Exam 1

Question 1

Nucelotide vs Nuceloside

Answer 1

-Nucleotide: three parts (sugar, a phosphate, and a base), purine or pyrimadine base
-Nucleoside: same as a nucleotide without a phosphate

Question 2

Complementary Base Pair Rules

Answer 2

-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

Question 3

What are the measurements of a DNA double helix?

Answer 3

-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

Question 4

Melting curve

Answer 4

-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

Question 5

How can you tell if a sequence is G-C rich or A-T rich

Answer 5

-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

Question 6

RNA structure

Answer 6

-Uracil replaces thymine
-single stranded
-ribose sugar
-can form hairpin structures

Question 7

DNA structure

Answer 7

-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

Question 8

A Form of DNA

Answer 8

same amount of bases as B form, thicker diameter, right-handed, dehydrated form

Question 9

B form

Answer 9

normal form of DNA, right-handed helix, long, thin

Question 10

Z form

Answer 10

G-C rich, left handed helix

Question 11

Purine vs Pyrimide

Answer 11

-Purines: double ring structure with 9 carbons
-Pyramidines: single ring structure

Question 12

How to tell the difference in Adenine and Guanine?

Answer 12

-amine group is on the 6 carbon of Adenine
-amine group is on the 2 carbon of Guanine

Question 13

How to tell the difference in Cytosine and Uracil?

Answer 13

-Thymine has 2 double bonded oxygens
-Cytosine: has an additional amine group when compared to thymine

Question 14

How many hydrogen bonds in A-T vs. G-C?

Answer 14

A=T (2 H bonds)
G-C (3 H bonds)

Question 15

Histones

Answer 15

-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

Question 16

5 main Types of Histones

Answer 16

-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)

Question 17

Histone Tails

Answer 17

provide potential targets along the chromatin fiber for chemical modifications that may include

Question 18

Acetylation

Answer 18

activation of genes (acetyl groups bring a negative charge)
-HAT: turn on
-Histone deactylase: catalyst for deacetylation

Question 19

Methylation

Answer 19

acctivation of genes

Question 20

Phosphorylation

Answer 20

activation or repression of genes

Question 21

Histone Code

Answer 21

making predictions about certain areas of chromosomes based on histones

Question 22

Nucleosome Structure

Answer 22

-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

Question 23

Hershey and Chase Experiment

Answer 23

-They did not know how phages reproduce
-Protein or DNA?

Question 24

Types of repeat DNA

Answer 24

-Repetitive DNA is approximently 150-300 bp long
-HIghly Repetitive DNA is less than 10 bp long

Question 25

Where is highly repetitive DNA found?

Answer 25

-cenromeres -telomeres -microsatellite DNA -Heterochromatin

Question 26

Semi-Conservative DNA replication

Question 27

Tandem vs. Interspersed Repeat Sequence

Answer 27

-Tandem: repeat sequence that is right beside itself (telomere) -Interspersed: repeat sequences that you find throughout the genome

Question 28

Viral Genetic Material

Answer 28

-Hershey and Chase

Question 29

DNA polymerase mechanisim in replicating DNA

Question 30

What phase in the cell cycle does DNA replication occur?

Answer 30

S phase

Question 31

Proof-reading in DNA Replication

Question 32

DNA Polymerase I

Question 33

DNA Polymerase III

Question 34

Characteristics of Genetic Material

Answer 34

-must contain complex information -must replicate faithfully -must encode the phenotype -must have the capacity to vary

Question 35

Chloroplast/Mitochondrial Genome Functions

Answer 35

-contain DNA -encodes some polypeptides used by the organelle, rRNA, and some tRNAs

Question 36

Mitochondrial genomes

Answer 36

-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

Question 37

Damage to what DNA is associated with aging and how does it work?

Answer 37

-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

Question 39

Griffith Experiment

Answer 39

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

Question 40

Avery, McCleod, and McCarty experiment

Answer 40

identification of the "transforming principle"; because DNase destroyed the transforming substance, the transforming substance is DNA

Question 41

Messelson/Stahl Experiment

Question 42

Chromatin Remodeling

Answer 42

-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

Question 43

Histone Features

Answer 43

-Histone Tails: provide potential targets along the chromatin fiber for chemical modification that may include acetylation, methylation, and phosphorylation

Question 44

Process of DNA Replication (Steps)

Answer 44

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