Exam 3 Review - Biology Past Paper

**Exam 3 Review** **[Chapter 11: Sexual Reproduction and Meiosis]** - **Meiosis** produces reproductive cells, called **gametes (sperm and egg)** - 4 genetically unique haploid (n) daughter cells - Meiosis involves one round of DNA replication, but **two** consecutive c...

**Exam 3 Review** **[Chapter 11: Sexual Reproduction and Meiosis]** - **Meiosis** produces reproductive cells, called **gametes (sperm and egg)** - 4 genetically unique haploid (n) daughter cells - Meiosis involves one round of DNA replication, but **two** consecutive cell divisions - Meiosis 1 and meiosis 2 - Each has prophase, metaphase, anaphase, and telophase stages - **Synapsis** - During early prophase 1 homologous chromosomes pair up to form **tetrads** - Connected structure called synaptonemal complexes - **Mitosis** produces all other cell types = **somatic cells** - 2 genetically identical diploid (2n) daughter cells - **Sexual life cycle** - Made up of **meiosis** and **fertilization** - **Zygote --** egg and sperm fuse to produce single cell - **Diploid** cells (2n) - Somatic cells of adults have 2 sets of chromosomes - **Haploid** cells (n) - Gametes have only 1 set of chromosomes - Requires meiosis to reduce the number of chromosomes - This prevents doubling of chromosomes at every fertilization - Offspring inherit genetic material from 2 parents - Zygote undergoes mitosis to produce somatic diploid cells - Early in development, some of these diploid cells are set aside (**germ-line cells)** and will undergo meiosis to produce the gametes - **Know what happens in the phases of meiosis I and II (slide 16 summarizes the phases nicely)** **[Meiosis I]** - **Prophase I** - Chromosomes coil tighter and become visible, nuclear envelope disappears, spindle forms - **Synapsis -** Homologues pair up and form **tetrads** - **Crossing over** occurs - Genetic recombination between non-sister chromatids - Allows the exchange of chromosomal material between homologs - **Chiasmata** -- site of crossing over - Contact maintained until anaphase 1 - **Metaphase I** - Microtubules from opposite poles attach to each homologue - Not each sister chromatid as in mitosis! - Monopolar attachment - Homologues are aligned at the metaphase plate **side-by-side** - Orientation of each pair of homologues on the spindle is random - Genetic variability - **Anaphase I** - Microtubules of the spindle shorten - Chiasmata break - Homologues are separated from each other and move to opposite poles - Sister chromatids remain attached to each other at their centromeres - Each pole has a complete haploid set of chromosomes consisting of one member of each homologous pair - **Independent assortment** of maternal and paternal chromosomes - **Telophase I** - Nuclear envelope re-forms around each daughter nucleus - Sister chromatids are no longer identical because of crossing over (prophase 1) - Cytokinesis occurs after telophase 1 - Meiosis 2 occurs after an interval of variable length - Period in between called interkinesis instead of interphase **[Meiosis II]** - Resembles mitosis - **Prophase 2**: nuclear envelopes dissolve and new spindle apparatus forms - **Metaphase 2**: chromosomes align on metaphase plate - **Anaphase 2**: sister chromatids are separated from each other - **Telophase 2**: nuclear envelope re-forms around 4 sets of daughter chromosomes; cytokinesis follows - Meiosis increases genetic variability - **Independent assortment** - reassortment of genetic material - **Crossing over** - DNA exchange between arms of non-sister chromatids - **Random fertilization** -- zygote forms a new individual fusion of two gametes **[Chapter 12: Patterns of Inheritance ]** - Gregor Mendel (1822--1884) laid groundwork for chromosome theory of inheritance through series of experiments on pea plants - Easy identifiable characteristics - Two distinct traits for each characteristic - Mendel performed hybridizations, which involve mating two true-breeding individuals that have different traits - **P~0~ (parental) generation** - plants used in first-generation crosses - **F~1~ (first filial) generation** - offspring of P~0~ generation - Allowed F~1~ generation to self fertilize - Collected and grew seeds from F~1~ plants to produce **the F~2~ (second filial) generation** - **Gene vs allele** - **Gene --** A hereditary factor that influences a particular trait - Located in specific place on chromosome - **Alleles** -- alternative version of a gene - Gene: flower color - Alleles: purple vs white - Make sure you are familiar with the following terms as they will be used in genetics problems - Mendel's principles - **Law of segregation** - Two alleles for a gene segregate during gamete formation and are rejoined at random, one from each parent, during fertilization - **Law of independent assortment** - genes do not influence each other with regard to the sorting of alleles into gametes, and every possible combination of alleles for every gene is equally likely to occur - In a dihybrid cross, the alleles of each gene assort independently - Independent alignment of different homologous chromosome pairs during metaphase I leads to the independent segregation of the different allele - **Test cross** - Mendel also developed a technique called the **test cross** to determine whether an organism that expressed a dominant trait was a heterozygote or a homozygote - The dominant-expressing organism is crossed with an organism that is homozygous recessive for the same characteristic - If F~1~ offspring are heterozygotes the dominant organism in question is homozygous dominant - If F~1~ offspring exhibit 1:1 ratio of heterozygotes and recessive homozygotes the dominant organism in question is a heterozygote - **Dihybrid cross -** Examination of 2 separate traits in a single cross - Mendel used this to test if the inheritance of one trait (such as seed shape) influences the inheritance of other traits (such as seed color) - **Rules of probability** -- know when to use each (lab 20 is a good place to practice these problems) - **Rule of addition --** if A and B are mutually exclusive, then P(A or B) = P(A) + P(B) - look for "OR" - **Rule of multiplication --** if A and B are independent, then P(A and B) = P(A) x P(B) - Events occur in sequence - Look for "and" - Extensions to Mendel - **Phenotypic plasticity -** the production of different phenotypes for the same genotype due to environmental conditions - **Polygenic inheritance -** Occurs when multiple genes are involved in controlling the phenotype of a trait - The phenotype is an accumulation of contributions by multiple genes - **Pleiotropy** - Refers to an allele which has more than one effect on the phenotype - **Multiple alleles -** May be more than 2 alleles for a gene in a population - Ex: blood type (3 alleles - **I^A^, I^B^, i )** - **Incomplete dominance -** the phenotype of a heterozygous organism is a blend between the phenotypes of its homozygous parents - **Codominance -** Phenotype of both alleles are simultaneously expressed in heterozygote - **Epistasis -** The action of one gene obscuring the effects of another gene - **Be able to use Punnett squares to solve genetics problems** - For complete dominance examples, refer to slides 16-19 practice problems, lab 17, or homework - For incomplete, codominance, and epistasis examples, refer to slides 30-35, lab 19, or homework - **Be able to use your probability rules to solve crosses involving 2 or more genes** - Refer to lab 20 for examples or homework **[Chapter 13: Chromosomal Basis of Inheritance ]** - **Sex-linked traits** - Sex chromosomes can be associated with certain traits - **X-linked -** when a gene being examined is present on the X, but not the Y, chromosome - Be able to do genetics problems/Punnett squares for sex linked traits - Refer to lab 21 - When female parent is **homozygous** for a **recessive** X-linked trait 100% male offspring will be - Females who are **heterozygous** for these diseases are **carriers** and may not exhibit any phenotypic effects - They will pass disease to **half of their male offspring** and will pass **carrier status** to **half of their female offspring** - Humans have 46 total chromosomes - 22 pairs are **autosomes** - 1 pair of **sex chromosomes** - Y chromosome is highly condensed - Recessive alleles on male's X have no active counterpart on Y - Has few active genes - **Dosage compensation** - Ensures an equal expression of genes from the sex chromosomes even though females have 2 X chromosomes and males have only 1 - In each female cell, 1 X chromosome is inactivated and is condensed into a **Barr body** - The particular X chromosome that is inactivated in each cell is **random** but once inactivation occurs, all cells descended from that cell will have the same inactive X chromosome - Human pedigree analysis - **Dominant** - Every affected individual will have an affected parent - Tend to appear in every generation - **Recessive** - Affected individuals can arise from unaffected parents - **Sex linked** - Seen more frequently in males - **Exceptions to chromosomal inheritance** - Genomic imprinting - The expression of an allele depends on which parent contributed - A type of epigenetic inheritance - Organellar inheritance - Mitochondria and chloroplasts carry their own genome - Typically inherited only from the mother - **Linkage** - Assortment of some genes is not independent, because they are linked together on a chromosome - Genetic recombination occurs less often between nearby genes - Linkage occurs between two genes that are close together and crossing over between them will be rare - With distance between genes, recombination (crossing over) can occur - **Karyotype** - the number and appearance of chromosomes, including their length, banding pattern, and centromere position - Cytologists photograph the chromosomes and then cut and paste each chromosome into a **karyogram** - **Nondisjunction** - when pairs of homologous chromosomes or sister chromatids fail to separate during meiosis - **Aneuploidy** -- gain or loss of a chromosome - **Monosomy** -- loss - **Trisomy** -- gain **[Chapter 14: DNA the Genetic Material]** - Chromosomes in living cells are complex of D N A and proteins: - Are genes made of DNA or protein? - Know the following important scientists and the experiments that led to discovery that DNA is the genetic material - **Frederick Griffith** did experiments using two strains of *Streptococcus pneumoniae,* a bacterium that causes pneumonia - **Rough (R**) - non-virulent (does not cause disease) - **Smooth (S)** -- virulent (causes pneumonia)  - Griffith concluded that information specifying virulence passed from the heat-killed S strain to the live R strain and **transformed** it into pathogenic S strain - **Transformation** - **Hershey and chase** studied bacteriophage T2 - T2 virus composed of only DNA and protein - Hershey and Chase grew virus in presence of one of the two radioactive isotopes - **^35^S, ^32^P** - Proteins contain sulfur but not phosphorous - **^35^S** incorporated into **proteins** - DNA contains phosphorus but not sulfur - **^32^P** incorporated into **D N A** - Only **radioactive D N A** was found inside cells: - Therefore, genes must be composed of **D N A** - **Erwin Chargaff established:** - \# of purines = \# of pyrimidines - \# A = \# T and \# G = \# C - **Rosalind Franklin** performed X-ray diffraction studies to identify 3D structure of molecules - **Discovered DNA is helical** - Using Maurice Wilkins' DNA fibers, she discovered that the molecule has a diameter of 2 nm and makes a complete turn of the helix every 3.4 nm - **James Watson and Francis Crick** deduced the structure of DNA using evidence from Chargaff, Franklin, and others - Proposed a double helix structure **DNA structure** - DNA is a nucleic acid - A **nucleic acid** is a polymer of **nucleotide** monomers - Three components of a nucleotide: 1. A phosphate group (PO~4~) 2. A five-carbon sugar 3. A nitrogenous (nitrogen-containing) base - Both the phosphate group and the nitrogenous base are bonded to the sugar molecule - Nucleic acids form when nucleotides polymerize via **condensation reactions** - **Phosphodiester linkage** (bond) occurs between - The phosphate group on the 5′ carbon of one nucleotide - And the --OH group on the 3′ carbon of another - Phosphodiester linkages form a sugar--phosphate backbone - DNA strands are antiparallel - One strand runs 3' 5', the other runs 5' 3' - DNA strands form double helix - Sugar-phosphate backbone faces exterior - Nitrogenous bases face interior **DNA replication** - DNA is replicated via **semiconservative replication** - Parental strands separate, and each is template for new **daughter strand** - Each daughter has one old and one new strand - DNA replication includes - **Initiation** -- replication begins - **Elongation** -- new strands of DNA are synthesized by **DNA polymerase** - **Termination** -- replication is terminated - **What enzymes are needed?** - **[DNA polymerase]** - Matches existing DNA bases with complementary nucleotides and links them - Several types of DNA polymerases - DNA polymerase 1 (Pol 1) - Acts on lagging strand to remove primers and replace them with DNA - DNA polymerase 2 (Pol 2) - Involved in DNA repair processes - DNA polymerase 3 (Pol 3) - Main replication enzyme - All have several common features - Add new bases to 3′ end of existing strands - Synthesize in 5′ 3′ direction - Require a primer of RNA - **[DNA helicase]** uses energy from ATP to break hydrogen bonds between two DNA strands to separate them - [**Single-strand DNA-binding proteins** (**SSBPs**]) attach to separated strands to prevent them from closing - **[Topoisomerase]** cuts and rejoins DNA to relieve tension - **DNA gyrase** is the topoisomerase used in replication - **[Primase]** -- type of RNA polymerase that makes primer - **[Ligase]** -- joins DNA segments - [**The** **replisome**] **-** Contains enzymes responsible for DNA synthesis around replication fork - Joined into one large macromolecular machine - **Initiation - prokaryotic cell** - Replication bubble forms when DNA is being synthesized - Forms at specific sequence---**origin of replication** - Bacteria have one and form one replication bubble - Each replication bubble has two **replication forks** - Because synthesis is **bidirectional**, replication bubbles grow in **two directions** - Replication ends at a specific site called the terminus - **Elongation - prokaryotic cell** - **Leading strand (continuous strand)** - Strand that is synthesized continuously toward replication fork in the 5′ → 3′ direction - **Lagging strand (discontinuous strand)** - Strand synthesized **away from** replication fork - Made up of short **Okazaki fragments** that are then linked to form continuous strand - **Leading** strand can be extended from a **single** primer, whereas lagging strand needs a new primer for each Okazaki fragments - **Termination- prokaryotic cell** - Replication ends at a specific site called the terminus **[Eukaryotic replication]** - Multiple origins of replications for each chromosome - Initiation requires more factors to assemble helicase and primase complexes onto the template - DNA polymerase epsilon (Pol ε) responsible for leading strand synthesis - DNA polymerase delta (Pol δ) responsible for lagging strand synthesis - **Telomeres**---region at end of eukaryotic chromosome - Replication of **telomeres** can be problematic - **Leading strand** is synthesized all the way to the end - **Lagging strand**, primase adds RNA primer close to end of chromosome - Final Okazaki fragment is made and primer is removed - **DNA polymerase cannot add to end with no primer** - Germ-line cells avoid this, with enzyme **telomerase** - The enzyme **telomerase** replicates telomeres, maintaining chromosome ends - Telomerase carries its own RNA template which it uses to extend parent strand **[Repairing mistakes and DNA damage]** - DNA polymerase can **proofread** its work - Mismatched bases have distinct shape - **Exonuclease** removes incorrect base and DNA polymerase can add the correct base - **Mismatch repair** - occurs when mismatched bases are corrected after DNA synthesis is complete - **Photorepair -** Specific repair mechanism for thymine dimers caused by UV light - Enzyme **photolyase** absorbs light in visible range and uses this energy to cleave thymine dimer - **Excision repair** - Nonspecific repair (a single mechanism to repair multiple kinds of lesions in DNA) **[Chapter 15: Genes and How They Work]** - The **central dogma** of molecular biology summarizes the flow of information in cells - **D N A → R N A → Proteins** - Genes are stretches of DNA that code for proteins - **Retroviruses** violate this order using reverse transcriptase to convert their RNA genome into DNA - **Transcription---**process of using D N A template to make complementary mRNA - Making a copy of information - Only template strand of DNA used - T (thymine) in DNA replaced by U (uracil) in RNA - **Translation---**process of using information in mRNA to synthesize proteins - Interprets nucleotide "language" to amino acids - Takes place at ribosome - Requires several kinds of RNA - In **eukaryotes** transcription occurs in the nucleus and translation occurs in the cytoplasm - In prokaryotes transcription and translation occur in cytoplasm - Translation starts before transcription is complete - **Genetic code** is read - In blocks of 3 DNA nucleotides ─ **Codon** - Continuously without punctuation between the codons - There is one **start codon** (**AUG**) that codes for **methionine** and signals where protein synthesis starts - There are three **stop codons** (**UGA, UAA, and UAG**) that signal the end of the protein-coding sequence - Code is **degenerate -** some amino acids are specified by more than one codon - Code is **universal** - [**Be able to use codon table to transcribe and translate a gene!** (refer to lab 24 or homework)] **[Transcription ]** - **Initiation -- prokaryotic cell** - **RNA core polymerase** and **sigma (**s) form **holoenzyme** - Sigma (s) recognizes **promoter** elements at -35 and -10 where transcription begins - Core polymerase synthesizes RNA - **Elongation -- prokaryotic cell** - Grows in the **5′-to-3′** direction as ribonucleotides are added - **Transcription bubble** -- contains RNA polymerase, DNA template, and growing RNA transcript - After the transcription bubble passes, the now-transcribed DNA is rewound as it leaves the bubble - **Termination --** prokaryotic cell - Marked by sequence that signals "stop" to polymerase - Causes the formation of phosphodiester bonds to cease - Codes for R N A that forms a hairpin structure - RNA--DNA hybrid within the transcription bubble dissociates - RNA polymerase releases the DNA - DNA rewinds **[Transcription -- differences in Eukaryotic cells ]** - 3 different RNA polymerases - Initiation - Requires a series of general transcription factors - Necessary to get the RNA polymerase II enzyme to a promoter and to initiate gene expression - Interact with RNA polymerase to form initiation complex at promoter - Termination - Termination sites not as well defined - RNA processing - the initial product of transcription is an immature **primary transcript** or **pre-m R N A.** Primary transcripts must undergo **R N A processing** before they can be translated - RNA splicing - **Introns -** Noncoding regions -- "junk DNA - not present in the final mRNA - snRNPs cluster with other proteins to form **spliceosome** which is responsible for removing introns - **Exons** - Coding regions of DNA - Will be translated -- will be **Ex**pressed - Present in final mRNA - **5′ cap**: modified guanine nucleotide with 3 phosphate groups that enables ribosomes to bind and protects from degradation - **Poly(A) tail**: 100--250 adenine nucleotides needed for translation and protects from degradation **[Translation]** - mRNA codons are translated into amino acids - Ribosomes are the site of protein synthesis - Also need **tRNA (transfer RNA)** that bring the amino acid to ribosome - Acts as an adapter molecule - **CCA** sequence at the 3′ end is amino acid binding site - The loop at the opposite end contains the **anticodon** - sequence of three nucleotides that base-pairs with the mRNA codon - 61 different codons but only about 40 t R N A s - One t R N A is able to read more than one codon - **wobble** **pairing:** anticodon's third position can form a nonstandard base pair - Ribosome structure - Ribosomes can be separated into two subunits - small subunit holds the mRNA in place - large subunit is where peptide bonds form - **Peptidyl transferase** - enzymatic component of the ribosome - The tRNA s fit into three sites in the ribosome, bound to corresponding mRNA codons - **A site** (acceptor or aminoacyl)---binds the tRNA carrying the next amino acid - **P site** (peptidyl)---binds the tRNA attached to the growing peptide chain - **E site** (exit)---binds the tRNA that carried the last amino acid - Translation has three phases: - Initiation - Elongation - Termination - **Initiation -- prokaryotic cells** - Initiation begins near the AUG start codon - Small subunit binds to **ribosome** **binding sequence (Shine--Dalgarno sequence)** of the mRNA - Mediated by **initiation factors** - Large subunit added - **Initiation -- eukaryotic cells** - Initiating amino acid is methionine - More complicated initiation complex - Lack of an RBS -- small subunit binds to 5′ cap of mRNA - **Elongation** - Initiator tRNA is in the P site - New charged tRNA will bind to A site if anticodon matched mRNA codon - Requires elongation factor called EF - Tu to bind to tRNA and GTP - Peptidyl transferase catlyzes formation of peptide bond between amino acid in A and P site - **Translocation** of ribosome -- ribosome moves down one codon The process diagram shows the elongation phase of translation. A new t R N A comes into the ribosome, forms a peptide bond, and then the ribosome moves over one codon. The three steps in the process are as follows. 1. Incoming aminoacyl t R N A. A new charged t R N A moves into A site, where its anticodon base pairs with the m R N A codon. A drawing shows the rectangular small subunit, the domed large subunit above, and the m R N A sandwiched between them, 5 prime end on the left. There are three tall cavities in the large subunit, from left to right. The Exit, E, site, the Peptidyl, P, site, and the Aminoacyl, A, site. The sites line up to three consecutive codons on the m R N A. A t R N A molecule is in the P site, with its anticodon UAC aligned to the start codon A U G on the m R N A. Bonded above the t R N A is f Met, located within a tunnel in the large subunit. Another t R N A, with the amino acid Glu and the anticodon C U U, is entering the A site. The sequence of the next m R N A codon, more 3 prime, is G A A, and is right below the A site. 2. Peptide bond formation. The amino acid attached to the t R N A in the P site is transferred by formation of a peptide bond to the amino acid of the t R N A in the A site. The new t R N A shown entering the A site in Step 1 has now entered the site. Its anticodon C U U is aligned to the next, 3 prime of the start codon, codon, G A A. The amino acid attached to that t R N A, G l u, is on the right of f M e t, in the ribosome's active site. A peptide bond has been formed between f M e t and G l u, and the first t R N A has detached from f M e t. 3. Translocation. The ribosome moves one codon down the m R N A with the help of elongation factors, not shown. The t R N A attached to the polypeptide chain moves into the P site. The A site is empty. The ribosome in the drawing has moved one codon, three bases, closer to the 3 prime end of m R N A. The first t R N A is in the E site and the second t R N A is in the P site.  - **Termination** - Termination occurs when the A site encounters stop codon - **release factor** enters A site - Resembles t R N A s in size and shape - Hydrolyzes bond linking the P-site tRNA to the polypeptide chain - The newly synthesized polypeptide, tRNA s, and ribosomal subunits separate from the mRNA - Mutation - **Mutation---**any heritable change in the genetic material - **Point mutations** result from one or a small number of base changes - **Missense** **mutations** change an amino acid in protein - **Silent mutations** do not change amino acid sequence due to redundancy in the code - **Nonsense mutations** change codon that specifies an amino acid into stop codon - **Frameshift muation** - **Chromosome-level mutation** are larger in scale - **Inversion---**segment of chromosome breaks off, flips around, and rejoins - **Translocation---**section of chromosome breaks off and becomes attached to another chromosome - **Deletion---**segment of a chromosome is lost - **Duplication---**segment of chromosome is present in multiple copies