Unit 3

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Unit 3

DNA replication

Lagging strand

multiple RNA primers are laid down then extended by DNA poly III

DNA polymerase I removes RNA and replaces with DNA nucleotides

primase

first makes RNA primers complementary to the DNA parent strand sequence

DNA polymerase III

synthesizes a leading strand, moving toward the replication fork.

then add nucleotides to the 3' end

SSB (single stranded proteins)

stabilize the unwound parental strands

topoisomerase

breaks and rejoins the parental DNA

Helicase

unwinds the parental DNA strands

Transcription

Travels

Towards 3' end of RNA and towards 5' end of DNA

towards 3' end of DNA and Towards 5' end of RNA

The synthesis of RNA using a DNA template.

Signals the termination of the translation process of the current protein.

A specific nucleotide sequence in the DNA of a gene that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place.

A type of RNA, synthesized using a DNA template, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.

The transcription of a protein-coding eukaryotic gene

A sequence within a primary transcript that remains in the RNA after RNA processing; also refers to the region of DNA from which this sequence was transcribed.

A noncoding, intervening sequence within a primary transcript that is removed from the transcript during RNA processing; also refers to the region of DNA from which this sequence was transcribed.

Translation

Includes

Eventually, the RNA transcript is released, the polymerase detaches from the DNA

The polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5' to 3'. After transcription has occurred, the DNA strands re-form a double helix.

After RNA polymerase binds to the promoter, the polymerase unwinds the DNA strands and initiates RNA synthesis at the start point on the template strands

The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of “language” from nucleotides to amino acids.

An RNA molecule that functions as a translator between nucleic acid and protein languages by picking up a specific amino acid and carrying it to the ribosome, where the tRNA recognizes the appropriate codon in the mRNA.

A complex of rRNA and protein molecules that functions as a site of protein synthesis in the cytoplasm; consists of a large subunit and a small subunit.

3 Active Sites

One of a ribosome’s three binding sites for tRNA during translation. The E site is the place where discharged tRNAs leave the ribosome. (E stands for exit.)

One of a ribosome’s three binding sites for tRNA during translation. The P site holds the tRNA carrying the growing polypeptide chain. (P stands for peptidyl tRNA.)

Definition To Know: Chromosomes: made of DNA and proteins; double stranded DNA with protein attached known as chromatin

When compacted, it's called a chromosome

Gene Regulation

*** BEST TO REGULATE GENE EXPRESSION AT TRANSCRIPTION LEVEL

Defintion to know: Differential Gene Expression: Differences between cell types result from differential gene expression; expression of different genes by cells with the same genome

Histones: Types: H1, H2A, H2B, H3, H4

Histone core: H2A, H2B, H3, H4

Eukaryotes

Process in steps:

Step 1: Activator proteins bind to distal control elements

Step 2: A DNA-bending protein brings activators closer to promoter, there are general transcription factors, mediator proteins, and RNA polymerase II

Step 3: Activators bind to certain mediator proteins and general transcription factors

There are control elements in DNA: Proximal control elements and distal control elements

Distal control elements: There are enhancers and bind to specific transcription factors (activators and repressors)

Location: Sequences in DNA upstream or downstream of gene; possibly close or far away from gene

Proximal control elements: sequences in DNA close to promoter as well as bind general transcription factors

There are transcription factors: General and Specific

Specific: Activators and repressors involved to either increase levels of transcription or decrease

General: background/basal level of transcription

Prokayotes

Example of regulation: Lac Operon

CAP is activated by cAMP; cAMP binds to CAP and helps RNAP bind to promoter to facilitate transcription = operon is on!

**If there is no cAMP because of the presence of glucose that blocks Adenylyl Cyclase, CAP cannot be activated and if CAP is not active, it cannot help RNAP bind to the promoter = operon is OFF!

When no lactose is present, Lac I makes a Lac repressor proteins that binds to the operator sequence and prevents expression of the lac operon structural genes

If there is also no glucose and no lactose present, the operon is ON!

When lactose is present, the gene expression will be turned on because Lac repressor protein binds to lactose; as a result, RNAp can bind to promoter

Organization of lac operon: DNA, promoter, regulatory gene, promoter for structural genes, operator, Z,Y,A genes

Structural genes for Lac Operon: LacZ, LacY, LacA

LacA: Trans-acetylase

LacY: Permease

LacZ: B-galactosidase

Positive and Negative Controls Exist

Negative Regulation: When repressor is bound to the operator, no transcription occurs; when no repressor is bound, transcription occurs

Positive Regulation: When activator is bound to the operator, transcription occurs; when no activator is present, no transcription will occur

DEFINITION TO KNOW: Operons: A cluster of functionally related genes can be under coordinated control of a single on-off "switch"