Bio 97 Midterm 1

What are the three components of a DNA nucleotide?

-Deoxyribose sugar

-Phosphate Group

-Nitrogenous Base: Thymine, Adenine, Cytosine, or Guanidine

How many hydrogen bonds does an A-T base pair have? How many does a G-C base pair have?

A-T = 2 bonds

G-C = 3 bonds

Origin of Replication (Def.)

The specific DNA sequence where DNA replication begins

Three Steps of a PCR Reaction:

1) Denaturing of DNA by heating (95 C)

2) Primer annealing (45 C-68 C; determined by length since the amount of hydrogen bonds that need to be broken)

3) Primer extension (72 C)

DNA Polymerase (Def.)

Synthesizes DNA; needs an RNA primer; has a proof-reading function; more active than exonuclease

DNA Exonuclease (Def.)

Part of proof-reading function, the exonuclease removes nucleotides that it just added that are wrong

Polymerase Chain Reaction (PCR)

-Requires a specific DNA sequence primer

-Requires a special polymerase (due to the high heat)

What is dideoxynucleotide triphosphate? How does it get used to sequence DNA?

Sugar missing both hydroxyl groups on the 3' and 2', this causes the chain to be terminated and ends DNA replication; fluorescence

***Next Generation Sequencing

Sequencing by synthesis

Three Key Structural/Chemical Differences between RNA & DNA:

1) Ribose Sugar (NTP)/ Deoxyribose Sugar (dNTP)

2) Uracil/ Thymine

3) RNA single stranded / DNA double stranded

mRNA (Def.)

messenger RNA; the RNA that is transcribed from the DNA to be translated by the ribosome

tRNA (Def.)

transfer RNA; bring amino acids to the ribosome to add to the polypeptide chain of amino acids; contains an anticodon

- Charged: with amino acid

- Uncharged: without amino acid

rRNA (Def.)

ribosomal RNA; make up the ribosome

Phosphodiester Bond

Bond between phosphate group and sugar group; covalent bond

Three Differences in Transcription between Prokaryotes & Eukaryotes:

1) Promoters are different: Eukaryotes have TATA & are more flexible

2) Eukaryotes have enhancers and silencers

3) Eukaryotes have splicing of introns and exon, as well as post-transcriptional modifications: Poly-A Tail & 5' Cap; eukaryotes do not have introns within their mRNA so splicing is not necessary

Promoter

RNA Polymerase will bind here to initiate transcription; consensus sequences: can be similar, don't have to be exact; located on the coding strand; can be read in either direction but it only makes sense in one direction

Enhancers

transcription factors that act as activators of transcription, upstream or downstream

Silencers

transcription factors that act as repressors of transcription, upstream or downstream

mRNA Splicing

- occurs at sites determined by the consensus sequences

- requires multiple proteins

- takes place in the nucleus

- the exon that remain after splicing make up the proteins by folding into domains, making many different proteins

- can give rise to variant proteins in different tissues

Three Mechanisms Eukaryotes use to increase the diversity of their proteins:

1) Alternative Splicing

2) Alternative Promoters: more than once sequence upstream can act as a promoter and initiate transcription

3) Alternative Polyadenylation: the poly A tail can occur whenever and cleave the mRNA, ending transcription

Translation

mRNA attaches to the small sub unit of the ribosome; the codons are read and the tRNA brings the proper amino acid for the designated anti codon that corresponds with it. A start codon (AUG) initiates translation, and stop codons initiate the end of translation. An mRNA strains is translated 5' to 3'. A polypeptide is synthesized N-terminus to C-terminus. Within a bacteria translation occurs within the cytoplasm, in a eukaryote it occurs within the cytoplasm as well.

UTR

Untranslated Region; The information helps them get there and initiation and how to terminate translation

Phases of Translation:

1) Initiation: the mRNA binds to the ribosomal small unit, it searches for a AUG codon, initiating translation and then the big sub unit comes and the tRNA brings Met

2) Elongation: A-P-E: peptide bond

3) Termination: there is no amino acid for termination, instead it is just released by binding factors

Polycistronic mRNA (Def.)

single mRNA codes for multiple proteins; differentiates prokaryotes from eukaryotes; can be turned on or off

Amino Acid

Differ by R group

- Carboxyl Group

- Amino Group

- Hydrogen

Peptide Bond

Covalent bond holding polypeptide together; made through hydrolysis

Third Base Wobble Position

Base pairing does not always have to be perfect for the third position within the codon; it is extremely likely that the base perfect will not be perfect, but it will still result in the same amino acid

Aminoacyl tRNA Synthetases

attach the amino acids to the tRNAs; one for each amino acid

Synonymous Codons (Def.)

Codons that code for the same amino acid

Silent Mutations

mutations within the codon that results for the same amino acid

Missense Mutation

mutation within the codon that results in a different amino acid, changing the protein

Nonsense Mutation

mutation within the codon that results in a stop codon, ending translation too soon

Frameshift Mutations

adding or deleting a nucleotide, altering the reading frameshift; this can alter every single amino acid after the mutation

Nucleoid (Def.)

a small region where bacterial chromosomes are densely compacted

What two mechanisms are used to compact a bacterial genome?

1) Proteins: shape the DNA into loops, and even smaller loops

2) Supercoiling: like a telephone cord

Five Differenced between Bacterial and Eukaryotic Chromosomes:

1)

2)

3)

4)

5)

Chromatin

proteins and DNA; chromatin makes up the chromosome; about 1/2 DNA & 1/2 protein

Histones

about 1/2 of the proteins used in chromatin; small basic proteins that bind DNA; positively charged

Chromatin Compaction

Nucleosome--> 10 nm Fiber --> 30 nm Fiber --> 300 nm Fiber --> Chromatin

Nucleosome

The core particle; octameric: 2 H2A, 2 H2B, 2 H3, and 2 H4

Euchromatin

not tightly condensed, ares of active gene expression

Heterochromatin

more tightly condensed, areas of less gene expression

- Facultative: sometimes tightly compacted other times loosely compacted

- Constitutive: Always tightly packed

Centromere

chromatin is highly condensed; made up of repetitive DNA sequences and kinetochore proteins

Histone Modifications

Methylation: chromatin condenses, repressing gene expression

Acetylation: decondenses the chromatin, thus increasing gene expression by making histone less positively charges

DNA Methylation

Methyl group added to the Cytosine, represses gene expression

Mendel's Experimental Design:

- Scientific Method

- Selection of traits with distinguishable features

- Pure-breeding strains

- Controlled crosses between plants

- Quantification of Results

- Replicate, Reciprocal, and Test Cross Analysis

Chi-Squared Value

test if the real experimental data is consistent with the hypothesis

x^2 = SUM(O-E)^2/ E

Larger the value, larger the difference

Degrees of Freedom

one less than the number of classes

P Value

the probability that we see the data, given our hypothesis is true

- small p value: very unlikely

p > 0.05 keep null hypothesis

p <= 0.05 reject null hypothesis

**Single Gene Inheritance

Carriers

Heterozygous genotype for a recessive trait; do not display the phenotype

G1 (Gap 1):

active gene expression

G0 (G Zero):

Cells that are terminally differentiated; their job doesn't require them to divide any longer; rarely do some cells re-enter the cell cycle

Chromosome

made up of DNA with a centromere

Chromatid

a DNA molecule

Sister Chromatids

two chromatids joined by a centromere

Homologous Chromosomes

found in diploid cells; they pair during meiosis I and separate during anaphase I

Mitosis

Prophase: chromosomes condense

Prometaphase: Chromosomes attach to the microtubules

Metaphase: chromosomes align at the metaphase plate

Anaphase: sister chromatids separate

Telophase & Cytokinesis: cleavage furrow splits the cell and the nuclei reform

- produces 2 identical diploid daughter cells

Meiosis I

Homologous chromosomes separate

Prophase: chromosomes condense & Crossing over takes place & attachment to the microtubules

Metaphase: align at the metaphase plate (Mendel's Law of segregation)

Anaphase: Homologous chromosomes separate

Telophase & Cytokinesis: cleavage furrow; haploid

Meiosis II

sister chromatids separate

Prophase: chromosomes condense & Attach to microtubules

Metaphase: align at the metaphase plate (Mendel's Law of independent assortment)

Anaphase: sister chromatids separate

Telophase & Cytokinesis: four haploid unique daughter cells; haploid

Prophase I

L: (Leptotene) condensation begins

Z: (Zygotene) synapsis

P: (Pachytene) Crossing over

D: (Diplotene) Chiasma

D: (Diakinesis) attach to microtubules

Synaptonemal Complex

proteins that hold the non sister chromatids together, enabling crossing over to take place

Chiasma

point where crossing over occurred

Crossing Over

exchange of genetic material between non-sister chromosomes or homologous chromosomes

Disjunction

the separation of chromosomes or sister chromatids

Dosage Compensation

females have 2 X chromosomes, while males have only 1 X Chromosome; dosage compensation equally distributes the concentration of gene products between the two sexes even though females have 2 X. Therefore, the dosage of genes may differ between the two sexes. To also compensate, one of the X chromosomes within females are inactivated.

Barr Body

one X chromosome that is inactivated; completely random; creates a mosaic for that character