Introduction

Linker Histones

(e.g. H1) occur between core octamers

Genome organization and gene expression (levels): Chromosome position in nucleus 1. Location 2. Affect gene transcription by doing what?

1. near the periphery, or internal 2. chromosomes are compacted into "territories" that affect gene transcription

Translation: 1. Start Codon 2. initiator tRNA 3. Why do Eukaryotes use Kozak consensus sequence? 4. ribosomes

1. needs a start codon "AUG" 2. a special methionine tRNA that binds to the initiation codon AUG that forms part of the initiation complex at the start of mRNA translation. 3. to correctly initiate translation 4. Made of rRNA and rprotein, rRNA is made constantly (housekeeping gene)

Genome organization and gene expression (levels): Chromatin: 1. define 2. Name two modes and define 3. Remodeling complexes can do what?

1. region of DNA wrapping around histone core octamer repressed DNA located in that region 2. can switch between two modes: heterochromatin - chromatin is condensed and suppresses transcription euchromatin - chromatin more open and allows for gene activation 3. remodeling complexes can change nucleosome positions

DNA sequencing diversity (calculation): How many nucleotide differences between you and your neighbor?

6,000,000 1 difference in 1000 3,000,000 nucleotides per set (n) 2 sets per person (2n)

Nucleosome: 1. define 2. form what complex?

DNA + Histone= Nucleosome they are condensed to make chromosome

Hershey-Chase Experiment

Studied bacteriophage, or viruses that attack bacteria. The phages used were simple particles composed of protein and DNA, with outer structures made of protein and inner core consisting of DNA. To establish whether the phage injected DNA or protein into host bacteria, they prepared two different batches of phage. In each batch, the phage were produced in the presence of a specific radioactive element, which was incorporated into the macromolecules (DNA and protein) that made up the phage: 1. One sample was produced in the presence of S35 a radioactive isotope of sulfur. Sulfur is found in many proteins and is absent from DNA, so only phage proteins were radioactively labeled by this treatment. 2. The other sample was produced in the presence of P32 a radioactive isotope of phosphorous. Phosphorous is found in DNA and not in proteins, so only phage DNA (and not phage proteins) was radioactively labeled by this treatment. each phage batch used to infect a different culture of bacteria. After infection occurred, each culture was whirled in a blender, removing any remaining phage and phage parts from the outside of the bacterial cells. Finally, the cultures were centrifuged, or spun at high speeds, to separate the bacteria from the phage debris. When Hershey and Chase measured radioactivity in the pellet and supernatant from both of their experiments, they found that a large amount of P 32 appeared in the pellet, whereas almost all of the S 35 appeared in the supernatant. Concluding that DNA, not protein, was injected into host cells and made up the genetic material of the phage.

Kozak sequence:

occurs on eukaryotic mRNA and has the consensus (gcc) gccRcc AUG G. The Kozak consensus sequence plays a major role in the initiation of the translation process. - lower case sequences may vary - upper case sequences are highly conserved (rarely changes) - R means purine (A or G, with A being more frequent) - (gcc) not clear how important - strength of translational initiation of a given mRNA depends on how close its Kozak sequence is to the consensus Kozak sequence - the cc between R and the AUG is a "spacer" needed for overall strength of translation, but not conserved

Central Doga of Molecular Biology

rRNA ( mRNA, tRNA, rRNA) The "central dogma" for molecular genetics: DNA codes for RNA and RNA codes for proteins

Transcription: - coding vs template strand - RNA polymerase - promoter - +1 site

- coding vs template strand: template: the sequence of DNA that is copied during the synthesis of mRNA coding: The opposite strand (that is, the strand with a base sequence directly corresponding to the mRNA sequence) or also called the mRNA-like strand because the sequence corresponds to the codons that are translated into protein. - RNA polymerase/ promoter: RNA polymerase binds the promoter (The promoter is usually found on the 5' side of the coding strand) and points in the correct direction. three types in EUK RNAPOL 1 (transcribes rRNA), RNAPOL 2 (transcribes mRNA, miRNA, snRNA, &snoRNA), RNAPOL3 ( transcribes tRNA) - +1 site: +1 site is the first nucleotide on the coding strand of the gene that gets transcribed into RNA. -1 site is the last nucleotide on the coding strand that does not get transcribed into RNA. There is no zero (0) strand

Dosage Effect: "X chromosome inactivation" 1. define 2. why it occurs 3. is an example of what?

- process by which one of the copies of the X chromosome present in female is inactivated by methylation. The inactive X chromosome is silenced by it being packaged in such a way that it has a transcriptionally inactive structure called heterochromatin. - Because females receive two X chromosomes, they inherit two copies of many of the genes that are needed for normal function. Extra copies of genes or chromosomes can affect normal development - X chromosome inactivation is an example of epigenetic change; not a change in the genotype, but switching off of genes (ex: calico cat)

Chromosomes: 1. define 2. Y chromosome 3. SRY 4. Must have? 5. composed of how many bp and genes

1. Chromosomal DNA + associate proteins Genomes are packaged into chromosomes... Each chromosome is a single piece of DNA 2. sex chromosome that is normally present only in male cells, which are designated XY. 3. sex determining region Y 4. Chromosome must have: - origins of DNA replication (many of them) - telomeres - centromere (has attachment region where fibers attach when cell divides) - genes 5. ~ 50-250 bp and ~ 400-4000 genes

Genome organization and gene expression: 1. Name the 3 major levels of regulation

1. DNA sequence 2. Chromatin 3. Chromosome position in nucleus

Histones: 1. Define 2. Histone core octamer 3. Number of wraps around it 4. Name types of histones

1. Positively-charged proteins where DNA is wrapped around it. 2. DNA is packed around histone core octamer, which is 2 molecules of each core histone - H2A, H2B, H3 and H4 3. DNA (negatively-charged) wraps twice around the histones (positively-charged) 4. A: core histones - H2A, H2B, H3 and H4 B: linker histones - H1 and H5

Onion Test: 1. What is the main purpose for this test. 2.State difference in genome sizes

1. if you believe that most genome is functional, why does an onion (Allium cepa) needs about five times more non-coding DNA for this function than a human? 2. - Humans - haploid genome size 3 billion bp (about 3.5 pg) Allium cepa - haploid genome size of about 16 billion bp (about 17 pg) - If there is something special about onions, then why is there such a large range in genome size (from 7 pg to 31.5 pg)?

C-value paradox 1. C-value 2. Expect what type of relationship? 3. Large and small c value

1. total amount of DNA in the genome (the amount of DNA per haploid cell (usually expressed as picograms) or the number of kilobases per haploid cell.) 2. Expect that the more complex the organism, the more DNA is needed to "run it"... Therefore expecting a linear relationship between genome size and organic complexity 3. - More complex the organism is, the MORE genetic information it needs (LARGE C value) - Smaller organisms (viruses and bacteria) there is no room for excess DNA (SMALL C value) On Choi's ppt: haploid human genome - 3 billion bp haploid frog (xenopus) genome -3 billion bp marbled lungfish genome - 130 billion bp paris japonica genome -149 billion bp

What is a gene?

A gene is a DNA sequence that is transcribed to produce a functional product. This definition also implies that regions that are functional but not transcribed (e.g. promoters) are NOT genes

Life Cycle

All cells in organisms are derived from one cell (fertilized egg). All cell in organism are clonal Sperm: complete set of DNA (chromosome n=haploid) Egg- complete set of DNA (chromosome n=haploid) Hence fertilized egg has two sets (2n= diploid number)

Why is DNA called the blueprint of life?

Because it contains the instructions needed for an organism to grow, develop, survive and reproduce. DNA does this by controlling protein synthesis. Proteins do most of the work in cells, and are the basic unit of structure and function in the cells of organism.

Explain Griffith Transformation Principle in Strep

Fred Griffith's experiment was the first experiment suggesting that bacteria are capable of transferring genetic information through a process known as transformation. He used two strands of Strep: - "R" (rough-non virulent )no protective coating - "S" (smooth-virulent) has protective coating He injected into mice the following: 1. S--> dead mouse 2. R--> healthy mouse 3. Heat Killed S cells--> healthy mouse 4. Living R cells plus heat killed S cells--> dead mouse Thus concluding R-strain bacteria must have taken up what he called a "transforming principle" from the heat-killed S bacteria, which allowed them to "transform" into smooth-coated bacteria and become virule. (because of step 4)

Functional RNA

Genes can make mRNA which make proteins rRNA: helps form the structure of a ribosome tRNA: translates amino acids forming proteins, or amino acids snRNA: involved in splicing or other RNA processing reactions (cuts introns) snoRNA: guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs miRNA: small non-coding RNA molecule functions in RNA silencing and post-transcriptional regulation of gene expression

Phenotype vs Genotype

Pheno: observable properties (includes molecular, behavioral properties) Geno: inferred cause...DNA sequences and chromosomes

Physical properties of DNA (charge and complementary pairing)

Physical molecule: 1. chain of subunits 2. two strands a. the strands are complementary i. A pairs with T ii. G pairs with C b. genetic info - the two strands can store complementary information Pairing achieved by H bonds Charge: Phosphate groups in the DNA backbone carry negatively-charged oxygen molecules giving the phosphate-sugar backbone of DNA an overall negative charge. The larger the DNA the slower is travels in gel the smaller DNA travels faster.

Karyotype: - define - male and female difference

Visual display of chromosomes found in cell nuclei -normal human karyotypes contain 22 pairs of autosomal chromosomes and one pair of sex chromosomes (allosomes). FEMALES: Normal karyotypes for females contain two X chromosomes and are denoted 46,XX; MALES: males have both an X and a Y chromosome denoted 46,XY.

Explain Avery Experiment

Wanted to identify Griffith's "transforming principle." Which was found out to be DNA Obtained large cultures of heat-killed S cells and, through a long series of biochemical steps, progressively purified the transforming principle by washing away, separating out, or enzymatically destroying the other cellular components. By this method, they were able to obtain small amounts of highly purified transforming principle, which they could then analyze through other tests to determine its identity... Which later showed could be DNA since: 1. The purified substance gave a negative result in chemical tests known to detect proteins, but a strongly positive result in a chemical test known to detect DNA. 2. The elemental composition of the purified transforming principle closely resembled DNA in its ratio of nitrogen and phosphorous. 3. Protein- and RNA-degrading enzymes had little effect on the transforming principle, but enzymes able to degrade DNA eliminated the transforming activity. Avery was still unsure if DNA was the transforming material. Which led to Hershey-Chase Experiment.

Genome is

a complete set of genetic material in an organism

Wobble position

allows some variability in the THIRD basepair position of the codon to anticodon relationship Codon (mRNA): read from 5'-->3'... position 3 Anticodon (tRNA): reads from 3'-->5'... if reading from 5-->3 position 1

Codon Bias

differences in the frequency of occurrence of synonymous codons in coding DNA....Certainly codons are more frequently used in some species, while other codons are less favored

Haploid vs Diploid

haploid and diploid cells is the number of chromosome sets found in the nucleus. Ploidy is the area of biology that refers to the number of chromosomes in a cell. Therefore, cells with two sets are diploid, and those with one set are haploid. In humans: Haploid number - 23 chromosomes (together human genome is made of 3 billion nucleotides) Diploid number- 46 chromosomes

Why is Genetic code known as universal and degenerate

the genetic code -- the three-letter codons -- direct the assembly of exactly the same amino acids in nearly every organism on Earth. The genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes for one of the 20 amino acids used in the synthesis of proteins. Degenerate because: Although each codon is specific for only one amino acid (or one stop signal), the genetic code is described as degenerate, or redundant, because a single amino acid may be coded for by more than one codon.

Codon degeneracy

the redundancy of the genetic code, exhibited as the multiplicity of three-base pair codon combinations that specify an amino acid. The degeneracy of the genetic code is what accounts for the existence of synonymous mutations

Genome organization and gene expression (levels): DNA sequence

tsc regulated by DNA binding proteins associating with regulatory elements

Core Histones

two H2A/H2B associate at either ends of the tetramer -2 H3/H4 dimers form a tetramer