Exam 1 Flashcards
Nucelotide vs Nuceloside
-Nucleotide: three parts (sugar, a phosphate, and a base), purine or pyrimadine base
-Nucleoside: same as a nucleotide without a phosphate
Complementary Base Pair Rules
-A binds to T and G binds to C
-Antiparallel: strands run in opposite directions
-complementary DNA strands; each base has a complementary base that pairs with it
What are the measurements of a DNA double helix?
-10 average bp per turn of the DNA helix -0.34 nm between bp
-entire helix is 2 nm in diameter
-The distance from minor groove to minor groove is 3.4 nm
Melting curve
-an analysis that you can do to see how fast DNA comes back together after the DNA is melted
-Denatures a nucelic acid via heat (makes it single stranded), cool it, and then detect how fast it comes back together
How can you tell if a sequence is G-C rich or A-T rich
-Melting curve will tell you if a substance is A-T or G-C rich. If a sequence took a lot more heat to melt than it is a G-C rich sequence due to having 3 hydrogen bonds
RNA structure
-Uracil replaces thymine
-single stranded
-ribose sugar
-can form hairpin structures
DNA structure
-double helix
-phosphodiester bonds form backbone
-hydrogen bonds cause base pairing between the strands
-Antiparallel (is important for stability) complementary base pairs
-terminal base does not have a phosphate, just a hydroxyl
-deoxyribose sugar
A Form of DNA
same amount of bases as B form, thicker diameter, right-handed, dehydrated form
B form
normal form of DNA, right-handed helix, long, thin
Z form
G-C rich, left handed helix
Purine vs Pyrimide
-Purines: double ring structure with 9 carbons
-Pyramidines: single ring structure
How to tell the difference in Adenine and Guanine?
-amine group is on the 6 carbon of Adenine
-amine group is on the 2 carbon of Guanine
How to tell the difference in Cytosine and Uracil?
-Thymine has 2 double bonded oxygens
-Cytosine: has an additional amine group when compared to thymine
How many hydrogen bonds in A-T vs. G-C?
A=T (2 H bonds)
G-C (3 H bonds)
Histones
-organize themselves into octamers
-relatively small (50-150 bp)
-one of the most abundant proteins that we make
-can have disordered sections
-chromatin remodeling must occur to allow the DNA to be accessed by DNA-binding proteins
5 main Types of Histones
-H1: not a core histone, lysine-rich
-H2A: slightly lysine-rich
-H2B: slightly lysine-rich
-H3: Argine-rich (positively charged)
-H4: Arginine-rich (positively-charged)
Histone Tails
provide potential targets along the chromatin fiber for chemical modifications that may include
Acetylation
activation of genes (acetyl groups bring a negative charge)
-HAT: turn on
-Histone deactylase: catalyst for deacetylation
Methylation
acctivation of genes
Phosphorylation
activation or repression of genes
Histone Code
making predictions about certain areas of chromosomes based on histones
Nucleosome Structure
-one histone type is sound in each nucleosome
-octamer of histones (~147 bp)
-each nucleosome consists of eight histone proteins around which the DNA wraps 1.65 times
-the nucleosomes fold up to produce 30 nm fiber
-chromatin remodeling (histones) must occur to allow the DNA to be accessed by DNA-binding proteins
-Linker DNA: 30 to 40 bp that seperates each nucleosome
Hershey and Chase Experiment
-They did not know how phages reproduce
-Protein or DNA?
Types of repeat DNA
-Repetitive DNA is approximently 150-300 bp long
-HIghly Repetitive DNA is less than 10 bp long
Where is highly repetitive DNA found?
-cenromeres
-telomeres
-microsatellite DNA
-Heterochromatin
Semi-Conservative DNA replication
Tandem vs. Interspersed Repeat Sequence
-Tandem: repeat sequence that is right beside itself (telomere)
-Interspersed: repeat sequences that you find throughout the genome
Viral Genetic Material
-Hershey and Chase
DNA polymerase mechanisim in replicating DNA
What phase in the cell cycle does DNA replication occur?
S phase
Proof-reading in DNA Replication
DNA Polymerase I
DNA Polymerase III
Characteristics of Genetic Material
-must contain complex information
-must replicate faithfully
-must encode the phenotype
-must have the capacity to vary
Chloroplast/Mitochondrial Genome Functions
-contain DNA
-encodes some polypeptides used by the organelle, rRNA, and some tRNAs
Mitochondrial genomes
-small and vary greatly
-Human mitochondrial DNA is circular, 16,569 bp, encodes two rRNAs, 22 tRNAs, and 13 proteins
-Yeast Mitochondrial DNA: five times as large as a human, encodes two rRNAs, 25 tRNAs, and 16 polypeptides
-Flowering plan mitochondrial DNA: extensice size variation
Damage to what DNA is associated with aging and how does it work?
-mitochondrial DNA
-many human genetic diseases associated with mitochondrial DNA appear in middle age or later
-mutations in mtDNA start life with decreased oxidative phosphorylation capacity
Griffith Experiment
discovering of a “transforming principle”; a substance in the heat killed virulent bacteria genetically transformed the type IIR bacteria into live, virulent type IIIS bacteria
Avery, McCleod, and McCarty experiment
identification of the “transforming principle”; because DNase destroyed the transforming substance, the transforming substance is DNA
Messelson/Stahl Experiment
Chromatin Remodeling
-Chromatin remodeling must occur to allow the DNA to be accessed by DNA binding proteins
-To allow replication and gene expression, chromatin must relax its compact structure and expose regions of DNA to regulatory proteins
Histone Features
-Histone Tails: provide potential targets along the chromatin fiber for chemical modification that may include acetylation, methylation, and phosphorylation
Process of DNA Replication (Steps)
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