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AU / Biology / BIO 1020 / How are acids and bases defined?

How are acids and bases defined?

How are acids and bases defined?


School: Auburn University
Department: Biology
Course: Principles of Biology
Professor: Zhong
Term: Fall 2015
Cost: 50
Name: Biology 1020: Final Review Study Guide
Description: This study guide covers the information the Dr. Zhong advised students to study during her study session for the exam. Good luck!
Uploaded: 12/10/2017
21 Pages 10 Views 6 Unlocks

Biology 1020: Final Exam Study Guide

How are acids and bases defined?

Chapter 2:

1. Isotope

a. Element with same protons, but different number of neutrons

2. Proton, neutron, electron

a. Proton: ​positively charged ion; atomic number

b. Neutron: ​neutrally charged particle; proton + neutrons = atomic mass c. Electrons: ​equal to proton number, negatively charged

3. Covalent bond

a. share electrons

4. Ionic bond

a. Most electronegative element pulls electrons towards nucleus

5. Nonpolar covalent bond

a. Equal sharing of electrons; determined by electronegativity

6. Polar covalent bond

a. Unequal sharing of electrons; Water

7. Hydrogen bond

a. attraction from the partial positive of Hydrogen and partial negative of Oxygen when water molecules bond

Chapter 3:

1. How are acids and bases defined? How is pH important to living organisms? a. Acids increase the [H+] and bases increase [OH-].

How is pH important to living organisms?

We also discuss several other topics like How do ethics and social responsibility relate to Marketing?

b. pH creates a stable environment according to the cell or organism

2. What are the specific heat and heat of vaporization of water?

a. Specific heat: temperature stability

i. Energy to raise the temperature of 1 gram of something 1 degree Celsius ii. 1 calorie / 1 gram degree C

b. Heat of Vaporization

i. Energy to move 1 gram from liquid to gas

3. Why can water moderate temperature?

a. Hydrogen bonds allow for a high absorption and release of energy without changing the overall temperature drastically

4. Why is water very necessary to life?

a. Allows for and established a stable cell environment for biochemical reactions b. Cohesion and adhesion abilities

c. Ability to moderate temperature

d. Expansion upon freezing

e. Versability as a solvent

Chapter 4:

1. Versatility of Carbon

What are the specific heat and heat of vaporization of water?

a. Four open valence electrons and has four bonding patterns possible because of them.

2. How are functional groups important in Chemical Reactions?

a. They attach to carbon backbone and determine the characteristics and chemical activity of the organic molecules.

3. Functional Groups:

a. Hydroxyl Group: --O-H; ​polar, found in alcohols

b. Carbonyl Group: carbon double bonded to oxygen and two lone single bonds available; ​polar found in aldehydes and ketones We also discuss several other topics like ross avilla uc merced

c. Carboxyl Group: carbon double bonded to oxygen and single bonded to hydroxide, with one long single bond; ​ weakly acidic, found in organic acids (amino acids)

d. Amino Group: Nitrogen bonded to two Hydrogens with one single lone bond; ​weakly basic, found in such things as amino acids

e. Sulfhydryl Group: S-H; ​essentially polar, found in some amino acids f. Phosphate Group: ​weakly acidic, found in such things as phospholipids and nucleic acids

g. Methyl Group: ​NONpolar group and thus hydrophobic; found in such things as lipids, and other membrane components Don't forget about the age old question of utd comm lab

Chapter 5:

1. Dehydration Synthesis vs. Hydrolysis

a. Dehydration Synthesis: ​brings monomers together through removing a water and building a polymer

b. Hydrolysis: ​breaks down polymers by adding a water to where one was removed

2. How are carbohydrates important to living organisms?

a. Monosaccharide: ​Glucose

b. Disaccharide: ​Maltose, Lactose, sucrose

c. Polysaccharide: ​Starch, Cellulose, Chitin

3. Glycosidic Linkage?

a. Links carbohydrates at Carbon 1 after dehydration synthesis

4. What are the characteristics of proteins? What is a peptide bond? a. Primary Structure: ​long chain of amino acids in a particular sequence; nonfunctional proteins

b. Secondary Structure: ​chain is folded into either an Alpha Helix or Beta Pleated Sheet; held together by Hydrogen bonds

c. Tertiary Structure: ​peptide chains stabilize by folding and coiling by the formation of ionic or hydrophobic bonds, disulfide bridges

d. Quaternary Structure: ​an assembly of more than 1 polypeptide or subunits of its own; insulin, blood, etc. (intermolecular forces)

5. Structure of Amino Acid?

a. Amino group-central carbon with Hydrogen and R functional group on top-Carboxyl group

6. What is phosphodiester bond? How does it link two nucleotides together? a. Links nucleotides by linking between Carbon 5 of one nucleotide and Carbon 3 of the next; sugar-phosphate backbone If you want to learn more check out su chem

7. Carbohydrates:

a. Monomers: ​monosaccharides

b. Polymers: ​disaccharides, polysaccharides

c. Bond: ​glycosidic link

d. Function:

i. Storage: Starch and Glycogen

ii. Structure: Cellulose and Chitin

8. Proteins:

a. Monomer: ​amino acids

b. Polymer: ​polypeptide

c. Bond: ​peptide bond

9. Lipids:

a. Monomers: ​fatty acids and triacylglycerols If you want to learn more check out physics 211 psu
Don't forget about the age old question of soup flashcard

b. Bond: ​ester bond

10. Nucleic Acids:

a. Monomer: ​nucleotides

b. Polymer: ​polynucleotides

c. Bond: phosphodiester bond

Chapter 6:

1. What is the Surface Area to Volume ratio? Why does it limit cell size? a. The surface area increases at a faster rate and causes the cell to be limited in size.

2. Prokaryotic vs. Eukaryotic Cells

a. Prokaryotic:

i. No membrane bound structures

ii. No nucleus

iii. Have ribosomes, membrane, DNA, RNA

b. Eukaryotic:

i. Membrane bound organelles

ii. Nucleus

3. Ribosomes

a. Protein synthesis

b. Attached to rough eR

4. ER

a. Enclosed, interconnected channels connected with nuclear envelope b. Rough​: protein synthesis

c. Smooth​: lipid synthesis; break down drugs and poisons

5. Vesicles

a. Transport modified proteins from Golgi, and then take them out of Golgi b. Membranous sacs

c. Transport substances

6. Golgi

a. Stacked, flattened sacs

b. Receives proteins from ER and sorts and packs them (modifies) c. Cis Face: receives protein

d. Trans face: sends protein out towards membrane

7. Lysosomes

a. Membranous sac

b. Buds from Golgi

c. Contains digestive enzymes

d. Low pH

8. Vacuoles

a. Food Vacuole

i. Membranous sac

ii. Bud from plasma membrane

iii. Fuse with lysosomes for digestion

b. Contractile Vacuoles

i. Maintain water balance

c. Central Vacuole

i. Plant cells

ii. Maintain water balance and ensure Turgor Pressure

iii. Store water

9. Mitochondria

a. Cellular Respiration

b. Double membrane

c. Circular DNA

d. Similar function to Chloroplast

10. Plastids

a. Amyloplasts

i. For starch storage

b. Chromoplasts

i. For color in petals/fruits

c. Chloroplasts

i. Photosynthesis

ii. Double membrane

iii. Own circular DNA

11. Peroxisomes

a. Membrane bound

b. Produce hydrogen peroxide and convert it to water

12. Cytoskeleton

a. Microfilaments

b. Microtubules

c. Intermediate Filaments

d. Network of protein fibers within the cytoplasm that maintains:

i. Cell shape

ii. Cell movement

iii. Organelle movement

iv. Facilitating cell division

Chapter 7:

1. How does the Sodium-Potassium Pump work?

a. Active transport

b. Binds 3 Na+ and 3 K+ ions, moves out 3 Na+, 2 K+ in

c. Consumes ATP every cycle and works against concentration gradient d. Changes the shape of the pumps

e. Pump is created so that charged particles can enter the membrane f. Creates membrane potential and maintains a more negative intracellular environment and positive extracellular environment

2. Hypotonic Solution:

a. More solution than solute; often more water.

b. Plants prefer Hypotonic environment because it increases the Turgor Pressure between their contractile vacuole and cell wall.

c. RBC will burst, along with any other cells in a hypotonic environment (lyse​) d. Water Flow

i. Water moves from [high water] → [low water] aka water flows HYPO → HYPER

3. Hypertonic Solution

a. More solute than solution

b. Plants will plasmolyze and RBC will shrink

c. Water Flow

i. Water moves towards because lower water concentration

4. Isotonic Solution

a. Equal amounts on solute and solution

b. RBC prefer

c. No water flow

5. Diffusion

a. Random movement of particles from [high] → [low] & is IN RESPONSE to a concentration gradient

6. Osmosis

a. Diffusion of water across a selectively permeable membrane

b. High ​osmotic potential in a hypertonic e​ nvironment

c. Low ​osmotic potential is a hypotonic ​environment

7. Dialysis Bag

a. Dialysis and Osmosis

i. Dialysis = diffusion of certain solutes

ii. Osmosis = diffusion of solvent

8. Active vs. Passive Transport

a. Active: ​transport against a concentration gradient; requires ATP; “pumps” such as the Sodium-Potassium

b. Passive: ​No energy needed to pass through membrane, goes with concentration gradient

i. Facilitated Diffusion​: channel/carrier proteins that bind to larger

molecules and allow them to pass through membrane

Chapter 8:

1. Endergonic vs. Exergonic reactions

a. Endergonic: ​requires an input of energy and creates larger molecules as a result; absorbs energy given off from Exergonic reactions. These reactions start at a lower energy level because they have to absorb energy in order to activate. Ex) amino acids building to create a protein.

b. Exergonic: ​gives off energy and breaks down larger molecules. The energy given off catalyzes most Endergonic reactions in catabolic coupled reactions. The activation energy is much lower, but these reactions begin at a higher energy state.

2. ATP Molecule

a. Structure: ​Adenine + Ribose + 3 Phosphate groups; u

b. Hydrolysis: ​ATP + H2O → ADP + Pi

i. Hydrolysis of ATP provides an energy coupling between catabolic and anabolic pathways

ii. Pi the active phosphate

c. High-energy bonds: ​located between last 2 phosphate groups; two phosphate bonds are unstable and release high energy during hydrolysis

3. How does ATP power endergonic reactions?

a. Through its energy released in its exergonic reaction of Hydrolysis, and the Pi activates the endergonic reaction

4. What are phosphorylated intermediates? Function?

a. When ATP hydrolysis is coupled to a reaction to provide energy, the Pi is transferred onto another compound rather than being immediately released b. Overall, Coupled Reactions are exergonic

5. ATP regeneration cycle:

a. Energy from catabolism (exergonic, energy-yielding processes) → ATP → energy for cellular work (endergonic reactions, energy-consuming processes) → ADP + Pi → then repeats cycle again

6. Define what an enzyme is, and be able to graph the effect an enzyme has on activation energy.

a. Enzyme: ​catalytic protein that lowers the activation energy of a process, without changing the overall free energy released; neither destroyed nor used up; recycle themselves

7. Why are enzymes important for us?

a. They assist energy processes within us while activating and inhibiting dangerous processes.

b. Competitive Inhibitor​: binds to the active site of an enzyme and prevents the substrate from binding, therefore inhibiting the activity; how medicines work c. Noncompetitive Inhibitor:​ binds to another part, causing enzyme to change shape

8. How do enzymes work with substrates to catalyze the reactions? a. Enzyme structure: ​specific to the substrate

b. Enzyme-substrate complex: ​active site where the substrate binds

c. Active Site: ​pocket-like structure where the substrate(reactant) binds; the shape of the active site is complementary to the shape of the substrate

9. What is substrate specificity?

a. Enzymes are specific to their substrates and vice versa; will not work otherwise.

Chapter 9:

1. Why do cells undergo respiration?

a. Cells need energy

2. What is the main function of cellular respiration?

a. To convert usable energy out of glucose

3. What is the chemical equation for respiration?

a. 6C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP

4. Four stages of Cellular Respiration:

a. Glycolysis

i. Overview: ​oxidation of glucose → pyruvate; does not require oxygen ii. Reactants: ​glucose + NAD+

iii. Products: ​2 ATP + 2 NADH

iv. 2 Phases:

1. Energy Investment Phase (activation)

a. Consume 2 ATPS

b. Products: 2 G3P molecules

2. Energy Payoff Phase (harvest energy)

a. Products: 2 Pyruvates + 2 NADH + 4 ATPS

b. Pyruvate Oxidation

i. Overview:

1. ​formation of acetyl CoA

2. NAD+ is reduced to NADH

3. pyruvate → CO2 and Acetyl CoA

4. ​Carboxyl group of pyruvate is removed as CO2 is released. The

remaining 2-carbon fragment is oxidized to acetate and NAD+ is

reduced to NADH

ii. Release of CO2 and synthesis of NADH

c. Krebs Cycle

i. Location: ​Matrix

ii. Net ATPS = 2 ATPS

iii. Acetyl CoA → CO2 (2)

iv. NAD+ reduced to NADH & FAD reduced to FADH2

1. Most NADH and FADH2 produced carry electrons to ETC

v. Overview:

1. CoA is removed and 2-carbon skeleton is attached to existing

4-carbon molecule(starting point of cycle), Carbon chain is broken

down releasing CO2, several electron carriers capture electrons

and more CO2 is released

2. “Cycle” = the 4-carbon acid that accepts acetyl CoA in first

step of cycle, is regenerated by the last step

vi. For each Pyruvate that enters the cycle:

1. 1 ATP produced

2. 3 NADH produced

3. 1 FADH produced

vii. For each Glucose that enters the cycle:

1. 4 CO2 produced

2. 2 ATP produced

3. 6 NADH

4. 2 FADH2

d. ETC

i. Location: ​Inner Membrane of Mitochondria

ii. Overview: ​after Hydrogen ions are pumped into the mitochondrial intermembrane space, they flow back through ATP synthase, which

produces most ATP associated with cellular respiration

iii. Chemiosmosis: ​energy from the flow of electrons along the ATC is used to pump H+ ions across the inner mitochondrial membrane and creating the chemiosmotic gradient.

iv. H+ ions accumulate along the mitochondrial intermembrane v. O2 is the final electron acceptor & forms water

vi. Total ATP: 28

5. By which step are all carbons broken down into CO2?

a. ETC

6. Which step needs CO2?

a. Krebs Cycle

7. Which step generates largest amount of NADH and FADH2?

a. Citric Acid Cycle

8. Which step generates largest amount of ATPS?

a. ETC; 18 due to oxidative phosphorylation

9. Which step occurs in the cytosol?

a. Glycolysis

10. What is the final electron acceptor?

a. oxygen

Chapter 10:

1. What is the chemical reaction for photosynthesis?

a. 6 CO2 + 6 H2O + light energy → C6H12O6 + 6O2

b. Carbon dioxide is reduced

c. Water is oxidized

d. 2 parts:

i. Part 1: PSII → PSI: energy from PSII and pump (cytochrome complex) produce ATP

ii. Part 2: PSI → NADP reductase: energy from PSI to reductase create NADPH as the final electron acceptor

2. What is the function of photosynthesis?

a. Plants need glucose to transform sunlight into chemical energy stored in complex organic molecules, releasing Oxygen as a by-product

3. Illustrate the Light Reactions

a. Reactants: ​water and light energy

b. Products: ​Oxygen, ADP, NADPH

c. Location: ​ thylakoid membranes

d. Overview: ​light energy is converted into high energy molecules, water is split providing oxygen that the basis for aerobic life (water is split as PSII and is similar to Oxidative Phosphorylation). Hydrogen atoms flow through ATP Synthase in the Light Reaction of Photosynthesis through the Thylakoid Space, stroma, and then to the Calvin Cycle.

4. Calvin Cycle

a. Reactants: ​CO2, ATP, NADPH

b. Products: ​ NADP+. ADP, Glucose

c. 3 Phases:

i. Carbon Fixation

1. Carbon capture → Rubisco

2. 6 RuBP + 6CO2 → 12 PGA

ii. Carbon Reduction

1. Synthesis of G3P

2. Energy is donated by ATP and NADPH

3. PGA → G3P

iii. RuBP Regeneration

1. 10 of 12 G3P molecules convert into 6 RuBP molecules

2. 2 of 12 G3P molecules are used to synthesize 1 Glucose


a. 2 G3P molecules (3 carbons each) are used to from 1

Glucose (6 carbons each)

3. ATP used as energy for these reactions

d. Intermediate RuBP: ​CO2 is captured and linked to RuBP by Rubisco e. PGA: ​result of Carbon Fixation

f. G3P: ​5 carbon starting molecule of the cycle which first combines CO2 & exits te Cycle as it is used as raw material to build other organic molecules

g. Location: ​Stroma

h. Overview: ​ builds sugars, uses ATP and NADP and recycles them

5. Connection between Light Reaction and Calvin Cycle:

a. NADPH carries electrons to the calvin cycle as it is the final electron acceptor for photosynthesis

6. Diagram Calvin Cycle

a. # of Carbon: ​6

b. How many CO2 are needed for one glucose synthesis? ​3 molecules due to 2 cycles

c. How many molecules of G3P are directly used for one glucose synthesis? ​1 due to 2 cycles

7. What is Rubisco?

a. Function: ​enzyme in plant that captures CO2 to begin the Calvin Cycle

Chapter 12 & 13:

1. How do you count chromosomes?

a. By their centromeres

2. How many chromosomes do we have in our body cells?

a. 46; 2 sets

3. How many chromosomes are there in our gametes?

a. 23

4. How many chromatids are there before/after DNA replication in somatic cells? a. Before:

i. 46

b. After:

i. 92

5. How many chromosomes are found in haploid/diploid cells?

a. Haploid (n) = a set of chromosomes has one member for each homologous pair; haploids have 1 set

b. Diploid (2n) = 2 complete sets

6. Be able to recognize and explain different phases of Mitosis and Meiosis. 7. Differences between Mitosis and Meiosis

a. Mitosis

i. Maintains ploidy

ii. Creates genetically identical offspring

iii. 2 diploid offspring

b. Meiosis

i. Reduces ploidy

ii. Increases genetic variability

iii. 4 haploid offspring

iv. 2 rounds

v. Separation of homologous chromosomes

vi. Crossing over (P1), Synapsis (P1), & Breaking of Homologous

Chromosomes (M1)

8. Be able to calculate Independent Assortment given number of homologous chromosomes.

9. Chromatin:​ less condensed; DNA and protein

10. Chromosome: ​condensed chromatin; carries DNA

11. Centromere: ​holds sister chromatids together

12. Sister Chromatid: ​identical copies of a chromosome; formed during DNA synthesis 13. Homologous Chromosome: ​2 pairs of chromosomes; 1 mom & 1 dad; have genes for some trait at the same loci

14. Fertilization: ​forming of a zygote; fusion of gametes

15. Mitotic Spindle: ​attaches to chromosomes during Metaphase

16. Zygote:​ fusion of gametes forms a diploid zygote

17. Gamete: ​haploid sperm or egg

Chapter 14 & 15:

1. Describe the Law of Segregation and the Law of Independent Assortment a. Segregation

i. The law of segregation states that alleles will separate accordingly during meiosis RANDOMLY

b. Independent Assortment

i. The law of independent assortment is shown during Metaphase I when homologous chromosomes line up variably 2-abreast and assort

independently of one another

2. Be able to use Punnett Squares to solve genetic problems of bother monohybrid and dihybrid crosses

3. Incomplete Dominance Inheritance

a. When both dominant and recessive alleles are shown, pink snap dragon plants 4. Multiple Alleles

a. ABO Blood Type System

b. A species may have more than 2 alleles for a given trait


d. ABO = Multiple Alleles

5. Be able to distinguish sex chromosomes and autosomes.

a. How many sex chromosomes do you have? Pairs?

i. 2 chromosomes; 1 Pair

b. How many autosomes do you have? Pairs?

i. 44 autosomes; 2 pair of 22

c. 23 chromosomes in a gamete and 1 sex chromosome

6. How is sex determined?

a. Father has XY & Female has XX

b. Sex is determined by whether the sperm cell contains an X and Y chromosome 7. What is a sex-linked gene?

a. Genes carried on the sex chromosomes; can be on either sex chromosome b. Eye-color

c. X-linked recessive alleles are expressed more often in males than females 8. Be able to draw punnett squares for sex-linked traits and infer parental or offspring’s genotypes.

9. Human Genetic Disorders:

a. Autosomal Recessive Disorders: 2 copies of abnormal gene must be present in order for the disorder to occur & if both parents have the recessive trait, a child has a 1 in 4 chance of inheriting the trait

i. Albinism

ii. Cystic Fibrosis

iii. Sickle-Cell Anemia

b. Autosomal Dominant Disorders: 1 copy of the abnormal gene must be present in order for the trait to represent itself

i. Achondroplasia

ii. Huntington's Disease

iii. Marfan Syndrome

iv. Polydactyl

v. Progneria

c. Sex-Linked Disorders: caused by genes located on X and Y chromosomes; since X chromosomes carry more genes that are not found in Y

chromosomes, X chromosomes are more commonly linked to genetic mutations and disorders

i. Hemophilia (recessive X trait)

ii. Red-Green Color-Blind (recessive X trait)

Chapter 16:

1. What is Chargaff's Rule?

a. Complementary base pairing: A=T & G=C

2. Explain how different nucleotides are assembled into a double helix. Describe what is meant by “complementary base pairing”. Be able to write the complementary strand given on DNA strand.

a. Complementary base pairing means that A-T and G-C on a DNA strand b. Nucleotides are assembled into a double helix through hydrogen bonds holding them together and their sugar-phosphate backbone stabilizing the structure 3. Explain the process of DNA replication, be able to draw a replication fork and label each enzyme and their functions, especially notice DNA helicase, SSDP, topoisomerase, primase, DNA polymerase and ligase.

a. DNA Replication

i. Semiconservative process

ii. Helicase unzips two strands of DNA and forms a replication bubble iii. SSDP keep the replication fork open and cover the nucleotide bases iv. Topoisomerase breaks and rejoins the strands

v. Primase starts the process by adding an RNA primer

vi. DNA Poly moves in 5’-->3’ direction in synthesizing the daughter strand and DNA Poly 1 replaces the RNA primer

1. DNA Poly also proofreads the new DNA and modifies it by

replacing any incorrect nucleotides

vii. Ligase joins the Okazaki Fragments on the Lagging strand

4. Illustrate the different mechanisms in leading and lagging strand. a. Leading Strand:

i. Synthesized completely

b. Lagging Strand:

i. Synthesized in fragments due to it running 3’--> 5”

Chapter 17:

1. Describe the process of transcription: DNA → mRNA

○ Where does it take place?​ Nucleus

○ Enzymes​? RNA Polymerase

○ Product​? mRNA

○ Start and Stop sites?​ Promoter (TATA box) with start codon ATG & Terminator (TAA)

○ Three Stages?

i. Initiation:

1. DNA strands are separated

2. Transcription factors facilitate RNA polymerase binding to


3. Transcription initiation complex is formed

4. RNA polymerase binds to promoter region of DNA


5. 5→3 direction

6. One DNA strand is used as the template

ii. Elongation:

1. RNA Polymerase adds free RNA nucleotides to elongate

the strand

2. RNA strand peels away

3. DNA strands repair and wind up

iii. Termination:

1. RNA Polymerase reaches the terminator and releases

completed RNA sequence

○ Direction? 5’ → 3’

2. How do Eukaryotic cells perform post-transcriptional modification (RNA processing) including 5’ capping, 3’ poly-a tail, or RNA splicing? ○ 5’ Cap​: modified guanine residue; required for binding to eukaryotic ribosomes and make mRNA more stable

○ 3’ Poly-a Tail​: facilitate the export of mRNA out of nucleus, make mRNA less susceptible to degradation, and initiation of Translation

○ RNA Splicing​: Introns are cut out by spliceosomes, exons remain 3. What is a ribozyme? Is it an enzyme (protein) or an RNA? Function? ○ Ribozyme is an enzymatic RNA that catalyzes RNA splicing 4. Understand tRNA structure and functions

○ Structure​:

○ Function​: brings amino acids to the ribosome

5. What are anticodons? Which molecules have anticodons? What are they used for translation?

○ Anticodons​: sequence of mRNA base pairs that are attached to tRNA ○ Molecules with Anticodons: ​tRNA

○ Role during Translation​: ensure the proper placement of the correct amino acid on the ribosomes.

6. Be able to draw a typical gene structure including promoter, terminator, 5’-UTR, coding-region (start codon, stop codon, exons, and introns). Use it as a template for gene expression. Understand the function of each structure in transcription, RNA-processing and translation.

7. What is a gene mutation? What is a mutagen?

○ Gene Mutation:​ changes in DNA sequences

○ Gene Mutagen​: environmental inducers

i. Cigarettes, chemicals etc

8. Understand each type of mutation and how they affect the gene expression? Which type is considered the least drastic for the gene expression? Which types can cause the reading-frame shift? ○ Substitution (point mutations):

i. Silent mutations= no effect on AA sequence

ii. Missense mutations = code for incorrect AA

iii. Nonsense mutations = change codon into stop codon

○ Insertions and Deletions (point mutations):

i. Change reading frame

ii. Change AA sequence

○ Inversions and Translocations:

i. Not problematic if entire gene is moved, but if genes is split in two, it will no longer code

○ Least drastic type: Substitution

○ Reading-frameshift: Insertion and deletions

9. Describe mutation in evolutionary concept, including neutral, bad, and good mutations.

○ Evolutionary Concept​: Mutations are an ultimate source of genetic variation that drives evolution

○ Neutral Mutations​: the point mutation doesn’t affect protein’s function i. Protein with unimportant AA change

ii. Protein with unchanged AA

○ Bad Mutation​: mutation causes the protein function to change and is harmful

○ Good Mutation​: mutation causes the protein function to be changed for the better

Chapter 22:

1. What is evolution?

a. Evolution is the change in a population, over time (Generations)

2. Define Natural Selection and explain.

a. Natural selection is the survival of the most fit organism in response to its environment.

b. Increases the adaptation of organisms to their environment over time c. Modifies populations over time

3. Describe and examine homologous features, analogous features, and vestigial features with examples.

a. Homologous​: similar in structure due to a common evolutionary origin (human arm, dolphin flipper, bat wing, bird wing)

b. Analogous​: similar in function, but not in structure, no common ancestry (bird and butterfly wing)

c. Vestigial​: once used, but are now no longer needed to survive so they have no purpose in our bodies; can be used to trace other populations that once had the functional feature

Chapter 23:

1. Understand Hardy-Weinberg equilibrium:

a. p^2 + 2pq + q^2 = 1

b. p= dominant trait

c. q= recessive trait

d. 2pq = frequency of heterozygous alleles

2. What are the five conditions necessary for Hardy-Weinberg equilibrium model? a. No natural selection

b. No mutation

c. No gene flow from populations

d. Random mating

e. No genetic drift

3. What is gene flow? Examples?

a. Gene flow: decreases allele frequency in old population, but increases the frequency in the new one; results from Migration of a species Ex) Min Zhong coming from China

4. What is genetic drift? Examples? How does population size effect genetic drift? a. Genetic drift​: random flow of alleles in a population; increase or decrease in a certain traits

b. Population size:​ smaller populations, bigger effect

5. What is the difference between the bottleneck effect and the founder effect? Examples?

a. Bottleneck​: A bottleneck effect dramatically reduces the number of the population due to disaster and lacks genetic variety

b. Founder: ​the founder effect results in a new colony being established and is isolated while it cuts the species off from a gene pool; disaster leaving few organisms alive and them creating a small/new colony

6. How does natural selection modify populations?

a. Natural selection​: it consistently works to adapt organisms to their environment, increases allele frequency of favored alleles; produces adaptations

7. 5 Causes of Microevolution and their consequences with examples. a. Genetic Drift: ​ random movement of alleles in a population

i. Bottleneck Effect: ​disaster wiping out large population and resulting in a lack of genetic variety

ii. Founder’s Effect: ​new colony is established after a disaster strikes and leaves only few surviving species in a single space away from gene pool b. Gene Flow: ​move of alleles from population to population due to migration of a species

c. Mutation:​ most mutations occur during lifetimes and do not affect all offspring (least likely cause of Microevolution)

d. Non-Random Mating: ​White Snow Geese only mate with white snow geese and blue snow geese only mate with blue snow geese. This causes distinctions between what is the exact same species.

e. Natural Selection: ​produces adaptations

8. Three types of Natural Selection and examples

a. Stabilization: ​most common; intermediate/average phenotype survives; ex: weight of born babies always being around 5-7 pounds on average

b. Directional: ​rare; one extreme trait is favored; ex) Giraffes long necks c. Disruptive: ​selection against the “mean” of the graph; ex) African Finches and their long beaks, small beaks, and no middle beaks because of only small and large seeds.

9. Sexual Selection

a. Sexual selection: ​ A process in which individuals with certain inherited characteristics are more likely than other individuals of the same sec to obtain mates → sexual dimphormisms (a difference in secondary sexual

characteristics between males and females of the same species)

Chapter 24:

1. What is a species? What is speciation?

a. Species​: a group of organisms that have the potential to produce vital and fertile offspring

b. Speciation​: ​making of species

2. Biological Species Concept:

a. Focuses on reproductive isolation; a group of populations whose members have the capability to interbreed in nature, fertile offspring, and reproduction isolation for other populations.

b. Can only apply to sexual organisms, not fossils

3. Phylogenetic Species Concept:

a. A species with a single line of descent that maintains its distinctive identity from other lineages

b. Applies to sexual and asexual species

i. Fossils

4. Morphological Species Concept:

a. Similar phenotypes within a population makes species more evident b. Sexual and asexual species

5. Ecological Species Concept:

a. Views a species in terms of its ecological niche

b. Sexual and asexual species

6. Reproductive Isolation & 2 Mechanisms:

a. Reproductive Isolation:

i. Means of preventing gene flow between two species

b. Prezygotic Barriers:

i. Habitat Isolation​: ecological isolation; isolation by differences in habitat occupied at the time of mating; 2 different locations for species

ii. Temporal Isolation​: isolation by difference in timing of mating; nocturnal vs. day active

iii. Behavioral Isolation​: differences in behavior that cause reproductive isolation; mating dance in blue footed boobies

iv. Mechanical Isolation:​ differences in physical structure of mating parts and make mating impossible

v. Gametic Isolation​: mating occurs, but the sperm and egg cannot fuse c. Postzygotic Barriers:

i. Hybrid Inviability:​ zygote formed from two species, but develops abnormally; crosses between two species in the same subspecies

ii. Hybrid Sterility: ​a zygote of a hybrid proceeds through normal

development, but is reproductively sterile; mules

iii. Hybrid Breakdown​: some first-generation hybrids are fertile, but when they mate interspecies, F2 generation and beyond are sterile; some

cultivated rice strains

7. Allopatric Speciation:

a. Form of Cladogenetic Speciation

i. The branching of a new species from a common ancestor-branching evolution

b. Gene flow is interrupted or reduced when a population is divided into geographically isolated ​subpopulations

8. Sympatric Speciation & leading mechanisms:

a. Form of Cladogenetic Speciation

b. Disruptive Selection

c. Speciation takes place in geographically overlapping populations d. Leading Mechanisms:

i. Polyploidy

1. Is the presence of extra sets of chromosomes due to accidents

during cell division

2. Major factor to sympatric speciation in plants

3. Autopolyploid: ​ an individual with more than two chromosome

sets; derived from one species

4. Allopolyploid: ​a species with multiple sets of chromosomes

derived from a different species

ii. Habitat Differentiation

1. Appearance of new ecological niches

iii. Sexual Selection

1. Also derives from sympatric speciation

Chapters 52 & 54:

1. Food Chain​: A food chain is a linear feeding relationship with just one representative at each trophic level

2. Food Web:​ A food web shows the actual net feeding relationships in a community, including its many interconnecting food chains

3. Producers & Consumers:

a. Autotrophs = producers

b. Heterotrophs = consumers

4. Trophic Levels:

5. Biomes on Earth:

a. Tropical Rainforest

i. High temps

ii. High rainfall

iii. High biodiversity

b. Savanna

i. Little rainfall

ii. Grass dominant

iii. Small shrubs

iv. Large mammals

c. Deserts

i. Low rainfall

ii. Vegetation is scattered

iii. Plants and animals are adapted to conserve water

d. Grasslands

i. Higher rainfall than a desert, but less than a forest

e. Temperate Forests

i. Higher rainfall

ii. Dominated by trees

f. Tundra

i. Low rainfall

ii. Cold temperature

iii. Slow growing vegetation

6. Zones of the Marine environment:

a. Photic Zone:

i. Occurs in the upper layer of water, where strong light can support photosynthesis

b. Aphotic Zone

i. Lies beneath the photic zone

ii. Only energy comes from organisms that swim there

iii. Start of “deep ocean”

c. Marine Benthic Zone

i. Seafloor and offshore pelagic zone

7. Main producers in Marine environment:

a. Phytoplankton

8. Community Interactions between living organisms (positive/negative for the individuals involved, understand examples of each type)

a. Predation (+/-)

i. Benefits predator, but harms prey

b. Competition (-/-)

i. Harms both species; Raccoons

c. Herbivory (+/-)

i. Herbivore eats part of algae

d. Commensalism (0/+)

i. One species is benefitted, but the other is unaffected; Whale tale and insect

e. Parasitism (+/-)

i. Benefits parasite, harms host

f. Mutualism (+/+)

i. Benefits both species; Nemo fish

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