DNA Structure, Replication, and Central Dogma: Key Concepts for Biology

What is DNA made of?

5-carbon sugar, phosphate group, nitrogenous base, and a free hydroxyl group

What are phosphodiester bonds?

Bonds between adjacent nucleotides formed between the phosphate group of one nucleotide and the 3' OH of the next nucleotide

Whart is Chargaff's rule?

There is always an equal proportion of two-ringed purines (A+G) and single-ringed pyrimidines (C + T)

Describe the structure of the DNA double helix

Two grooves are formed, the major and minor grooves

- Strands connect via hydrogen bonds between bases on opposite strands (Ex: A + T)

How many hydrogen bonds are formed between A and T?

2 hydrogen bonds

How many hydrogen bonds are formed between C and G?

3 hydrogen bonds

What is antiparallel configuration?

The two strands of a single DNA have opposite polarity to one another, one end terminates in 3' OH and the other terminates in 5' PO4

What is the conservative model of DNA Replication

both strands of parental duplex remain intact; new DNA copies consist of all new molecules

What is the semiconservative model of DNA replication?

Correct model (one p + one new strand)

What three things does DNA replication require?

1. Template (Parental DNA molecules)

2. Something to do the copying (enzymes)

3. Building blocks to make copies (nucleotides)

List the stages of DNA replication

1. Initiation

2. Elongation

3. Termination

What is the function of DNA Polymerase?

to add and link nucleotides to the end of a growing DNA strand in the 5' to 3' direction

What does DNA Polymerase require to build DNA?

primer which acts as starting point for DNA synthesis, provides hydroxyl group

What does DNA Pol I do?

Replaces RNA primer (nucleotides) with DNA nucleotides

What does DNA Pol II do?

DNA repair

What does DNA Pol III do?

main replication enzyme, starts DNA synthesis at 3' end of primer, continues in 5' to 3' direction.

Define endonucleases

an enzyme that breaks down phosphodiester bonds between nucleotides internally

Define exonuclease

removes nucleotide 1 at a time from the end of a sequence (either direction 3' or 5')

What does helicase do?

Uses energy from ATP to unwind DNA

What causes supercoiling?

When unwinding of DNA introduces torsional strain it can lead to additional twisting of the helix

What are the eznymes that prevent supercoiling called?

Topoismerases

What is DNA Gyrase?

Topoisomerase II, relieves strain

How are the leading and lagging strands synthesized?

The leading strand is synthesized continiously from a initial primer while the lagging strand is synthesized discontinuously w/ multiple priming events

What are Okazaki fragments?

DNA fragments on the lagging strand

What is the replication fork?

A partial opening of helix formed where double stranded DNA is being unwound and synthesis occurs

What is the B subunit?

A ring-shaped protein in bacteria that acts like a sliding clamp on the leading strand to keep DNA POl III attached to DNA

What is processivity?

The ability of a polymerase to stay attached (Ex: DNA Pol III in leading strand synthesis bc sliding clamp results in high processivity)

Why does lagging strand synthesis require additional enzymes?

- Primase has to make RNA primer for EACH Okazaki fragment

- Requires DNA Ligase to join Okazaki fragments

- DNA Pol I has to remove multiple RNA primers

What is a replisome?

Collection of all enzymes involved in DNA replication at replication fork

What are the two main components of a replisome?

A) Primosome: Primase, helicase, and accessory proteins

B) Complex of two DNA Pol III

Why is eukaryotic replication more complex than prokaryotic replication?

A) Larger amount of DNA in multiple chromosomes

B) Linear structure

C) Chromatin

DNA Polymerase Epsilon synthesizes the ________ strand and DNA Pol Delta synthesizes the __________ strand

leading, lagging

What are telomeres?

DNA at the tips of chromosomes

What do telomeres do?

Protect ends of chromosomes from nucleases and maintain the integrity of linear chromosomes

What is telomerase?

An enzyme that adds bases to the ends of telomeres; abundant in young cells but eventually runs out.

What enzyme has proofreading abilities?

DNA Polymerase

What are the two categories of DNA repair?

Specific repairwhich targets a single kind of lesion, and nonspecific repair which uses a single mechanism for multiple lesions.

What is mismatch repair?

Removal of incorrect bases incorporated during DNA replication

- Replaces them with the correct base by copying the template strand

What is the function of the photolyase enzyme?

To absorb light in the visible range and use this energy to cleave thymine dimers (prevents cancer essentially)

List the central dogma information flow

DNA to RNA to protein

Transcription is ____ to _____

DNA to RNA

Trnaslation is ___ to ___

RNA to protein

Define transcription

The production of an RNA copy of DNA using RNA Polymerase

What is the coding strand

The strand of DNA not used as a template in transcription

What does mRNA do?

messenger, contains the information from DNA to make protein by translation

The mRNA carries information from the ____ to _____

nucleus to cyptoplasm

Define Ribosomal RNA (rRNA)

Class of RNA that makes up ribosomes, the organelles that translate mRNA

Define small nuclear RNA

Forms complexes that are used in processing of pre-mRNA (splicing)

What is a framshift mutation?

Additions or deletions of 1 or 2 nucleotides

What are the three stop codons?

UAA, UGA, UAG

"U Are Annoying, U Go Away, U Are Gone"

What is AUG

Start codon used to signify the beginning of translation

What does it mean when a code is degenerate?

Some amino acids are specified by more than one codon

What are the requirements for transcription?

1. Promoter

2. Start Site

3. Terminator

What is a promoter?

Recognition and binding site for RNA Pol

- Indicates site of initiation and direction in transcription

What does RNA Pol I do?

transcribes rRNA

What does RNA Pol II do?

Transcribes mRNA and some snRNA

What does RNA Pol III do?

transcribes tRNA and some other small RNAs

Discuss the RNA polymerase promoters

Each RNA Polymerase has its own promoter

Pol I: Promoters are species specifc

Pol II: Consists of core promoter and TATA box

Pol III: Most are found within the gene itself (downstream)

What modifications are made to mRNA in eukaryotes?

Addition of a 5' cap, a 3' poly-A tail, and removal of introns.

Introns

Non-coding sequences

Exons

Sequences that will be translated (expressed)

Describe the pre-mRNA splicing process

snRNPs recognize the intron-exon boundaries, snRNPs cluster w other proteins to form spliceosome whic does the splicing

What is splicing?

Removal of introns

Transcriptome

all the RNAs produced from a genome

Proteome

All the proteins produced from a genome

What is alternative splicing?

Process of a single primary transcript being spliced into different mRNAs by including different sets of exons

Gene _____ refers to the combined processes of transcription and translation

expression

What are the tRNA binding sites?

Aminoactylm peptidyl, exit (APE)

What happens at the Aminoacyl (A) site in translation?

Where the tRNA carrying the next amino acid binds

What is the peptidyl site?

Where the tRNA attached to the growing peptide chain binds

What is the exit site?

Holds tRNA after amino acid is released

Define Transfer RNA (tRNA)

The type of RNA that shuttles amino acids to the ribosomes;it functions as the translator from nucleotide into amino acid in protein synthesis

What is the function of peptidyl transferase?

It forms peptide bonds between AAs

- Part of the large subunit

What is the function of the small subunit in the ribosome?

To read mRNA

What is the function of the large subunit in the ribosome?

To catalyze peptide bonds between AAs

Translation elongation steps

codon recognition or decoding (A site), peptide bond formation, translocation (P + E sites)

What is the function of EF-Tu

binding and delivering aminoacyl-tRNA to the A-site of the ribosome, enahnces speed and accuracy of translation

GTP versus GDP

A GTP-bound form is active and a GDP-bound form is inactive

translation termination

Stop codons are recognized by release factors which release the protein from the ribosome

What is base substitution?

Substitution of one base for another, two categories (transition and transversion)

- Specific type of point mutation

Transition mutation

DNA substitutions within the same base class—purine to purine (A to G) or pyrimidine to pyrimidine (T to C)

Transversion mutation

purine to pyrimidine or vice versa

Silent mutation

Same AA inserted, no net effect

What is a missense mutation

Point mutation in which a single nucleotide is changed, resulting in a different amino acid

Nonsense mutation

changes the amino acid to a stop codon

What is the function of regulatory proteins?

Blocking transcription by preventing the binding of RNA Polymerase OR stimulating transcription by facilitating the binding of RNA Polymerase to promoter

What are effector molecules?

Molecules that bind in a location other than the active site that can activate or inhibit enzyme function

- act on both repressors and activators

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide into a number not divisble by three

point mutation

Gene mutation involving changes in one or a few nucleotides (swapping but not insertion/deletion)

Operon

group of genes operating together

What is the operator?

A segment of DNA within or near the promoter that acts as a switch, where a repressor protein binds to block transcription.

The leading strand synthesizes ______ the replication fork and the lagging strand synthesizes ________ the replication fork

towards, away from

Holoenzyme

the complete, catalytically active form of an enzyme, consisting of an inactive protein component (apoenzyme) and a non-protein component (cofactor or coenzyme)

How does DNA methylation affect gene expression?

methyl groups are added to segments of DNA, silencing or turning off that particular gene so no protein is produced from that gene

histone acetylation

relaxes chromatin structure (euchromatin), facilitating increased access for transcription factors and accelerating gene expression

Enhancers

Binding sites for SPECIFIC transcription factors (different than promoter which is for general transcription factors)

DNA replication in order

1. Helicase unwinds DNA

2. Supercoiling relieved by DNA Gyrase

3. Primase adds RNA Primers

4. DNA POlymerase extends DNA

5. DNA Pol replaces RNA primers

6. DNA ligase seals fragments

Translation to transcription steps in order

1. RNA Poly binds to promoter

2. Initation

3. Transcription elongation

4. RNA processng

5. RNA exits nucleus

6. Ribosome translates mRNA

SSB Protein Function

Bind to unwound DNA strand during replication so that the strands don't go back together AND to protect from degradation by nucleases

As your cells keep dividing the telomeres get shorter but this is fixed by ________ so that doesn't happen