CHEM 1010-02 CHAPTER 1-4 EXAM STUDY GUIDE

what is reductionism?

This study guide will include key concepts from Dr. V’s lectures and from the  textbook. For a more in-depth look at these concepts, be sure to check out my  lecture notes. In this study guide I’ll also include the main ideas from the two  readings she posted on Canvas. I won’t include anything from her powerpoint slides  (unless she specifically talked about it) because they’re already available on canvas.

I’ll be updating lectures notes and this study guide even after posting to StudySoup, just in case she adds any more important concepts that may be tested.

Alright, let’s do this.

Chapter 1 – Evolution and the Foundation of Biology

Biology- The scientific study of life

When studying biology, it is important to keep in mind the following common  themes:

∙ Organization 

∙ Information 

∙ Energy and matter 

∙ Interactions 

what is Homeostasis-?

∙ Evolution 

∙ Emergent properties

1. New properties that emerge at each level of progression that are lacking  in the previous level

∙ Correlation between structure and function

1. Structure defines function and function defines structure

Organization

Biology follows a hierarchy of complexity (Complex -> Simple)

∙ In reductionism, we study complex systems by reducing them to their  simple components, allowing them to be studied more easily.

∙ A reductive approach to studying cells would be looking at a cell’s organelles, or the macromolecules inside the cell, or the molecules that make up the  macromolecule, etc.

Matter is built of atoms, the smallest forms of matter that cannot be broken down  by chemical or physical means

∙ Atoms combine to form molecules and compounds, which combine and react  together to allow cells to function

what is Electronegativity?

We also discuss several other topics like jackson lowman afrikan american women

All cells share certain characteristics, such as…

∙ Being enclosed by a membrane that regulates the passage of materials  between the cell and its surroundings

∙ Containing genetic information in the form of DNA (as well as cytoplasm and  ribosomes)

Although these similarities exist, it is important to classify cells based off their  differences. We do this by classifying them into two groups… Don't forget about the age old question of hoda mirafzal

Eukaryotic Cells

∙ These cells have membrane-bound organelles, including a true, well-defined  nucleus (a membrane-bound structure that holds DNA)

∙ Example: plants and animals

Prokaryotic Cells

∙ Do not have membrane-enclosed organelles or a nucleus

∙ Example: bacteria and archaea

How do we organize an organism? Let’s take it step by step…

∙ Cell -> Tissue -> Organs -> Organ System -> Organism

If we look on a broader scale, we see the following progression…

∙ Organism -> Species -> Population -> Community -> Ecosystem ->  Biosphere

It is easier to study the biosphere when reduced to these smaller, simpler parts, an  example of reductionism

∙ Some organisms evolved through reductive evolution, such as viruses. They  are believed to have once been complex, but were more suitable to survive  as simpler organisms

Systems Biology goes hand in hand with reductionism; it is breaking down each  system into smaller systems in order to identify emergent properties and other  characteristics more easily.

When studying biology in all aspects, its important to remember that structure  defines function and function defines structure. We also discuss several other topics like hum100 textbook notes

∙ Looking at why or how an organism or molecule functions can give us clues  as to why its structured a certain way If you want to learn more check out launchpad learning curve answers

∙ Looking at an organism or molecules’ structure can give us clues as to what it does or how it functions

∙ This is a crucial idea in studying biology, so underline it, bold it, highlight it,  just don’t forget it

Dr. V says that organization allows us to understand growth and development INFORMATION

Deoxyribonucleic Acid (DNA)- genetic material in chromosomes

DNA stores information to make an organism by making copies through cell division

∙ Cell division for prokaryotic cells is simply reproduction

∙ Cell division for eukaryotic cells is multicellularity, or GROWTH What is DNA? What does it do?

∙ It makes copies

∙ Its building blocks are nucleotides

∙ It stores information in sequences of nucleotides, and these sequences are  responsible for passing on traits

The two fundamental roles of DNA as our source of information 

∙    Make copies

∙    Undergo variations Don't forget about the age old question of What are the three main clusters of personality disorders?

 1. THIS IS THE RAW MATERIAL OF EVOLUTION 

2. We call mutations the capacity to undergo variation

Dr. V tells us that our source of information allows us to maintain continuity of  life because our genes live on in the gene pool after we die

Gene- sequence of nucleotides/segment of DNA that codes for a specific function

∙ These hold blueprints for making proteins, which are the tools of gene  expression 

∙ Nucleotides along a gene are transcribed into mRNA, which is then  translated into an amino acid chain

∙ Transcription- The creation of a specific type of RNA molecule, called mRNA, through information in the sequence of DNA nucleotides

∙ Translation- The decoding of information of an mRNA nucleotide, creating a  chain of amino acids

∙ Protein folding- The process in which amino acid chains fold in specific  shapes, creating a specific protein

Genome- All of the genes in all 46 chromosomes

Genomics- the techniques employed to analyze the genome

Proteome- the sum of all proteins in the body

Proteomics- the techniques used to study the proteome

Bioinformatics display a reductive method of analysis; different labs from different  walks of science come together to break down data into individual parts for efficient analysis Don't forget about the age old question of redcap fiu

∙ This speed and technology of bioinformatics is an emergent property that is  relatively new to the analysis of data

ENERGY

Energy- capacity to do work/ability to cause change

∙ Energy flows through an ecosystem in a cycle, while chemical elements  remain and are recycled

∙ The primary source of energy for life on Earth is the sun

∙ Photoautotrophs, or plants, are able to make their own energy through  photosynthesis, the process by which radiant energy is converted into  chemical energy (ATP).

∙ Consumers can’t undergo photosynthesis, so they undergo cellular  respiration instead

1. Cellular respiration deals with metabolism- the sum of all reactions that  take place in our body (anabolism + catabolism = metabolism)

2. Anabolism- set of reactions used to make larger substances from smaller  substances

3. Catabolism- breaking large substances into smaller substances with  release of energy

INTERACTIONS

Interactions are simply adaptations to the environment; they can be a result of  biotic or abiotic stimuli

∙ God knows living with a roommate requires interactions and adaptations ∙ These adaptations can be temporary, like plants turning towards a source of  light

∙ These adaptations can be long-term, like the arctic fox’s coat of hair growing  thick in the winter and thin in the summer

Organisms interacting with each other in a community brings up some important  concepts…

∙ Commensalism- relationships between two organisms living in the same  place and time in which one benefits and the other is unaffected 1. Example: sucker fish and whale

∙ Mutualism- relationships between two organisms living in the same place  and time in which both organisms benefit

∙ Parasitism- relationships between two organisms living in the same place  and time in which one benefits and the other is harmed

Organisms also interact with abiotic factors, like heat

∙ Homeostasis- regulation of internal processes

1. Our (human) body temperature is regulated at a fixed temperature,  making us warm blooded, but other animals can change their internal  temperatures by interacting with surroundings (like alligators in the  shade)

EVOLUTION

Evolution- Scientific theory that accounts for environmental adaptations as well as diversity and unity among organisms

∙ When we say unity, we mainly think of DNA, because ALL living organisms have it

Nature conserves traits that allow for survival

∙ Survival is measured by propagation/reproduction rate

∙ Beneficial traits that give better chances of survival and reproduction are conserved

ALL organisms can be classified into three domains; Archaea, Bacteria, and Eukarya

∙ Eukarya are all organisms with eukaryotic cells

∙ Bacteria are the prokaryotes with the most diversity and are the most widespread

∙ Archaea are prokaryotes that live in Earth’s extreme ecosystems Why are Bacteria and Archaea classified differently if they’re both prokaryotic?

∙ Archaea have a lot more introns than Bacteria

∙ Archaea have more complicated cell membranes than Bacteria ∙ In some cases, Archaea are more similar to Eukarya than Bacteria!

Classification through taxonomy allows us to unite and differentiate between organisms and their species

∙ Humans and leopards are identical in taxonomy up until order. ∙ Taxonomy shows us how certain aspects are conserved (united) and certain aspects are diversified

∙ Structure modifies function and function modifies structure; this core idea accounts for diversity 

1. A cat’s limbs are built for stealthy movement, while a human’s arms are modified for grasping

When we look at the different Kingdoms of Domain Eukarya, we classify them by nutrition. An organism’s source of energy shows a correlation between structure and function, illuminating the diversity of life

∙ Kingdom Fungi- Main source of energy is extracellular digestion; the secretion of digestive juices outside their bodies to break down and absorb nutrients ∙ Kingdom Plantae- Main source of energy comes from cellulose in cell wall, allowing photosynthesis

∙ Kingdom Animalia- Main source of energy is cellular respiration/metabolism ∙ Kingdom Protist- Generally unicellular, very diverse kingdom, with some protists more closely related to animals than other protists.

1. Some protists are autotrophs¸ other protists eat these autotrophs. They’re super diverse.

Whenever we talk about evolution, we say that organisms that are better adapted to the environment will evolve

∙ As I said before, evolution is looked at in terms of survival and reproduction rate, but we also look at descent with modification

1. Organisms descend from ancestors with mutations that increase their chances of survival

2. Dr. V’s example: glyptodont and armadillo

3. Natural Selection is a primary cause of descent with modification

When formulating his theory of natural selection, Darwin made three essential observations…

∙ The individual organisms that make up a population are diversified in their traits, and these traits are passed on through generations

∙ A population has the ability to have more offspring than can survive long enough to make their own

1. In other words, an organism can produce a lot of babies, but chances are a lot of these babies won’t live to make babies of their own

2. Competition is a part of nature

∙ Species are normally adapted to their environments (well-suited for their circumstances)

Therefore, we know that Darwin’s theory of natural selection tells us that organisms with inherited characteristics that are better adapted to their surroundings are more likely to survive and produce offspring of their own than those less-adapted organisms. Over time, well-suited organisms will outnumber the worse-suited organisms. 

Dr. V tells us that Origins of Species, Darwin’s book, highlights that…

∙ Function relates to structure and structure relates back to function  1. Example: Galapagos finches

∙ The capacity to survive is key

∙ Diversification gives us new variations; new species come along ∙ Overcoming competition gives high capacity to reproduce more 1. Example: giraffes with tallest necks will continue to eat highest leaves wile short-necked giraffes will die out

Natural selection goes hand in hand with beneficial mutations 

 ∙     Galapagos Finches- the forces behind the finches evolving were beneficial mutations AND natural selection 

There are two forces of evolution; vertical and horizontal

∙ Vertical Evolution deals with the tree of life- the evolution of one species 1. The driving motion here is beneficial mutations with natural selection ∙ Horizontal Evolution deals with the web of life- bringing in an exchange of genes from unrelated species

1. Gene recombination is the driving force here 

The main aspect that sheds light on unity and diversity is looking at other species

Homologous structures- similar structures with different functions, therefore sharing a common ancestor 

Analogous structures- structures that share the same function, but have no common ancestor

SCIENCE

Science follows a process; observation -> questioning -> hypothesis -> experiments -> conclusions

Hypotheses are educated guesses based on prior knowledge

Hypotheses are validated by predictions (‘because’ statements) and are followed by experimental verification

Deductive reasoning- applying general principles and making a conclusion

∙ Example: If an archaeologist finds a fossil, he doesn’t know everything about  the organism right away. Maybe he observes the bone structure and comes  up with the conclusion that ‘this fossil may be from a mammal.’ This is an  example of deductive reasoning because he applied what he already knew  about mammalian bone structure in order to make a conclusion of the fossil

∙ The textbook explains that deductions are usually predictions of results; “If…  Then…”

Inductive reasoning- making specific observations and constructing onto general  principles with new information

∙ Let’s take the fossil found by the archaeologist in the previous example. The  fossil is brought back to the lab for further analysis, and it is found that there  is no way the organism could have given birth to live young, meaning it could only lay eggs.

Deductive reasoning results in inductive reasoning

∙ You apply generalizations through deductive reasoning, and by experiments  and learning more through inductive reasoning, you add on to these  

generalizations

Quantitative Data- Number of measurements, something mathematical that you  can observe and write down as clear information

Qualitative Data- observations of behavior

∙ This is the textbook definition, but it raises too many possible  

misconceptions. This is why science gives more weight to quantitative data

When discussing experimental control, Dr. V gave the following example of mice  in cages

Cage C

Same as Cage B,

but with an i.v. injection of Chemical X and .9% saline once a week.

Cage A

5 male mice

100-120 g in weight

5 months old

Cage B

Same as Cage A,

 but with an injection of .9% saline once a week

Which cage holds the  experimental control?

∙ Cage B is  

the experimental  control because B and  C are exposed to the  same experience

1. If you only had Cage A and C, you wouldn’t be  

sure if problems or inconsistencies arose from saline or Chemical X. 2. Between B and C, you are reducing the variable to one.

∙ Cage A is not the control because its purpose is to ensure the health of the  experimental mice

∙ Cage C is not the control because it is the main experiment

Independent variable- factor manipulated by researchers

Dependent variable- factor being observed to be affected by the independent  variable

∙ The book uses an experiment of mice and camouflage to display this. The  experiment placed mice of different shades of camouflage in different  environments and observed their rate of predation

∙ The independent variable was the color of the mice, while the dependent  variable was the rate of predation

Basic research- working on technologies that are already known (university-level  research)

Applied research- taking technologies to the industry and introducing it to the  economy (pharmaceutical compounds)

Theory- broad explanation leading to a large concept

Law- indisputable principle of science, even if it is not proven (like gravity)

Science and technology are interdisciplinary; science depends on technology and  technology depends on science

Chapter 2 – The Chemical Context of Life

In the eyes of a chemist, we are nothing but moving masses of chemical reactions Matter- anything that has mass and takes up space

∙ Atoms are the building blocks of matter

∙ Atoms of different elements come together to form compounds with new  characteristics

1. Compound- a fixed ratio of two or more different elements combined to  form a substance

2. Compounds are emergent properties of atoms

Periodic table- a chat that categorizes elements based off their properties and  characteristics (made by Dmitri Mendeleev)

∙ Groups (vertical columns)- share the same chemical properties a. As you shift to the right, valence electrons in these groups increases,  indicating a shift in chemical properties 

∙ Periods (horizontal rows)- tell us how many electron shells are in an atom ∙ There are 118 elements on the periodic table, 92% of which are naturally  occurring elements

1. All naturally occurring elements have decimal mass numbers because  they represent the average of all possible isotopic forms

 ∙     The elements essential for life are carbon, hydrogen, and nitrogen ∙ Trace elements are necessary for proper function, but are only required in  minute quantities  

1. These are most notable in enzymes- compounds that increase the rate of  a reaction

Mass number- sum of number of protons and neutrons in an atom

∙ When dealing with atomic mass scale, we use Carbon-12 as a reference 1. Atomic mass scale- how we actually denote the mass of an atom 2. When finding the atomic mass of Hydrogen, we say it is 1/12 that of  Carbon

∙ Although electrons aren’t very important in terms of mass, they play a huge  role in giving an atom volume 

While mass number is the total number of neutrons and protons, the atomic  mass is the average mass of all of an element’s isotopes

Atomic number- Number of protons in the nucleus

Isotopes- various forms of an element which have the same atomic number, but  different mass number (more neutrons than protons in the nucleus)

∙ All isotopic forms share the same chemical characteristics because they have the same number of electrons, but physical properties are changed ∙ Isotopes are constantly decaying; they are always trying to break down into  elements with lower atomic numbers

∙ Each element has its own rate of propensity- also known as the rate of  decay or half-life, it is the time taken for one half of a sample to break down Energy levels and how electrons are arranged in an atom 

Orbit- the path taken by electrons

Orbital- the space around the nucleus with the highest chance of finding electrons

Energy shell- An area around the nucleus where electrons have certain amounts of energy

Energy level- an electron’s average distance away from the nucleus

If an electron is bombarded with photons, it will go from grounded to excited and  move up an energy shell. If you continue to bombard the electron with photons, it  will not keep moving up energy shells. The capacity of the electron is the deciding  factor

An orbital can have a maximum of two electrons 

∙ s (spin) – 1 orbital, holds maximum of 2 electrons

∙ p (principle) – 3 orbitals, holds maximum of 6 electrons

∙ d (diffuse) – 5 orbitals, holds maximum of 10 electrons

∙ f (fundamental) – 7 orbitals, holds maximum of 14 electrons

We classify electron shells into groups based off their energy levels. In order of  ascending energy, we will look at shells K, L, M, and N

I offered a detailed view of this in my 9/7/17 lectures notes, which I will include here just in case there is confusion on this important topic (see next page)

Looking at Figure A, we can understand the notation of electron arrangement. The number out front tells us which shell we are dealing with. The letter tells us which orbital we are dealing with. The exponent number tells us how many electrons are in that orbital based off the atom we are given.

Looking at the chart (Figure B), we see that the first shell (K shell) has one orbital: an s orbital. We know that s orbitals can only hold 2 electrons, so the total number of possible electrons in the K shell is 2 electrons.  

The second shell (L shell) has two orbitals; an s orbital and a p orbital. P orbitals are composed of three sub-orbitals, which hold 2 electrons each. This means that the p orbital gives us a total of 6 electrons. Add this to the 2 electrons that the s orbital gives us, and we have 8 possible total electrons in the L shell.

The third shell (M shell) has three orbitals; an s orbital, a p orbital, and a d orbital. Just like in the L shell, the s and p orbitals give us 8 electrons total, but the d orbital gives us 10. This is because the d orbital is composed of five sub-orbitals, each with 2 electrons. Adding up all electrons present in these orbitals gives us a grant total of 18 possible electrons in the M shell.

The fourth shell (N shell) has four orbitals; an s orbital, a p orbital, a d orbital, and an f orbital. Just like in the M shell, the s, p, and d orbitals give us 18 electrons. The f orbital is composed of seven sub-orbitals, each with 2 electrons. Adding up the 14 electrons given from the f orbital with the other 18 gives us a grand total of 32 possible electrons in the N shell.

I say ‘possible’ because the exact number of electrons in each shell depends on the element you are arranging. Let’s take Oxygen for example, an element with 8 electrons.

With 8 electrons to work with, I added them in a sequence. The first 2 go to the s  orbital in the K shell. The next 6 go to the s and p orbitals in the L shell. Notice how  the p orbital has 4 electrons in this case, while it can hold a possible 6. This is  because oxygen doesn’t have enough electrons to fill the p orbital. Exact electrons  in an orbital depend on what atom you are arranging, but the possible number of  electrons is always constant in each orbital and shell.

Octet rule- all elements require 8 electrons in the outermost shell in order to fulfill  the energy component for that element (EXCEPT FOR HYDROGEN AND HELIUM)

Bond- force that holds chemicals together when they react

 ∙     The formation and function of molecules depend on chemical bonding  between atoms 

∙ Nonpolar covalent bond- equal sharing of electrons

∙ Polar covalent- unequal electronegativity and sharing of electrons, resulting in a partial charge separation across a compound

1. Electronegativity- measure of capacity of an atom to attract bonded  electrons to itself

2. Keep in mind that the charges are called partial because an electron is not being given away, it is still shared

3. Remember that you are still sharing electrons in both polar and nonpolar  covalent bonds, so no matter the polarity, covalent bonds are always  signified by a dash [(H – H) or (C – C)]

a. Structural formula- H – H (the line represents a single bond, a pair of shared electrons)

b. Molecular formula- H2

∙ Hydrogen bonds- arise from polar compounds where the hydrogen with a  partial positive charge extend a weak force of attraction (signified by a dotted line)

∙ Key difference between covalent bonds and hydrogen bonds is the aspect of  sharing. There is no sharing in hydrogen bonds, they are forces of attraction 1. Van der Waals interactions are forces of weak attraction, hydrogen bonds  

are forces of weak attraction, but neither of them share electrons 2. Van der Waals interactions are only present within a tiny radius, they  depend on attraction and repulsion from changing electron densities ∙ Ionic bond- when one atom loses an electron and gives it to another atom,  resulting in two oppositely charged ions

1. Cation- positively charged atom (has less electrons than protons by  giving away electrons)

2. Anion- negatively charged atom (has more electrons than protons by  receiving electrons)

3. Atoms give and take electrons in order to fulfill the octet rule 

Induced fit- when a compound initially fits loosely, then fits precisely with the  active side of the reactants so that bonds can be broken and new ones can be  formed

∙ This has to do with the flexibility of molecules

1. They are capable of being so flexible because they can rotate around their bond angles, allowing them to make shapes within their structure. This  lets molecules fit into reactants to start chemical reactions 

The prerequisites of a chemical reaction (breaking of old bonds and the formation of new ones) 

∙ A chemical reaction needs reactants 

∙ The purpose of energy in a reaction, specifically heat, is to excite the reactant molecules, allowing them to collide, break bonds, and form new ones

∙ Reactions happen at the speed they do inside our bodies because of  enzymes/catalysts- they do not participate in the reaction, but they speed the rate of it

∙ These reactions also require an aqueous environment; moisture is necessary  for reaction (water is a great hydrolytic agent; it helps in breaking down) ∙ Equilibrium of a reversible reaction is reached when the rate of the  forward reaction equals the rate of the reverse reaction  

∙ Equilibrium of a forward reaction is reached when all the reactants are  converted to products

The Properties and Characteristics of Water 

The bonds inside water molecules which hold the atoms together are polar covalent  bonds 

The bonds between water molecules which hold them together are hydrogen bonds 

∙ The main point the textbook makes in this chapter is that all of these  properties are somehow connected to water’s hydrogen bonds

Because of polarity, the most important quality of water, which we attribute to  survival, is cohesion 

∙ Cohesion- capacity of molecules of the same type to bond with each other  ∙      Cohesion is the main force of water entering plants from soil ∙ When water moves from the soil, through the roots, up the plants, it goes  against gravity

∙ You usually have to expend energy in order to counteract gravity, but plants  don’t use any energy in this energy efficient process thanks to water’s  cohesive property

∙ Cohesion of water is due to its polarity and therefore its ability to form  hydrogen bonds

∙ Adhesion prevents water molecules from slipping down on their way up the  plant

1. Cohesion deals with water molecules interacting with other water  molecules, adhesion deals with water molecules interacting with different  compounds

∙ Since all animals in the food chain rely on either herbivores or plants, life is  sustainable because of the cohesive force of water 

Hydrostatic skeleton- water; it allows the basic structure of plants, just like we  have bones

Turgor pressure- the primary force applied by water; it is the pressure exerted by  water upon exiting a cell

Energy and Temperature

Kinetic Energy- energy of motion

Thermal Energy- measure of average kinetic energy

Temperature- sum of ALL kinetic energy (a measure of heat)

Heat- movement of particles from one location to another (generally random  motions of particles)

There are two properties of water that allow us to maintain constant internal  temperature; high specific heat andhigh heat of vaporization 

∙ Specific heat- the amount of energy required to increase 1 g of water 1- degree C (1 calorie or .239 Joules)

1. Water has a very high specific heat because of its polarity

2. Heat is always released in chemical reactions in some way

3. All the heat given out from all the reactions in your body are absorbed  by water, and when this heat is absorbed, hydrogen bonds are broken 4. Specific heat can be thought of as a substance’s resistance to changes  in temperature

5. Heat applied to water doesn’t change temperature too much because  it is used to break hydrogen bonds before it excites molecules

6. Organisms made up of mostly water can resist temperature change  exceptionally well because of this property

∙ Heat of vaporization- the amount of energy required to change 1 mole of a  substance to a gas at its boiling point

1. Water has a high heat of vaporization

2. When hydrogen bonds break, the next step is reforming bonds, which  releases heat, condensing liquid water into water vapor, which comes in  contact with the cool atmospheric air outside

3. This process of evaporating sweat cools the body, regulating temperature 4. Evaporative cooling- the surface of a liquid cools down as it evaporates a. If the fastest runners of a track team flew off into the skies as gases,  the average speed of the team would decline

The property that keeps water from freezing completely is heat of fusion

∙ Heat of fusion- amount of energy released by a compound in order to  convert itself from a liquid to a solid

1. Water releases energy as its temperature lowers, forming hydrogen bonds with fewer molecules

2. This allows it to expand, becoming less dense, allowing ice to float in  water

3. Water’s capacity to expand is why live continues under frozen lakes High heat of vaporization allows water to exist in gaseous form High heat of fusion allows water to exist in solid form 

Surface tension- measure of the force of attraction between the water molecules  on a liquid surface to the water molecules in air

∙ Both water molecules in air and on the surface of a liquid exhibit hydrogen  bonds with each other; proving an elastic nature on the surface of liquid

∙ The hydrogen bonds of the liquid water and water vapor creates a water-air  interface, where gases mix

∙ Colligative property- capacity to extent boiling and freezing point 1. Organisms that live in harsh environments (under frozen lakes or in  volcanic zones) are able to survive by secreting organic substances into  the water in their body, extending the boiling and freezing points of it Solubility of Water

Solution- substance with a solvent and a solute

∙ Solvent- liquid medium in which a solute is dissolved (water) ∙ Solute- a substance dissolved in a medium (sugar)

Water is an almost universal solvent because it is polar, so nonpolar compounds  don’t dissolve

The solubility factor of water is important for survival of organisms because… 

∙ It lubricates our organs 

1. Many parts of our body are moist because aqueous environments are  necessary for reactions

∙ Allows us to excrete waste from the body 

1. Water is an effective solvent necessary to excrete harmful substances 2. Harmful substances are broken down into hydrophilic metabolites (water soluble parts)

3. Kidneys take these metabolites and filter them through a medium of water in order to excrete them

When ions like Na and Cl dissolve in water, hydration shells are formed, which are spheres of water that engulf them

The capacity of a solute to dissolve in water is categorized in three groups;  hydrophilic, hydrophobic, and amphipathic

Hydrophilic- has the capacity to dissolve

Hydrophobic- substances that don’t dissolve in water

∙ We call these substances water fearing because of hydrophobic exclusion 1. This is the principle that water pushes non-polar, non-soluble substances  together, allowing them to form clumps, but never diffuse with the water

Amphipathic- substances that have both hydrophilic and hydrophobic properties

∙ The phospholipid bilayer is an example of amphipathic properties in our cells 1. Polar heads (hydrophilic) and nonpolar tails (hydrophobic) make up  phospholipids, and when these phospholipids are mixed with water, the  hydrophobic, nonpolar tails face inward because of hydrophobic exclusion. The polar, hydrophilic heads face the opposite direction, facing the water  head-on (pun intended)

Capacity of water to ionize is another important characteristic

∙ Water acts as a buffer because of its ability to break down into hydrogen and hydroxyl ions

pH- concentration of hydrogen ions, measured on a scale of 1-14

∙ pH is the negative logarithm of hydrogen ion concentration to the base 10 1. Negative logarithm signifies that as hydrogen concentration goes up, pH  goes down

Acid- a solution that increases the concentration of hydrogen ions, or decreases the concentration of hydroxyl ions

∙ A strong acid completely dissociates in water, thereby increasing the  concentration of hydrogen atoms

∙ A weak acid partially dissociates in water

Base- a solution that increases the concentration of hydroxyl ions, or decreases the  concentration of hydrogen ions

∙ A strong base completely dissociates in water, thereby increasing the  concentration of hydroxyl atoms

Buffer- a weak reservoir of acids and bases 

∙ Buffers have the capacity to increase or decrease hydrogen concentrations Importance of pH

∙ pH is necessary to maintain the structural integrity of compounds, especially  proteins 

∙ pH allows optimal rate of reaction 

∙ pH allows substances to dissolve in water 

∙ pH allows substances to react with each other 

CHAPTER 3 – Carbon and the Molecular Diversity of Life

Life depends on four macromolecules: proteins, carbohydrates, lipids, and  nucleic acids

∙    The first function of carbohydrates that always comes to mind is energy ∙    The first function of lipids that always come to mind is storage of energy ∙ The first function of proteins that always come to mind is enzymes ∙ The first function of nucleic acids that always come to mind is storing  information 

∙    Nucleic acids are the only class of macromolecules that don’t give energy 

Polymers are long molecules made up of identical or similar building blocks  attached by covalent bonds, like a train and its individual cars

∙ Carbohydrates, proteins, and nucleic acids are all polymers

∙ Monomers are the building blocks that make up a polymer

∙ Polymers have emergent properties not present in monomers

We call molecules organic if they contain hydrocarbons (hydrogen and carbon) Carbon is super important because it has a very high reactive potential

∙ It reacts readily with a wide array of elements, giving it the ability to form  different types of compounds with tons of variety in structure and function

Carbon chains are skeletons of organic molecules, varying in shape, length, and  bond type

In carbon-carbon double bonds (C=C), the length of the bond is very short

∙ Adverse conditions cannot break these bonds easily in organisms (under  frozen lakes or in volcanic zones)

The two different molecules and properties that help maintain life in adverse  conditions are water’s colligative property and carbon’s short double bond  length 

Functional group- group of elements that come together but don’t fulfill the octet  rule

∙ They have their own properties and characteristics, but do not fulfill the octet rule

∙ Hydroxyl, Carbonyl, Carboxyl, Amino, Sulfhydryl, Phosphate, and  Methyl are important functional groups you should know the structure and  compositions of (they are in Dr. V’s PowerPoint slides)

Isomer- compounds that share the same chemical formula and composition of  elements, but differ in structure

Structural Isomer- compounds that share the same chemical formula and  composition of elements, but with different bonding relationships 

Stereoisomer- compounds that share the same chemical formula and composition  of elements, same bonding relationships, but with different spatial organizations 

∙ There are two different types of stereoisomers; geometric and enantiomers ∙ When talking about geometric stereoisomers, the book talks about cis and  trans

1. Cis isomers (same side as double bond, left image) are more stable than  Trans isomers (opposite sides of double bond, right image)

2. These subtle differences in geometric makeup can have big effects  biologically

∙ An example of a geometric isomer is Glucose because it can exist as linear or  as a ring

1. Alpha glucose- hydroxyl group is below the ring and can be metabolized 2. Beta glucose- hydroxyl group is above the ring and cannot be  metabolized 

3. As glucose forms a ring, it can form alpha glucose or beta glucose depending on the placement of its functional groups, as highlighted below  with blue boxes

Enantiomer-also known as optical isomers because they are isomers that are  mirror images of each other

∙ Classic example is L glucose vs D glucose in their ringed form 

∙ Notice how the two are mirror images of each other

Glucose is also an enantiomer to galactose in its linear form 

1. Notice how glucose and galactose are similar except for their mirrored  hydroxyl group on the 5th carbon

ISOMER REVIEW

Isomer Subtype  

Examples 

Structural (no subtypes)  

Glucose and Fructose

 Isopropyl alcohol and propyl

alcohol Stereoisomer Geometric  Cis and Trans isomers

 Alpha and Beta  

glucose

 Enantiomers L Glucose and D  

glucose (ring form) 

 Glucose and Galactose  

(linear form)

Adenosine Triphosphate (ATP)- ATP is an organic molecule composed of a  nitrogenous base, a sugar, and a phosphate chain

∙ As pictured below, the nitrogenous base is Adenine, and it is bonded to the  first carbon

∙ The phosphate chain is connected to the 5th carbon

∙ The 3 phosphates (highlighted by the blue box) give ATP its name 1. The 3 negative charges of phosphate produce a lot of repulsion, therefore  it is easier to break ATP than glucose, for example, because glucose  doesn’t contain such repulsion. The activation energy of ATP is lower than  glucose

2. Activation Energy- the energy supplied to break the bonds

∙ ATP is the universal energy currency from prokaryotes to eukaryotes because  it can be used directly to give energy

∙ Energy is stored in ATP through electrostatic repulsion because of the  repulsive forces that exist between the three negatively charged phosphates

Let’s get back to the four basic macromolecules, remember…

∙    The first function of carbohydrates that always comes to mind is energy ∙    The first function of lipids that always come to mind is storage of energy ∙ The first function of proteins that always come to mind is enzymes ∙ The first function of nucleic acids that always come to mind is storing  information 

Synthesis relates all macromolecules through dehydration synthesis and hydrolytic  cleavage

∙ Dehydration synthesis- when water is released through the attachment of  two or more monomers (also called polymerization)

∙ Hydrolytic cleavage- water inserting itself in order to break a polymer into  monomers

1. This process of disassembling monomers is also called hydrolysis

∙ The way all four macromolecules are made and the way they are  broken is constant though these two processes involving water 

Carbohydrates, looking at the name alone, are hydrated carbon 

∙ They are basically sugars and polymers of sugars  

∙ They are a very easy source of storing energy

Monosaccharides- simple carbohydrates, or simple sugars, which are categorized  into hexos, pentos, tetros, or tiny trios, depending on how many carbons are  present

∙ Most sugars form rings in aqueous solutions

∙ The most common trios is glyceraldehyde, a biproduct of glucose, that is  used for making fat

 ∙     Carbohydrates are the basis for all other macromolecules to form; they form  proteins by forming amino acids. Metabolites are carbohydrates that form  lipids or nucleic acids  

∙    Tetrose sugar- 4 carbon sugar

1. 4 carbon sugars are much easier to assemble than 5 carbon sugars ∙    The two 5 carbon sugars, pentose sugars, we look at decide whether a  molecule will be deoxyribonucleic acid or a ribonucleic acid

1. These pentose sugars are the core molecules that decide the nature of  nucleic acids

2. In the following picture, we have a 5-carbon sugar that could be either  ribose or deoxyribose; depending on what is attached to the 2nd carbon

1. The 5’ end contains the phosphate group

2. The 3’ end contains the hydroxyl group at the third carbon free to add on  another nucleotide to extend the length of nucleic acids; nucleotides (the  building blocks of nucleic acids) will be added to the 3rd carbon

 3. The 2nd 

 carbon tells us whether this 5-carbon sugar is ribose or  

 deoxyribose; if a hydrogen is bonded on top of the 2nd carbon and a

hydroxyl group (OH) on the bottom, you have a ribose sugar. If a hydrogen is bonded on top of the 2nd carbon AND a hydrogen is bonded on the  bottom, you have a deoxyribose sugar.

a. The de- means ‘absence of,’ which makes sense because we have an  absence oxygen in on the 2nd carbon of deoxyribose

 ∙     To sum up the numbering of carbons in a pentose sugar… 

1. The first carbon in a core sugar connects to the nitrogen base 2. The second carbon decides the nature of the sugar (ribose or deoxyribose) 3. The third carbon should always be free for forming the covalent bond  between nucleotides to extend the length of the compound

4. The fourth carbon isn’t really important to us right now

5. The fifth carbon is always attached to the phosphate group 

∙ Hexose sugars- we have three different hexose sugars which are all isomers of each other

1. Glucose (transport sugar)

2. Fructose (glucose’s structural isomer)

3. Galactose (glucose’s enantiomer)

Glycosidic covalent bonds are covalent bonds formed between monosaccharides

∙ In the picture above, we see a covalent bond formed between the 1st carbon  of one sugar and the 5th carbon of another, forming a ‘1-4 glycosidic bond’  with the liberation of water

Disaccharides- two monosaccharides joining together via glycosidic bonds

∙ We know of three disaccharides; sucrose (fructose + glucose), lactose  (glucose + galactose), maltose (glucose + glucose)

Polysaccharides- many numbers of monosaccharides coming together via  glycosidic linkages

∙ Storage polysaccharides and structural polysaccharides 1. Structural polysaccharides give structural support

2. Storage polysaccharide give storage

Lipids- small class of molecules that are not soluble in water

∙ Fats- made up of glycerol and fatty acids through dehydration synthesis in  order to store energy

1. Fatty acids- long carbon skeletons

∙ The building blocks of fats in our body are triacylglycerol

∙ Let’s look at the 3-carbon compound glycerol

∙ Notice the 3 long chains of fatty acids

∙ When the 3 long chains of fatty acids combine with glycerol through an ester  linkage, 3 water molecules are released; hydroxyl group goes away from acid  part and hydrogen goes away from glycerol

1. Ester linkage- a bond between a carboxyl group and hydroxyl group ∙ This highlights the complexity of the building block of lipids

∙ Fats are classified as saturated vs unsaturated

1. Saturated fats have a stable, solid structure at room temperature  because most of the carbons are saturated with hydrogen (C-H single  bonds)

2. Unsaturated fats are liquids, and are composed of carbon-carbon double bonds (C=C)

∙ Essential fat- cannot synthesize, must be taken through your diet ∙ Trans fat is unsaturated, and is more dangerous because it lowers the  concentration of HDL and raises the concentration of LDL

∙ Phospholipids are amphipathic molecules similar to fats, but only have 2  fatty acids instead of 3

∙ Here we have the long chains of fatty acids in glycerol again, but in a  phospholipid, a phosphorylated amino acid is connected to one of the  carbons

∙ When you take a nonpolar amino acid and phosphorylate it, it becomes polar, and that gives one carbon a hydrophilic property, while the other two have  hydrophobic properties, making this an amphipathic phospholipid 1. Phospholipids are in all cell membranes, and therefore, all membranes are semi-permeable 

a. We have two layers of phospholipids in our cell membranes

b. By hydrophobic exclusion, water from outside the cell pushes the  hydrophobic parts away, while water from inside the cell pushes the  hydrophobic parts away, leaving the hydrophobic parts in the middle,  while the hydrophilic parts face the water on both sides

c. Phospholipids gives the property of semi-permeability to the  membrane 

d. Tails allow hydrophobic substances to pass through while preventing  hydrophilic substances from going through (SEMI-PERMEABLE) 

∙ Steroids- highly nonpolar lipids; 4 carbon interconnected rings form steroids 1. Adding a hydroxyl group to steroids gives you cholesterol, which is  important for maintaining membrane integrity and hormones 

a. Small changes in hormones give male cardinals their beautiful red coat of feathers, while female cardinals do not have such a luxury

2. Steroids form the basis for hormones, cholesterol, and are all extremely  nonpolar

Waxes give protection against water and pressure changes 

Terpenes are types of lipids (very long chains of fatty acids)

PROTEINS

Proteins are tools of gene expression and the workhorses of a cell Proteins are made up of carbon, hydrogen, oxygen, nitrogen, and sulfur

Building blocks of proteins are amino acids

∙ Amino acids are divided into an amino part and an acid part

∙ You will always have an amino group and a carboxyl group, and, at a neutral  pH, there is always a positively and negatively charged end on an amino acid ∙ The n terminal is the positively charged end of an amino acid, while the c  terminal is the negatively charged end; THESE TWO NEVER SWITCH; if an  amino acid forms an isomer, the R group and the hydrogen will be flipped

Proteins are made of amino acids which are linked by peptide bonds Primary Structure- arrangement of amino acids based on codes present in mRNA

 ∙     NEVER WILL YOU FIND A PROTEIN IN ITS PRIMARY STRUCTURE  ∙     Primary structure is the most important structure 

1. Sickle cell anemia is a result of one mutation in hemoglobin’s primary  structure

 ∙     Primary structure dictates the structure and function of a protein Secondary Structure- first folding that occurs of the protein

∙ HYDROGEN BONDS 

1. The only bonds you see as soon the amino acids are formed are hydrogen  bonds

∙ Two possible shapes in secondary structure: alpha helical and beta pleated  sheet

1. The main difference between the two lies in how the amino acids organize  themselves

∙ Alpha helical- amino end of one amino acid in the chain forms a hydrogen  bond with the carboxyl end of a distant amino acid within the chain ∙ Beta pleated- Adjacent amino acids form hydrogen bonds together ∙ The secondary structure determines the strength of a protein 

Tertiary Structure- the ultimate folding that occurs, giving 3d structure of the  protein

∙ Tertiary structure includes hydrogen bonds, polar ionic bonds, hydrophobic  forces of exclusion, van der Waals forces of weak attraction, and one covalent disulfide bond, but this disulfide bond is not very common because there are  only two amino acids that contain sulfur

∙ Domain- parts of the protein that have their own composition of amino acids, their own 3d structure, and have their own function that aids in the function  of the protein

Denaturation is the unfolding of a protein by breaking its bonds

Renaturation- forming bonds again and folding proteins back to their intended  shape

∙ Chaperones are classes of heat-shock proteins that identify denatured  proteins, grasp these proteins, and provide them with the optimal  environment to renature

Quaternary structure deals with proteins composed of more than one polypeptide

∙ All bonds that work with tertiary structure also work with quaternary structure (listed above, hydrogen, polar ionic, etc…)

∙ Dissociation occurs when two polypeptides come together to make a  protein. After the protein is synthesized, the two polypeptides move away, or  dissociate, and there is no unfolding, or harmful side effects

∙ A protein with quaternary structure also has tertiary structure Protein-Protein interactions

∙ Milky way chocolate proteins react with receptors on taste buds. There are  hydrogen, polar, hydrophobic, van der Waals forces all acting towards  temporary bonding

∙ Disulfide bridges are not involved in protein-protein interactions because  covalent bonds are not temporary in this case

Nucleic Acids are composed of nucleotides, which are bonded via  phosphodiester covalent bonds  

∙ Composed of carbon, hydrogen, oxygen, and nitrogen

∙ Primary functions include storing and accessing information, as well as  certain RNA molecules acting as enzymes (ribozymes)

∙ Nucleotides come together to form a long string of nucleic acid ∙ Nucleotides -> Nucleic Acid -> 2 strands of nucleic acids bonded by hydrogen bonds (DNA) -> DNA + histone -> chromosomes -> genomes

a. This is the hierarchy of nucleic acid

Building blocks of nucleotides

∙ 5-carbon pentose sugar

∙ Nitrogenous base + sugar = nucleoside 

∙ Nucleoside + phosphate = nucleotide 

∙ The phosphate and sugar gives continuity of the strand, while nitrogenous  bases protrude from the strand

1. There are two kinds of nitrogenous bases based off number of rings:  purines and pyrimidines

2. Purines of RNA- 2 rings (adenine and guanine)

3. Pyrimidines of RNA- 3 rings (uracil and cytosine)

Differences/similarities between RNA and DNA

∙ A pyrimidine in DNA is Thymine, while RNA has Uracil

∙ Phosphates in DNA and RNA are the same

1. In DNA, there are two hydrogen bonds between Adenine and Thymine and three hydrogen bonds between Cytosine and Guanine

2. Two strands of DNA are antiparallel (one goes 5’ -> 3’ while the other goes 3’ -> 5’)

a. This represents complimentary nature of nitrogenous bases (polarity  makes hydrogen bonds, but for it to be polar, the sugar direction needs to be flipped)

∙ Within a strand of nucleic acid, you have phosphodiester bonds ∙    Between two strands of nucleic acids, you have hydrogen bonds ∙ DNA’s unique shape is that of a helical cord

∙ RNA’s shape has a lot of different possible shapes; clumped, long linear  molecule, ribbon shaped, etc.

CHAPTER 4

Cell theory

∙ All living organisms are composed of one or more cells

∙ A cell is the simplest fundamental unit of life

∙ New cells arise from old cells by division

We share a few common features among all cells; plasma membrane,  DNA, ribosomes, and cytoplasm

Microscope- an instrument of magnification

∙ Light microscopes use light as their source of illumination ∙ Staining microscopes increases contrast and resolution

Phosphodiest er bonds

Reading Key Points

“Are Viruses Alive?”

∙ Looking at viruses’ evolutionary history shows strong evidence that they are  living

∙ Viruses do not metabolize; they only carry out one life process, reproduction,  which they undergo by hijacking another cell and injecting their DNA into it ∙ Looking at a virus’ genetic history is challenging because a virus’ DNA  replicates itself and mixes with host DNA so often, mutations are very  common

∙ To combat this, researchers instead looked at protein folds, which are coded  by genes, and do not drastically mutate over time

∙ It was found that 442 folds were shared by viruses and cells; indicating a  branching of some sort

∙ This tells us that viruses share properties with cells, and are thereby living ∙ It is thought that viruses underwent reductive evolution; they simplified  instead of becoming complex. It is theorized that viruses were “more cellular  in nature” and “existed in the form o primitive cells”

∙ The last common ancestor linking cells and viruses may have lived around  2.45 billion years ago

∙ Viruses restore their lost abilities when they hijack a host cell; it is possible  that viruses and cells existed as a unit together at some point, and even  today that can restore their association upon infection

Motorized molecules drill through cells

∙ Rotors in single-molecule, light-powered cells can drill through cell  membranes, giving way to new possibilities in infection treatment ∙ These rotors spin 2 to 3 million times per second in order to get through  adjacent molecules and the membrane itself

∙ These rotors can be used to deliver drugs to a cell or rip open its membrane,  killing it

∙ The labs made 10 variants of these molecules, with different functions and  variations

∙ They tested these rotors by placing a dye in a synthetic lipid bilayer, drilling  into a membrane, and watching the fluorescent dye fade as it entered the cell ∙ It takes about a minute to get through the membrane

∙ These present a possible solution to certain cancers, which can be killed in 1  to 3 minutes