Genetics Exam 3

Semiconservative DNA Replication

Each progeny molecule retains one of the parental strands

Conservative DNA Replication

The two parental strands of DNA remain together or pair again after replication and, as a whole, serve as a template for the synthesis of new progeny DNA double helices.

Dispersive DNA Replication

The parental double helix is cleaved into double-stranded DNA segments that act as templates for the synthesis of new double-stranded DNA segments.

What did the Meselson-Stahl Experiment confirm?

Confirmed that the semiconservative replication model is correct.

How did Meselson and Stahl test DNA Replication models?

The DNA of E. coli was labeled across several replication cycles using isotopes of nitrogen. From the patterns of DNA labeling they saw the DNA is replicated Semi-conservatively.

DNA Polymerase

Enzymes that catalyze DNA synthesis.

What direction is DNA synthesized?

5' to 3'

3' to 5' exonuclease activity

Proofreading/ Error Correction. Can remove nucleotides from the 3' end of a DNA chain.

(DNA Pol I & DNA Pol III)

5' to 3' Synthetic activity

The direction of DNA synthesis

Origin of Replication

The specific region where the DNA double helix denatures into single strands and within which replication commences.

Replication Bubble

The locally denatured segment of DNA.

Replication Fork

A Y-shaped structure created when DNA untwist to expose the two single-stranded template strands for DNA replication.

DNA Helicase

The helicases untwist the DNA in both directions from the origin of replication by breaking the hydrogen bonds between the bases.

What untwist DNA in both directions of the Origin of Replication?

DNA Helicase

DNA Primase

Binds to helicase and then denatured DNA and synthesizes a short RNA primer.

Why is DNA Primase important?

It is important because DNA polymerases cannot initiate the synthesis of a DNA strand; they can add nucleotides only to a pre-existing strand. The DNA primer creates a short RNA primer that adds new nucleotides by DNA polymerase.

RNA Primer

Is extended by DNA polymerase as new DNA is made. (Will be removed later).

Single-strand DNA-binding (SSB)

Bind to each single-stranded DNA, stabilizing them and preventing them from reforming double-stranded DNA by complementary base pairing.

DNA Ligase

- Seals the gaps between adjacent DNA fragments (Okazaki Fragments) with phosphodiester bonds to form a longer, covalently continuous chain.

What fragments does DNA ligase seal?

Okazaki Fragments

Semidiscontinous DNA Replication

The leading strand is synthesized continuously, whereas the lagging strand is synthesized in pieces, or discontinuously. Thus, DNA replication as a whole occurs in a semidiscontinuous manner.

Which DNA strand is synthesized continuously?

Leading Strand

Which DNA strand is synthesized discontinuously or in pieces?

Lagging Strand

Okazaki fragments

The fragments of lagging strand DNA made in semidiscontinuous replication.

Bi-directional Replication

Synthesis of DNA is in both directions away from the origin of replication.

Leading Strand

The new strand being made in the same direction as the replication fork.

Lagging Strand

The new strand being made in the direction opposite of the replication fork.

Telomere

- A specific set of sequences at the end of a linear chromosome, stabilizes the chromosome, and is required for replication.

- Has tandem repeats at the ends of chromosomes.

Tandem repeats at the ends of chromosomes.

Telomere

Telomerase

- Where a chromosome end has been produced after primer removal with an overhang extending beyond the 5' end of the new DNA.

- Extends telomeres

Metabolic Pathway

Set of actions or interactions between genes and their products that results in the formation or change of some component or system, essential for the correct functioning of a biological system.

One-Gene-One-Enzyme Hypothesis

Each gene controls the synthesis or activity of a single gene

One-Gene-One-Polypeptide Hypothesis

Changes one-gene-one-enzyme hypothesis because some enzymes may consists of more that one polypeptide each coded by a different gene.

PKU (phenylketonuria)

- Commonly caused by a recessive mutation of a gene on the long arm of chromosome 12 (an autosome).

- People with PKU cannot make tyrosine, an amino acid needed for protein synthesis, production of thyroxine and melanin.

- People tend to be very fair skin, blue eyes, and low levels of epinephrine (adrenaline).

Amino Acid

A sequence of 3 nucleotides

Polypeptides

Made of amino acids strung together.

Protein

A high-molecular-weight, nitrogen-containing organic compound of complex shape and composition.

Consists of one or more macromolecular sub-units called polypeptides.

Each cell type had a characteristic set of proteins that gives it its functional properties.

Enzyme

A biological catalyst

Four main enzymes that facilitate DNA Replication: Helicase, Primase, DNA Polymerase, and Ligase.

What is Sickle Cell Anemia?

A genetic disease affecting Hemoglobin. In conditions of low oxygen tension, red blood cells from ppl w/ the disease lose their characteristic disc shape and assume the shape of a sickle. The sickled red blood cells are fragile and break easily, resulting in the anemia. Blood circulation is impaired and tissues become deprived of oxygen.

What disease causes red blood cells to lose their characteristic disc shape?

Sickle Cell Anemia

What genetic disorder causes fair skin, blue eyes, and low levels of adrenaline?

PKU

What happens molecularly for Sickle Cell Anemia to occur?

Substituting the amino acid glutamic acid with valine at the 6th position from the N-terminal end of the B-polypeptide causes the B-polypeptide to fold up in a different way. Hemoglobin with this mutant version of the B-polypeptide aggregates readily, falling out of solution and leading to extreme sickling of red blood cells in ppl with sickle cell anemia and mild sickling of the red blood cells in ppl with sickle cell trait.

Hemoglobin

The oxygen-transporting protein in red blood cells.

Transcription

The synthesis of a single-stranded RNA copy of a segment of DNA; only one of the two DNA strands is transcribed into an RNA.

Translation

(Protein Synthesis) is the conversion of the messenger RNA base-sequence information into the amino acid sequence of a polypeptide.

Pre-mRNA

The first form of RNA created through transcription in protein synthesis and controls both non-coding sequences (introns) and coding sequences (exons).

Mature mRNA

The second product of a transcribed gene which controls only coding sequences (exons)

RNA Polymerase

- An enzyme that catalyzes the process of transcription.

- The enzyme is also known as DNA-dependent RNA Polymerase because it uses a DNA template for the synthesis of an RNA chain.

Where does the template strand come from for the synthesis of an RNA chain?

The template strand is the 3' to 5' strand of DNA.

What direction is the synthesis of an RNA molecule?

5' to 3' direction

tRNA (Transfer RNA)

Brings amino amino acids to ribosomes during translation.

rRNA (Ribosomal RNA)

With ribosomal proteins, makes up the ribosomes--the structures on which mRNA is translated.

snRNA (small nuclear RNA)

With proteins, forms complexes that are used in eukaryotic RNA processing to produce functional mRNAs.

Promoter

A sequence upstream of the start of the gene that encodes the RNA.

The sequence serves to orient the RNA Polymerase to start transcribing at the beginning of the gene and ensures that the initiation of synthesis of every RNA occurs at the same site.

Sigma Factor

Ensures that the RNA polymerase binds in a stable way only at promoters.

Without the___________, the core enzyme can bind to any sequence of DNA and initiate RNA synthesis, but this transcription initiation is not at the correct sites.

Structural Genes

Genes that encode for a polypeptide = protein coding (enzymes and structural proteins)

Consensus Sequence

The base found most frequently at each position.

rho-dependent termination

The protein rho plays a role in the termination of transcription.

Binds to recognition site in terminator region (on mRNA). RNA Polymerase and RNA are released.

Steps of rho-independent termination

A. Sequence upstream from terminator has 2 fold symmetry.

B. RNA transcript forms stem-loop structure followed by series of Us in RNA.

C. Stem-loop plus Us causes termination of transcription - may destabilize RNA-DNA complex.

Steps of rho-dependent termination

A. rho protein with 2 domains: 1 binds RNA, 1 binds to ATP.

B. Binds to recognition site in terminator region (on mRNA)

C. When RNA Polymerase reaches the terminator, it pauses. ATP is hydrolyzed by rho and RNA is unwound from DNA template. RNA polymerase and RNA are released.

rho-independent termination

The core RNA polymerase terminates transcription. (NO rho protein).

Transcription Factors

Specific proteins required for initiation of transcription in Eukaryotes.

TATA Element

Specify where the transcription machinery assembles and determine where transcription will begin.

5' TATAAAA 3'

-30 position

CAAT Element

upstream from TATA; Promoter-proximal element; 5' CAAT 3'; -75 position.

CG element

upstream from TATA; promoter-proximal element; 5' GGGCGG 3'; -90 position.

Leader Sequence

5' untranslated region

Trailer sequence

3' untranslated region

Intron

non-coding region

Exon

Amino acid coding region

5' cap

Once RNA Polymerase III has made about 20-30 nucleotides of pre-mRNA, a capping enzyme adds a guanine, nucleotide---most commonly, 7-methyl guanosine-- to the 5' end. The addition involves an unusual 5' to 5' linkage, rather than a 5' to 3' linkage.

Poly (A) tail

Modification at 3' ends by the addition of a sequence of about 50 to 250 adenine nucleotides.

- Required for efficient export of the mRNA from the nucleus to the cytoplasm.

- Protects the 3' end of the mRNA by buffering coding sequences against early degradation by exonucleases.

Nontranscribed Spacer

Contains the promoter and terminator of the previous repeat unit.

External transcribed spacer

A piece of nonfunctional RNA, closely related to the internal transcribed space, which is situated outside structural rRNAs on a common precursor transcript.

Internal transcribed spacer

A piece of non functional RNA located between structural rRNAs of a common precursor transcript.

What spacers are removed to make a final functional rRNA molecule?

External and Internal transcribed spacers

Internal Control Region

Location of promoter elements

gene redundancy

A biochemical function is redundantly encoded by two or more genes.

Anticodon

A group of three adjacent nucleotides in a tRNA molecule that pairs with a codon in mRNA by complementary base pairing.

Peptide Bond

A covalent bond in a polypeptide chain that joins the carboxyl group of one amino acid to the amino group of the adjacent amino acid.

C-terminus

The end of a polypeptide with a free carboxyl group