Exam 1 BIOL 1A Study Guide Flashcards

Topic 1: The Study of Life

• 1. Describe the elements of the scientific method

  • Steps: make an observation, ask a question, form a hypothesis that answers the question, make a prediction based on the hypothesis, do an experiment to test the prediction, analyze the results, determine if the hypothesis is correct or incorrect and report the results.
  • If the hypothesis is incorrect, form a new hypothesis and repeat the steps.

• 2. Qualifications for a valid hypothesis; examples of a "good" vs a "bad" hypothesis

  • A hypothesis must be testable and falsifiable and must offer an explanation.
  • A good hypothesis is testable, falsifiable, and explanations-based; a bad hypothesis is not testable or falsifiable or does not offer a plausible mechanism.

• 3. Distinguish between basic and applied science; provide examples

  • Basic science: aims to answer fundamental questions about biology.
  • i. Decades of studies have informed our understanding of how genes are regulated. Scientists look for genes that are up-regulated in cancer cells as a drug target.
  • ii. Scientists study the replication cycle of retroviruses. Researchers develop drugs to block different stages of the HIV replication cycle.
  • iii. Scientists study the function of plant genes. Researchers create a drought-resistant strain of rice.
  • Applied science: uses information from basic science to solve real-world problems.

• 4. Distinguish between inductive and deductive reasoning; examples

  • Deductive reasoning: starts with a general idea and becomes more specific. For deductive reasoning to work, the hypothesis/theory you are working with must be true.
  • Example: all people are mortal. Sheila is a person, therefore Sheila is mortal.
  • Inductive reasoning: starts with a specific observation to make more general claims about the world.
  • Example: bob died. Jim died. Susan died. Conclusion: people are mortal.

• 5. Describe the process of peer-review and explain its significance in science

  • Peer-reviewed manuscripts are reviewed by other scientists before publication to ensure the quality of the scientific work.

• 6. Primary vs Secondary sources in science

  • Primary Source: reports of original research that follow IMRaD format (Introduction, Methods, Results, and Discussion).
  • Secondary Sources: summarize and compile many primary sources; most common type is literature reviews.

• Take Homes from Chapter PPT

  • Science is both a noun and a verb: it is an existing body of knowledge (noun) and also something people do (verb).
  • The scientific process is complex and every scientific discovery has followed a different path.
  • A scientific hypothesis is both testable and falsifiable.
  • Scientists use inductive reasoning to develop a hypothesis and deductive reasoning to test it.
  • Deductive reasoning only works if the hypothesis you’re working with is correct.
  • Basic and applied science produce applications/technologies that are beneficial to humans.
  • Life defies a one-sentence definition. Living things from single-celled bacteria to the tallest redwoods share common characteristics.

Topic 2: Chemistry Basics

• 1. Elements found in the highest abundance in humans

  • Oxygen, Carbon, Hydrogen, Nitrogen

• 2. Protons, neutrons, and electrons; their arrangements within an atom; determining counts for atoms in the first three rows

  • Protons = atomic number; dictate the chemical properties of an atom.
  • Neutrons = mass number − atomic number.
  • Electrons = number of protons.

• 3. What is an isotope?

  • Isotopes have the same chemical reactivity but differ in their number of neutrons.

• 4. How is the half-life of an isotope defined?

  • The amount of time it takes for half of the isotope to decay. (Practice problems are noted for class.)

• 5. Uses of radioisotopes in biology

  • Various applications not listed in detail here; generally include tracing, dating, and diagnostic/therapeutic uses.

• 6. Electron configuration and interaction with other atoms

  • Given an element in the first three rows of the periodic table, determine the number of protons, electrons, and neutrons based on atomic number and mass.
  • The electron configuration helps predict chemical behavior and reactivity with other atoms.

• 7. Covalent vs. Ionic bonds; define anion and cation

  • Covalent bonds: sharing of electrons; generally the strongest type of bond.
  • Ionic bonds: formed when one atom transfers electrons to another, creating positively charged (cation) and negatively charged (anion) ions.
  • Cation: positively charged ion.
  • Anion: negatively charged ion.

• 8. Polar covalent vs. nonpolar covalent bonds

  • Polar covalent bonds: electrons shared unequally due to different electronegativities; one atom pulls electrons more strongly.
  • Nonpolar covalent bonds: electrons shared more equally due to similar electronegativities.

• 9. Hydrogen bonds

  • Hydrogen bonds are the weakest interactions, resulting from hydrogen covalently bonded to an electronegative atom and another electronegative atom that it can weakly interact with.
  • They are present in DNA.

• Take Homes from Chapter PPT

  • The number of protons determines which element it is and how it behaves.
  • Isotopes differ in the number of neutrons; some isotopes are unstable and decay over time (radioactive).
  • The half-life is the time for half of the substance to decay.
  • The number of electrons in the valence shell determines how an atom interacts with others.
  • Atoms that share electrons form covalent bonds (strongest). Covalent bonds can be polar or nonpolar.
  • Atoms that donate or accept electrons become ions and form ionic bonds; ionic bonds ionize in water.
  • Hydrogen bonds are weak interactions between a partially positive hydrogen and another electronegative atom.

Topic 3: Water

• 1. Water molecule interactions and hydrogen bonding

  • Draw a diagram of several water molecules interacting with one another (description): Oxygen is partially negative; hydrogens are partially positive.
  • Type of bond that forms between water molecules: hydrogen bonds.

• 2. The four properties of life that water makes an ideal medium for life; explain the why

  • Water as solvent of life; high specific heat: water resists changes in temperature, helping stabilize Earth’s climate and maintain stable internal temperatures.
  • Ice floats on water: water is less dense as a solid than as a liquid.
  • Moderation of temperature by water.
  • Cohesion and adhesion of water molecules; hydrogen bonding between polar water molecules; cohesion (water bonds to itself) and adhesion (water bonds to other surfaces).

• 3. Relationship between hydrogen ion concentration, hydroxide ion concentration, and pH

  • Hydrogen ions (H+)
  • Hydroxide ions (OH-)
  • pH: a measure of H+ concentration.
  • Higher H+ → lower pH → more acidic.
  • Lower H+ → higher pH → more basic.

• 4. Calculate pH, [H+], or [OH-] from one value

  • ext{pH} = - ext{log} [H^+]
  • [H^+][OH^-] = 10^{-14}

• 5. The properties of buffers and their importance in biology

  • A buffer is a weak acid + its conjugate base that stabilizes solutions against changes in pH.
  • Buffers help minimize pH changes in biological systems.

• Take Homes from Chapter PPT

  • Water is polar due to the polar covalent bonds between oxygen and hydrogen; oxygen is partially negative and hydrogens are partially positive.
  • Emergent properties of water: (1) moderation of temperature, (2) ice floats, (3) cohesion and adhesion, (4) polar solvent.
  • At low concentrations, water produces H+ and OH- ions in solution.
  • pH represents the concentration of hydrogen ions: ext{pH} = -\log [H^+].
  • Buffers are weak acids that minimize changes in pH; understand the direction a buffer would move in response to adding an acid or base.

Topic 4: Carbon and Macromolecules

• 1. Why is carbon considered a "versatile" element?

  • Carbon can form covalent bonds with up to four atoms.

• 2. Identify the seven functional groups and their basic properties

  • -OH: hydroxyl
  • Found in alcohols, carbohydrates
  • Can form hydrogen bonds
  • Polar
  • C=O: carbonyl
  • Within a molecule: ketone
  • At the end of a molecule: aldehyde
  • Polar
  • C=O-OH: carboxyl
  • Highly polar; can donate a proton in water to become COO-
  • -NH2: amino
  • Very polar; nitrogen attracts a proton (H+) in water; Found in amino acids
  • -SH: sulfhydryl
  • Polar group
  • O-P=O-O- -O- : phosphate
  • Very polar group
  • -CH3: methyl
  • Hydrophobic; nonpolar; important for DNA

• 3. The three types of isomers; diagrams and examples from topics 5 and 6

  • Structural isomers: same number of each type of atom, but different shapes
  • Cis-trans isomers:
  • Cis: the two substituents (the two X groups) are on the same side
  • Trans: the two substituents are on opposite sides
  • Enantiomers: a carbon bonded to four different groups is an asymmetric carbon; molecules can exist as non-superimposable mirror images.

• 4. Definitions: polymer, monomer, catabolic, anabolic, dehydration reaction, hydrolysis; diagrams of polymer assembly and breakdown

  • Polymer: a large molecule made up of many repeating smaller units (monomers) linked by covalent bonds.
  • Monomer: the small repeating unit that bonds with others to form a polymer.
  • Catabolic: metabolic pathways that break down molecules into smaller ones; release energy (often stored in ATP).
  • Anabolic: metabolic pathways that build larger molecules from smaller ones; require energy input.
  • Dehydration reaction: a chemical reaction that links monomers together to form polymers by removing a molecule of water.
  • Hydrolysis: polymers are broken down into monomers by adding water (split water).

• Take Homes from Chapter PPT

  • Biological macromolecules are made of carbon-hydrogen skeletons and functional groups.
  • C–H bonds have substantial biological energy.
  • Structural isomers have the same atoms but different arrangement.
  • Cis–trans isomers differ in the position of two groups around a double-bonded carbon or within a ring.
  • A carbon bound to four unique groups is an asymmetric/chiral carbon; can have enantiomers.
  • Know all seven functional groups, which macromolecules feature them, and whether they are polar or nonpolar.
  • Polymers are built from monomers via dehydration reactions and broken down by hydrolysis.

Topic 5: Carbohydrates and Lipids

• 1. How monosaccharides are classified; why ring structures for 5- and 6-carbon sugars in biology; relationship to disaccharides and polysaccharides

  • Monosaccharides classification:
  • i. Number of carbons: triose (3) — glyceraldehyde; pentose (5) — ribose (RNA), deoxyribose (DNA); hexose (6) — glucose, fructose, galactose
  • ii. Location of carbonyl group: aldose (on first or last carbon) vs ketose (internal carbon)
  • iii. Handedness (asymmetric carbon)
  • iv. For 5- and 6-carbon sugars, there are linear and ring forms
  • Disaccharides: two sugars covalently joined at a glycosidic bond
  • Sucrose = glucose + fructose
  • Lactose = glucose + galactose
  • Maltose = glucose + glucose
  • Polysaccharides: long polymers of monosaccharides
  • Energy storage: polymers of α-glucose used to store energy
  • Structural: polymers of β-glucose — cellulose

• 2. Polysaccharides learned in class; where found; function; structural differences and how they relate to function

  • a. Amylose
  • b. Amylopectin
  • c. Cellulose
  • d. Chitin

• 3. Triglycerides: what they are made of; three types (two natural, one man-made); chemical differences and health implications

  • a. Triglycerides are made of glycerol + three fatty acids joined by dehydration reactions.
  • b. Types:
  • i. Saturated fats (natural)
  • ii. Unsaturated fats (natural)
  • iii. Trans fats (unnatural)
  • How differences relate to health:
  • Saturated fats have only single bonds in tails; typically solid at room temp.
  • Unsaturated fats have one or more double bonds; often liquid at room temp.
  • Trans fats have trans double bonds; associated with negative health effects.

• 4. Phospholipid structure and self-assembly in water

  • A phospholipid has two fatty acids and a modified phosphate group attached to a glycerol backbone.
  • In water, the hydrophilic (polar) head groups face the aqueous solution, while the hydrophobic tails face inward, forming a bilayer.

• 5. Steroids: what they are and why important

  • Steroids are lipids with a carbon skeleton of four fused rings.
  • They are hydrophobic, though some have polar functional groups that give partial solubility.
  • The liver synthesizes cholesterol, a steroid; cholesterol is a precursor to many steroid hormones (e.g., testosterone, estradiol) secreted by gonads and endocrine glands; cholesterol is also a precursor to Vitamin D and bile salts (which emulsify fats and aid absorption).
  • Cholesterol is necessary for proper bodily function.

• Take Homes from Chapter PPT

  • Carbohydrates provide energy and structural roles.
  • Monosaccharides are classified by carbon count and carbonyl position.
  • 5- and 6-carbon sugars form ring structures in water; glucose can form alpha or beta rings.
  • Monosaccharides join via dehydration synthesis to form disaccharides and polysaccharides.
  • Starch and glycogen are made of α-glucose and function to store energy.
  • Cellulose is a structural polysaccharide made of β-glucose; strands hydrogen-bond to form strong fibers.
  • Lipids are hydrophobic.
  • Triglycerides store energy and are made of glycerol plus three fatty acids.
  • Saturated fats have no double bonds; unsaturated fats have at least one double bond.
  • Unsaturated fats can be cis or trans.
  • Phospholipids make up the plasma membrane and have both hydrophilic and hydrophobic regions; they form a bilayer in water.
  • Steroids are lipids used in signaling and as membrane components.

Topic 6: Proteins and Nucleic Acids

• 1. Amino acids: general structure and chiral center

  • Draw a general amino acid structure: an a-carbon bonded to an amino group, a carboxyl group, a hydrogen, and an R group (side chain).
  • All amino acids (except glycine) have a chiral (asymmetric) center and exist in two enantiomeric forms.
  • The functional groups present in every amino acid: amino group (-NH2), carboxyl group (-COOH), hydrogen, and an R group.
  • Hydrophobic vs hydrophilic amino acids can be depicted by R group characteristics.

• 2. Polypeptide synthesis; bond type and involved functional groups; direction of growth

  • Process: building a polypeptide (protein) via peptide bonds formed between the carboxyl group of one amino acid and the amino group of the next.
  • Bond type: peptide (amide) bond.
  • Growth direction: the polypeptide grows in the 5′ to 3′ direction (N-terminus to C-terminus) as new amino acids are added to the free amino end of the chain.

• 3. Protein structure: primary, secondary, tertiary, and quaternary; what happens in unfavorable conditions

  • Primary structure: the unique sequence of amino acids in a polypeptide.
  • Secondary structure: local folding (e.g., alpha helices and beta sheets) formed by hydrogen bonds between the amine and carboxyl groups.
  • Tertiary structure: the three-dimensional shape of a single polypeptide, determined by interactions among R groups.
  • Quaternary structure: the arrangement of two or more polypeptide chains into a functional protein.
  • Unfavorable conditions (e.g., excessive heat or altered pH) can cause denaturation, disrupting structure and function.

• 4. Functions of nucleic acids; differences between RNA and DNA; pyrimidines vs purines

  • Functions: information storage (DNA) and gene expression (RNA).
  • RNA: single-stranded; ribonucleotides; phosphodiester bonds; bases are A, U, G, C.
  • DNA: double helix; antiparallel and complementary strands held by hydrogen bonds.
  • Pyrimidines: cytosine, thymine (DNA), uracil (RNA).
  • Purines: adenine and guanine.

• 5. Three parts of a nucleotide; the 2′, 3′, and 5′ carbons; importance

  • Parts: phosphate group, pentose sugar (ribose in RNA or deoxyribose in DNA), nitrogenous base.
  • 2′ carbon: in RNA has an -OH group; in DNA it has a hydrogen (absence of 2′-OH).
  • 3′ carbon: bears a hydroxyl group used to form phosphodiester bonds.
  • 5′ carbon: bears the phosphate group of the incoming nucleotide.

• 6. Building a DNA polymer; the two functional groups involved; direction of growth

  • Monomers: deoxyribonucleotides (DNA).
  • Components: phosphate group, deoxyribose sugar, nitrogenous base (A, T, G, C).
  • Functional Groups Involved:
  • 3′-hydroxyl (–OH) of the sugar on the existing strand
  • 5′-phosphate (–PO4^3−) of the incoming nucleotide
  • Bond Formation: the 3′–OH attacks the phosphate on the 5′ carbon of the next nucleotide, forming a phosphodiester bond; this is a dehydration reaction (water released).
  • Directionality: DNA polymerization occurs in the 5′ → 3′ direction; nucleotides are added to the 3′ end.

• Take Home: Proteins

  • Proteins are the products of gene expression and are made of long polymers of amino acids.

• Take Home: Nucleic Acids

  • Nucleic acids are long polymers of nucleotides that store information (DNA) and express genes (RNA).
  • DNA is double-stranded, antiparallel, and complementary.
  • Adenine pairs with thymine (A–T) via two hydrogen bonds; cytosine pairs with guanine (C–G) via three hydrogen bonds.
  • A pyrimidine always pairs with a purine (to maintain the width of the helix).
  • Phosphodiester bonds form between the 3′-OH of one nucleotide and the 5′-phosphate of the next, creating a polymer.
  • RNA differs from DNA: usually single-stranded, contains uracil instead of thymine, and uses ribose sugar; ribose has an -OH on the 2′ carbon, whereas DNA’s deoxyribose lacks this 2′-OH.