A. Heredity (8%)

  1. Meiosis and gametogenesis
  2. Eukaryotic chromosomes
  3. Inheritance patterns

B. Molecular Genetics (9%)

  1. RNA and DNA structure and function
  2. Gene regulation
  3. Mutation
  4. Viral structure and replication
  5. Nucleic acid technology and applications

JFMcL. Although we talked about bacterial transformation and recombinant DNA, we did not actually perform this lab. Review the steps of the process by going to the following website below:

Below is a good movie that reviews Griffith's discovery of transformation as well as the steps needed to carry out the process in the lab.

The organization of a chromosome confused me when we were covering this topic, but it follows these steps:
1.) Nucleosomes (10-nm fiber)- These are like beads on a string and are composed of DNA and histone molecules
external image nucleosome.gif
2.) 30-nm fiber- When the string of nucleosomes coils to form a chromatin
external image f05-13-0.jpg
3.)Looped Domains (300-nm fiber)- Folding of the 30nm fibers during during prophase
external image ch8f18.gif
4.) Metaphase Chromosome- The chromatin folds even further which results in a compacted chromosome
external image images?q=tbn:ANd9GcQ0CDMjrbR8H9gqAJrMriE86PKj0VefJMgIAw1Bi6_5nXc1Fn_kZ0JpLMB4-Q

Here's a video I found that explains the difference between chromosomes, chromatin, and chromatids. I always had a hard time remembering which one was which. This video is a little long, but very helpful. It also goes into transcription, translation, and replication.


This video is about 7 minutes, and I think it provides a good review of DNA replication in general. The main idea that always confused me about DNA replication was the 5' and 3' ends, and this provides a good illustration and explanation of that process. It also goes over leading/lagging strands and Okazaki fragments, DNA polymerase III, and other enzymes and molecules involved with replication. The video makes it pretty easy to understand.

I didn't understand the life cycle of a virus.
external image 450px-Life-cycle.jpg
1. Mature virus binds to the outside of a cell. This binding is mediated by the glycoproteins on the surface of the virus, and cell receptors on this surface of the cell.
2. The virus membrane (the envelope) fuses with the cell, and the insides of the virus are released into the cytoplasm of the cell.
3. Depending on virus type, various stages must occur with its genome. HIV uses RNA for its genome, and must reverse transcribe it into DNA and integrate it in the cell's genome before proceeding. HSV's genome must circularize and enter the nucleus.
4. Virus proteins are produces in stages, typically called immediate early, early, and late. The first proteins made are typically regulatory proteins; the last proteins made are typically structural proteins. Genomic copies are often made last.
5. New virus particles assemble. This is typically just the core, and does not include the envelope (outer membrane).
6. The virus is transported to the outer membrane of the cell, and buds, picking up its envelope (membrane). Some viruses (like HSV) bud inside of the cell first, and then are transported to the membrane.
7. Some have a maturation step, which involves the cleavage of proteins.

I often get confused when it comes to the terms for complex inheritance:

Incomplete dominance- F generation appears between the phenotypes of the two parents (Red and White P Generations - Pink F generation)

Codominance: two alleles affect the phenotypes in separate distinguishable ways

(AB Blood type, Roan Cattle)

Multiple Alleles: there are more than two possible alleles for a gene

(Fur colors in many animals, blood type in humans)

Polygenic Inheritance: traits that are controlled by more than one pair of alleles, resulting in a wide range of phenotypes

(Most traits in humans; height, skin color, eye color)

Epistasis: when the expression of one gene interferes with the expression of another

(Albino gene)

Pleiotropy: a single gene has multiple phenotypic effects

(Sickle-cell disease)

SRF- Operons were probably my least favorite topic, and that's why I forced myself to do them. There were a lot of really helpful diagrams on this site so I attached the link.

Prokaryotic cells have linear sequences of DNA called operons. The operon is composed of a promoter sequence, followed by an operator gene, followed by one or more structural genes that act as blueprints for proteins. The operon is controlled by a regulator gene found elsewhere on the chromosome.
Operons can be inducible (turned on by a substrate) or repressible (turned off by a product).


RAMThis is just something extra I found to supplement the operon post and provide a bit of a visual aid. I had a LOT of trouble trying to understand them and these two videos made a huge difference, plus provided me with an essay example
keep in mind these videos provide examples for the Inducible operon only =)

KGT I know that we all had a lot of trouble with Chi Squares. I found a really simple tutorial online that walks you through the basic steps of creating a Chi Square and interpreting the data. It only takes a few minutes but is definitely worth checking out.

Basically, the purpose of a Chi Square is to compare the observed distribution of a population with the hypothesized distribution of a population. It can be used to see how close your actual data is to your hypothesis.

JM:Types of Mutations
A substitution is a mutation that exchanges one base for another (i.e., a change in a single "chemical letter" such as switching an A to a G). Such a substitution could:
  1. change a codon to one that encodes a different amino acid and cause a small change in the protein produced. For example, [[@/evolibrary/glossary/glossary_popup.php?word=sickle+cell+anemia|sickle cell anemia]]is caused by a substitution in the beta-hemoglobin gene, which alters a single amino acid in the protein produced.
  2. change a codon to one that encodes the same amino acid and causes no change in the protein produced. These are called silent mutations.
  3. change an amino-acid-coding codon to a single "stop" codon and cause an incomplete protein. This can have serious effects since the incomplete protein probably won't function

Insertion Insertions are mutations in which extra base pairs are inserted into a new place in the DNA
Deletion Deletions are mutations in which a section of DNA is lost, or deleted.

Frameshift Since protein-coding DNA is divided into codons three bases long, insertions and deletions can alter a gene so that its message is no longer correctly parsed. These changes are called frameshifts.
For example, consider the sentence, "The fat cat sat." Each word represents a codon. If we delete the first letter and parse the sentence in the same way, it doesn't make sense.
In frameshifts, a similar error occurs at the DNA level, causing the codons to be parsed incorrectly. This usually generates truncated proteins that are as useless as "hef atc ats at" is uninformative.
There are other types of mutations as well, but this short list should give you an idea of the possibilities

JMcL. Insertions and deletions can both give rise to frameshift mutations.

I couldn't remember gene splicing so this gives a brief explantation.

After today's review I was not totally clear on gametogenesis.
Gametogenesis is the overall process of gamete production. In animals, there are two types of gametogenesis: spermatogenesis, which is sperm production, and oogenesis, which is production of the ovum or egg.
The sperm cell, or spermatozoon, is highly specialized for travel, to find an egg to fertilize. Most spermatozoa have flagella that allow them to swim. All spermatozoa derive from immature premeiotic stem cells called spermatogonia, which reproduce mitotically. Some spermatogonia begin to differentiate into primary spermatocytes, which then undergo the first meiotic division. This division produces two haploid secondary spermatocytes from each primary spermatocyte. Secondary spermatocytes undergo meiosis II, producing two spermatids from each secondary spermatocyte. Overall, therefore, each primary spermatocyte divides by meiosis to produce four haploid spermatids.
The ovum, or egg, must store large quantities of materials needed for the development of the new individual after fertilization. The cell that produces ova is called an oogonium. Oogonia reproduce by mitosis, although some differentiate into primary oocytes, which begin meiosis. These oocytes only get as far as prophase I, at which point they stop the cycle temporatrily. The oocytes stay in this dormant state until they are about to be ovulated. In humans, the prophase arrest occurs before the female is even born, and the oocytes stay dormant until at least puberty, which is approximately 12 years later. Prior to ovulation, the primary oocyte completes meiosis I, producing two haploid cells. The cell that receives most of the cytoplasm is called a secondary oocyte; the cell receiving little is called a polar body. The secondary oocyte undergoes meiosis II (often the polar body does as well). Once again, cytokinesis is unequal, with one cell receiving almost all of cytoplasm. This cell becomes the ovum; the other cell, which receives little cytoplasm, is another polar body. Oogenesis, therefore, produces one haploid ovum and three haploid polar bodies from each primary oocyte. Only the ovum is capable of being fertilized; the polar bodies eventually die. Oogenesis works this way so that important materials can be stockpiled more easily for later in development.
(paraphrased from

Looking at the genetics essay I don't remember the scientists nearly as well as I probably should. I shortened it from the original so you wouldn't have to be reading for an hour, I thought this was the most essential information.
The link below is a more detailed description of some of their important experiments in case you still don't remember.

04/08/1866 Gregor Mendel Gregor Mendel, an Augustinian monk, became known as the "father of genetics." This is for many good reasons, starting with his findings after crossing abnormal pea plants. First, he self-pollinated pea plants (P generation.) Next, he cross-pollinated the P gen., and it became known as the F1 generation. After that, the F1 gen. self-pollinated, and became known as the F2 generation. His results after doing this were way ahead of his time. Next, we'll examine Mendel's findings/ contributions. Mendel found that traits were inherited in certain ratios, and that dominance and segregation played roles in the development of traits.The Law of Segregation stated that when gametes are produced, copies of genes separate so that each gamete only receives one copy. The Law ofInd. Assort. stated that there was no relation between how traits were inherited. They are inherited independently.
04/10/1928 Frederick Griffith Griffith extensively researched the bacteria which could cause pneumonia. He realized that seemingly harmless strains of a bacteria (R-strain) when mixed with a harmful S-strain, would be potentially fatal. His first experiment was performed on mice, which he injected with a heated form of the S-bacteria. This mice lived on! However, when he injected a mixture of the R-strain and heat-killed S-strain into the mice, they ended up dying. 04/10/1928 Frederick Griffith Cont. This happened because when mixed, the R-strain was "transformed" into the S-strain by picking up the S-strain's DNA.Griffith's major contribution to the world of genetics was in his finding of bacterial transformation
04/10/1949 Erwin Chargaff Chargaff's Rules, as they later became known, consisted of 2 parts. The first was that in DNA, the amount of guanine = the amount of cytosine, and that the amount of adenine = the amount of thymine units. The second part of Chargaff's Rules is in the fact that different species have different amounts of A+T or G+C.
04/08/1952 Maurice Wilkins and Rosalind Franklin These two geneticists set out to answer the unknown question of what DNA looked like. To do this, they'd use a technique called X-ray crystallography.Through many trial and errors, Franklin and Wilkins figured out that the sugar-phosphate backbone of DNA is located on the outside of the molecule, verses where others thought it was located (inside). Another discovery made was in the structure of DNA itself. It was found that DNA had two strands, verses the previously thought 3 strands.
04/10/1952 Alfred Hershey and Martha Chase These two scientists performed a series of experiments to confirm that DNA was the genetic material. To do this, they made radioactive phage DNA and infected bacteria. When they separated the phage and bacteria by centrifuging the mixture, the radioactivity went with the bacteria. Since the phage inject their DNA into the bacteria, then this proved that the DNA must have been the genetic material, not the protein.
04/10/1953 James Watson and Francis Crick Rosalind Franklin, who had passed away because of cancer, also helped Watson and Crick to determine the structure of DNA. They usedFranklin's X-ray "pictures" to determine that the shape of DNA was a double helix. They received the Nobel Prize for that discovery.

Nondisjunction is an important alteration that can occur in chromosomes. It often results in odd chromosomal numbers, or some disorders. Nondisjunction is when the chromosomes in a homologous pair do not separate correctly during meiosis 1, or the sister chromatids do not separate correctly during the meiosis 2 phase.

Nondisjunction causes one of the gametes to receive too many, or too few chromosomes, which can be very harmful to the offspring which will later develop from the gamete. An incorrect number of chromosomes is known as aneuploidy.

Trisomic is when the fertilized egg receives three copies of the chromosomes
Monosomic is when the fertilized egg receives only one copy of the chromosomes
Polyploidy is when an organism has more than two complete sets of chromosomes, and it is virtually unheard of in animals, as it would be nearly impossible for the organism to live

Klinefelter's Syndrome and Down Syndrome are aneuploid conditions, that result from having an extra chromosome. For Klinefelter's, the chromosome is an extra X chromosome (a sex chromosome). For Down Syndrome, there is an extra chromosome 21, which gives the syndrome another name of Trisomy 21.

I was very confused on the regulation of gene expression. Someone above already reveiwed gene expression in prokaryotes so heres a review of gene expression in eukaryotes.
  • The expression of eukaryotic genes can be turned off and on at any point along the pathway from gene to functional protein. In eukaryotes these changes are usually permanent.
  • The more tightly bound DNA is to its histones, the less accessible it is for transcription
  • This relationship is governed by two chemical interactions:
1. DNA methylation which is the addition of methyl groups to DNA. It causes the DNA to be more tightly packaged, thus reducing gene expression.
2. In histone acetylation, acetyl groups are added to amino acids of histone proteins, thus making the chromatin less tightly packed and encouraging transcription.
*Notice that methylation occurs primarily on DNA and reduces gene expression, whereas acetylation occurs on histones and increases gene expression
This website below describes and plays through an animation of the formation of a transcription initiation complex which also plays a key role in gene expression:

Sometimes I can't remember between the difference between autosome and allosome chromosome. Autosomes are chromosomes that are NOT sex chromosomes, meaning only the other 22 pairs of chromosomes. Allosomes are sex chromosomes, which can either be X or Y chromosomes.
Protein Synthesis

Transcription- When the DNA code is transcribed onto the mRNA in the nucleus.
Translation- When the mRNA is out in the cytoplasm and is being edited by the Introns and Exons. It also includes the whole process that occurs at the ribosome.

This diagram briefly displays what occurs in the processes of Transcription and Translation.

external image biotrans.gif

When the mRNA is at the ribosome, it goes through the three steps of Initiation, Elongation, and Termination.

Initiation- The first codon (set of 3 nucleotides) signals the ribosome that it the Translation Process is about to begin. During initiation, the smaller piece of the ribosome attaches to the larger portion of the ribosome.
Elongation- Each codon codes for a separate corresponding tRNA which has a specific amino acid attached to it. The tRNA molecules will attach to the mRNA at the correct location and attach their amino acid to the existing chain of amino acids. This process will continue to occur until Termination occurs.
Termination- The final codon is a termination codon which causes the long chain of amino acids to be released into the cytoplasm. The final codon will either have the code of UAA, UAG, or UGA. These are the only three codons which code for "stop."

Below is a diagram that displays the elongation process.

external image 404_113_q10.jpg

While doing the essay test, I realized that it is definitely important to understand Alfred Hershey and Martha Chase's experiment with bacteriophages. I found this animation that explains the experiment excellently, it is definitely beneficial to check it out, especially if you need help with the essays!
One important thing to note, this experiment helped scientists determine that DNA and not proteins carried genetic material. Enjoy!

JFMcL. Good work on info for the essays!

This animation goes through DNA replication and the different enzymes involved. I found this very helpfule while studying.

There were a few questions on the diagnostic test about the enzymes involved in DNA replication, and I realized I needed to go over that. I know Maddie just posted a video about it but I personally like studying from diagrams, so I thought this was a pretty good one.


tRNA transfers amino acids from the cytoplasm to a ribosome, which then incorporates the amino acid into a growing polypeptide chain
- Each type of tRNA is for a specific amino acid: at one end it binds the amino acid and at the other end it has the nucleotide triplet anticodon, which allows it to pair with a codon (triplet) on mRNA
- mRNA is read one codon at a time and one amino acid is added to the chain for each codon read
- Wobble is the relaxation of base-pairing rules between the third base of a codon and the complementary anticodon base
- Ribosomes have 3 binding sites for mRNA:
P site: holds the tRNA that carries the growing polypeptide chain
A site: holds the tRNA that carries the amino acid that will be added to the chain next
E site: exit site for tRNA

This video does a great job explaining the enzymes and Okazaki fragments during transcription - plus he has a cool accent! AND it's a really short video

I often forget the key differences between mitosis and meiosis, and questions asking about how many chromosomes are left in the daughter cells after division always screw me up.
The DNA is replicated before both mitosis & meiosis, but meiosis has two stages of cell division: meiosis I and meiosis II.
The result of meiosis is four genetically different daughter cells, each with half as many chromosomes (haploid number) as the parent cell.
There are a few unique processes in meiosis I that do not occur in mitosis:
In prophase I-
1. Synapsis occurs, forming tetrads (joining of homologous chromosomes along their length)
2. Tetrads undergo crossing over (DNA from one homologue is cut and exchanged with an exact portion of DNA from another homologue- increases genetic variation) these areas are called chiasma
In metaphase I-
1. Paired homologous chromosomes (tetrads) line up at the metaphase plate rather than individual replicated chromosomes
2. Independent assortment of chromosomes: when they are lined up at the metaphase plate, they can pair up in any combination
In anaphase I
1. Duplicated chromosomes of each homologous pair move toward opposite poles, but the sister chromatids of each duplicated chromosome stay attached. In mitosis the chromatids separate

All of this information can be found in the review book.

I realized I needed to review some of the applications of DNA technology
  1. Diagnosis of Disease- If a virus's DNA or RNA is know then the plymerase chain reaction can amplify a patient's blood samples and detect even small traces of the virus
  2. Gene Therapy- This holds a lot of potential for treating disorders traceable to a single defective gene like cystic fibrosis
  3. Production of Pharmaceuticals- gene splicing and cloning can be used to produce large amounts of particular proteins in lab
  4. Forensic Applications- DNA samples can be taken from a suspect and compared to those that were found at the crime scene
  5. Environmental Cleanup- Scientists engineer metabolic activities into microorganisms to help clean up heavy metals
  6. Agricultural Applications- Certain genes that produce desirable traits have been inserted into crop plants to increase producivity like frost resistance

I know that someone wrote a short explanation of regulation of gene expression in eukaryotes above, but this was a topic that I was very unclear on when writing my Genetics essays Tuesday night. I find diagrams to be helpful because sometimes it is hard to visualize a process in your head.

DNA Methylation/Histone Acetylation
  • The depiction of the tightly packed heterochromatin vs. the loosely packed euchromatin here gave me a much better mental image of chromatin structure. Previously to writing the essay about eukaryotic gene expression, I did not know that heterochromatin is not able to be transcribed because it is too tightly packed. This helped me to understand why DNA methylation and histone acetylation are needed to loosen up the structure of the heterochromatin so that its genes can be expressed.
external image epiq_pis.jpg

RP. After that essay on genetics, I really wish I remembered scientists and their contributions a little better. So here is a short summary on the scientists that Sam and I studied, Watson and Crick!
Also, here's a short video actually featuring both of them. And it's in their favorite place, the bar!

When I was looking over my notes of the discoveries in DNA, I noticed that I did not have a lot written down for Barbara McClintock. She discovered jumping genes, also know as transposable genetic elements, which are genes that are able to move from one place to another in an organism's genome. This website does a good job of explaining her experiment and what jumping genes are.

I always thought this was an interesting topic and i dont think anyone mentioned it yet, cloning DNA genes. Theres a good picture in the review book on page 135 but i found this similar one online
external image 22487-004-5347D587.gif
1.) identify and isolate the gene of interest and a cloning vector(the plasmid, thats usually bacterial, that will carry DNA sequence to be cloned)
2.) cut both the gene of interest and the vector with the same restriction enzyme (provides matching sticky ends)
3.) join the two peices of DNA (forms recombinant plasmids, the human DNA fragments are sealed into the vector using DNA ligase)
4.) get the vector carrying the gene of interest into a host cell (plasmids taken up in the bacterium by transformation)
5.) select for cells that have been transformed (this can be done by linking the gene of interest to an antibiotic resistance gene or a reporter gene

Good Review for the process of DNA replication

Operons are my weakness. I found a good video online that explains how they regulate genes.

Here are some of the scientists and their experiments that were not mentioned.

Avery, MacLeoud, McCarthy
- Were able to isolate DNA as the agent that caused Griffith's "transformation"
- They took extracts from heat killed smooth bacteria cells and used DNAase to remove the DNA in the cells. This is then mixed with rough bacteria and injected to mices. The result was that the mices were alive.
-They then took on the same experiment but rather than using DNAase, they used protease(to digest proteins). The reuslt was that the mices died.
-This supports that the DNA is the genetic material and also the factor that caused Griffith's transformation.

Here is a video animation describing Messelson & Stahl's Experiment


My group struggled a lot with the gel electrophoresis Lab, and just rereading expected results and sample labs hasn't really helped me too much to understand it. However, I found this interactive virtual lab and it has really helped me to understand it. If anyone else is having a problem with it, check it out.

When going through my labs I remembered that I had trouble with the one having to do with cutting and recombining the DNA. The concept of that was a little tricky also. This diagram is a simple explanation on how it works.
external image restriction%20enzymes.jpg

I never really got to know and remember all the levels of organization for chromosomes. Here is a picture that helps me to visualize how DNA is packed and winded into a chromosome.
external image pierce_11_5_large_2.jpg

The essay the other night reminded me that the regulation of gene expression can occur at any step in eukaryotes and involves operons in prokaryotes, but the processes are very detailed and specific. This site is extensive but it is related to our AP Bio book and it goes over regulation in both types of cells, I found it very informative in reminding me of these processes.

For some reason, I always had a hard time doing crosses with blood type. These two charts cleared up both the cross itself and the blood types created by each genotype.
external image File.aspx?f=2C37F6FF-419F-4545-8230-D4F0682CE493


I was having some trouble understanding the Hardy-Weinberg equations, there for I investigated. In investigating, I found this extremely good video, encompassing the gene pool, equations, alleles, and processes involved in the equations step by step. Also the video encompasses how to solve the problems.

Happy Studying!

JJS During the genetics unit, we spent a lot of time learning about different genetic diseases. Since then, I have forgotten most of them. As began to study these diseases again, I was shocked by the amount and complexity of them. I thought I would be able to copy and paste a simple table for all of us to review, but instead I found this:

JJS A common multiple choice question I have come across in the diagnostic tests includes:
The rule of multiplication: When calculating the probability that two or more independent events will occur together in a specific combination, multiply the probabilities of each of the two events. Thus, the probability of a coin landing face up two times in two flips is 1/2x1/2=1/4. If you cross two organisms with the genotypes AABbCc and AaBbCc, the probability of an offspring having the genotype AaBbcc is 1/2x1/2x1/4=1/16.
(bio review book)

JJS This definition, listed below the rule of multiplication, I had never hear of before...
The rule of addition: When calculating the probability that any two or more mutually exclusive events will occur, you need to add together their individual probabilities. For example, if you are tossing a die, what is the probability that it will land on either side with 4 spot or the side with 5 spots? 1/6 + 1/6 = 1/3
(bio review book)

I know I still dont fully understand the operon. I found a really helpful and simple video that helped me understand the concept a lot better
This video is on the LAC operon
This is another McGraw/Hill video (I posted another on the Hershey and Chase experiment), I find these videos to explain whatever topic they are describing very well.

Here's a website on Chi-square analysis! This is actually a mathematic web site, but I thought it explained the concept well. There are also a few examples, which really help cement the information

The tables on the second and third pages of this website have extremely good information on the differences between asexual and sexual reproduction. This seems to be a common topic for ap questions so make sure you're familiar with the advantages and disadvantages!

  • Codon recognition: anticodon of tRNA hydrogen binds to codon of mRNA
  • § tRNA then enters A site,
  • § Requires elongation factor and GTP hydrolysis
  • § Peptide bond formation catalyzed by ribosome (by ribozyme)
  • § Joins polypeptide extended from tRNA in P site to the amino acid carried by the tRNA in the A site; transfer polypeptide from tRNA in P site to tRNA in A site
  • § tRNA in A site is translocated to P site; empty tRNA in P site translocated to E site, then exits the ribosome
  • § mRNA moves through the ribosome in one direction
  • § Energy supplied by GTP hydrolysis
  • Peptide bond formation
  • Translocation


I keep forgetting how certain genetic disorders are inherited, and it seems like there are always questions on certain ones, so hope this helps! This website was pretty helpful with genetic disorders.

Autosomal Recessive:
cystic fibrosis
sickle-cell disease

Autosomal Dominant:

Duchenne muscular dystrophy


Epigenetics is the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence. It refers to functionally relevant modifications to the genome that do not involve a change in the nucleotide sequence. Examples of such changes are DNA methylation and histone modification, both of which serve to regulate gene expression without altering the underlying DNA sequence.

Interesting article about epigenetics and fruit flys!
Basically the eye color can change from white to red if there is a brief change in temperature of the embryo.
This would have been a perfect example for a certain essay...