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ASU / Biology / BIO 181 / How does the hydrophobic effect work?

How does the hydrophobic effect work?

How does the hydrophobic effect work?


School: Arizona State University
Department: Biology
Course: General Biology I
Term: Fall 2017
Tags: general and Biology
Cost: 50
Name: BIO 181, Exam 1 Study Guide
Description: This upload is a study guide for the first exam covering the first 3 weeks of class and chapters 1-4 of the textbook.
Uploaded: 01/29/2018
10 Pages 204 Views 8 Unlocks

Marissa Welch (mjwelch3@asu.edu)

How does the hydrophobic effect work?

General Biology I

Zachary Shaffer

Exam 1 Study Guide

Highlight = Key Term/Concept

Chapter 1: Life (pdf textbook pg. 68-89)

Core Concepts

- 1.1: The scientific method is a deliberate way of asking and answering questions about the natural world.

- 1.2: Life works according to fundamental principles of chemistry and physics. - 1.3: The fundamental unit of life is the cell.

- 1.4: Evolution explains the features that organisms share and those that set them apart. - 1.5: Organisms interact with one another and with their physical environment, shaping ecological systems that sustain life.

 - 1.6: In the 21st century, humans have become major agents in ecology and evolution.

Why is it called the central dogma?

1.1: The Scientific Method

- Observation allows us to draw tentative explanations called hypotheses.

- Hypotheses: Tentative explanations that are proposed when questions are observed. - A hypothesis makes predictions that can be tested by observation and experiments. - Variable: Something that can be deliberately added into an experiment. Don't forget about the age old question of What are the three main kinds of neurons that carry information?

- Test Group: The group that is expected to be affected by the experimental variable. - Control Group: The group that is not affected by any experimental variable.

- General explanations of natural phenomena supported by many experiments and observations are called theories.

- Theory: A statement that generally explains the world that supported by a large body of experiments and observations.

What does dna deoxyribonucleic acid mean?

1.2: Chemical and Physical Principles

- The living and nonliving worlds follow the same chemical rules and obey the same physical laws. - The First Law of Thermodynamics: States that energy can neither be created nor destroyed; it can only be transformed from one to another.

- The Second Law of Thermodynamics: States that the degree of disorder (or the number of possible positions and motions of molecules) in the universe tends to increase as time goes on.

Marissa Welch (mjwelch3@asu.edu)

- Entropy: Quantification of the amount of disorder in a system.

- The scientific method shows that living organisms come from other living organisms.

1.3: The Cell

- Nucleic acids store and transmit information needed for growth, function, and reproduction. We also discuss several other topics like What is the science of describing the earth?
Don't forget about the age old question of Why did the children's crusade attempt to appeal to muslims?

- Deoxyribonucleic Acid (DNA): A molecule that is the information archive

in all organisms.

- Proteins: The key structural and functional molecules that do the work of

the cell.

- Ribonucleic Acid (RNA): A copy of DNA’s information in the form of a

closely related molecule.

- Transcription: The synthesis of RNA from a DNA template.

- Translation: The process that converts information in the language of We also discuss several other topics like Who is ibn khaldun in sociology?


- Central Dogma: The molecular biological pathway from DNA to RNA to


- Gene: The DNA sequence that corresponds to a specific protein product.

- Replicated: The process of copying stored information.

- Membranes define cells and spaces within cells.

- Plasma Membrane: The second essential feature of all cells.

- Nucleus: The part of the cell which houses the cell’s DNA.

- Cytoplasm: The space in the cell separate from the nucleus.

- Prokaryotes: Cells without a nucleus.

- Eukaryotes: Cells without a nucleus.

- Bacteria: One of the three domains of life. Lack of a nucleus


- Archaea: One of the three domains of life. Lack of a nucleus Don't forget about the age old question of Observation law refers to what?

(prokaryotic). Single-celled microorganisms.

- Eukarya: One of the three domains of life. Eukaryotic.

- Metabolism converts energy from the environment into a form that can be used by cells. - Metabolism: Chemical reactions by which cells convert energy from one

form to another.

- Adenosine Triphosphate (ATP): Released energy storage in a chemical


- A virus is genetic material in need of a cell.

1.4: Evolution

- Variation in populations provides the raw material for evolution.

- Natural Selection: Complex mathematical formulations of evolution through selection. - Environmental Variation: Differences in the experiment. We also discuss several other topics like Spherical space is how many degrees?

- Genetic Variation: Differences in the genetic material that is transmitted from parents to offspring.

- Evolution predicts a nested pattern of relatedness among species, depicted as a tree. - Evolution can be studied by means of experiments.

1.5: Ecological Systems

Marissa Welch (mjwelch3@asu.edu)

- Basic features of anatomy, physiology, and behavior shape ecological systems. - Ecological interactions play an important role in evolution.

Chapter 2: The Molecules of Life (pdf textbook pg. 94-113)

Core Concepts

- 2.1: The atom is the fundamental unit of matter.

- 2.2: Atoms can combine to form molecules linked by chemical bonds. - 2.3: Carbon is the backbone of organic molecules.

- 2.4: 4 Carbon is the backbone of organic molecules.

- 2.5: Organic molecules include proteins, nucleic acids, carbohydrates, and lipids, each of which is built from simpler units.

- 2.6: Life likely originated on Earth by a set of chemical reactions that gave rise to the molecules of life.

2.1: Properties of Atoms

- Atoms consist of protons, neutrons, and electrons.

- Nucleus: The dense center of an atom made up of positively charged particles and electrically neutral particles.

- Protons: Positively charged particles found inside the nucleus of an atom.

- Neutrons: Electrically neutral particles found inside the nucleus of an atom.

- Atomic mass: The mass of the protons and neutrons (the nucleus).

- Isotopes: Atoms of the same element that have different numbers of neutrons. - Ions: Electrically charged atoms.

- Electrons occupy regions of space called orbitals.

- Orbital: a region of space circling the atom’s nucleus.

- Shell: A given energy level of several orbitals.

- Elements have recurring, or periodic, chemical properties.

- Periodic Table of Elements: The tabular arrangement of chemical elements.

2.2: Molecules and Chemical Bonds

- A covalent bond results when two atoms share electrons.

- Valence Electrons: The electrons in the outermost orbitals of an atom.

- Molecular Orbital: The merged orbital.

- Covalent Bond: Each shared pair of electrons that holds the atoms together. - A polar covalent bond is characterized by unequal sharing of electrons.

- Electronegativity: The ability of atoms to attract electrons.

- Polar Covalent Bond: When electrons are shared unequally between the two atoms. - Nonpolar Covalent Bond: A covalent bond between two atoms that have the same, or nearly the same, electronegativity.

- An ionic bond forms between oppositely charged ions.

- Ionic Bond: Non-covalent bonds attracted through opposite forces.

- A chemical reaction involves breaking and forming chemical bonds.

Marissa Welch (mjwelch3@asu.edu)

- Chemical Reaction: A process by which atoms or molecules are transformed into different


- Reactants: Starting atoms or molecules in a chemical reaction.

- Products: Ending atoms or molecules in a chemical reaction.

2.3: Water: The Medium of Life

- Water is a polar molecule.

- Polar: A molecule that has regions of positive and negative charge.

- Hydrophilic: Water loving.

- Hydrophobic: Water fearing.

- Solvent: A substance that is capable of dissolving many other substances.

- Aqueous: Watery.

- Nonpolar: A molecule that doesn’t have regions of positive and negative charge. - Hydrophobic Effect: Polar molecules like water exclude nonpolar ones.

- A hydrogen bond is an interaction between a hydrogen atom and an electronegative atom. - Hydrogen Bond: The interaction between a hydrogen atom with a slight positive charge and an electronegative atom of another molecule.

- Hydrogen bonds give water many unusual properties.

- Cohesion: A property of molecules tending to stick together.

- pH is a measure of the concentration of protons in a solution.

- Acidic: pH < 7

- Basic: pH > 7

2.4: Carbon: Life’s Chemical Background

- Carbon atoms form four covalent bonds.

- Carbon-based molecules are structurally and functionally diverse.

- Isomers: Molecules that have the same chemical formula but different structures.

2.5: Organic Molecules

- Functional groups add chemical character to carbon chains.

- Functional Groups: groups of one or more atoms that have particular chemical properties on their own, regardless of what they are attached to.

- Proteins are composed of amino acids.

- Enzymes: Catalysts that accelerate the rates of chemical reactions.

- α (alpha) Carbon: A central carbon atom in an amino acid.

- Amino Group: One of the four groups in an amino acid. (-NH2)

- Carboxyl Group: One of the four groups in an amino acid. (-COOH)

- R Group/Side Chain: One of the four groups in an amino acid. Differs from one amino acid to the next.

- Peptide Bond: A covalent linkage between nitrogen atoms in each amino acid. - Nucleic acids encode genetic information in their nucleotide sequence.

- Deoxyribonucleic Acids (DNA): Genetic material in all organisms.

- Ribonucleic Acid (RNA): The key player in protein synthesis and the regulation of gene expression.

- Base: A nitrogen-containing compound.

- Pyrimidine: A single-ringed base. Cytosine (C), Thymine (T), and Uracil (U).

Marissa Welch (mjwelch3@asu.edu)

- Purines: A double-ringed base. Guanine (G) and Adenine (A).

- Phosphodiester Bond: A bond between a phosphate group in one nucleotide and a sugar unit of another nucleotide.

- Double Helix: The form that DNA in cells usually consisting of two strands of nucleotides take.

- Complex carbohydrates are made up of simple sugars.

- Carbohydrates: Distinctive molecules composed of C, H and O atoms, usually in the ratio 1:2:1.

- Saccharides: Simplest form of carbohydrates. AKA sugar.

- Monosaccharide: A simple sugar.

- Polysaccharides: Polymers of simple sugars.

- Complex Carbohydrates: Long, branched chains of monosaccharides.

- Glycosidic Bonds: Covalent bonds between attached monosaccharides.

- Lipids are hydrophobic molecules.

- Triacylglycerol: An example of a lipid that is used for energy storage.

- Glycerol: A 3-carbon molecule with OH groups attached to each carbon.

- Saturated: Fatty acids that do not contain any double bonds.

- Unsaturated: Fatty acids that contain carbon-carbon double bonds.

- Van der Waals Forces: The weak attraction of opposite charges in molecules. - Steroids: A second type of liquid.

- Phospholipids: A third type of liquid.

2.6: How Did the Molecules of Life Form?

- The building blocks of life can be generated in the laboratory.

- Experiments show how life’s building blocks can form macromolecules.

Chapter 3: Nucleic Acids and Transcription (pdf textbook pg. 114-133)

Core Concepts

- 3.1: Deoxyribonucleic acid (DNA) stores and transmits genetic information.

- 3.2: DNA is a polymer of nucleotides and forms a double helix.

- 3.3: Transcription is the process by which RNA is synthesized from a DNA template. - 3.4: The primary transcript is processed to become messenger RNA (mRNA).

3.1: Major Biological Functions of DNA

- DNA can transfer biological characteristics from one organism to another.

- Transformation: Conversion.

- DNA molecules are copied in the process of replication.

- Replication: The copying process.

- Mutation: An unrepaired error in DNA replication.

- Genetic information flows from DNA to Rna to protein.

- Ribonucleic Acid (RNA): Another type of a linear polymer.

- Central Dogma: The flow of information from DNA to RNA to protein.

- Transcription: Genetic information in a molecule of DNA is used as a template, or pattern, to generate a molecule of RNA.

Marissa Welch (mjwelch3@asu.edu)

- Template: A pattern.

- Translation: A molecule of RNA is used as a code for the sequence of amino acids in a protein.

3.2: Chemical Composition and Structure of DNA

- A DNA strand consists of subunits called nucleotides.

- Nucleotides: DNA’s subunits.

- Sugar: One of the three components of a nucleotide.

- Base: One of the three components of a nucleotide.

- Phosphate Groups: One of the three components of a nucleotide.

- Deoxyribose: The sugar molecule in the DNA.

- Purines: Bases A & G.

- Pyrimidines: Bases T & C (and U in RNA).

- Nucleoside: The combination of sugar and base.

- DNA is a linear polymer of nucleotides linked by phosphodiester bonds.

- Phosphodiester Bond: A relatively stable bond in DNA that can withstand stress like heat and substantial changes in pH that would break weaker bonds.

- Polarity: One end differing from the other.

- 5’ End: The nucleotide at the top with a free 5’ phosphate.

- 3’ End: The nucleotide at the bottom with a free 3’ hydroxyl.

- Cellular DNA molecules take the form of a double helix.

- Major Groove: The outside contours of the twisted strands from an uneven pair of grooves.

- Minor Groove: The outside contours of the twisted strands from an uneven pair of grooves.

- Antiparallel: Run in opposite directions.

- Complimentary: A-T or A-U and C-G base pairs.

- Base Stacking: The stabilizing force in a double helix.

- The three-dimensional structure of DNA gave important clues about its functions. - Cellular DNA is coiled and packaged with proteins.

- Supercoils: The circular molecule’s coiling upon itself.

- Topoisomerases: Enzymes that cleave, partially unwind, and reattach a DNA strand, which puts strain on the DNA double helix.

- Chromosome: DNA molecules formation.

- Chromatin: A complex of DNA and proteins referred to as chromatin.

- Evolutionarily Conserved: Very similar in sequence from one organism to the next.

3.3: Retrieval of Genetic Information Stored In DNA: Transcription

- What was the first nucleic acid molecule, and how did it arise?

- RNA world hypothesis: The idea that RNA, not DNA, was the original

information-storage molecule in the earliest forms of life on Earth.

- RNA is a polymer of nucleotides in which the 5-carbon sugar is ribose.

- Ribose: The sugar in RNA which carries a hydroxyl group on the 2’


- Uracil: One of the bases in RNA that replaces thymine in DNA.

- In transcription, DNA is used as a template to make complementary RNA.

Marissa Welch (mjwelch3@asu.edu)

- RNA Transcript: Complimentary in sequence to the template according to

the base-pairing rules.

- RNA Polymerase: The enzyme which carries out the polymerization.

- Nontemplate Strand: The partner strand to the transcribed DNA strand.

The strand of DNA that is not transcribed.

- Transcription starts at a promoter and ends at a terminator.

- Promoters: Regions of typically a few hundred base pairs where RNA

polymerase and associated proteins bind to the DNA duplex.

- TATA Box: A sequence in the promoter region similar to 5’-TATAAA-3’.

- Terminator: A sequence that stops the process of transcription.

- Housekeeping Genes: Genes whose products are needed at all times in

all cells, transcription takes place continually.

- Sigma Factor: A protein that mediates promoter recognition. Associated

with RNA polymerase and facilitates its binding to specific promoters.

- General Transcription Factors: Six proteins that assemble at the

promoter of a gene.

- Transcriptional Activator Protein: Binds to a specific DNA sequence

known as an enhancer.

- Enhancer: A specific DNA sequence that binds to a transcriptional

activator protein.

- Mediator Complex: A complex of proteins that is recruited by enhancer

DNA sequences.

- Pol II: Protein-coding genes.

- Initiation: When transcription begins.

- RNA polymerase adds successive nucleotides to the 3’ end of the transcript.

3.4: Fate of the RNA Primary Transcript

- Messenger RNA carries information for the synthesis of a specific protein.

- Polycistronic mRNA: Molecules of mRNA that code for multiple proteins.

- Primary transcripts in eukaryotes undergo several types of chemical modification. - RNA Processing: A complex chemical modification of the primary


- 5’ Cap: The addition of a special nucleotide attached in a un unusual


- Polyadenylation: The second major modification of eukaryotic primary


- Poly(A) Tail: A-bearing ribonucleotides to the 3’ end.

- Exons: Regions of protein-coding sequence often found in eukaryotes.

- Introns: Regions of noncoding-proteins often found in eukaryotes.

- RNA Splicing: The process of intron removal.

- Spliceosome: A complex of RNA and protein that catalyzes the process

of RNA splicing.

- Lariat: The loop and tail that is formed when the cleaved end of an intron

connects back on itself.

- Alternative Splicing: Primary transcripts from the same gene can be

spliced in different ways to yield different mRNASs and therefore

different protein products.

Marissa Welch (mjwelch3@asu.edu)

- Some RNA transcripts are processed differently from protein-coding transcripts and have functions of their own.

- Ribosomal RNA (rRNA): Found in all ribosomes that aid in translation.

- Nucleolus: A distinct, dense, non-membrane-bound spherical structure

observed within the nucleus.

- Transfer RNA (tRNA): Carries individual amino acids for use in


- Small Nuclear RNA (snRNA): Found in eukaryotes and involved in

splicing, polyadenylation, and other processes in the nucleus.

- MicroRNA (mRNA): One of the two major types of small regulatory RNA.

- Small Interfering RNA (siRNA): One of the two major types of small

regulatory RNA.

Chapter 4: Translation and Protein Structure (pdf textbook pg. 134-153)

Core Concepts

- 4.1: Proteins are linear polymers of amino acids that form three dimensional structures with specific functions.

- 4.2: Translation is the process in which the sequence of bases in messenger RNA specifies the order of successive amino acids in a newly synthesized protein.

- 4.3: Proteins evolve through mutation and selection and by combining functional units.

4.1: Molecular Structure of Proteins

- Amino acids differ in their side chains.

- α (Alpha) Carbon: A central carbon atom. 

- Amino Group: (-NH2) One of the four different chemical groups covalently bonded to the central carbon of an amino acid.

- Carboxyl Group: (-COOH) One of the four different chemical groups covalently bonded to the central carbon of an amino acid.

- Side Chain/R Group: One of the four different chemical groups covalently bonded to the central carbon of an amino acid.

- Successive amino acids in proteins are connected by peptide bonds.

- Peptide Bond: The bond formed between the two amino acids.

- Amino End: One end of the amino acid that has a free amino group.

- Carboxyl End: Another end of the amino acid that has a free carboxyl group. - Protein: Used as a synonym for polypeptide, especially when the polypeptide chain has folded into a stable, three-dimensional conformation.

- Residues: Amino acids that are incorporated into a protein.

- The sequence of amino acids dictates protein folding, which determines function. - Primary Structure: The sequence of amino acids in a protein.

- Secondary Structures: Interactions between stretches of amino acids in a protein. - Tertiary Structure: The overall three-dimensional shape of the polypeptide.

- Quaternary Structure: Proteins made of several polypeptides interacting with each other. - Secondary structures result from hydrogen bonding in the polypeptide backbone. - α (Alpha) Helix: One of the two types of secondary structure found in many different

Marissa Welch (mjwelch3@asu.edu)


- β (Beta) Sheet: One of the two types of secondary structure found in many different proteins. 

- Tertiary structures result from interactions between amino acid side chains.

- Denatured: Unfolded Proteins.

- Polypeptide subunits can come together to form quaternary structures.

- Chaperones help some proteins fold properly.

- Chaperones: Evolved proteins that help protect slow-folding or denatured proteins until they can attain their proper three-dimensional structure.

4.2: Translation: How Proteins are Synthesized

- Translation uses many molecules found in all cells.

- Ribosomes: Complex structures of RNA and protein that find with mRNA and the site of translation.

- A (Aminoacyl) Site: One of the three bonding sites of the large subunit of the ribosome. Beginning site for entering tRNAs.

- P (Peptidyl) Site: One of the three bonding sites of the large subunit of the ribosome. Middle site for tRNAs.

- E (Exit) Site: One of the three bonding sites of the large subunit of the ribosome. Ending site for leaving tRNAs.

- Reading Frames: The different ways of parsing the string into three-letter words. - Anticodon: Three bases in the anticodon loop of a tRNA.

- Aminoacyl tRNA Synthetases: Enzymes that connect specific amino acids to specific tRNA molecules.

- The genetic code shows the correspondence between codons and amino acids. - Genetic Code: What most codons use to specify an amino acid.

- Translation consists of initiation, elongation, and termination.

- Initiation: One of the three separate processes of translation. Initiator AUG codon is recognized and Met is established as the first amino acid in the new polypeptide chain. - Elongation: One of the three separate processes of translation. Successive amino acids are added one by one to the growing chain.

- Termination: One of the three separate processes of translation. The addition of amino acids stops and the completed polypeptide chain is released from the ribosome. - Initiation Factors: Proteins that bind to the mRNA to initiate translation.

- Elongation Factors: Proteins that are bound to GTP molecules (energy), and break their high-energy bonds to provide energy for the elongation of the polypeptide.

- Release Factor: A protein that binds to the A site of the ribosome when a stop codon is encountered.

- Polycistronic mRNA: Prokaryotic mRNAs that can code for more than one protein. - Operons: A group of functionally related genes located in tandem (having two things arranged one in front of the other) along the DNA and transcribed as a single unit from one promoter.

- How did the genetic code originate?

4.3: Protein Evolution and The Origin of New Proteins

- Most proteins are composed of modular folding domains.

Marissa Welch (mjwelch3@asu.edu)

- Folding Domain: A region of a protein that folds in a similar way relatively independent of the rest of the protein.

- Amino acid sequences evolve through mutation and selection.

- Mutation: A change in the sequence of a gene.

- Selection: The process that eliminates or retains random mutations.

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