Exam 1 Study Guide
Chapter 1: Genomics vs. Genetics
● Genetics: the study of biologically inherited traits including traits that are influenced in part by the environment
● Genomics: the study of all the genes in an organism to understand their molecular organization, function, and interaction
● Genes: The basic unit of biological information made of specific segments of DNA on a chromosome that encodes a particular protein or structural DNA molecule
● Genome: the entire collection of genes in chromosomes in each cell ● DNA+Histone = Chromatin
● Chromatin condenses to form chromosomes during cell division ● Proteome: the entire collection of proteins encoded by an organism. Types of Genetic disorders
● Chromosome disorders
● Single-gene disorders
● Multifactorial disorders
● Mitochondrial diseases (small fraction of diseases)
● Proved that genetic material can be transferred
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Avery- Macleod- McCarty experiment
● Proved that DNA is the substance that causes bacterial transformation, therefore DNA is the genetic material.
Hershey and Chase Experiment
● Confirmed that DNA is the genetic material
● There is a 1:1 ratio of pyrimidine and purine bases within DNA
DNA consists of two strands of polynucleotides and forms a right-handed double-helix Each nucleotide has:
● A five carbon sugar
● A phosphate group
● A nitrogen-containing base
Pyrimidines have longer names and smaller bases (thymine and cytosine) Purines have shorter names and bigger bases (adenine and guanine ● The inside of the helix contains hydrophobic bases while the outside of the helix is a sugar-phosphate backbone which is hydrophilic Don't forget about the age old question of How did tobacco impact the development of the virginia colony?
Each strand of DNA runs in an antiparallel direction
● One strand runs in a 5’-->3’ direction and the other runs in a 3’-->5 direction ○ The 5’ end attaches to a phosphate
○ The 3’ end attaches to OH
The strands are connected by hydrogen bonds between the bases ● A-T are connected by a double bond
● G-C are connected by a triple bond
Watson and Crick’s DNA double helix
● Showed how DNA acts as a code, specifying how proteins are made by the cell. The sequence of the bases determines the genetic code.
Types of DNA Don't forget about the age old question of What are the functions of instructional materials?
1. A DNA- right handed, RNA-DNA hybrid
2. B DNA- right handed , Watson-Crick double helix
3. Z DNA- left handed
DNA replication: the copying process in which a single DNA molecule gives rise to two identical molecules.
● Each strand serves as a template for complementary base pairing ● Daughter strand synthesis occurs in a 5’-->3’ direction
● nucleotide is added to the 3’ end of DNA
Genes and Protein
● Genes are DNA segments that carry genetic information. It is normally a stretch of DNA that codes for a type of protein or for an RNA chain that has a function in the organism. Genes pass genetic traits onto offspring.
● Proteins are responsible for most of the biochemical activities in a cell ○ Structural protein: cellular rigidity and mobility
○ channel/ pore: traffic small molecules in and out of cell
○ Receptor: cellular activities in response to extracellular signal
○ Enzymes: break down organic molecules
● A mutation in the gene causes a mutated protein. The defective enzyme results in lack of function and disease.
● Proved that any hereditary disease in which cellular metabolism is abnormal results from an inherited defect in an enzyme If you want to learn more check out Why do lower social classes have poorer health?
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Beadle and Tatum’s experiment
● Proved that metabolic pathways are regulated by genes. Don't forget about the age old question of What testing is run on an infant who is preterm?
Central Dogma of Molecular Biology
● Genetic information flows in one direction
○ DNA→ RNA→ protein
● Transcription: the flow of information from DNA to RNA
○ Transcriptional control: the rate at which RNA is synthesized
● Translation: the flow of information for RNA to protein
○ Post translational control: the location of protein in eukaryotic cells RNA is made of nucleotides called ribonucleotides.
-ribonucleotides are linked by 3’-5’ phosphodiester bonds
DNA vs. RNA
-DNA stores RNA and protein-encoding information. RNA carries protein-encoding information and helps to make proteins.
-DNA is double stranded, while RNA is usually single stranded.
-The sugar of DNA is Deoxyribose, while the sugar of RNA is Ribose. RNA can basepair within itself for functional purposes.
Types of RNA
● rRNA (ribosomal)- Produces ribosomes
● mRNA (messenger)- Brings genetic information to the ribosome ● tRNA (transfer)- Translates information from RNA to ribosomes Transcription
● Coding strand of DNA: not used as a template, but is identical in sequence to the mRNA. However, in mRNA all the T’s are replaced with Uracil.
● Template strand of DNA: strand of the DNA used to make RNA
● The synthesis of a polypeptide under the direction of an mRNA molecule ● A codon is 3 bases of mRNA that specify one amino acid
● AUG is the start codon
● UAG, UGA, and UAA are the start codons
DNA cleavage by Restriction enzyme
● Restriction endonuclease recognizes specific base sequences in DNA, in which they cut the DNA at that site.
○ Endonuclease: enzymes that cleave the phosphodiester bonds from within the nucleic acid molecule
○ Exonucleases: enzymes that cleave the phosphodiester bonds from the end of the nucleic acid molecule
● Most restriction endonucleases recognize only one short base sequence, which is usually only made up of 4-6 bases
● Some restriction enzymes generate “sticky ends” while others generate “blunt ends”
● The restriction sites are palindromic
● The restriction site is recognized without regard to the source of DNA ● The number of cuts in the DNA is determined by the number of restriction sites present
DNA is negatively charged due to its PO4- and moves toward a positively charged electrode
● Ethidium bromide-stained DNA can be seen under UV lighting
○ Largest DNA fragment moves the least, while the smallest moves the most
● Restriction map: a diagram showing sites of cleavage of one or more restriction sites along a DNA molecule
○ Sorts fragments by size using gel electrophoresis
Forces stabilizing DNA double helix
1. Hydrogen Bonding
○ At high pH, the solution is rich in hydroxide ions can pull hydrogen ions off of molecules. At a pH greater than 11.3, all hydrogen bonds are eliminated resulting in the denaturation of DNA
2. Base stacking
○ Stabilizes the double helix by stacking hydrophobic bases to minimize contact with water.
3. Electrostatic forces
○ Monovalent cations interact electrostatically with nucleic acids so that the electrostatic repulsion between the two strands of the duplex decreases with increasing salt concentration
DNA denaturation: separation of DNA double strand
● Heating temperature
● Low or no amount of monovalent cations in the DNA solution
● High pH
● H-bond breaker (Urea or formamide)
DNA renaturation: formation of DNA, also known as annealing
● Cooling temperature
● High amount of monovalent cations in the DNA solution
● Neutral pH
● Removal of H-bond breaker
Nucleic acid hybridization
Probe: A fragment of DNA to detect the presence of nucleotide sequences in the DNA ● The nucleotide sequence in the probe is complementary to the sequence in the target DNA
● Probes are usually labeled with a radioisotope or light-emitting molecules Southern blot: the presence of a specific nucleotide sequence in DNA
● Northern blot: detection of a nucleotide sequence in RNA
● Southern blot analysis:
a. DNA is cleaved; electrophoresis is used to separate DNA fragments
b. DNA fragments are transferred onto filter
c. Filter is exposed to radioactive probe
d. Filter is exposed to photographic film and then developed
DNA replication: the process of producing two identical copies from one original DNA molecule ● PCR: Polymerase Chain reaction
● PCR reaction requires
○ Template DNA
○ A primer with free 3’-OH
○ DNA polymerase enzyme
○ Deoxyribonucleotides (dNTPs)
● Used to amplify the amount of a particular DNA molecule in a sample. Thermal cycling
● A PCR machine (gene machine) controls temperature
● Typical PCR goes through 3 steps
○ Denaturation- Heating denatures the DNA
○ Annealing- two primers bind to the complementary region of DNA
○ Extension- DNA polymerase duplicates DNA
● Human genome is organized into 46 chromosomes
● 2 sex chromosomes (X, Y):
○ XY- in males
○ XX-in females
● 22 pairs of autosomes
● Homologous chromosomes are pairs of chromosomes- one from mother and one from the father- with identical loci and structure.
Alleles: alternative forms or a gene
● Different types of the same gene
Locus: The specific place on a chromosome where a gene is located.
At each locus of the homologous chromosome, there are 2 alleles. These constitute the individual's genotype at the locus
● Homozygous condition: identical alleles
● Heterozygous condition: different alleles
A phenotype is a physical expression of a genotype.
● Genetic markers which can be detected by direct analysis of DNA
● DNA markers are based on naturally occurring polymorphism in DNA sequence ○ DNA polymorphism is a sequence difference that is present in at least 1-2% of a population
○ Polymorphisms can be single bases or thousands of bases
○ Polymorphisms may or may not have phenotypic effects
● DNA markers are sequences of DNA which have been traced to specific locations on the chromosomes and associated with particular traits
SNP-Single Nucleotide Polymorphism
● A single base change in DNA sequence that occurs in a significant proportion of a large population
● A SNP defines two alleles. Therefore, there could be three genotypes among individuals in the population
Tandem repeat polymorphism
● Short repetitive sequences that are abundantly interspersed throughout a species’ genome.
● # of genotypes=n(n+1)/2, n= # of alleles
Copy number Variation
● Structural variation in which a segment of DNA is 1000 base pairs or more in length exhibit copy number