetic material composed of DNA and associated proteins. Eukaryotes have chromosomes in their cell nuclei and in plastids and mitochondria
The complex formed between DNA and such proteins is termed chromatin
Another way to say it is the complex of DNA and proteins in a eukaryotic cell is referred to as chromatin
The nuclear matrix consists of two parts: the nuclear lamina, which is composed of intermediate filaments that line the inner nuclear membrane, and an internal nuclear matrix, which is connected to the lamina and fills the interior of the nucleus.
Chromosome territory: A distinct area where each chromosome is located within the cell nucleus of eukaryotic cells; chromosome territories do not overlay
The primary functions of the nucleus are the protection, organization, replication, and expression of the genetic material
Another important function is the assembly of ribosomal subunits–cellular structures involved in producing polypeptides during the process of translation
The assembly of ribosomal subunits occurs in the nucleolus (plural, nucleoli), which is a droplet organelle in the nucleus of nondividing cells
Ribosome assembly occurs in an area of the nucleus called the nucleolus
A ribosome is composed of two subunits: one small and one large. Each subunit contains one or more RNA molecules and several types of proteins
The endoplasmic reticulum (ER) is a network of membranes that form flattened, fluid-filled tubes, or cisternae. The terms endoplasmic (Greek, for in the cytoplasm) and reticulum (Latin, for little net) refer to the location and shape of this organelle when viewed under a microscope
The membranes of the endoplasmic reticulum form cisternae and fluid-filled tubules
Lumen: The internal space of an organelle (or an organ). The ER membrane encloses a single compartment called the ER lumen
There are two distinct, but continuous types of ER: Rough ER and smooth ER
The outer surface of the rough endoplasmic reticulum (rough ER) is studded with ribosomes, giving it a bumpy appearance.
Rough ER plays a key role in the sorting of proteins that are destined for the ER, Golgi apparatus, lysosomes, vacuoles, plasma membrane, or extracellular environment.
The organelles that play a role in sorting proteins that are destined for the Golgi apparatus, lysosomes, vacuoles, plasma membrane, or outside of the cell is the rough endoplasmic reticulum
Proteins are packaged into membrane vesicles—small spheres enclosed by a membrane–and moved from one location in the endomembrane system to another
Organelles of the endomembrane system can pass proteins to each other via small, membrane-enclosed spheres known as vesicles
Glycosylation: The covalent attachment of a carbohydrate to a protein or lipid, producing a glycoprotein or glycolipid, respectively
The smooth endoplasmic reticulum (smooth ER), which lacks ribosomes, functions in diverse metabolic processes
The smooth ER is continuous with the rough ER
The organelle that consists of an extensive network of membranes which provides a large surface area for enzymes that play important metabolic roles is the smooth ER
Metabolism: The extensive network of smooth ER membranes provides a large surface area for enzymes that play important metabolic roles
Golgi apparatus (also called the Golgi body, Golgi complex, or simply Golgi): was discovered by microscopist Camillo Golgi in 1898.
Consists of a stack of flattened membranes, with each flattened membrane enclosing a single compartment called a cisterna (plural, cisternae).
The cis Golgi is near the ER membrane, the trans Golgi is closest to the plasma membrane, and the medial Golgi is found in the middle
Vesicular transport model: Materials are transported between the golgi cisternae via membrane vesicles that bud from one compartment in the golgi and fuse with another compartment
Cisternal maturation model: Vesicles from the ER fuse to form a cisterna at the cis face; the cisterna that was previously at the cis face becomes a medial cisterna. This addition of a cisterna moves the other medial cisternae toward the trans face. A cisterna at the trans face is lost as a result of the export of vesicles from its surface
The Golgi apparatus performs three overlapping functions: processing, protein sorting, and secretion
Proteolysis: A processing event within a cell in which enzymes called proteases cut proteins into smaller polypeptides
Secretory vesicle: A membrane vesicle carrying different types of materials that fuses with the cell’s plasma membrane to release the contents extracellularly
Secretory pathway: A pathway for the movement of larger substances, such as carbohydrates and proteins, from the ER to the outside of a cell
Palade chose to study the cells of the pancreas. This organ secretes enzymes and protein hormones that play a role in digestion and metabolism. Therefore, these cells were chosen because their primary activity is protein secretion.
To study the pathway for protein secretion, the researchers injected a radioactive version of the amino acid leucine into the bloodstream of male guinea pigs. The radiolabeled leucine traveled in the bloodstream and was quickly taken up by the guinea pigs’ cells, including those in the pancreas
At various times after the second injection, samples of pancreatic cells were removed from the animals. The cells were then prepared for transmission electron microscopy (TEM)
The same was stained with osmium tetroxide, a heavy metal compound that became bound to membranes and showed the locations of the cell organelles. In addition, the sample was coated with a radiation-sensitive emulsion containing silver
When radiation was emitted from the radiolabeled proteins, it interacted with the emulsion in a way that caused the precipitation of silver, which became tightly bound to the sample.
In this way, the precipitated silver marked the location of the radiolabeled proteins. Unprecipitated silver in the emulsion was later washed away. Because silver atoms are electron-dense (allowing few electrons to pass), they produce dark spots in a TEM. Therefore, dark spots revealed the locations of radiolabeled proteins.
Palade’s pulse-chase experiment in order:
Inject guinea pigs with a radioactive amino acid, [3H]-leucine
Inject guinea pigs with nonlabeled leucine
Remove samples of pancreatic cells at various times
Stain the sample with osmium tetroxide, which a heavy metal that binds to membranes
Cut thin sections of the samples and place a thin layer of radiation-sensitive emulsion over the sample
Observe the sample under a transmission electron microscope
Lysosomes: Small organelles that are found in animal cells and break down molecules and macromolecules.
Lysosomes contain many acid hydrolases, which are hydrolytic enzymes that use a molecule of water to break a covalent bond
Vacuoles use prominent organelles in plant cells, fungal cells, and certain protists. The term vacuole (Latin, for empty space) came from early microscopic observations of these compartments.
We now know that vacuoles are not empty but instead contain fluid and sometimes even solid substances.
Most vacuoles are made from the fusion of many smaller membrane vesicles. Vacuoles in animal cells tend to be smaller than those in plants and are more commonly used to temporarily store materials or transport substances. Such vacuoles are sometimes called storage vesicles.
Contractile vacuole: A small, membrane-enclosed, water-filled compartment that eliminates excess liquid from the cells of certain protists.
Peroxisomes, discovered by Christian de Duve in 1965, are small organelles found in all eukaryotic cells
Peroxisomes catalyze certain cell reactions are found in all eukaryotic cells, therefore, all eukaryotic cells contain peroxisomes
The cytoplasm of eukaryotic cells is surrounded by a plasma membrane, which is part of the endomembrane system and provides a boundary between a cell and the extracellular environment. Proteins in the plasma membrane perform many important functions that affect the activities inside the cell
4.7 Protein Sorting to Organelles
In eukaryotes, most proteins contain short stretches of amino acid sequences that direct them to their correct cellular location. These sequences are called sorting signals, or traffic signals.
Each sorting signal is recognized by specific cellular components that facilitate the proper movement of the protein carrying that signal to its correct location
To be directed to the rough ER membrane, a polypeptide must contain a sorting signal called an ER signal sequence, which is a sequence of about 6-12 amino acids that are predominantly hydrophobic and usually located near the N-terminus of the polypeptide
4.8 Systems Biology of Cells: A summary
System biology, the study of how new properties of life emerge through complex interactions of its components. The system being studied can be anything from a metabolic pathway to a cell, an organ, or even an entire organism.
Bacterial cells are relatively small and lack the extensive internal compartmentalization characteristic of eukaryotic cells.
On the outside, bacterial cells are surrounded by a cell wall, and many species have flagella.
Animal cells lack a cell wall, and only certain cell types have flagella or cilia.
Like bacteria, plant cells also have cell walls but the chemical composition of these walls is different from that of bacterial cells.
Plant cells rarely have flagella
The inner membrane of a mitochondrion is highly invaginated to form projections called cristae
The membranous system of flattened sacs in a chloroplast are called thylakoids
Smartbook #9-Chapter 5 Sections 5.1-5.2, 5.4, 5.6
Cystic Fibrosis is a genetic disease caused by a mutation in a gene called CFTR, which codes a protein named the cystic fibrosis conductance transmembrane regulator
CFTR is a protein that functions in the transport of chloride ions across the plasma membrane of certain types of cells, such as those in the lungs and in the pancreas
CF illustrates the importance of the plasma membrane, which encloses the cytoplasm. In addition, eukaryotic cells have internal membranes that surround organelles. Both types are also called biological membranes
The plasma membrane separates the internal contents of a cell from its external environment
All biological membranes, including the plasma membrane are thin (typically 5-10 nm) and somewhat fluid. It would take 5,000-10,000 of these membranes stacked on top of each other to equal the thickness of a piece of paper
Biological membranes exhibit the property of fluidity, which means that individual molecules remain in close association yet have the ability to readily move within the membrane
Though membranes are often described as fluid, it’s more appropriate to say they are semifluid because the movement of membrane components occurs only in two dimensions. In a fluid substance, molecules can move in three dimensions.
Most phospholipids can rotate freely around their long axes and move laterally within the membrane leaflet. This type of motion occurs in two dimensions, that is, within the plane of the membrane
Rotational and lateral movements keep the lipid tails within the hydrophobic interior, such movements are energetically favorable.
Lipid raft is a group of lipids that float together as a unit within a larger sea of lipids.
Lipid rafts have a lipid composition that differs from the surrounding membrane. Like usually having a high amount of cholesterol. In addition, lipid rafts may contain unique sets of lipid-anchored proteins and transmembrane proteins.
The presence of membrane proteins within lipid rafts may facilitate interactions between the membrane proteins in a given raft.
The functional importance of lipid rafts is the subject of a large amount of current research.
Unsaturated is the property of certain lipids that contain one or more C==C double bonds
A third factor affecting fluidity is the presence of cholesterol, a short and rigid molecule produced by animal cells.
The cells of many species adapt to changes in temperature by altering the lipid composition of their membranes.
For example, when the water temperature drops, the cells of certain fish will incorporate more cholesterol into their membranes, making the membrane more fluid.
If a plant cell is exposed to high temperatures for many hours or days, it will alter the lipid composition of its cell membranes to have longer lipid tails and fewer double bonds, which will make the membrane less fluid
If the cells were maintained at 0 degrees celsius, a temperature that greatly inhibits lateral movement, the fluorescence was seen on only one side of the fused cell.
If the cells were incubated for several hours at 37 degrees celsius, and then cooled to 0 degrees celsius, the fluorescence was distributed throughout the plasma membrane of the fused cell. This occurred because the higher temperature allowed the lateral movement of the H-2 protein throughout the fused cell
The lipids made in the ER membrane are transferred to other membranes in the cell by a variety of mechanisms
Phospholipids in the ER can diffuse laterally to the nuclear envelope.
Lipids are transported via vesicles to the Golgi, lysomes, vacuoles, or plasma membrane
A third mode of lipid transfer involves lipid exchange proteins, which extract a lipid from one membrane, diffuse through the cell, and insert the lipid into another membrane. Such transfer can occur between any two membranes, even between the endomembrane system and semiautonomous organelles.
Example: The lipid exchange proteins transfer lipids between the ER and mitochondria. In addition, chloroplasts and mitochondria synthesize certain types of lipids that are transferred from these organelles to other cellular membranes via lipid exchange proteins.
Glycosylation is the process of covalently attaching a carbohydrate to a lipid or protein
When a carbohydrate is attached to a lipid, a glycolipid is created, whereas attachment of a carbohydrate to a protein produces a glycoprotein
Glycolipids and glycoproteins often play a role in cell surface recognition. When glycolipids and glycoproteins are found in the plasma membrane, the carbohydrate portion is located in the extracellular region.
Two forms of protein glycosylation occur in eukaryotes: N-linked and O-linked.
N-linked glycosylation, which also occurs in archaea, involves the attachment of a carbohydrate to the amino acid asparagine in a polypeptide.
It’s called N-linked because the carbohydrate is attached to a nitrogen atom of the asparagine side chain
O-linked glycosylation occurs only in the Golgi apparatus, and involves the addition of a string of sugars to the oxygen atom of a serine or threonine side chain in a polypeptide.
Membrane transport-the movement of ions and molecules across biological membranes. All cells contain a plasma membrane that exhibits selective permeability, allowing the passage of some ions and molecules but not others.
Substances can move directly across a membrane in three ways:
Simple diffusion occurs when a substance moves across a membrane from an area of high concentration to one of lower concentration by passing directly through the phospholipid bilayer. This direction of movement is also referred to as a movement down a concentration gradient or downhill movement
A second mechanism of membrane transport is facilitated diffusion, in which a transport protein provides a passageway for a substance to cross a membrane from an area of higher concentration to one of lower concentration. Both simple diffusion and facilitated diffusion are types of passive transport–the movement of a substance across a membrane from an area of high concentration to one of lower concentration, which does not require an input of energy
The third mode of membrane transport, called active transport, moves a substance from an area of low concentration to one of high concentration with the aid of a transmembrane protein. This direction of movement is also referred to as movement against a concentration gradient or uphill movement. Active transport requires an input of energy from a source such as ATP
The phospholipid bilayer is a barrier to the simple diffusion of ions and polar (hydrophilic) molecules because of their hydrophobic interiors
Such ions and molecules are called solutes; they are dissolved in water, which is a solvent. Four factors affect the ability of solutes to pass through a phospholipid bilayer:
Size: small solutes cross bilayers faster than larger ones
Polarity: nonpolar solutes cross bilayers faster than polar ones
Charge: noncharged solutes cross bilayers faster than charged ones
Concentration: the rate of movement of a solute across a membrane will be higher when its concentration is higher
When we speak of a transmembrane gradient or concentration gradient, we mean that the concentration of a solute is higher on one side of a membrane than on the other. Transmembrane gradients of solutes are a universal feature of all living cells.
For example, immediately after you eat a meal containing carbohydrates, a higher concentration of a glucose is found outside your cells than inside; this is an example of a chemical gradient
Electrochemical gradient: a dual gradient across a membrane, having both electrical and chemical components; determines the direction in which ions will move.
When the concentrations of solutes on both sides of the plasma membrane are equal, the two concentrations are said to be isotonic
When the concentration of solutes outside the cell is higher, the outside is said to be hypertonic relative to the inside of the cell. Alternatively, the outside of the cell could be hypotonic–have a lower concentration of solutes than the inside
If solutes cannot readily move across the membrane, water will do so and tend to balance the solute concentrations. In this process, called osmosis, water moves across a membrane from the hypotonic compartment (with a lower solute concentration) into the hypertonic compartment (with a higher solute concentration)
How does osmosis affect cells with a rigid cell wall, such as bacteria, fungi, algae, and plant cells? If the extracellular fluid is hypotonic, a plant cell will take up a small amount of water, but cell wall prevents osmotic lysis from occurring.
Alternatively, if the extracellular fluid surrounding a plant cell is hypertonic, water will exit the cell and the plasma membrane will pull away from the cell wall, a process called plasmolysis.
Eukaryotic cells have two other mechanisms, exocytosis and endocytosis, for transporting larger molecules, such as proteins and polysaccharides, and even very large particles
During exocytosis, material inside the cell is packaged into vesicles and then excreted into the extracellular environment. These vesicles are usually derived from the Golgi apparatus.
During endocytosis, the plasma membrane invaginates, or folds inward, to form a vesicle that brings substances or particles into the cell. Three types of endocytosis are receptor-mediated endocytosis, pinocytosis, and phagocytosis.
Receptor-mediated endocytosis: A common type of endocytosis in which a receptor in the membrane is specific for a given cargo
Pinocytosis: A type of endocytosis that involves the formation of membrane vesicles from the plasma membrane as a way for cells to internalize the extracellular fluid
Phagocytosis: A type of endocytosis that involves the formation of a membrane vesicle, called a phagosome or phagocytic vacuoles, which engulfs a particle such as a bacterium
Questions for 5.1-5.6
The three main molecular components of cellular membranes are phospholipids, carbohydrates, proteins
The structure that separates the internal contents of a cell from the extracellular environment is the plasma membrane
The plasma membrane consists of a lipid bilayer
The fatty acid tails of phospholipids are nonpolar and are found in the interior of the phospholipid bilayer
The plasma membrane is enclosed in the cytoplasm
The cell membrane is referred to as a mosaic because it is a mixture of lipids, carbohydrates, and proteins
The three main molecular components of the plasma membrane are lipids, proteins, and carbohydrates
Membrane proteins and lipids are able to move relative to one another within the plasma membrane according to the fluid-mosaic
The basic structure of the plasma membrane is a phospholipid bilayer
Transmembrane protein: A segment of amino acids is inserted into the phospholipid bilayer; lipid-anchored protein: A lipid molecule is covalently attached to an amino acid side chain of the membrane protein; peripheral membrane protein: Noncovalent associations form with phospholipids or other membrane proteins
Membrane proteins that span both leaflets of the lipid bilayer have transmembrane segments that are composed of nonpolar amino acids
Phospholipids have a hydrophilic head region that will interact with aqueous environments
Most transmembrane segments of integral membrane proteins are folded into alpha-helix secondary structures
Because the plasma membrane contains lipids, proteins, and carbohydrates, it is often described as a mosaic
Integral membrane proteins include: Lipid-anchored proteins and transmembrane proteins
The model used to explain the structure, organization and dynamics of biological membranes is the fluid mosaic model
The peripheral membrane proteins are most likely to be located: attached to the polar head group of phospholipids on the membrane surface & bound to regions of integral membrane proteins that project from the membrane
Transmembrane protein is when regions inserted into the hydrophobic interior are usually alpha helices; Peripheral membrane protein is not covalently bound to membrane; Lipid-anchored protein-Lipid tails are inserted into the hydrophobic portion of the membrane
Smartbook #10: Chapter 6, sections 6.1-6.2
Crazy that over 2,000 years ago, pain medication began with power from tree bark and leaves from a willow tree?
Go salicylic acid (the og pain relief med compound)
Cyclooxygenase is the enzyme that makes molecules called prostaglandins (#itsthereasonwehavepainfuckthatguy)
Aspirin and Ibuprofen are the ones that like stop that shit (the shit in question being cyclooxygenase)
A chemical reaction is when 1 + substances are turned into other substances (#thatshitsjusttransgenderlol)
The reactions could involve other molecules attaching to each other to form larger molecules (like bubbles), molecules breaking apart to form two or more smaller molecules (like bubbles), rearrangements of atoms within molecules (not like bubbles…probably), or the transfer of electrons from one atom to another (trans you say? hehe)
Metabolism is the sum total of all chemical reactions that occur within an organism to maintain life (so the flash has like hella fast metabolism cause my boy be speeding)
Metabolism also refers to a specific set of chemical reactions occurring at the cellular level
For example, biologists may speak of sugar metabolism or fat metabolism (this is where the flash and spider man come in…also L from death note and Edogawa Ranpo from bsd)
Most types of metabolism involve the breakdown or synthesis of organic molecules
In case you didn’t know this, energy is the ability to cause change or do work (like right now, where I’m using my fucking energy to get this assignment done)
Physicists (cough cough isaiah cough cough) often consider energy in two general forms: kinetic energy (zoom boy zoom) and potential energy (am i or am i not going to move lol im edging u over the potential of me moving)
Kinetic energy is energy associated with movement, such as the movement of a baseball bat from one location to another (hence the zoomies)
Potential energy is the energy that a substance or object possesses due to its structure or location (hence the edging)
An electron in an atom has potential energy based on its position relative to other electrons and the positively charged nucleus. Electrons occupy orbitals of different shapes and sizes, which are found within electron shells, or energy levels. (They like vibe around the nucleus kinda like how planets orbit the sun, the electron is the planets)
An electron in an outer shell has a higher amount of potential energy than one in an inner shell (further away from the nucleus = more potential energy, the closer to the nucleus the less energy so bitch gets lazy)
If an electron drops to a lower shell, some of its potential energy is converted to kinetic energy (cause my boys no longer edging he got the zoomies 🙂↕)
The study of energy interconversions is called thermodynamics (oooh big word). There are two laws of thermodynamics that govern energy conversions (only two?):
First law of thermodynamics aka the law of conservation of energy: Says that energy can’t be created or destroyed (cause like no matter how tiny something gets you can’t break it bruv). Howeverrrr, energy can be transferred from one place to another and can be transformed from one type to another (like when chemical energy is transformed into heat)
Second law of thermodynamics: Is basically that any energy transfer or transformation from one form to another increases the degree of disorder of a system, called entropy
Entropy is a measure of the randomness of molecules in a system (bro’s a lil silly)
When a physical system becomes more disordered, the entropy increases. As the energy becomes more evenly distributed, that energy is less able to promote change or do work. When energy is converted from one form to another, some energy may become unusable by living organisms.
Energy is required for many cellular processes, including chemical reactions, cellular movements such as those occurring in muscle contraction, and the maintenance of cell organization. To understand how organisms use energy, we need to distinguish between the energy that can be used to promote change or do work (usable energy) and the energy that cannot (unusable energy)
Some of that shit is unusable because of fucking entropy. Like when glucose is metabolized to make ATP, some of the usable energy is lost in the form of heat (so sad hey siri play despacito)
The total energy of a system is termed enthalpy (H), and the usable energy–the amount of energy that is available and can be used to promote change or do work–is called the free energy (G)
The letter G is used to represent the free energy in recognition of physicist J. Willard Gibbs (Gibbs?! Like from Pirates of the Carribean?!) who proposed the concept in 1878. The amount of unusable energy in a system is the entropy (S).
Gibbs proposed that these three components of a system’s energy are related to each other in the following way:
H = G +TS
Where T is the absolute temperature in Kelvins. Because our focus is on free energy, we rearrange this equation as follows:
G = H - TS
The key way to evaluate if a chemical reaction is spontaneous is to determine the free-energy change that occurs as a result of the reaction: (insert fuck ass change symbol) G = (insert fuck ass change symbol) H - T(insert fuck ass change symbol)S
If a chemical reaction has a negative free-energy change (change symbol G < 0), the products have less free energy than the reactants, and, therefore, free energy is released during product formation. Such a reaction is said to be exergonic (i know it’s not but it feels exotic).
Exergonic reactions are spontaneous. Alternatively, if a reaction has a positive free-energy change (Change symbol G > 0), requiring the addition of free energy, it is termed endergonic (ender? Endermen 🙂↕) An endergonic reaction is not a spontaneous reaction
Many biological processes require the addition of free energy; that is, they are endergonic and don’t occur spontaneously (why not 🙁) How do cells overcome this problem? One strategy is to couple exergonic reactions with endergonic reactions. If an exergonic reaction is coupled with an endergonic reaction, the endergonic reaction will proceed spontaneously if the combined net free-energy change for both processes is negative.