Unit 6 AP Biology, Unit 5 AP Biology Review, Cells, Cell Membrane, Cell Transport Review, Unit 4/Part 5 AP Biology Review, Cellular Energetics Review, Biochemistry Unit Review Terms, AP Biology Cell Parts Review

Bacteria Background

- Bacteria are one-celled prokaryotes, reproduce by binary fission, incredibly diverse. Their genome consists of one single circular chromosome, with naked DNA and no histone proteins. They do not have introns and not enough dna to pack for regulation - Bacteria are opportunists. In a stressful environment they pick up any DNA they come across and take in that gene in order to survive, mechanism for them to survive over stress. They can pick up something from dead ones and convert them into something harmful - Bacterial Transformation is either a natural or artificial process that provides a mechanism for the recombination of genetic information in some bacteria. Small pieces of extracellular DNA are taken up by a living bacterium, ultimately leading to a stable genetic change in the recipient cell. - They pick up naked, foreign DNA wherever it may be hanging out. They have surface transport proteins that are specialized for the uptake of naked DNA. They can import bits and pieces of chromosomes from other bacteria and into their own chromosome which is transformation, or a form of recombination

Prokaryotic Gene Regulation Background

- Bacteria need to respond quickly to changes in their environment. If they have enough of their product they need to stop its production because its a waste of energy to produce more. They can stop it by stopping the production of enzymes of synthesis. - If they find new food or energy source, they need to be able to utilize it quickly for metabolism, growth, and reproduction. They do this by starting the production of enzymes for digestion (they don't need the enzyme until it obtains a particular food source)

Control of Translation

- Blocking the initiation of translation by attaching regulatory proteins to the 5' end of mRNA strand which prevents the attachment of ribosomal subunits and initiator tRNA. Prevents ribosome from grabbing mRNA and blocks translation

Protein Synthesis Background

- DNA codes for proteins which codes for traits - triplet code is transcribed into a codon sequence in mRNA, inside the nucleus. The newly formed strand of RNA known as pre-RNA is modified in the nucleus. The codon sequence leaves the nucleus and is translated into an amino acid (a poly-peptide) in the cytoplasm at the ribosome. - DNA to mRNA (complementary sequence except there's Uracil instead of thymine and those codons match amino acids. Anticodon is complementary to the mRNA strand.

DNA Structure and Details

- DNA makes up chromosomes and that genes are located on chromosomes. We can even see the location of certain genes by tagging them with a fluorescent dye. - double helix, shaped like a twisted ladder which has two strands running in opposite directions (anti-parallel) One strand runs 5' to 3' and one runs 3' to 5'. - a polymer consisting of nucleotides. They are made of a 5C sugar called deoxyribose (carbon is number 1 to 5, 5 is closet to the phosphate or CH2), a phosphate group, and a nitrogenous base (A,G,T,C) - its function is to store and transmit genetic information by coding for the process of protein synthesis - The 5' end is near the phosphate and the 3' end is near the hydroxide. There are 5 different carbons - The backbone is made out of phosphate and sugars Covalent Phosphodiester bonds are strong and hold the backbone together and hydrogen bonds which are weak-hold the nitrogenous bases together. - DNA gets packed and unpacked as needed. DNA combines with a large amount of proteins called histones which it separates from during replication. DNA plus histones is called chromatin. When the DNA wraps around twice around the core of histones it is called a nucleosome.

Transcription

- DNA nucleic acid to RNA nucleic acid language (we are making mRNA). Transfer of genetic information from DNA to RNA. It produces mRNA and processes it before it can be read. mRNA carries instructions from the nucleus to the cytoplasm. 1. The transcribed DNA strand is the template strand and untranscribed DNA strand is the coding strand which is same as the RNA sequence except there is Thymine instead of Uracil. RNA is built from 5 prime to 3 prime The enzyme that does this is RNA polymerase (transcribes genes into mRNA) and each one has a specific promoter sequence it recognizes - Promoter Region - the binding site before the beginning of the gene. This has the TATA box binding site which is for RNA Polymerase and transcription factors. You can have the Enhancer Regin which is the binding site far upstream of gene. Transcription factors bind to promoter region to trigger the binding of RNA Polymerase to DNA 2. Transcription factors like proteins bind to the promoter region. It could be hormones and that helps turn transcription on or off. It then triggers the binding of RNA Polymerase to DNA. The transcription initiation complex is made up of transcription factors, promoter region (TATA box because of its repeating thymine and adenine), and the RNA Polymerase. Once RNA Polymerase is attached, transcription begins. 3. RNA bases are matched to DNA bases on the DNA strand by RNA Polymerase from 5 to 3 prime by RNA Polymerase 4. The RNA Polymerase continues to add nucleotides to the 3' end. Each unit that is transcribed consists of a triplet of bases or a codon that code for a specific amino acid. RNA Polymerase has proofreading during transcription, mRNA is usually short-lived, errors don't have a major effect. 5. RNA Polymerase transcribes the termination sequence. At this point, mRNA is cut free from DNA Template. Then it gets processed

Eukaryotic Gene Regulation

- Eukaryotic organisms need to turn genes of and off rapidly; adjust levels of enzymes for synthesis and digestion - This is to maintain homeostasis, regulate growth and development, cell specialization, must coordinate the body as a whole. The control of gene expression can occur at any step in the pathway from gene to functional protein

Protein processing (post-translation)

- Folding, cleaving, adding sugar groups, targeting for transport, modified by the cell - a newly made protein may stimutaneously fold into its correct shape and begin working - some new proteins must be activated before they function. For example, insulin which is released from a ribosome in inactive form, and only becomes and active hormone after being cleaved by an enzyme.

Cells are Small

- For importing large quantities of materials for transfer, the smaller the size, the larger the SA:V ration. Small cells are more efficient and allows for transfer of food and materials to other places more quickly. The surface area of the cell membrane must be able to accomadte the metabolic needs based on the volume of the cytoplasm - The cell membrane of the smaller cell will be faster and more efficient at supplying needed materials and removing waster than the cell membrane of the larger cell. In fact, if a cell grows and the volume of the cytoplasm becomes too great for the area, a pathway is triggered and the cell divides - The ratio decreases as size increases.

DNA History

- Frederick Griffith performed experiments with several different strains of bacteria Diplococcus pneumonia. Some strains are virulent and cause pneumonia in humans and some strains are harmless. He discovered that bacteria have the ability to transform harmless cells into virulent ones by transferring some genetic factor from one bacteria cell to another. This is known as bacterial transformation. He showed that a substance could be transferred to harmless bacteria and make it harmful. - Hershey and Chase carried out experiments that support the theory that DNA is the genetic material. Viruses are not made of cell. Its DNA inside a protein coat. To reproduce, a virus must insert its own genetic material into the cell. - Watson and Crick proposed the double helix structure of DNA.

Translation Background

- From nucleic acid language to amino acid language mRNA codes for proteins in triplets called codons. mRNA carries the directions for making protein. Read by codons, or three letter triplet bases. Different codons code for one of the 20 amino acids. - Codons are the code for all life and is the strongest support to show common origin - Code is redundant because it has a third wobble base. DNA matches to the mRNA which matches to a piece of tRNA that has the anticodon on it - tRNA has one side with anticodon that links with codon on mRNA and other side has the place for the amino acid that is bringing to the protein on 3 prime end - Ribosomes facilitate the coupling of tRNA anticodon to mRNA codon. The ribosome has two subunits (large and small) and doesn't come together until they grab onto the mRNA - codons on an mRNA seqeunce are changed into an amino acid sequence.

Chromosomal Mutations

- Mutations are any change in the genome. They can occurs in somatic (body cells) and be responsible for development of cancer, or affect future offspring during gameteosis. - there are two types of mutations: gene mutations and chromosome mutations. - Gene mutations are caused by a change in DNA sequence. Chromosome mutations can be seen under a microscope through a technique called karotype. This shows the number and shape of chromosomes and can reveal the precense of certain abnormalities. 1. Deletion:loss of chromosomal segment 2. Duplication: repetition of a segment. (these two are caused by errors in replication) 3. Inversion: reverses a segment 4. Translocation: moving segment from one chromosome to another. ( these are due to errors of crossing over)

Plasmids

- Plasmids are small supplemental circles of DNA that carry extra DNA. - They are used to insert new genes into bacteria. This is the DNA that bacteria swaps when hunting in the environment or during conjugation. - This provides bacteria with genes for antibiotic resistance. You can get plasmids by cutting the plasmid dna and getting the gene from the other organism, inserting the plasmid into the bacteria (vector) and the bacteria now expresses a new gene and a new protein. - Cut the bacteria's DNA, insert the new gene unto the plasmid, glue the DNA, make a recombinant plasmid, insert plasmid into bacteria, the bacteria now expresses a new gene and makes a new protein. OR Cut specific Gene/DNA we want, cut plasmid DNA, insert the gene we want into the plasmid, glue together by ligase to form recombinant plasmid. - A plasmid is a foreign, small, circular, self-replicating DNA molecule that inhabits a bacterium. A bacteria can harbor many plasmids and will express the genes carried by the plasmid. These genes may impart an advantage to the bacteria.

Regulating Metabolism - Feedback Inhibition

- Product acts as an allosteric inhibitor of the 1st enzyme in the tryptophan pathway, but this is still a wasteful production of enzymes. -There are multiple steps and each step has its own enzyme. If we produce enough, tryptophan will go back and bind as an inhibitor. This is still wasting energy making enzymes used in the steps. - You can regulate gene transcription by turning them on or off depending on what you need

Steps to DNA Replication

- Replication begins at special sites called origins of replication. DNA can have multiple points of origin. The two-strand separate to form a replication bubble. A replication bubble expands as replication proceeds in both directions at once. At each end of the replication, the bubble is the replication fork, a Y-shaped region where the strands of DNA are elongating. The leading strand works toward the replication fork. 1. Unwind DNA - Helicase comes in and unwinds part of DNA Helix by breaking hydrogen bonds; stabilized by single-stranded binding proteins act as scaffolding at the replication fork which helps keep the two strands separated. Topoisomerase prevents coiling from happening or it becomes super twisted as the strands are unzipping. 2. RNA Primers are built from Primase which serves as a starter sequence for DNA Polymerase III which can only build on an existing sequence. 3. DNA Polymerase 3 (cannot initiate synthesis) builds the daughter DNA strand by adding complementary bases and it can only add to the 3' end of a growing DNA Strand (5 to 3 ONLY) 4. Leading and Lagging Strand( away from the replication fork): The leading strand is the continuous synthesis and the lagging strand has Okazaki fragments joined by ligase. The lagging strand unzips small sections from the 5' to 3' and then RNA primer is laid down by Primase. DNA Polymerase 3 goes in and builds. (the leading and lagging strand are going in the opposite directions 5. DNA Polymerase I is used to removing the RNA Primer and replace sections with DNA nucleotides (then ligase seals it). This can only build onto the 3' end of an existing DNA strand. DNA polymerase I also proofread and corrects errors in DNA, by carrying out mismatch repair. Damaged regions of DNA are excised by DNA nuclease. 6. All DNA polymerases can only add to the 3' end of an existing DNA strand. So there is a loss of bases at 5' ends in every replication because you can't replace RNA on the 5' end, you can only add to 3' end. Chromosomes get smaller and limit the number of cell divisions. For protection, there are repeating, non-coding sequences (protective ends) at the end of chromosomes called telomeres. So every time you copy, the 5' end erodes off a little bit. Cells that divide more have more telomeres. Telomerase is the enzyme that puts the junk DNA on and it's not always active depending on the number of times the cell has to divide. This may serve as a clock that counts cell divisions and causes the cells to stop dividing as it ages.

Operon Summary/ Other Facts

- Some operons are inducible, meaning that they can be turned on by the presence of a particular small molecule. Others are repressible, meaning that they are on by default but can be turned off by a small molecule. - Trp operon is like feedback inhibition

Incomplete Dominance

- The heterozygote shows an intermediate blended phenotype. - This is a situation where neither allele is completely dominant. - The phenotype intermediate between 2 parental phenotypes - characterized by blending. - A homozygous red flower (PP) is crossed with a homozygous white flower (WW) , and you get a pink flower (PW- makes 50% less color). - describes the relationship of 2 alleles in a single gene that codes for a trait P: PP * WW F1: 100% one blended color F2: 25 % P, 25% W, and 50% PW

Operon

- These are genes grouped together with related functions. - Essentially a set of genes and the switches control the expression of those genes - Examples include all the enzymes in a metabolic pathway. One RNA polymerase can transcribe all 5 genes onto one piece of DNA. Ex. all enzymes needed to make tryptophan are on the trp operon - There are different parts: 1. Promoter - (RNA polymerase binding site and there is only one for all genes and tells RNA polymerase to start here to make a single mRNA 2. Operator - DNA binding site of the repressor protein (on/off switch) when repressor is in, transcription is off 3. Repressor Protein - binds to the DNA at operator site, blocking RNA Polymerase, and blocks transcription. Repressor will fit if the operator has the correct shape

Packing/Unpacking DNA (Regulation at Chromatin Structure Level)

- This is about how DNA fits in the nucleus and how there are multiple structure levels wrapped around the histone proteins (positively charged amino acids bound tightly to negatively charged DNA) - Eukaroytic DNA is packed with proteins called histones into an elaborate complex known as chromatin, the basic unit of which is the nucleosome. Changes to the histone structure alter chromatin configuration, binding it more tightly or loosely, thus making DNA more or less accessible for transcription and expression. This inhibiton is reversible. 1. The degree of DNA packing regulates transcription - Heterochromatin: darker staining, tightly packed. We don't use this that much so we wrap these sections. - Euchromatin: lighter, more loosely packed, cell uses more of this 2. DNA methylation -This blocks transcription factors; turning the genes off. A methyl group attaches to the cytosine, nearly permanent, example is inactivated mammalian X chromosome or a Barr Body - methylation for certain bases silences the DNA temporarily or for long periods of time. Reversing this and removing the groups can turn genes on. - Causes Barr bodies and long-term deactivation of genes neccesary for normal cell differentiation in embroyic development. 3. Histone Acetylation - Loosely wrapped around histones; unwinds the DNA turning the genes on or allowing transcription. This promotes the loosening of the chromatin structure and permits transcription. Removing Acetyl groups BLOCK transcription. - Attachment of acetyl groups to histones; causing a conformational change in histone proteins and transcription factors have easier access to the genes, they don't wrap so tightly.

Linked Genes

- This is when genes are located on the same chromosome. They do not assort independently of eachother. - There are many more genes than chromosomes, thousands of genes are linked. Humans have 46 chromosoms in every cell. Therefore, humans have 46 linkage groups. - Linked genes tend to be inherited together and do not assort independently unless they are separated by a crossover event during meiosis and gamete formation - When genes are linked, you can map the location of a gene on the chromosome (relative to eachother) by using cross-over frequencies. - For example, genes for eye color and hair color are linked. The closer together two genes are on the chromosome, the less likely their alleles will be separated by crossing over. - When performing a cross for this, two alleles are on each gene. For exampe, if you cross a short and long fly (llAa) with long and long fly (LlAA). One chromosome for a parent would be lA and the other would be la. This would be the top of the punnet on one side. Alleles for the same trait will not be on the same chromosome. The other parent would be LA and lA. These would then be the other sides of the punnet and then you would cross these.

Epistasis

- This is when one gene completely masks another gene. This describes the relationship between 2 genes. - The expression of one gene is modified by the expression by one or several other genes. Ex. Some mice have no color in their fur even though the alleles for color are present. One gene could be present that does not allow the gene for coat color to be expressed - one gene depends on another gene to be expressed - Can be seen in dihybrid crosses -In Labrador retrievers, the coat color is epistatic. There are three coat colors, black, chocolate, and yellow; but there are only two genes, coat color and the ability to express color. Black (B) coat color is dominant to chocolate (b) coat color and the expression of color (E) is dominant to the inability to express the color (e). Regardless of the genotype for color, the expression of the color gene influences the final coat color of the dogs. In other words, if a dog has the genotype, BBee, the dog will be yellow, even though it carries the dominant genes to produce a black coat. A type of gene interaction in which one gene alters the phenotypic effects of another gene that is independently inherited.

Transcription initiation (controlling regions on DNA) ~ Transcriptional Level

- Transcription is a highly regulated process. To initiate transcription, RNA Polymerase must bind to the promoter. This process requires the assistane of transcription factors. These turn transcription on or off. 1. Promoter- nearby control sequence on DNA that established base rate of transcription; binding site for RNA polymerase and transcription factors 2. Enhancer- distant control sequence on DNA that establishes base rate of transcription, binding site for activator proteins, enhanced rate (high level) of transcription

gel electrophoresis

- Used to compare DNA for the purposes of forensics, medical diagnostics, paternity, evolutionary relationships, and more - This is when we separate fragments by size by running it through gelatin. It's a method of separating DNA in a gelatin-like material using an electrical field. DNA is negatively charged so that's why when it's in an electrical field it moves to the positive side. Small pieces travel the farthest and large pieces travel slower and lag behind. The thicker the piece, the larger the DNA. - Everyone's sections of junk DNA is so different because of the junk dna, repeated patterns on our 23 chromosomes that is why everyone's DNA pattern is so different. - A child should have bands that come from either mom or dad.

Chi Square Test

- Way to compare if the variation in data is due to chance or the variables you are actually testing. The chi square tests helps you decide if the difference between the observed and the expected is due to chance or if there is some other factor influencing the results, such as an alternative inheritance mechanism. X^2 = E (Sum) (O [observed] - E [Expected]) sqaured divided by Expected - Null Hypothesis: There is no significant difference between the observed and expected frequencies. No statistical significance. - accept or reject null hypothesis - Degrees of Freedom: Need atleast two outcomes. Subtract one from the total outcomes to find the degree of freedom. - Critical Value: Look at 0.05 value. That is where you are 95% sure if you are accepting or rejecting the null hypothesis. If you get a number higher than the critical value, reject the null hypothesis and there is something aside from chance that is causing you to get your results. If you don't exceed the critical value, you accept the null hypothesis that the results are due to chance.There is no statistical significance if you accept the null hypothesis. - To find your expected values, you multiply the ratio expected by the total number of things in your experiment. For most genetics test, a significance level of 0.05 is used (which means 95 times out of 100, you will see what you are expecting, with variation occuring 5 times out of 100 purely due to random chance). - - If we accept the null hypothesis that means with 95% confidence, there is no difference between the expected and observed results. If we rejected the hypothesis then we would accept the fact there is a satistically significant difference between the numbers we observed and the numbers we were expecting, and the items are not behaving the way they are suppose to.

Bacteria Transformation Lab

- We are trying to see in what environments the bacteria will grow in order to glow. If the bacteria glow, that means they took the plasmid in. The more shocked the bacteria were, the more chance or higher possibilty they will take up the plasmid. 1. First plate: Luria Broth and not plasmid: The bacteria would simply grow because there is food present. The result is a lawn of bacteria present on the plate. 2.Second Plate:Luria Broth and the plasmid: The bacteria would grow because the food was there but they would not contain the new DNA because they were not stressed out. The result was a lawn of bacteria 3. Third Plate: LB/ampicillin and no plasmid: The bacteria would die because of all the ampicillin. This was the control group. This was to see the experimental change. The result was no growth 4. Fourth Plate: LB/amp and the plasmid: The bacteria would survive the stress and the ampicillin because it has the plasmid. The result was the formation of many colonies. There were isolated colonies because the bacteria took up the plasmid and was able to withstand the amp.

Repressible Operon (Tryptophan)

- consists of a promoter, operator, and 5 adjacent structural genes (A,B,C,D,E) that code for five separate enzymes necessary to synthesize the amino acid tryptophan. - As long as RNA Polymerase binds to the promoter, one long strand of mRNA containing the start and stop codon is transcribed - Repressible Operon, meaning it is always switched on unless the repressor is activated. 1. ON: enzymes are synthesized and making tryptophan. 2. OFF: The repressor is attached with the tryptophan (repressor protein complex) which binds to the DNA. When excess tryptophan is present this happens, and blocks transcription. The changes (conformational change in shape) shape to stop - This is when it changes shape to stop. This is a synthesis pathway model. When excess tryptophan is present, it binds to tryp repressor protein and triggers a repressor to bind to the DNA. This blocks transcription. - The excess product must attach to the repressor protein to stop - Normally is on and when it is the goal is to make proteins that lead to tryptophan - Found in Anabolic pathways, synthesizing end products, when the end product is in excess - Trp is the allosteric regulator of the repressor protein.

Chloroplast

- contain green pigment called chlorpophyll, along with other enzymes that absorb light energy and synthesize sugar. Double outer membrane and inner membrane system called thylakoids. Site of photosynthesis.

Nucleus

- contains genes that control eukaryotic cells, genetic information that controls structure and function of the organisms. It contains chromosomes that are wrapped around special proteins into a chromatin network. Surrounded by a selectively permeable membrane called the nuclear envelope that has pores whihc allows for transport of molecules, like mRNA. Gene is a segment of DNA that has information to encode

Restriction Fragment Length Polymorphisms (RFLPs)

- differences in DNA between the individuals. A change in DNA sequence affects the restriction enzyme's cut site and creates different fragment sizes and different band patterns - restriction fragment is a segment of DNA that results when treated with restriction enzymes. When scientist compared noncoding regions or JUNK DNA or introns of human DNA across a population, they discovered that restriction fragment pattern is different in every individual - these differences have been named Restriction Fragment Length Polymorphisms - A RFLP anaylsis of someone's DNA gives a human DNA fingerprint that look likes a barcode - Differences in DNA sequence on homologous chromosomes that can result in different patterns of restriction fragment lengths (DNA segments resulting from treatment with restriction enzymes). - each person's RFLP are unique, except in identical twins.

Viruses

- parasite that can live only inside of another cell. They cannot replicate without a host. - It comandeeers the host cell machinery to transcribe and translate all the proteins it needs to fashion new viruses. In the process, thousand of new viruses are formed and the host cell is often destroyed. - Virus has a capsid (protein coat) which holds the DNA or RNA - each type of virus can only infect one specific type of cell because it gains entrance into the cell by binding to SPECIFIC receptors on the cell surface. For example, the virus that causes the cold only binds to the membranes of the respiratory system.

Nucleolus

- ribosomes (rRNA) are synthesized and assembled (large and small subunits), found in the nucleus, non-membrane bound structures, a tangle of chromatin and unfinished ribosomal precursors

Plasma Membrane

- seletively permable membrane that regulates the steady traffic that enters and leaves the cell - Phospholipid bilayer where tails are toward the middle and hydrophobic and heads are toward the outsides and hydrophilic -Fluid Mosaic Model: fluid because it's not to liquid or too solid. Mosaic because it has proteins dispersed between the layers. Altering the fatty acids can alter fluidity (saturated vs. unsaturated) Saturated would be solid and unsaturated would be more liquid. Fish have more unsaturated so its resistant to freezing in water - Nonpolar molecules such as hydrocarbons, carbon dioxide, oxygen can dissolve and pass through the ayer without any proteins because the interior is hydrophobic - Polar molecules, except water, such as glucose, do not cross without the aid of a protein.

DNA Replication Background

- semi-conservative process; each strand serves as the template for a new strand composed of complementary nucleotides. - the new molecules consist of one old parent strand and one new daughter strand. - occurs during the S phase (DNA replication) during the cell cycle. - the separate process not a part of protein synthesis - Many replication forks develop along a chromosome. This process continues until the replication forks meet, and all of the DNA in a chromosome has been copied. Each new strand that has formed is complementary to the strand used as the template. Each resulting DNA molecule is identical to the original DNA molecule. During prophase of mitosis or prophase I of meiosis, these molecules of DNA condense into a chromosome made of two identical "sister" chromatids. This process ensures that cells that result from cell division have identical sets of genetic material and that the DNA is an exact copy of the parent cell's DNA.

Inducible Operon (Lac Operon)

- series of genes that produce lactase enzymes to breakdown lactose - The lac operon is regulated by the availability of lactose. The lac operon consists of a promoter, an operator, three adjacent structural genes which code for enzymes and a terminator. The three genes are: lacZ, lacY, and lacA. The Z gene encodes β-galactosidase, the Y gene encodes permease, and the A gene encodes transacetylase. All three genes are controlled by the same regulatory elements. - This is when it changes shape to start - When lactose attaches to the repressor, it changes his shape causing him to go away and allow for RNA Polymerase to make enzymes to help break down; induces transcription - Found in Catabolic pathways, digesting nutrients to simpler molecules - Produces enzymes only when the nutrient is available ON: the food is available such as lactose which attaches to the repressor, causing it to change shape and fall off the operator allowing for RNA polymerase to transcribe. Lac is attached to the repressor protein OFF: The repressor is attached without anything, entirely blocking transcription. No enzymes are created, LAC is NOT attached to so there is no shape change which prevents lac from being broken down. **** a lactose metabolite called allolactose binds to the allosteric site on the repressor. This interaction causes a conformational change in the repressor shape and the repressor falls off the operator, allowing RNA polymerase to bind to the promoter and initiate transcription. Allolactose is called an inducer because it turns on, or induces the expression of the lac genes. - Three enzymes are synthesized to break down lactose into glucose and galactose to get energy from lactose. When lactose is present, it binds to the repressor protein and causes a shape change that triggers the repressor to release the DNA. - the repressor which causes the protein to change shape, causing it to release DNA and fall allows RNA Polymerase to attach to the promoter region and transcribe lactose digesting enzymes. Lactose is the allosteric regulator of the repressor protein.

RNA

- single-stranded helix which consisting of nucleotides (A, G, C, U). The 5 Carbon sugar is ribose. It still has direction. There are different types of RNA that are used in protein synthesis such as mRNA and tRNA and rRNA.

Mitochondria

- site of cellular respiration; outer double membrane and inner series of membrane called cristae; have their own DNA; constantly divide and fuse with eachother to exchange DNA and compensate for one another's defects. Produces ATP from sugars and other fuels

Gregor Mendel

- the father of modern genetics. He was an Austrian Monk, who bred pea plants in order to study patterns of inheritance. He had a parent generation which was generally homozygous for the traits and then a F1 Generation who ended up being heterozygous, and then a F2 generation. - He used the experimental method, quantitive analysis to document his research. He cross pollinated true breeding parents, which resulted in F1 generation. Allowed offspring to cross-pollinate and observe next generation (f2 - 3:1 ratio). If bred a true breeding purple and a true breeding white flower

Sex-Linked Genes

- there are 2 sex chromosomes and NOT ON 44 (22 pairs) of autosomal diseases. - Traits are carried on the X chromosome and are called sex-linked. There are a few genes carried on the Y-Chromosome - the male determines the sex of the child. - If a sex-linked trait is due to recessive mutation, the female needs both copies of the mutated gene to have the disease, but if she has only one then she is a carrier - Males only need one mutated gene because they only have one X chromosome. (XY) - All daughters of affected fathers are carriers of the disorder; sons cannot inherit a sex-linked trait from the father because the son inherits the Y chromosome from the father - Males cannot ever be carriers. They either have it or they don't - In order for a female to have a recessive sex-linked condition, she must inherit the mutant gene from both parents - The Y chromosome has few genes other than SRY. This is the master regulator for maleness; it turns on genes for the production of male hormones. The X chromosomes have other genes/traits beyond sex determinations and has some mutations like hemophilia and Duchenne muscular dystrophy. - Because females have two X chromosomes, they have two alleles for any X-linked trait. Therefore, they must inherit two copies of the recessive allele to express the recessive trait. This explains why X-linked recessive traits are less common in females than males. - An example of a recessive X-linked trait is red-green color blindness. People with this trait cannot distinguish between the colors red and green. More than one recessive gene on the X chromosome codes for this trait, which is fairly common in males but relatively rare in females

Pedigrees

- these are udes to predict the probability the offspring will inherit the genetic disorder. Pedigrees reveal Mendelian Pattern of inheritance - family tree indicates the phenotype of one trait being studied for every member of the family. - Females are circles, Males are squares, if you have the disease, the shape is circled - It can show if something is dominant or recessive Dominant: these traits do not skip generations. If a trait is dominant and the child has it, one of the parents must have it. Recessive: these traits tend to skip generations. If a child has a recessive trait, both parents need to have atleast one allele to donate - It can show if the trait is autosomal or sex-linked. Sex-Linked Traits are found when more males have the disorder than females. - If a trait is autosomal recessive, then all those who have it homozygous recessie. - With dominant inheritance, all affect individuals will have atleast one dominant allele.

Basics of Probability

- this is the likelihood that a particular event will occur. If an event is absolutely certain, its probability is 1. If it cannot even happen, the probability is zero. Probability can predict an average outcome. Multiplication: Independent events in a sequence. If it uses the word and, generally means multiplication. Multiply all the probabilties out to find the final chance. Ex. In a cross between AaBbCc * AaBBCC, what is the probability that the offspring will be AaBbCC. Work the A's then the B's then the C's, multiply the probaiblites for each outcome to find the final. Ex. A couple having two boys depend on two independent events. The chance of the first child being a boy is 1/2 and the chance of the second child being a boy is 1/2. Multiply to find the overall probability. Addition: mutually exlusive events. Two things that could go either way. The question uses the word or. Ex. In a cross between AaBbCc * AaBBCC, what is the probability that the offspring will be AABbCc or AABBCC? Multiply first to find the individuals then add the grouped numbers together. - When more than one arrangement of events producing the specified outcome is pososible, the probabilites are added together. (Having a boy and one girl in any order - do multiplication first then multiply.

Methods of Bacterial Reproduction

1. Binary Fission: DNA copies itself, bacterium grows larger, and DNA separates into two distinct strands. Bacteria contracts in the middle, dividing the cell, 2 identical daughter cells are made 2. Conjugation - Requires direct contact, primitive form of sexual reproduction. Bacteria that contain F+ plasmid (fertility) and the Bacteria that don't contain fertility are called F-. The F+ plasmid contains genes for the production of pili, cytoplasmic bridges that connect the adjacent cell and allow the DNA to move from one cell to another. Both cells end up as F+. The F factor is cut at a specfic region called the origin of transfer. OR Conjugation is the process of genetic transfer between bacterial cells that require direct contant. The F Factor is a plasmid. There are F+ and F-. F+ cell are donors that produces a pili which connects to the other cell. The F+ factor is cut at the origin of transfer. The DNA is trasnferred to the recipient cell, it makes a circular DNA molecule. It is replicated and it becomes double stranded. F factor DNA was aso replicated. Both cells wind up with a complete F+ and can conjugate with other cells. 3. Transduction: A segment of DNA is carried from one bacterial cell to another by a bacteriophage. The phage attaches to the bacterial cell and injects its nucleic acid into the host. A phage enzyme is produced that breaks down the host DNA into smaller fragments. Phage DNA is replicated and phage coat proteins are produced. During formation of phage particle, some phage heads may have host DNA and not phage DNA. The phage particle carring the bacterial DNA infects another cell, transferring the bacterial DNA to the new cell. When the bacterial DNA is introduces into the new cell, it can become part of the host chromosome, transferring genes to the recipient. THe cell then multiples and carries new genetic material. Forms recombinant bacteria. 4. Transformation: transfer of naked DNA into a recipient cell. Double stranded donor DNA binds to a specific receptors on the surface of the recipient cell. One stand of the donor DNA is degraded by nucleases and the other strand enters the cell. The single-stranded donor pairs with an homologous region on the recipient DNA and is integrated into the recipient genome by a breakage and reunion mechanism. The repair system removes the donor or recipient , and replaces it with a complementary sequence. Since either stand can be replaced, some cells have the donor DNA and others have the orignal DNA. In labs, cells are plated on selective media so that only the transformants will grow.

Cells only found in Plant Cells

1. Central Vacuole: stores salts, minerals, water and other nutrients while providing structure to the cell 2. Cell Wall: provides structural support for the cell, made of complex polysaccharides known as cellulose, prevents the cell from expanding or contracting too much as water levels vary, holes (plasmodesmata) allow for communication between adjacent plant cells. Fungi cell walls are made of chitin. The primary cell wall is immediately outside the plasma membrane. 3. Chloroplast: the site of photosynthesis; light energy is used to produce food such as glucose.

Law of Independent Assortment

1. Each pair of alleles of one gene segregates into gametes independently of another gene's alleles. 4 classes of gametes are produced in equal amounts. - During gamete formation, the alleles for one trait such as height, assort independently from the alleles of a gene for another trait, such as seed color. Established by Meiosis 1 The law of independent assortment applies when a cross is carried out between two individuals for two or more traits that ARE not on the same chromosome. -Alleles of a gene on nonhomologous chromosomes assort independently during gamete formation. - supports a dihybrid cross, where traits assort independently. - Multiple Genes: for separate traits that are passed independently of one another from parent to offspring. The trait for flower color assorts independently of the trait for height ** THIS APPLIES FOR TRAITS THAT ARE NOT LINKED. Two traits do not influence one another. Each pair of alleles for one gene separate independently of another pair of alleles.

mRNA Processing

1. Eukaryotic genes are not continuous and they have junk. - Exons are the real genes (expressed/ coding DNA) - Introns are the junk (in between sequence, non-coding regions) which comes out. This is called post-transcriptional processing. mRNA splicing is done to edit out introns out of the primary mRNA transcript - Splicing must be accurate. A single base added or lost throws off the reading frame. Splicing is done to edit out introns and make transcribed RNA short and remove junk DNA. 2. RNA Splicing Enzyme - snRNPS (small nuclear RNA and proteins) grab on to the ends of the intron and recognize specific codes. Then they look up the intron and come together and altogether they are called a spliceosome. Several snRNPS (small nuclear ribonucleoproteins) make a splicesome that cut and paste the gene. When they are done the intron is cut/excised out. 3. Alternative Splicing - Alternative mRNAs can be produced from the same gene. The same piece of DNA can code for more than one protein depending on what is cut - RNA can code for more than one protein depending on what is cut or what is considered the intron or exon. Different RNA molecules are produced from the primary same transcript. This depends on what is treated as introns and what is exons. Different segments can be exons making different proteins. - alternative splicing allows one mRNA to produce many polypeptides. 4. Post-Transcriptional Processing - Need to protect mRNA on its trip from the nucleus to the cytoplasm because of enzymes in the cytoplasm attack mRNA. In order to protect the end of the molecule, we add 5' GTP cap (modified guanine nucleotide which helps the RNA strand bind to the ribosome during translation) and a poly-A tail (string of adenine nucleotides) to the 3' end. It protects the mRNA strand from degradation by hydrolytic enzymes and facilitates the release of mRNA into the cytoplasm. Protects it from exonucleases which are proteins that degrade nucleic acids. The longer the tails the more the mRNA lasts and the more protein it produces

Translation Steps

1. Initiation: mRNA is attached to the subunits of the ribosome. The first codon, the start codon is always AUG or Methionine. It must be positioned correctly in order for translation to start. 2. Elongation: tRNA attaches to the different sites and reads the mRNA code. The anticodon on the tRNA binds to the codon on the mRNA which carries an amino acid that matches the mRNA codon. A polypeptide chain is formed. There are 64 possible codon sequences for 4 nitrogenous bases. The ribosome moves along the mRNA. The three sites are - A site: [aminoactyl tRNA] tRNA brings in the next amino acid. The ribosome moves along not the tRNA. It bonds here - P site: [Peptidyl tRNA] holds the growing tRNA polypeptide chain - E site: [Exit site] empty tRNA leaves ribosome from the exit site. Termination is dependent on end codon which is UAA, UGA, or UAG. 3. Termination: When a ribosome reaches a stop codon. A release factor breaks the bond between the tRNA and the last amino acid of the polypeptide chain. The chain is freed from the ribosome and mRNA is broken down.

Regulation of mRNA degradation

1. Life span of mRNA determines amount of protein synthesis, can last from hours to weeks this depends on the size of Poly A tails and 5' GTP caps. 2. RNA Interference by small interfering RNA (siRNA) these are short siRNA segments that bind to mRNA creating sections of double stranded mRNA, this is the death tag for mRNA and triggers degradation, causing gene-silencing and turning genes off. They come to the mRNA strand when we need to get rid of and when they come they bind to mRNA and make it double stranded and transcription cannot occur causing death and enzymes that like to kill to come kill RNA (DEATH TAG FOR mRNA) - human mRNA may continually translate protein for hours and weeks.

Cells only found in Animal Cells

1. Lysosomes: Membrane-bound sac of Hydrolytic Enzymes that used to digest food, other molecules, and worn-out cell parts. Principle site of intracellular digestion. Cells can renew itself by breaking down and recycling cell parts (autophagy) 2. Centrosome: paired structure found n animal cells that consist of triples of a 9+0 arrangement, involved in cell division 3. Flagella

Law of Segregation

1. The two alleles for each gene separate during gamete formation. Created by Meiosis 1 During the formation of gametes, the two traits carried by each parent separate. - The two factors of a characteristic separate during the formation of gametes - When gametes are produced from meiosis, homologous chromosomes separate from each other. Each allele for a trait is package in a separate gamete. If you as an individual have Tt for a genotype for seed color, one gamete will egg will get t and one will get T. - When an individual produces gametes, the copies of a gene separate so that each gamete receives one copy. A sperm or egg will receive only ONE allele of a gene. - The cross that supports this law is a monohybrid cross. More: For example, if an individual carries the alleles for brown and blue eyes, as inherited from their parents, when they produce sex cells, each sex cell will have only one allele; either the allele for brown eyes, or the allele for blue eyes. This process occurs during meiosis, as the paternal and maternal chromosomes are separated and the alleles are segregated into two different haploid daughter cells.

Plasma Membrane Functions

1. Transport: molecules and electrons, and ions are carried through the channels, pumps, carriers, and electron transport chains, which manufacture ATP 2. Enzymatic Activity: one membrane-bound enzyme is adenylate cyclase, which synthesizes cyclic AMP (cAMP) from ATP. 3. Signal Transduction: binding sites on protein receptors fit chemical messengers like hormones. The protein changes shape and relays the message to the inside of the cell. 4. Cell to Cell Recognition: some glycoproteins and lipids serve as identification flags that are recognized by other cells. 5. Cell to cell attachments: - Gap Junctions: (a type of cell surface in animals) analogous (similar) to plasmodesmata in plant cells. They directly connect the cytoplasm of 2 cells, which allows various molecules, ions, and electrical impulses to directly pass through a regulated gate between cells. - Glycocalyx: (a type of cell surface in animals) made of carbohydrates, strengthens cell surface, helps glue animal cells together, helps in cell recognition. - Tight junctions: (a type of cell surface in animals) holds the cell together, two membranes bond into one, the function is to block transport and limit permeability 6. Attachment to the cytoskeleton and extracellular matrix: this helps maintain cell shape and stabilize the locations of certain membrane proteins.

Protein degradation(post-translation)

1. Unwanted proteins are tagged by ubiquitin, a polypeptide, and broken down into 7-9 amino acid fragments by proteasome. 2. Ubiquitin is the protein death tag and this is chopped into little pieces. Proteasome chops proteins into short amino acids chains for reuse

Restriction Enzymes

1. We cut DNA through restriction enzymes and we get these from bacteria. In bacteria, they evolved to cut up foreign DNA and protect us from viruses. They only cut a specific sequence of bases which prevents them from cutting their own DNA. Bacteria protect their own DNA with methylation group, so if the sequence does exist, if you put a methylation group on the cytosine, it is not even there anymore. Mixing genes together is important because it produces new proteins in different organisms. 2. They cut a specific DNA sequence also called restriction sites. They cut at symmetrical palindromes (a sequence in which the top strand read from 3 to 5 end is the same as the bottom strand read from 5 to 3, reads the same backward and forward) and produce either protruding ends, which are sticky ends because they will bind to any complementary DNA. After you cut other DNA with the same enzyme, you can glue the DNA together at the sticky ends. DNA ligase joins the two strands together OR these enzymes cut DNA at specific recognition sequences or sites, such as GAATTC. Often, these cuts are staggered, leaving single-stranded sticky ends to form a tempoary union with other sticky ends The fragments that result from the cuts are called restriction fragments. They are called sticky ends because they are easy to rejoin to the complementary stick ends. Some enzymes cut two strands of DNA directly across eachother, producing a blunt end. 3. Gene produces proteins in different organisms or individuals. Bacteria can read the human DNA because the code is universal and they will end up with the same protein. Restriction Enzymes are named for the bacteria they are found in. Each restriction enzyme has its own restriction site. - Genetic Engineering is possibly due to special enzymes that cut DNA. Special Proteins, restriction enzymes, produced by bacteria to prevent or restrict invasion by foreign DNA. They act as DNA scissors and cut foreign DNA into pieces so it cannot function.

Different types of RNA

1. mRNA - Messenger RNA: involved in transcription. When a sequence of DNA is expressed, one of the two strands of DNA is copied into mRNA, according to the base-pairing rule. Carries instructions from the nucleus to the cytoplasm 2. rRNA - ribosomal RNA. Involved in Translation. It is structural. It makes up the ribosome which is made up of a large and small subunit. The ribosome is the site of protein synthesis and has one mRNA binding site and three tRNA binding sites (A,P,E) 3. tRNA - Transfer RNA. Carries amino acids from cytoplasm to mRNA at the ribosome. Shaped like a cloverleaf and has a binding site for amino acids on one end and another binding site for an anticodon sequence that binds to the mRNA at the other. Anticodon is one cloverleaf end and amino acid is on 3' end. Aminoacytl tRNA synthetase is the enzyme that bonds amino acids to tRNA. Require energy so it can release amino acid at ribosome so ATP goes to AMP and makes it unstable.

Codominance

2 alleles affect the phenotype equally and separately. - not blended phenotype, both traits show - both alleles influence the phenotype. - An example is the human blood type. The alleles IA and IB are codominant. Meaning if they are present, the individual has Type AB Blood with Type-A and Type B antigens.

Biotechnology

A form of technology that uses living organisms, usually genes, to modify products, to make or modify plants and animals, or to develop other microorganisms for specific purposes. - Genetic engineering is the manipulation of DNA. - Genetically modified organisms Enabling plants to produce new proteins: Protect crops from toxins Extend growing season and Improve quality of food

polymerase chain reaction (PCR)

A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules, and nucleotides. - method for making many copies of a specific segment of DNA and only need about one cell to start. This is copying DNA in a test tube and you need a template strand, DNA polymerase enzyme, nucleotides, and a prime - cell-free automated technique by which a piece of DNA can be rapidly copied or amplified within a few hours. The DNA piece that is to be amplified is placed in a test tube with Taq polymerase (a heat stable form of DNA polymerase extracted from extremophile bacteria) along with a supply of nucleotides, primers necessary for DNA synthesis. Once the DNA is amplified, these copies, can be studied or used in a comparison with other DNA samples. The size of the piece that is amplified must be very small and avoidant of skin cell contamination. Billions of copies of fragments of DNA can be produced in a few hours.

Post-transcriptional control (mRNA processing)

Alternative RNA Splicing: alternative RNA Splicing, variable processing of exons create a family of proteins, you can cut different ways to make different proteins. - important in regulating gene expression in which different mRNA molecules are produced from the same primary transcript, depending on which segments are treated as introns and which are treated as exons.

Reverse Transcriptase

An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis. - HIV infects and destroys cells in the immune system, weakening a person's ability to fight off other infections. A combination of drugs can make HIV infection a treatable chronic disease. The drug AZT or azidothymidine is a drug commonly used and targets a critical step in HIV replication: revere transcriptase. During reverse transcriptase, an HIV enzyme converts the HIV RNA into DNA so that it can be inserted into the host cell's genome. The genome of HIV is made up of a single-stranded RNA. - AZT is structurally very similar to the nucleoside (does not have a phosphate, nucleotide has a phosphate) thymidine. In a cell, AZT can be linked to a phosphate group to form a nucleotide that can be incorporated into a growing nucleic acid chain. - HIV contains the enzyme called reverse transcriptase that transcribes RNA into DNA. When HIV enters the cell, the reverse transcriptase transcribes the viral genome into a complementary DNA strand. The enzyme then catalyzes the synthesis of a second DNA strand, complementary to the first. The double-stranded viral DNA is then inserted into the host cell's chromsome. The host cell's RNA Polymerase transcribes the viral DNA into RNA molecules that can serve both to provide instructions for synthesis of viral proteins and as genomes for new viruses. - AZT works as a drug against HIV because where we would attach the next phosphate group when making DNA, at the 3' end, there is a nitrogen group, blocking the attachment. This won't produce a complete copy of the viral HIV's genome. The rest of the complementary strand won't be made.This is a drug that stops reverse transcriptase due to the nitrogen group at the 3' end instead of a hydroxyl. The phosphate needs to attach to a hydroxyl and create a phosphodiester bond. The prevents the rest of the reverse transcriptase from working.

Translation Based on Animation

Begins when messenger RNA binds to the ribosome. The initial tRNA occupied the P site. Other tRNA with amino acids enter the ribosome at the A site. The matching of the anticodon on the TRNA and the three nucleuotides on MRNA ensures correct sequence. Another tRNA enters A site. Each time a new codon sequence moves into the A site, a new transfer RNA brings an amino acid. The ribosome moves along the mRNA. As the ribosome proceeds down, a stop codon is encountered and the ribosomal complex falls apart and the protein is released into the cell.

Eukaryotes vs. Prokaryotes

Both: DNA (genetic material), Cytoplasm, Cell Membrane, Ribosomes, Flagella (Sperm and Bacteria), sometimes Cell Wall Prokaryotes: simple cells that contain no nuclei or other internal membranes. An example is Bacteria. They have a nucleoid region instead of a nucleus and even that is non-membrane bound. 1. No internal membrane-bounded organelles, Circular naked DNA (nucleoid region), small ribosomes, metabolism is anaerobic and aerobic, no cytoskeleton, mainly unicellular, very small cells Eukaryotes: They have a nucleus bound by a double membrane, internal organelles, and membranes that compartmentalize each cell so that complex chemical reactions can occur. Examples include animal cells, plant cells, protists, and fungi. 1. Distinct membrane-bound organelles, DNA wrapped with histone proteins protected into chromosomes (nucleus), larger ribosomes, metabolism is aerobic, the cytoskeleton is present, mainly multicellular, cells are larger.

Chromosomal Mutations

Chromosomal mutations include deletions (a piece of the chromosome breaks off and is lost), inversions( a piece of the chromosome breaks off and reattaches itself in reverse order), translocations(a broken piece attaches to a nonhomologous chromosome), and nondisjuction( a pair of chromosomes fail to separate during Anaphase 1 of meiotic cell divison, results in trisomy or monosomy.

Other Form of Transcription

DNA's code for building a particular protein must be copied onto a piece of messenger RNA first. The mRNA can then travel out of the nucleus and head to the ribosome for translation, the actual production of the protein. 1. During preinitiation, RNA polymerase binds to a promoter sequence in the presence of specific transcription factors. RNA polymerase II, and therefore the initiation of transcription, requires the presence of a core promoter sequence in the DNA. The TATA box is a highly characterized core promoter sequence found in most eukaryotic promoters. The TATA box is the binding site for a transcription factor known as TATA-binding protein. Only after this factor and a number of other factors bind to this complex can RNA polymerase complete the preinitiation complex and initiate transcription. 2. Initiation of transcription only occurs when all transcription factors are aligned along the promoter correctly. Transcription factors are usually proteins that bind to the DNA sequence of the promoter. Once all these factors are in place, RNA polymerase can begin transcription. 3. Transcription begins with the binding of RNA polymerase to the promoter of a gene. he promoter usually includes specific sequences that are recognized by transcription factors, which are proteins that aid in the binding of RNA polymerase to the correct place on the DNA. The transcription initiation complex formed by the promoter, transcription factors, and RNA polymerase signals the start, or initiation, of transcription. 4. The DNA unwinds as the hydrogen bonds between the bases are broken, and produces a small open complex, which allows RNA polymerase to "read" the DNA template and begin the synthesis of RNA. 5. Elongation: Transcription elongation involves the further addition of RNA nucleotides and the change to a transcriptional complex. As the RNA transcript is assembled, DNA in front of RNA polymerase unwinds by breaking the hydrogen bonds between the bases, and transcription continues. As transcription progresses, RNA nucleotides are added to the 3' end of the growing RNA transcript. The DNA template (non-coding) strand is read in the 3' → 5' direction, so the complementary RNA stand in created in the 5' → 3' direction. This produces an RNA molecule from 5' → 3', an exact copy of genetic instructions in the DNA coding strand. Of course the newly made RNA is composed of RNA nucleotides with uracil bases and ribose sugars. Termination: proteins cut the RNA transcript free from the RNA polymerase and the enzyme eventually falls off the DNA. This process produces a pre-mRNA, an mRNA that is not quite ready to be translated. Then it is processed

Splicing More Information

Eukaryotic pre-mRNA contains introns and exons. An exon is the region of a gene that contains the code for producing a protein. Most genes contain many exons, with each exon containing the information for a specific portion of a complete protein. In many species, a gene's exons are separated by long regions of DNA that have no identified function. These long regions are introns, and must be removed prior to translation. Splicing is the process by which introns are removed (Figure below). Sometimes a process called alternative splicing allows pre-mRNA messages to be spliced in several different configurations, allowing a single gene to encode multiple proteins. Splicing is usually performed by an RNA-protein complex called the spliceosome,

X Inactivation (Barr Body)

Females inherit 2 X chromosomes. One X becomes inactivated during embroyic development. That inactivated chromosome X condenses into a compact object known as a Barr body. Which X becomes the barr body is random. - one of the X chromosomes inactivated in every somatic (body)cell. This process results in an embroyo that is a genetic mosaic, some cells have activated X chromosomes and some are inactivated X chromosomes. All cells of female mammals are not identical. - a Barr body is a dak spot of chromatin and can be seen as the outer edge of the nucleus of all somatic cells in the female. Ex. this can be seen in multicolor cats which can only be females. This leads to patches of different colors. Humans might have patches of normal skin and patches of skin that lack sweat glands

Important Concept with Cells

Function dictates form. The shape of the cell affects the function and therefore cells are all different. 1. Nerve Cells are long and thin for long-distance communication (large surface area) 2. Fat Cell - spherical and rounded shape for storage like vacuoles. 3. Long, thin for stretching like smooth muscle cells 4. Sheet-like for large surface area for skin cells, protection and covering

Extranuclear Genes

Genes outside the nucleus, in the mitochondria and chloroplasts - The DNA in these organelles is small and circular anr carries a small number of genes. - they have been linked to several rare and inherited diseases. - the produce of most mitochondrial genes are invovled with energy production, defects in these genes can cuase weakness and deteriation is muscles - Mitchondrial DNA is ONLY INHERITED FROM MOM (its maternal, the father's mitochondrial DNA does not enter the egg during intercourse)

Gene Mutations

Genetic mutations may also occur within the actual gene in a chromosome. These are permanent changes and occur spontaneously and randomly. It can be caused by mutagenic agents like toxic chemicals and radiation. A mutation in a somatic (body cell) disrupts normal cell function. Mutations that occur in gametes are transmitted to offspring and can change the gene pool for the population. MUTATIONS ARE THE RAW MATERIAL FOR NATURAL SELECTION. Some regions are more vulnerable to mutations than others (A::T is more vulnerable than G:C because it only has double hydrogen bonds) 1. Point Mutation: Single base change and it is a base-pair substitution - Silent: no amino acid change and redundancy in code - Missense: change the amino acid - Nonsense: change to stop codon 2. Frameshift (is it more dangerous in the beginning or the end) ~ Shift in the reading frame; changes everything downstream - Insertions: adding bases - Deletions: losing bases

Epigenetic Inheritance

Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence. - Environmental factors can alter gene expressions such as diet, stresss, prenatal nutrition (what your mother ate as well) - not like regular genetics. These changes are reversible and not permanent.

Parts of the Plasma Membrane

Membrane Proteins: proteins can send/recieve signals from outside the cell 1. Intergral Protein: nonpolar regions hat span the hydrophobic interir of the membrane. This is like channel or pumps. 2. Peripheral Proteins are loosely bound to the surface of the membrane. 3. Cholesterol molecules are embedded in the interior of the bilayer to stabilise the membrane and its fluidity. 4. Glycolipids: carbohydrates chain covalently bonded to lipids and serve as cell recognition markers. 5. Glycoproteins: carbohydrate chain covalently bonded to proteins for cell recognition and to help neighboring cells interact. (for cell recognition, carbohydrates check for tags and destroy them otherwise) 6. Transport/Channel Proteins: proteins that carry substances across a membrane or allow molecules to pass through a channel. 7. Cytoskeleton Filaments: long protein chains that help cells hold their shape. Organelles and other molecules can travel along with this as a highway.

Pleitropy

Most genes are pleiotrophic or have multiple phenotypic effects. - one gene affects more than one phenotypic character - one gene affects more than one trait - Ex. in a garden, the gene that determines flower color also determines the outer coating. - the ability of one gene to have multiple affects - causes some diseases such as Sickle Cell and Cystic Fibrosis

Nitrogenous Bases; Base Pairing Rule

Purine: Double Carbon Ring Structure 1. Adenine 2. Guanine Pyrimidine: Single Ring Carbon Structure 1. Cytosine 2. Thymine 3. Uracil (replaces thymine in RNA) Pairings - A::T (double hydrogen bonds) - G:::C (triple hydrogen bonds)

Ribosomes

Site of protein synthesis; some are freely suspended in the cytosol and are associated with protein production for the cell's own use. Ribosomes attached to the ER are meant for export out of the cell.

Multiple Alleles

Some traits have multiple alleles which influence the genotypic and phenotypic makeup of that trait - the traits are controlled by 3 or more alleles of the same gene. - An example is human blood type. An individuals' blood can be determined from Ia and Ib, or i (recessive allele) - there are MORE THAN two allele forms.

Genes and the environment

The environment can alter the expression of genes. In fruit flies, the mutation for vestigial wings can be altered by the temperature of the environment - Many human diseases have a multifactorial basis. This is when there is an underlying genetic component with a significant environmental influence. Examples include heart disease, canccer, alcoholism, and more. * nature vs. nurture for intelligence

Crossover and Linkage Mapping

The farther apart the chromosomes are on one chromosome, the more likely they will be seperated from eachother during meiosis bcause of a crossover event that will occur between them. - Where the crossover and recombination occurs, is the chiasma, the physical bridge built around the point of exchange - the probability that genes on the same chromosome will segregate as a unit is a function of the DISTANCE between the genes known as map units. The closely the genes are, the less likely they are to cross over. - one map unit distance on a chromosome is the distance within which recombination occurs one percent of the time. The rate of crossover gives us no information about the actual distance of genes, but it tells us the order of the linked genes on the chromosome. This can be drawn by recombination frequencies to construct the linkage map.

Dibhybrid Cross

The inheritance of two distinct character traits. Like flower color and flower height. Cross can produce four gametes for each individual . - Each gamete must have one allele for each gene, to find the gametes FOIL the parent's alleles individually. If you cross two heterozygotes, you will get a 9:3:3:1 phenotypic ration (D/D, D/R, R/D, R/R)

Where does Energy come from for Replication and DNA Polymerase?

The nucleotides arrive as nucleosides. These are DNA bases with three phosphates. They are bonded by the enzyme DNA Polymerase 3 and 2 come off for energy since it is an endergonic building reaction to make the complementary strand.

Ethic Issues with Biotechnology

There could be saftey issues of the possiblity of the modified hormone or molecule to find its way into the human body and affect humans negatively. - Ethical issues that arise from modern biotechnologies include the availability and use of privileged information, potential for ecological harm, access to new drugs and treatments, and the idea of interfering with nature - Gene flow from all cultivated plants to wild relatives and to traditional landraces may be a problem because cultivated plants are suited for specific conditions, including traits that may not be beneficial in wild plants. In addition, gene flow from all cultivated plants can reduce genetic diversity in landrace or wild populations. - may develop a resistance of something

Peroxisomes

They contain catalase which converts hydrogen peroxide (h2O2) a waste product of respiration, into water with the release of oxygen atoms. They also detoxify alcohol in liver cells. Contains enzymes that transfer H from substrates to oxygen to produce water.

Polygenic Inheritance

This indicates that more than 2 (or more) genes itneract in order to produce a single phenotype or trait - A trait is the produce of multiple genes - Skin color and eye color and height are influenced by the additive effects of 3-6 genes in a single character. Each of these genes result in the formation of a certain amount of pigment called melatonin. The more genes expressed, the darker the skin is. - MULTIPLE GENES HAVE ONE EFFECT - Ex. AaBBCc (for height, you inherit one allele for each of the height genes) -

Nondisjunction

This is an incorrect number of chromosomes because the chromosomes did not separate properly during meiosis. This is an error that occurs when homologous chromosomes fail to separate as they should - one gamete receives two copies of the same type of chromosomes and one could receive none. The resulting zygote could have an abnormal number of chromosomes. - An example is Down Syndrome also known as Trisomy 21. These are three chromosomes on the 21st pair. - this is due to problems in the meiotic spindle which causes errors in daughter cells. Homologous chromosomes do not separate properly during Meiosis I. Sister chromatids do not separate properly during Meiosis 2. This all results in too many or too few chromosomes which can lead to cancer or a mutation or a chromosomal abnormality. 1. Trisomy: three copies of the chromosome 2. Monosomy: one copy of the chromosome

Test-Cross

This is when you cross-breed the dominant (A_ unknown genotype which could be homozygous dominant or heterozygous) with a homozygous recessive to determine the identity of the unknown allele. - If the individual being tested is hybrid, one-half of the offspring can be expected to show the recessive trait. If any offspring shows the recessive trait, the unknown parent has to be a hybrid - If the individual being tested is the homozygous dominant, all offspring will be Bb and show the dominant trait.

Fact about Traits

Traits are inherited as discrete units. For each characteristic, an organism inherits two alleles, one from mom and one from dad, this creates a diploid organism. Inherits two sets of chromosomes, 1 from each parent

Fact

Traits come in alternative versions. Different alleles vary in the sequence of nucleotides at the specific locus of a gene. Purple flower allele and white flower allele are different version of the gene on homologous chromosomes at the flower color locus.

Human Blood Type

Type A: IA, IA or IA, i Type B: IB, IB, or IB, i Type AB: IA, IB Type O: i, i Antigens: for each blood type antigens, are ID tags found on the surface of red blood cells. Type A has Type-A antigens, Type B has Type B antigens, Type AB has both antigens, and Type O has no antigens so it is the universal donor. - Antibodies: these kill the unknown cells, cause blood to clot which might kill you. A: Anti-B antibodies B: Anti-A antibodies AB: no antibodies, makes it the universal receptor O: anti-A and anti-B antibodies.

Law of Dominance

When two organisms, each homozygous (pure) for two opposing traits are crossed, the offspring will be hybrid (carry two different alleles) but will only exhibit the DOMINANT trait. The trait remains hidden is known as the recessive trait. Recessive allele has a gene that makes it a non-functional protein. 2 Organisms can have the same phenotype but a different genotype. - In parents that are homo for contrasting traits, only one form of the trait will appear in the next generation. - Principles of Dominance: one factor of a pair may mask the effect of another. - DOMINANT allele is fully expressed.

Monohybrid Cross

a cross in which only one characteristic is tracked, inheritance of a single characteristic like flower color or seed color Example: Plant Height (tall vs. short) P Generation: TT * tt F1 Generation: Tt F2: TT, Tt,tt (3:1 phenotypic ration)

Microfilamets

assembled from actin filaments and help support the shape of the cell 1. allow animal cells to form cleavage furrow when they divide

Cytoskeleton

complex mesh of protein filaments that extend throughout the cytoplasm. It consists of microtubules and microfilaments. Has several functions 1. maintains cell's shape 2. controls the position of organelles within the cell by anchoring them to plasma membrane 3. involved with the flow of cytoplasm ( helps things move inside the cell) 4. Anchors cell in place by interacting with other elements

Theory of Endosymbiosis

eukaryotic cells once emerged when mitochondria and chloroplast, once-free living prokaryotes, took up permanent residence inside other larger cells. Mitochondria and chloroplast evolved from small prokaryotic organisms being engulfed by larger ones. Evidence for this includes both mitochondria and chloroplast have their own DNA (similar to that of a bacteria), have a double membrane, can produce their own ribosomes, and they can reproduce through binary fission like bacteria

Golgi Apparatus

flattened membranous sacs stacked next to eachother. There are two sides reffered to as a cis face (recieving department near Rough ER) and a trans face (shipping department - away from ER). Processes and packages proteins into vesicles. Produces secretory vesicles.

Microtubules

hollow tubes made of protein tubulin that make up cilia, flagella, and spindle fibers - cilia and flagella consist of 9 pairs of microtubules organized around 2 singlet microtubules and are used to move cells around. Flagella are not the same in Prokaryotes. - Spindle fibers help separate chromosomes during cell division in mitosis and meiosis.

Endoplasmic Reticulum

is a membraneous system of channels and flattened sacs that traverse the cytoplasm and account for more than half the total membrane in eukaryotic cells. 1. Rough ER - has ribosomes studded throughout it and folds proteins/modifies proteins. Channels proteins to transport vesicles that can bud off because they are made of the same substance. Involved in membrane production. 2. Smooth ER - no ribosomes on it. - Assists in the synthesis of lipids such as steroid hormones like sex hormones - Stores Calcium ions in muscle cells to facilitate normal muscle contractions - Detoxifies drugs and poisons from the body through liver cells - metabolizes carbohydrates

Vacoules

membrane bound organelles used for structure and storage. Large vesicles derived from ER and Golgi. Freshwater protists have contractile vacoules to pump out excess water. Food vacuoles are formed by phagocytosis of foreign material.

Centrioles, Centrosomes, and the Microtubule Organizing Centers

nonmembraneous structures that lie outside the nuclear membranes. They organize spindle fibers needed for cell divison Two centrioles oriented at a right angle to eachother make a centrosome consisted of 9 triplets of microtubules. Plants have MTOC.

Prions

not cells, nor are they viruses. - they are misfolded versions of a protein normally found in the brain. - If prions get into a normal brain, they cause all the normal versions of the protein to misfold in some way - infectious and cause severe brain diseases such as Cruetzfeldt-Jakob Disease - all known diseases are fatal

Non-Mendelian Inheritance

refers to any pattern of inheritance in which traits do not segregate in accordance with Mendel's laws (ex. incomplete dominance, codominance, multiple alleles, polygenic traits, sex-linked traits) - Mendelian principles apply to traits determined by a single gene for which there are only two alleles.

Endomembrane System

regulates protein traffic and performs metabolic functions in the cell; The path of a protein - Ribosomes (made in the nucleolus) to the cytoplasm or rough ER to create protein - Rough ER folds and modifies them into the secondary or tertiary structure and for export - transport vesicle ( takes to the Golgi) - Golgi Bodies sorts, tags, ships them - Secretory Vesicle - take them to the plasma membrane to fuse and leave the cell.

Punnet Square

shows the different combinations of alleles that can result.

recombination frequency;

the percentage of recombinant offspring among the total - this is the recombinant (or the traits that the parents don't have and are due to crossover) over the total number of offspring.

Bacteriophages

viruses that infect bacteria. This can reproduce in two ways. It has a capsid head that holds the nucleic acid which can be RNA or DNA. It has a long sheath body, spikes used for piercing into the cell membrane. 1. Lytic Cycle:A very selective virus attaches to a host cell and binds to a receptor the cell has, gives access to attach. Virus injects its DNA or RNA into the cell. The cell takes the genetic material and follows its instructions. Starts making copies of the DNA which causes the membrane to rupture or lyse (burst) causing the virus to affect other cells. OR The bacteriapahge enters the host cell, takes control of the cell's machinery, replicates itself, and causes the cell to burst, releasing new generation of infections phage viruses. These viruses kil thousands of cells in the same manner. This is a virulent phage. 2. Lysogenic Cycle: The bacteriophage injects its DNA, however the genetic material stays hidden. When the host cell makes new cells, it replicates its own DNA and the viral DNA. These leads to daughter cells making more daughter cells with its own DNA and the viral DNA. This is bad if it then goes to the lytic cycle because all those cells can start making viruses. OR viruses replicatie without destroying the host cell. The virus becomes incorporated into a specifc site in the host's DNA and remains hidden or dormant. Replicates with the host cell's DNA. Some point, environmental triggers cause the prophase (calm viral DNA) to switch to lytic cycle.