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Bio Study Guide-Outline

Bio Study Guide-Outline

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BELLARMINE COLLEGE PREP

Biology Honors Semester Two
All-inclusive Study Guide
Evan W. Noronha 5/23/2010

The contents of this study guide include absolutely everything needed to earn an A on Mark Riese’s Biology Honors Semester Two final. All data was collected from BSCS Biology: A Molecular Approach and compiled into outline format by Evan Noronha ‘13. Roughly 20% of the diagrams used were created by Kevin Korb ’13. All rights reserved. ©Evan Noronha and Kevin Korb 2010.

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide I. Chapter 8- The Cell Cycle A. 8.2 The Phases of the Cell Cycle (ref. to figure 1 on following page) 1. Single Cell -> Cell cycle -> 2 daughter cells 2. When Eukaryotic cell breaks down, nuclear membrane breaks down a) Individual chromosomes separate and are sorted into daughter cells 3. Mitosis: Process of sorting and distributing of chromosomes 4. Interphase: period between divisions a) Chromosomes not visible during this stage b) Divided into 3 parts i. G1, S, G2 5. Cell is ALWAYS in one of 5 stages of cell cycle a) G1- Gap one (AKA prereplication) b) S- DNA Synthesis c) G2-Gap 2 (AKA premitosis) d) M- Mitosis e) G0- Gap 0 (Non-dividing cell) 6. Gap Stages a) Cells grow and synthesize RNA, proteins, and other macromolecules i. Preparing for either next S or M phase b) Sequence same for all cells i. Different cells spend diff. amounts of time in various stages 7. When a cell in G0 or G1 receives signal to divide, it passes the restriction point a) “Point-of-no-return” b) Commits the cell to a full 8. Different cells vary in ability to pass restriction point a) Ex. Stem Cells- constantly dividing b) Liver cells almost always in G0 9. After passing restriction point, cell enters S Phase a) DNA of each chromosome replicate i. Exact copying ensure that each daughter cell gets a complete copy of genetic information 10. After S phase, cell enters G2 a) Prepares for mitosis by synthesizing specific types of RNA and proteins i. Required by mitosis in upcoming M Phase 11. M phase easiest to recognize because chromosomes are condensed and in the center a) Visible through a light microscope b) Sometimes called nuclear division because nucleus divides into two nuclei w/ identical sets of nuclei 12. After Mitosis, who cell divides in cytokinesis then enters G1 2|P age

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide

Figure 1: The Cell Cycle

B. 8.3 DNA Structure (ref. to figure 2) 1. Process of DNA replication depends on the molecular shape of DNA and its nucleotide bases 2. Base pairing depends on how many hydrogen bonds Figure 2 DNA Structure ea. nitrogen base can form w/ its counterpart a) Adenine(A) pairs Thymine(T) i. 2 hydrogen bonds b) Guanine(G) pairs Cytosine(C) i. 3 hydrogen bonds c) Sugar-phosphate backbones have opposite orientations i. Strands are parallel but run in opposite directions- known as antiparallel structure  Important to DNA replication C. 8.4 DNA Synthesis (ref to figure 3 on following page) 1. Synthesis of DNA is a multi-step process a) Divided into 3 major partd i. Binding of enzymes to existing DNA 3|P age

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide ii. iii. Unwinding of the double helix Synthesis of a new matching strand for each existing strand

2. Process: a) Enzymes and other proteins bind to regions of chromosomes called replicator origins i. Chromosomes have more than one replication origin  But Prokaryotes only have one ii. Proteins includes an unwinding enzyme, and RNA synthesizing enzyme, and DNA polymerase which catalyzes the formation of new DNA strands iii. Combination of DNA and proteins is a replisome b) DNA splits at the origin and enzyme (RNA primer) prepares ea. individual strand for synthesis of a matching strand i. Synthesis is continuous on leading strand  DNA Polymerase adds nucleotides to the end of the RNA primer ii. On lagging strand, DNA synthesis occurs in short unconnected bursts due to antiparallel structure c) Replisomes move away from replication origin in both directions d) End result is to replace the original double helix strand with two new ones i. Each is half old strand half new strand- known as semiconservative ii. Once replication is complete, there are two new chromosomes in place of the original one Figure 3 Replication Forks

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Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide

D. 8.6 The Stages of Cell Division (ref. to figure 4) 1. Cell goes to G2 phase after S 2. Copies of chromosomes made in S phase are called sister chromatids a) Now rady to be separated and delived to the new nuclei b) Still attached by centromere at the center of the chromosomes 3. Separation of sister chromatids called chromosome segregation a) Mistakes result in daughter cells w/ abnormal number of chromosomes i. AKA aneuploid cells 4. Mitosis is continuous but usually divided into 4 steps a) Prophase i. Membrane breaks down into small vesicles ii. Chromosomes condense; become visible under a light microscope iii. Microtubules form around the nucleus and join forming a mitotic spindle iv. If cell has centrioles, they are pushed to the opposite ends by microtubules  Microtubules at the end of spindle are anchored to protein structures that surround the centrioles- these sites known as spindle poles v. Each centriole contains a protein complex called a kinetochore  Microtubules in the spindle bind to the kinitochores b) Metaphase i. By this time, motor proteins in kinetochores have pulled chromosomes into a ring between the two poles  Forms metaphase plate- perpendicular to the spindle c) Anaphase i. Enzymes break down protein holding sister chromatids together  Separate and kinetochores pull them along the spindle microtubules to opposite spindle poles  Each segregated chromatid is now a chromosome d) Telophase i. Chromosomes expand and nuclear envelope forms around them- produces two nuclei ii. Cytokinesis divides the cell in two new daughter cells  Both enter G1  May enter G0 or start another cycle

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Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide

Figure 4 Stages of the Cell Cycle

E. 8.8 and 8.9- Regulation of the cell cycle (ref to figure 5) Figure 5 Control of the Cell Cycle

II.

Chapter 9- Expressing Genetic Information A. 9.1 Genetic Material (ref to figure 6) 1. Consists of two biomolecules a) DNA b) RNA 2. Living cells store genetic information in Dan 6|P age

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide a) Indirectly direct protein function 3. When a gene becomes active, an enzyme makes a temporary RNA copy of the gene in process called transcription a) Messenger RNA- provides the pattern that is used to assemble proteins 4. Synthesis takes place on ribosomes a) Ribosomes are made of proteins and ribosomal RNA 5. Each amino acid that is used in making a protein is attached to transfer RNA

Figure 6 Types of RNA

Figure 7 Codons and Anticodons

6. Eukaryotic cells also have a variety of small nuclear RNA that can interact with proteins during RNA processing 7. Genetic code describes how a sequence of bases in DNA and RNA translates into amino acids then proteins a) Similar to a Language- needs at least 20 different code words, one for each amino acid i. 4 Nucleotides are letters (A,T,G,C) ii. 3 nucleotides in a row is a “word” that codes for a particular amino acid iii. Different “words” or codons, can mean the same thing  Ex. UAA, UAG, and GUA are all “stop” codons  GGU, GGA, GGC, GGG all code for glycine  UUU and UUC code for phenylanine iv. In translation, a codon pairs with a tRNA molecule with the correct amino acid  Pairs according to which tRNA has the correct anticodon(ref to figure 7) 7|P age

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide v. Studies indicate that this genetic code is nearly universal

B. 9.2 Importance of Proteins 1. Proteins serve as material that makes op cells or tissues a) Keratin- main structural material in skin, hair, and feathers b) Colagen- major component of connective tissues c) Myosin- molecular motor that makes your muscles contract 2. Serve as enzymes a) Makes chemical reactions of a living system fast enough to be useful 3. Bind to specific molecules a) Ex. Hemoglobin in red blood cells binds to oxygen 4. Help with internal communication a) Ex. Insulin is a protein hormone that helps maintain homeostasis i. Hormones- chemical signals given off by cells in one part of an organism that regulate behavior of cells in another part C. 9.3 RNA Synthesis (ref. to figure 8 on following page) 1. Transcription enzyme- RNA Polymerase joins RNA nucleotides according to base sequence in DNA 2. Transcription is more complex in Eukaryotes, but general process is the same 3. In eukaryotes, protein synthesis occurs outsife the nucleus using mRNA, rRNA and tRNA made in the nucleus a) RNA molecules then modified, moved out of the nucleus into the cytoplasm b) rRNA transcriptions takes place in nucleolus- specialized region of the nucleus i. Also where as many as 70 proteins are assembled into ribosomal subunits ii. 2 ribosomal subunits and an mRNA come together during protein synthesis to form a functional, intact ribosome 4. Only one strand of DNA directs RNA synthesis 5. Transcription has three stages a) Initiation i. RNA polymerase attaches to a specific region of DNA called the promoter site  Site promotes transcription  Located right before the segment of the DNA coding strand that will be transcribed  Proteins called initation factors must be presen for the RNA to attach to the promoter site b) Elongation 8|P age

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide RNA polymerase partially unwinds the DNA, exposing the coding strand ii. Enzyme moves along the DNA away from the promoter site  Sequence of DNA determines sequence of RNA transcript c) Termination i. RNA polymerase reaches terminator reigon ii. Enzyme and primary transcript are released from the DNA i.

Figure 8 Transcription

D. 9.4 RNA Processing (ref. to figure 9 on following page) 1. In prokaryotes, new mRNA is translated and broken down rapidly 2. Life span depends on how the primary transcript is processed 3. Primary mRNA transcript can contain up to 200,000 nucleotides a) Average for humans is 5000) 4. mRNA in the cytoplasm averages only 1000 a) In processing of the primary transcript, enzymes modify, add, and remove additional nucleotides 5. Processing Steps 9|P age

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide a) Enzymes add a cap of modified guanine nucleotides(methyl-guanine) i. AKA mG cap ii. Helps the mRNA attach to a ribosome and begin translation b) Other enzymes replace part of the opposite end with a tail of 100-200 adenine nucleotides i. AKA poly-A tail ii. Helps transport mRNA out of the nucleus iii. Cap and tail help protect the mRNA from enzymes that break down nucleic acids c) Splicing of introns i. Introns- segments of the RNA that don’t code for proteins ii. Remaining pieces of code are called exons iii. Process recognizes the sequence GU at the end of an intron and AG at the other end Figure 9 RNA Processing

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Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide E. 9.5 Translation 1. Protein synthesis translates the codon sequence of mRNA into amino-acid sequence of proteins a) Happens on the ribosome where tRNA acts as a molecular adapter i. One end carries specific amino acid while other end has anticodon that pairs with the mRNA codon (see figure 10) that Figure 10 Structure of a codes for the corresponding amino acid tRNA molecule 2. Attachment of the amino acid to tRNA molecule is called tRNA charging a) Carried out by 20 different enzymes b) Each enzyme forms a bond between a specific amino acid and its matching tRNA i. A molecule of ATP provides energy to form bond c) Charged tRNA, mRNA and the growing poly-peptide chain meet at ribosomal binding sites where anticodons base-pair with codons i. This is how the codon sequence dictates the amino-acid sequence 3. Binding Sites (ref to figure 11) a) P site i. Holds the tRNA carrying the growing polypeptide chain b) A site i. Holds the tRNA carrying the next amino acid to be added c) E site i. Exit Site where uncharged RNA leaves the E site Figure 11 Protein Synthesis

4. Stages of translation- same stages as transcription a) Initiation i. Ribosome attaches at a specific site on the mRNA 11 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide  This site is the start codon- AUG b) Elongation i. Peptide bonds join each amino acid with the next in sequence ii. Charged tRNA w/ an anticodon matching the next codon enters at the A site  Positions the attached amino acid to be added to the growing chain w/ a peptide bond iii. Once bond is formed, the polypeptide chain transfers to the tRNA at the A site  Entire ribosome moves down to the next codon iv. Uncharged tRNA exits at the E site c) Termination i. Translation ends when stop codon reaches the A site  3 possible stop codons- UAA, UAG, UGA ii. tRNA releases the polypeptide; ribosome lets go of the mRNA and tRNA and ribosomal subunits separate F. 9.7 Translation Errors (ref. to figure 12) 1. Most errors in translation are caught and corrected 2. Most common errors result from misreading nucleotide sequence 3. Initiation determines where the translation will begin a) From this point onward, grouping of bases into codons is the reading frame b) If start begins one or two nucleotides in either direction, there will be a frame shift Figure 12 Frame Shifts

4. Some errors caused by splicing mistakes or changes in DNA a) Ex. If one nucleotide is lost, a frame shift results 12 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide b) Ex. If one nucleotide changes so that a stop codon is produced, translation will terminate early i. Results in partial polypeptide III. Chapter 10- Animal Growth and Development A. 10.1 Beginnings of an Embryo 1. Development of animals begins with fertilization a) Union of male and female parent’s cells i. Sperm and Egg (known as gametes) ii. Animal Sperm usually very small and have flagellum they use to swim towards an egg iii. Eggs are much larger and their cytoplasm contains a yolk  Energy rich collection of lipids and proteins and a variety of RNA molecules iv. Each parent cell has half the chromosome set found in each of the parents cells 2. Begin fertilization- sperm cell touches the surface of the egg cell and fuses with it a) Sperm nucleus and egg nucleus fuse Figure 13 The Process of Cellular Differentiation i. Reestablishes the full chromosome set 3. Fertilized cell- zygote, is the earliest stage of the human embryo 4. Before fertilization, eggs are metabolically inactive a) Use little energy and make almost no proteins and RNA b) Fertilization turns on the eggs metabolism i. This is known as activation ii. Cell respiration increases and new proteins are made using mRNA already in the cytoplasm iii. Results in rapid change in the plasma membrane which blocks fertilization by a second sperm iv. Rearrangement of the zygote cytoplasm by movements in the cytoskeleton  Helps to produce differences among cells when they divide c) When zygote begins to divide, it is as metabolically active as mature cells B. 10.2 Growth, Differentiation, and Form 1. Animal development consists of growth, cell specialization, and formation of tissues and organs 2. Embryo becomes multicellular through cell division a) Increased number of cells causes it to grow larger b) As it continues to divide, some cells become different from others i. Process called differentiation (ref. to figure 13) 13 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide 3. Cell is completely differentiated when it possesses all features of a specific cell type a) Ex. Muscle cell b) Ex. Skin Cell 4. As cells differentiate, they form tissues and organs a) Period of development is called morphogenesis 5. Cells that differentiate have special structure a) Ex. Skin Cells i. Tough, thin, and flat; designed to protect the body b) Ex. Muscle Cells i. Filled with protein fiber that help them contract 6. Each cell type has a specific location and each performs a specialized role 7. Proteins are key to differentiation in animals a) Cell movements in morphogenesis involves proteins on each cells surface b) Specific genes are expressed in each cell i. Leads to production of specific proteins c) Differences between cells in protein synthesis lead to differences in cells C. 10.5 Human Development (ref to figure 14) 1. Development of humans and most mammals is unique- Develop within the mother a) Mother provides a warm protected environment b) Blood circulation provides nutrition and oxygen to the embryo and tkes away wastes and CO2 2. Human egg is roughly 0.1mm; contains little yolk 3. Zygote cleaves as it moves into the uterus 4. After about 5 days, the embryo, called a blastocyst, resembles the hollow blastula of other animals

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Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide a) Sinks into the wall of the uterus to develop and grow Figure 14 A Developing Fetus

IV.

5. Part of a thick mass of cells inside the blastocyst forms the disk that becomes the embryo a) Rest of the blastocyst becomes membranes that surround, nourish, and protect the embryo. i. Amnion immediately surrounds the embryo ii. Chorion encloses all the other membranes; forms thin outer wall  Extends fingerlike projections (villi) into the lining of the uterus  Villi and uterine lining form the placentaexchanges nutrients, wastes, oxygen and carbon dioxide with the mother  6. Human takes about 40 weeks to develop in the uterus a) After 8th week, the embryo is a fetus b) After 3 months(first trimester) most organ have begun to form; skeleton can be seen through ultrasound c) Last 3 months (last trimester) is a period of rapid growth and maturation of organ systems Chapter 11 Plant Growth and Development (ref. to figure 15) A. Put a plant in the ground, give it water, it grows 15 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide 1. Whoopdy-Doo… 2. Figure 15 A Tree...

V.

Figure 16 Binary Fission Chapter 12- Reproduction A. 12.1 Asexual Reproduction 1. Requires a single parent 2. Results in a genetically identical clone 3. Prokaryotes reproduce by dividing in two a) Process called binary fission(ref to figure 16) B. 12.2 Chromosome number (ref to figure 17) 1. Each species has characteristic number of chromosomes a) Prokaryotes typically have 1 i. Single circle of DNA b) Number varies among eukaryotes i. Ex. Humans and fish called Black Mollies have 46 ii. Ex. Turkeys have 82 iii. Ex. Giant Redwoods have 22 2. Cells of organism that reproduce sexually have pairs of similar chromosomes a) Each parent provides one member of each pair b) Cells that have a double set of chromosomes are diploid i. Represented by 2n 16 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide c) Cells with only one set are haploid i. Represented by n 3. In diploid organisms, two chromosomes in a pair are called homologous a) These chromosomes, homologues, are similar in structure b) Carry the same genes; DNA sequence may be slightly different i. Differences produce the variety among members of the same species 4. In sexual reproduction, each parent Figure 17 contributes half the normal number of Changes in chromosome Number chromosomes (haploid number) a) Otherwise, if parents each contributed diploid number, chromosome number would double with every generation b) Parent gametes are all haploid i. Haploid sperm and Haploid egg join to form a diploid zygote 5. Meiosis produces haploid gametes a) Complementary to Fertilization; Meiosis produces haploid gametes and fertilization reunites them as diploid cells C. 12.3 Meiosis and the Production of Gametes (ref. to figure 18 on following page) 1. Different from mitosis in 3 important ways a) Cells divide twice in meiosis, but are only duplicated after first division b) Meiosis distributes random mixture of maternal and paternal chromosomes to each gamete i. Results in new genetic combinations c) Homologous chromosomes pair up during the first meiotic cell division where they exchange corresponding pieces of DNA i. Process known as crossing-over; adds to genetic variety of the gametes 2. Meiosis has 2 nuclear divisions- Meiosis I and Meiosis II a) Produces four haploid cells b) Both divisions have same four steps as mitosis, but small differences i. Meiosis I vs. Mitosis  In prophase I, homologues cross-over  Sister chromatids don’t separate in anaphase I  Migrate [together] to opposite poles 17 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide  Results in a pair of cells, each with a single pair of chromosomes; each chromosome consists of a pair of sister chromatids

Meiosis II  Chromatids separate iii. Overall it’s a complex process for three reasons  Reduces chromosomes to the haploid number  Provides genetic variation  Ensures correct distribution of chromosomes 3. Doesn’t always divide cytoplasm equally a) In most males, meiosis produces four equal sized sperm b) In females, most cytoplasm remains in one cell i. Largest cell becomes the ovum ii. 2 small cells-polar bodies, usually break down and disintegrate D. 12.6 Sexual Reproduction in Animals [as relevant to humans] 1. Animals that reproduce sexually have organs called gonads that produce gametes a) Ovaries that produce ova b) Testes that produces sperm 2. Land animals and a few aquatic animals like whales use internal fertilization a) Male releases sperm into a female reproductive organ b) Fertilization occurs within the body of the female c) Protects gametes and requires fewer gametes than external fertilization d) Most efficient i. Fewer eggs are required 3. Internal fertilization is an evolutionary trend among larger, more complex organisms a) Mammals are the most extreme examples of this trend 4. Sperm are usually much smaller than eggs

ii.

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Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide a) Egg is adapted as a storehouse for nutrients and organelles that support the embryo’s development Figure 18 Stages of Meiosis for a cell with 2n=4

b) Sperm just the nucleus and the flagellum and a few mitochondria to sustain itself for a short time i. Most still die before reaching the egg E. Egg production and the Menstrual Cycle 1. In human females, ovaries are contained within body cavities a) Usually release eggs one at a time 19 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide Egg travels through one of two oviducts to the uterus where embryo develops(if fertilized)  During birth, baby is pushed out from the uterus through the vagina  This route also functions as passageway for male to deposit sperm 2. Egg releasing cycle-menstrual cycle, usually lasts 28 days a) Inner lining of the uterus builds up in prep for receiving a fertilized egg i. If not fertilized, the lining and rich blood is sloughed out through the vagina b) First day of menstrual flow marks the first day of the cycle 3. Regulated by nervous system and several other glands and organs; Hypothalamus acts like a thermostat (fluctuates to adjust hormone levels) a) Start of menstrual flow, estrogen and progesterone released into the bloodstream by the ovaries are at low levels i. Low levels cause hypothalamus to secrete gonadotropinreleasing hormone (GnRH) that is received by the pituitary gland ii. GnRH stimulates the pituitary to release follicle –stimulating hormone (FSH) and luteinizing hormone (LH)  FSH causes the egg to start maturing  Both stimulate the follicle to release more estrogensignals the lining of the uterus to thicken b) 14-day of the cycle i. Sudden increase of LH makes the follicle burst and release the egg  Process called ovulation ii. Ruptured follicle becomes corpus luteum and continues to release estrogen and progesterone iii. Hypothalamus detects high levels of estrogen and slows release of FSH and LH c) If egg not fertilized, corpus luteum degenerates and levels of progesterone and estrogen decline i. Signals lining of uterus to break down and menstruation begins, marking a new cycle d) If egg is fertilized, undergoes mitosis and becomes an embryo, implanting itself in the uterus upon entry; forms a placenta i. Releases the human chorionic gonadotropin  Signals the corpus luteum to continue releasing high levels of progesterone and estrogen which support the uterine lining and indirectly prevent menstruation 20 | P a g e i.

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide Corpus Luteum functions for first three months of gestation (development of embryo within the uterus) iii. After first trimester, placenta stops releasing HCG and replaces the corpus luteum as the main source of estrogen and progesterone e) At birth, small peptide known as oxytocin is released that makes the muscles of the uterus contract i. After birth, it causes the uterus to contract and stimulates milk release ii. Placenta separates from the uterine wall shortly after and is expelled as the afterbirth F. 12.8 Sperm Production 1. In human males, the testes are located within the scrotum a) Outer pocket of the body wall b) Keeps them cooler than body temperature 2. Sperm are produced by meiotic cell division in highly coiled tubes called seminiferous tubules in the testes then stores in the epididymis, a coiled part of the sperm duct 3. Prostate glands and seminal vesicles produce seminal fluid which transports sperm a) Seminal fluid also contains fructose i. Provides energy for sperm b) Released during ejaculation with sperm in a mixture called semen i. If not ejaculated, sperm are eventually reabsorbed by the tissues in the male reproductive tract 4. Males have same regulatory hormones as females a) GnRH stimulates the pituitary gland to release FSH and LH b) LH stimulates cells between tubules to secrete androgens, group of male hormones i. Major androgen is testosterone c) FSH stimulates other cells in testes to produce sperm d) No evidence that males have a reproductive cycle like females Chapter 13- Patterns of Inheritance A. 13.2 Mendel and the Idea of Alleles 1. 1860’s, Gregor Mendel studied pea plants to study heredity and genetics a) Choice of peas was important i. Easy to grow ii. Self-fertilizing b) Only studied traits found in the either-or form i. Found Seven of those traits (ref. to figure 19) Figure 19 Pea Plant Traits studied by Mendel 21 | P a g e ii.

VI.

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide

c) Worked to make sure he had true-breeding plants i. Produce identical offspring generation after generation d) Crossbred his plants ant classified the offspring; looked for patterns of inheritance i. Ex. Crossed green pods and yellow pods  First gen. offspring were all green  First generation self-fertilized and some produced offspring with green pods ii. Blending theory couldn’t explain these results iii. Demonstrated that both parent pass on genetic factors that remain separate  Ex. Yellow pod factor remained hidden in the first generation offspring, but appeared in the second generation 2. Genes have now replaced Mendel’s idea of factors 22 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide a) Gene- a segment of DNA whose sequence of nucleotides codes for a specific functional product b) Most exist in more than one form or allele i. Each allele has a different base sequence 3. Change in gene for a protein can result in a different sequence, thereby producing a different protein 4. All organism have alleles a) Ex. Widow’s Peak b) Ex. Male-pattern baldness c) Many traits controlled by multiple alleles B. 3.3 Genes and Chromosomes 1. Arrangement of genes on Eukaryotic chromosomes a) Eukaryotic Chromosomes are long DNA molecules w/ some non-coding regions i. Only about 1% of eukaryotic DNA is expressed 2. Prokaryotic Chromosomes a) Have a single circular chromosome b) Don’t have introns i. About 90% is translated c) May also contain plasmids i. Circles of DNA that contain genes ii. Can be moved from one bacterium to another  Used in genetic engineering 3. Karyotypes (ref. to figure 20) a) A display of all the chromosomes in a person’s genome i. Sorted by size, and homologous chromosomes are placed sideby-side Figure 20 A Karyotype of a Human Cell

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Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide C. 13.4 Probability and Genetics 1. Distribution of alleles in diploid organisms is up to chance a) Probability is used to predict the chance of particular alleles being passed on i. Probability- branch of math that predicts chance of a particular event  Ex. Flip a coin- ½ heads, ½ tails  Ex. Draw a card from a deck - 1/13 chance it’s an ace  Each event is Independent  Ex. If you flip a coin 3 times, the 4th flip isn’t influenced by the other 3  Chance of two or more independent events both happening is their probability multiplied together  Ex. Flipping heads twice= ½*½= ¼ chance  Ex. Pulling 2 aces out of a deck =1/13*1/13=1/169 2. Geneticists use probability to predict the alleles of offspring a) Predictions can be compared with results of breeding experiments b) Mathematical tests show whether the prediction and observations are significantly different 3. Genetic ratios are estimations; not absolute numbers; the larger the sample size, the closer the numbers will be to the prediction D. 13.5 Inheritance of Alleles (ref. to figure 21) Figure 21 A monohybrid cross 1. Mendel crossed plants that differed in only one trait a) Known as a monohybrid cross- diagramed with a Punnett square as in figure 21 b) Crossed plants with true-breeding, green-podded peas with truebreeding yellow-podded peas i. Plants involved in the first cross(first generation) are called the parental (P) generation ii. Offspring from P generation are called first filial, or F1 Generation  Absolutely all were green-podded  Allowed these to self fertilize iii. Offspring from the F1 Generation are the second filial, or F2 generation  428 were green-podded and 152 were yellow-podded  3:1 ratio 2. Of all traits that Mendel studied, only one of the two would appear in the F 1 offspring a) He called this trait the dominant trait 24 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide b) He called the other trait (that was hidden in the F1 generation but showed up in the F2)the recessive gene 3. Mendel used his observations to form the principle of segregation a) Says that through meiosis and gamete formation, each parent passes on only one factor (today called allele) to its offspring b) Alleles segregate during gamete formation and meiosis 4. Today, allele for dominant genes is represented by a capital letter and recessive allele is represented by the lowercase letter a) Ex. G for green pods and g for yellow pods b) Ex. T for tall stem and t for short stem c) Since most multicellular organisms are diploid, their genotype consists of two alleles i. Genotype- genetic makeup, of true-breeding green-podded plants would be GG  Two dominant alleles is homozygous dominant ii. Genotype of true-breeding yellow plants would be gg  Two recessive alleles is homozygous recessive iii. If the two alleles are different (Gg), then the plant is heterozygous d) Phenotype- physical appearance, is dictated by the genotype i. Ex. GG and Gg (homozygous dominant and heterozygous) both have the dominant allele so they will be green-podded while gg (heterozygous) will be yellow-podded because there is no dominant allele to “hide” the recessive one 5. F2 Genotype Explained (ref to figure 21 on previous page) a) Half of the gametes produced by F1 Generation had g allele and half had the G allele i. Chance that a plant would receive a g allele from one parent is ½ ii. Chance that a plant would receive the G allele from one parent is ½  Therefore, chance of receiving g allele from both parents (and thereby being homozygous recessive) is 25%  Would be a true-breeding yellow-podded plant  Chance of receiving G allele from both parents (and thereby being homozygous dominant) is 25%  Would be true-breeding green-podded pea  50% chance of receiving one of each (Gg or gG have same result)  Would be green-podded pea plant carrying the recessive allele 25 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide Figure 22 Dihybrid Cross

6. Following inheritance of two characteristics is done with a dihybrid cross (ref. to figure 22) a) Cross of organisms with two differing traits b) Organisms that are heterozygous for both traits will return a ratio of 9:3:3:1 i. Ratio is characteristic of the F2 generation in a dihybrid cross ii. This led Mendel to the principle of independent assortment  Alleles for one characteristic divide up among gametes independently of alleles of other characteristics E. 13.6 Sex Determination (ref to figure 23 on following page) 1. All chromosomes come in matching pairs except for the sex chromosomes a) Labeled X and Y b) Females have 2 X chromosomes while males have 1 X and 1 Y 2. All eggs have 1 X chromosome while 50% of sperm have an X and 50% have a Y 26 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide a) Therefore, the sperm determine the sex of offspring

Figure 23 Distribution of X and Y chromosomes

F. 13.7 Multiple Alleles and alleles without Dominance(ref to figure 24) 1. Some genes don’t follow the dominant-recessive pattern a) Ex. Red-flowered snapdragons cross with White-Flowered snapdragons to produce pink-flowered snapdragons i. Known as incomplete dominance b) Ex. Human blood type depends on the presence of A or B carbohydrates on the surface of red blood cells i. Possible alleles: IA and IB code for different forms of an enzyme that add different sugars to the carbohydrate bound to the blood cell’s membrane  IA and IB are codominant alleles while i codes for no active enzybe  Possible genotypes:  IAIA and IAi =type A  IBIB and IBi =type B  IAIB- type AB  Ii- type O  While there are three alleles, any individual can only possess two at a time G. 13.8 Linked Genes (ref. to figure 24 on following page) 1. Genes on the same chromosome are said to be linked 27 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide a) Often inherited together b) Somewhat goes against the principle of independent assortment 2. Alleles of linked genes sometimes separate a) Could be exchanged with other chromosomes during crossing-over b) The farther apart they are, the more likely they are to separate 3. Frequency of separation of linked traits indicated where they are in relation to each other on a chromosome a) Enables people to identify-disease related genes i. Ex. Huntington’s disease H. 13.9 X-Linked Traits 1. Researchers found that when a white-eyed male fly mated with a normal red-eyed female, all offspring had red eyes a) Confirmed that white eyes were recessive trait b) Only males had white eyes c) Crossed white-eyed females and red-eyed males i. F1 offspring included only red-eyed females and white-eyed males ii. Explanation was that the gene for eye color in a fly is passed on the X Figure 24 chromosome Crossing over and Separation  No eye-color gene on the Y of Linked genes chromosome  Whatever allele the male receives will be exhibited in its phenotype  Females will display the dominant eye-color because they have 2 X chromosomes and therefore two alleles 2. Mary Lyon suggested that one X chromosome becomes deactivated early in female development a) Occurs at random b) In some cells, the maternal X-linked genes are expressed while in others, the paternal ones are c) Explained that this deactivation could explain the dark stain in a nucleus called a Barr Body i. Errors in meiosis could give a female an extra X chromosome  Cells of these females have two Barr Bodies, indicating that one X chromosome remains active 28 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide  Embryos with extra chromosomes typically don’t survive, but females with more than 2 X chromosomes do Chapter 14- Other forms of inheritance A. 14.1 Understanding Gene function (ref. to figure 25) 1. Genetics builds on previous research a) Ex. Mendel’s observations formed basis of modern genetics 50 yrs later 2. Modern scientific explanations are in keeping with evidence and well-reasoned thinking 3. We learn a lot from mutations a) Provide important clues about how the gene is supposed to work 4. Particular mutations could have different results in different people a) Ex. One abnormal allele can produce stomach ulcers in one family member, but cause kidney stones in another 5. Expression of genes depends on binding or RNA polymerase on nearby site called promoter; RNA polymerase must bind to promoter and pass the operator sequence before a gene is transcribed 6. Entire set of genes and its control sequence is called an operon Figure 25 Bacterial Operon

VII.

7. Repressor can bind to the operator, blocking RNA polymerase from transcribing mRNA, thereby stopping expression of that gene a) Environmental factors can make the repressor protein change shape, allowing the RNA polymerase to transcribe the mRNA, expressing the gene 8. Eukaryotic gene regulation a) Variety of factors can influence which gene is expressed, at what level, at what time 29 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide Ex. Steroids hormones influence gene transcription  Hormone enters cell and binds to a receptor protein  Combination of Hormone and receptor protein enters nucleus and acts as a transcription factor; binds to regulatory DNA sequence known as response element  Response element responds to outside stimulus  Binding transcription factor at response element activates the nearby gene b) Other hormones regulate through a “domino effect” of biochemical reactions B. 14.2 Cytoplasmic Inheritance 1. Mitochondria and Chloroplasts have their own DNA a) Because they are found in the cytoplasm, their DNA is the sourse of Cytoplasmic inheritance b) Eukaryotic cells have 100’s~1000’s of mitochondria, and each had several copies of mitochondrial DNA (mtDNA) i. Double-stranded, circular molecule Figure 26 Mitochondrial Inheritance ii. Codes for 13 polypeptides, 2 rRNAs, 2 tRNAs  Not sufficient for all mitochondrial activities; rest is controlled by DNA molecules in the nucleus iii. mtDNA is copied independently; new mitochondria are made through fission like prokaryotes  Do not sort evenly between daughter cells during meiosis and mitosis c) Mitochondria (and mtDNA) is always passed on through the mother(ref. to figure 26) i. Ovum is a large cell with lots of mitochondria to sustain its growth ii. Sperm have few mitochondria in its tail  At fertilization, the sperm loses its tail and at that point, the zygote that will develop into a new organism only has maternal mitochondria C. 14.5 Genetic anticipation(ref to fig 27 on following page) 1. Doctors observed that with certain inherited diseases, symptoms would develop at younger ages as generations progressed a) Shift toward earlier symptoms is called genetic anticipation i. Best known ex. Huntington’s Disease  In certain genes, number of copies of a repeated sequence of three bases can increase or decrease within a normal range 30 | P a g e i.

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide  If there are too many copies, the gene becomes unstable; then number of bases will always increase with each generation  Situation is called trinucleotide repeat expansion

Figure 27 Huntington's disease pedigree

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Chapter 15- Advances in molecular Genetics A. 15.6 Mutations and DNA Repair 1. Mutations are changes in the DNA sequence a) Many different causes i. Chemical exposure ii. Radiation iii. Etc. 31 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide 2. Most common cause of mutation is errors in copying DNA a) Can affect protein structure directly, or occur in regulatory regions of the genome b) Most common type of mutation is point mutation- one base pair changes into a different one i. If it changes an important amino acid, it is a missense mutation ii. If it changes to a stop codon, it is called a nonsense mutation  Results in an abnormally short protein c) Frameshift Mutations delete one or two base pairs (see section 9.7) i. Change every subsequent codon ii. Usually produces a new stop codon iii. Results in a shortened, nonfunctional protein 3. Different mutations in same gene can cause same phenotype a) Ex. Different mutations found in phenylalanine hydroxylase i. Normally converts phenylalanine to tyrosine ii. Any mutation that reduces the activity of this enzyme results in a physical disorder called phenylketonuria (PKU) 4. Some genetic disorders are caused by one specific point mutation a) Ex. Sickle-cell anemia b) Ex. Form of dwarfism called achondroplasia i. 98% of cases are caused by the same point mutation in the gene that encodes the receptor for a growth hormone c) Detection tends to be easy 5. When many mutations lead to the same disease, detection is more difficult a) Ex. PKU, cystic fibrosis, breast cancer b) Testing is more difficult if the gene is large 6. Large regions of chromosomes can also be mutated by deletion or mutation of genetic material a) Common in cancer cells b) Clue to how chromosomal rearrangements leads to cancer was revealed in leukemia study i. 70% of patients had cancer cells with a mutation called the Philadelphia chromosome  Parts of 9 and 22 chromosome break off and are translocated  Result is a fused gene  Consists of the promoter and beginning of one gene from chromosome 22 and the end of a different gene from chromosome 9  Promoter ensures that the mutant protein is continuously expressed 32 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide 7. Mutations can occur in somatic cells of multicellular organisms a) Some not so bad- worst case is that mutant cell dies b) Others cause uncontrolled cell growth that leads to cancer c) Gene Amplification- normal part of development in many animal species (but not humans) i. Creates extra copies of specific genes ii. Specialized cells produce large quantities of particular proteins  Ex. Glandular cells in the pancreas produce insulin IX. Chapter 17 A. 17.1 The Big Bang 1. Life on Earth can’t be older than earth itself 2. Measurements of light coming from deep space indicates that the universe used to be smaller a) Hubble telescope consistently detects redshifts, indicating things it is viewing are moving away from it 3. By calculating the rate of expansion, scientists think that 15 billion years ago, the universe was one super dense mass that exploded a) Following this hypothesis, Earth was formed 4.6 Billion years ago b) Analysis of moon rocks indicate that the moon is also this age i. Could have formed when a meteor hit Earth and blew a chunk of it into orbit

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Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide c) Geologists have worked out a history of Earth from evidence in its rocks (ref. to figure 28) Figure 28 Geologic Timescale

B. 17.2 Early Earth 1. Evidence indicates that Earth’s interior is hot a) Miners experience higher temps deep underground b) Volcanoes and hot springs 34 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide 2. Decay of radioactive elements (Uranium, Thorium, and some isotopes of potassium) is primary source of heat 3. Entire planet was probably hot when it first formed a) As it cooled, gasses were released from the crust, forming the primitive atmosphere i. Nitrogen, Carbon Dioxide, Water Vapor, Hydrogen and small amounts of Carbon Monoxide ii. Probably didn’t have much oxygen  Only became present after photosynthetic organisms produced it 3-3.5 billion years ago  Would have been bound in compounds like iron oxide  Earliest rocks we have found have very little oxygen containing compounds C. 17.3 The beginnings of Life 1. Surface of early earth probably wouldn’t sustain modern life a) Organic compounds don’t form easily in an atmosphere rich in nitrogen and carbon dioxide b) UV radiation from the sun zapped everything i. Is harmful to DNA ii. Today, we are protected by the ozone layer  Made of ozone (O3) gas 2. Three popular explanations for the origin of life a) Life originated on some other planet and traveled to Earth i. Doesn’t explain origin of life b) Life originated by unknown means i. Earliest life could have been very different from today’s organisms ii. Very difficult to investigate c) Life evolved from nonliving substances through interactions with the environment i. Can be tested in nature and labs ii. Most suited to scientific investigation iii. Can be stated in the form of a hypothesis D. 17.4 Chemical Evolution (ref. to figure 29) 1. 1920’s Soviet- Alexander Oparin and British- J.B.S. Haldane both described the hypothesis that life evolved on Earth from nonliving substances a) Worked separately b) Said that energy sources like radioactivity, lightning, etc., caused gasses in the atmosphere to react and form organic compounds i. Organic compounds accumulated in oceans 35 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide ii. Figure 29 The heterotroph hypothesis Hypothesized that life further evolved in the oceans trough complex chemical reactions

2. Their ideas led to the heterotrophy hypothesis a) Oparin-Haldane version requires three major steps i. There had to be a supply of organic molecules, produced by nonbiological processes ii. Some processes had to assemble those small molecules into polymers such as nucleic acids and proteins. iii. Other processes had to organize the polymers into a system that could replicate itself, using the organic molecules produced in step 1. b) Each step is a major change from nonliving to living 3. Explaining Step 1 a) Harold Urey and Stanley Miller (Urey and Miller) i. Recreated conditions of early Earth in an airtight apparatus  Methane, hydrogen, ammonia gas circulated through an electric spark  Boiling water added water vapor  Cooled and formed “rain” ii. Recorded two visible changes  Small mass of tar appeared in the apparatus  Water turned red  Found many organic compounds including amino acids in the water iii. Repeated with only water vapor, hydrogen, carbon dioxide and nitrogen  Produced only simple amino acids  Noted that a little methane is needed to produce complex amino acids iv. Their experiments produces 13 of 20 common amino acids 4. Explaining step 2 a) 1985, A.G. Cairns-Smith i. Suggested clay could have formed the first organic polymers  Consists of tiny layered crystals that can attract and contain certain molecules  Crystals could have catalyzed the bonding of these small molecules concentrated on their surface 36 | P a g e

Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide 5. Explaining step 3 a) Self replication of life presents a “chicken-and-egg problem” i. Structure of proteins are coded by DNA ii. Replication of DNA requires proteins b) RNA has provided a possible solution i. Components can be produced nonbiologically ii. Can join spontaneously iii. Some catalyze their own reactions c) According to this RNA-world hypothesis, RNA was the information molecule and catalyst and DNA showed up later d) RNA can also undergo simulated Darwinian evolution E. 17.7 Eukaryotes 1. Lynn Margulis hypothesized that mitochondria and plastids were once freeliving prokaryotes a) Said that eukaryotes evolved from a symbiotic relationship between large anaerobic prokaryotes and smaller photosynthetic prokaryotes b) Large cells absorbed the small ones, and instead of being digested, the smaller cells survived i. Smaller cells produced sugars and ATP that benefitted the host cells ii. Eventually, the internal partners- endosymbionts -lost the ability to exist separately 2. Now known as the endosymbiont hypothesis a) Supported by large body of evidence: i. Mitochondria have their own DNA and ribosomes ii. Genes and ribosomes are similar to those of bacteria iii. Both have double membranes Chapter 20 A. I’m tired, and there’s only six questions on this chapter, so just use this: B. Evolutionary Advancements 1. Opposable thumbs and big toes (fine manipulations) 2. Nails instead of claws 3. Binocular vision (depth perception 4. Omnivores (eat many things) 5. Color vision 6. Bipedalism (leaves hands free) 7. Single births C. Early Homos 1. Australopithecines a) -“Southern Apes” b) -Lived 4 MYA to 2.5 MYA c) -First hominids d) -About 50 pounds and 1m tall e) -cranial capacity=400 37 | P a g e

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Evan Noronha Mr. Riese Bio Honors Semester Two Study Guide f) -“Handyman” g) -Used crude stone tools h) -Lived 2.5 MYA to 1.5 MYA i) -cranial capacity=600-700 j) -May have had fire 2. Homo Erectus a) -“Traveling Man” b) -Lived 1.5 MYA to 500,000 years ago in Africa c) -Lived 1.5 MYA to 250,000 years ago in Europe d) -About 5 feet tall and 100 pounds e) -cranial capacity=900-1000 f) -Had crude wooden shelters and fire g) -Lived in groups of 20-50 h) -Hunter Gatherers 3. Homo Sapien Neanderthalensis a) -Big game hunters b) -strong and robust c) -Lived 250,000 years ago to 30,000 years ago d) -cranial capacity=1750 e) -Buried dead with weapons, jewelry, food, etc. 4. Homo Sapien/Cro Magnon a) -“Modern Man” b) -Lived 30,000 years ago to present c) -Cave dwellers (artistic) d) -Taller and more slender e) -cranial capacity=1350

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