• synthesized in fragments of RNA primer, RNA, and DNA ligase
• synthesized discontinuously
• synthesized away from replication fork

1. backbone made from sugar and phosphate group of deoxyribonucleic acid

2. series of nitrogen-containing bases that project from backbone

• one end has exposed hydroxyl group on the 3' carbon
• Other end has exposed phosphate group at the 5' carbon

A-hydrogen bonds-T

G-hydrogen bonds-C

parent strands of DNA separate and each strand is used as a template for synthesis of a new strand

daughter strands consist of one old and one new strand of DNA

• enzyme that catalyzes the synthesis of DNA
•  (DNA ONLY)
• can only work in one direction
• can add deoxyribonucleotides at the 3' end
• therefore they only work in 5-3 direction
• EXERGONIC

• monomers that act as substrate
• high potential energy due to 3 phosphate groups

• forms in chromosomes that are being replicated
• grow as DNA replication proceeds because it is bidirectional
• eukaryotic cells have multiple replication bubbles (because they have multiple origins of replication)

• the specific point in bacterial chromosomes where replication occurs
• prokaryotes have only 1 because they are circular
• eukaryotic cells have multiple origins because they are linear

• begining of all DNA synthesis
• y shaped regionwhere DNA is split into 2 separate strands for replication

• enzyme that catalyzes the breaking of hydrogen bonds between 2 DNA strands

• few nucleotides bonded to template strand
• needed by DNA polymerase (because it provides a free hydroxyl group that can be combined with an incoming dNTP to form a phosphodiesther bond)

• type of RNA polymerase
• synthesizes a short strand of RNA
• this RNA strand serves as a primer for DNA synthesis

• DO NOT CONTAIN GENES
• short repeating stretches of bases

telomerase adds enough of a repeating base to the end of the lagging strand catalyzing DNA synthesis.

Primase makes and RNA primer for the telomeres, DNA polymerase uses that primer to synthesize the lagging strand, and ligase connects them

removes deoxyribonucleotides from DNA

DNA polymerase III's epsilon subunit can do this

• Often cause of cancer
• mutations in genes often lead to tumors if they go unrepaired
• Defects in repair genes make the cell more susceptible to the mutations that cause cancer

changes in DNA ranging from one base to a whole section of a chromosome

MAY or MAY NOT result in a phenotype

null/loss-of-function allele

Nonfunctioning alleles

• Beadle & Tatum
• proposes that each gene contains info on how to make 1 enzyme

requires the action of 3 enzymes to produce an amino acid

ex: Arginine in N. crassa (Srb & Horowitz tested this)

DNA codes for RNA which codes for proteins

DNA codes for sequence of bases in the RNA which codes for specific amino acids in proteins

• DNA is transcribed to mRNA by RNA polymerase
• process by which hereditary information from DNA is copied to RNA

• generate DNA from RNA
• viral polymerase

• AUG
• found in mRNA

• found in mRNA
• stop coding for amino acids
• UGA, UAA, UAG

• redundant - all (but 2) amino acids encoded by more than 1 codon
• unambiguous - 1 codon never codes for more than 1 amino acid
• universal - almost all codons specify same amino acid in other living species
• conservative - when codons specify same amino acid, they usually have the same first 2 bases

do not affect organism's fitness

ex: silent mutation

addition or deletion of a chromosome

(chromosome level mutation)

when sections of the chromosome breaks and moves around before rejoining the chromsome again

chromosome composition change

when section of a chromosome breaks off and attaches to another (different) chromosome

chromosome composition change

• occurs when the cell does not produce mRNAfor a specific enzyme.
• slow but efficient
• the cell avoids the production of these enzymes by utilizing regulatory proteins that prevent RNA polymerase from binding to a promoter

• allows the cell to prevent translation of an mRNA molecule that has already been transcribed

1. regulatory molecules can speed up mRNA degredation
2. translation initiation can be altered
3. translation proteins can be affected

translational control info flow

• cell fails to activate a manufactured protein by chemical modification
• controls actual polypeptides

• enzyme (in E. coli cells) cleaves lactose in order to produce glucose and galactose. 
• only present when lactose is in cell

molecule that stimulates expression of a specific gene

ex: lactose in E. coli, it induces Beta-galactoside to cleave the lactose and form glucose and galactose

deiscovered that mutant E. coli cells could not metabolize lactose

gene must be present to produce enzyme and thus protein

1. isolte large number of individuals with mutations in random locations in their genome
2. use genetic screening on the mutant individuals with defects in the process or pathway in question

• used to identify mutant cells

• 4 steps:

1. grow bacterial colonies on "master plates" containing a medium with many sugars
2. transfer cells from each colony to a piece of sterilized velvet
3. trnsfer cells to a plate with a medium of only lactose to screen for colonies that could not grow on lactose. This is the replica plate
4. compare colonies on the master plate and replica plate

• allow researchers to direclty observe with metabolic deficiencies

• produce Beta-galactosidase and galactosdie permease when lactose is abset
• aka constitutive mutants

the inducer binds to the repressor which causes it to release from the operator (this ends negative control)

ex: lactos (inducer) binds to lacI (repressor) and ti then releases from the operator

transcription is reduced because when its product(s) is already present the cell does not need to produce more

ex: if glucose (a product of lactose) is already present then the transcription of the lac operon is reduced because it does not need to produce more by cleaving lactose and thus using more energy

when one of the product molecules (catabolite) of reactions represses production of enzymes responsible for reaction

ex: glucose is the catabolite repressor for lac operon

• regulates CAP by binding to it
• when CAP and cAMP are bound they can bind to DNA
• low levels, CAP not active and transcription is not increased

translate mRNA into protein (with help of tRNA)

used for transcription

does NOT require a primer

5'-3' direction

used for templated-directed synthesis in 5'-3' direction

requires RNA primer to begin transcription

First step in transcription

requires Sigma to bind to polymerase first

protein subunit in bacteria

binds to RNA polymerase to make it "active"

type of allosteric regulation

binding site of holoenzymes and where transcription begins

40-50 base pairs

10 bases upstream from transcription start site

TATAAT sequence

35 bases upstream from +1 site (starting site of transcription)

TTGACA

proteins that bind to DNA promotors and start transcription

Eukaryotic cells only

similar function as Sigma in bacteria, but NOT a holoenzyme, it is a group of proteins

• Allows Sigma to open DNA and let a template strand go into RNA polymerase active site
• ribonuceloside triphosphate goes in and binds to complementary base on the DNA strand and allows polymerazation to begin
• Sigma then dissociates the core enzymes when initiation is finished

• transcription ends
• RNA polymerase encounters termination signal in DNA template

• Bacteria
• termination signal
• causes RNA polymerase to separate from RNA, this causes the process to end

coding area in Eukaryotic cells

part of final mRNA product

intervening, non-coding sequence

spliced from mRNA (edited)

NOT part of mRNA

product of RNA polymerase synthesis in eukaryotic cells

contains introns and exons

• spliced
• 5' Cap
• Poly (A) tail

recognition signal for translation machinery

directs the ribosomes for translation process

1. mRNA codons and amino acids interact directly
2. Crick said an adapter molecule holds amino acids in place while interacting directly and specifically with a codon in mRNA

(Crick) because there are 61 codons and only abour 40 tRNA, Crick said that some anticodons from tRNAs can still pair with a codon whose third base pair is nonstandard

SO 1 tRNA can bind with more than one codon

protein in ribosome

• small subunit holds mRNA in place during translation
• large subunit where peptide bonds form
• during translation, 3 distinct tRNAs line up with ribosome

acceptor site for aminacyl tRNA

1. aminoacyl tRNA carries correct anticodon for mRNA codon enters A site
2. peptide bond forms between amino acid on the aminoacyl tRNA in the A site and the growing polypeptide on the tRNA in the P site
3. ribosome moves ahead 3 bases and all 3 tRNAs move down 1 position, then tRNA exits ribosome through E site

1. mRNA binds to small subunit in ribosome
2. initiator aminacyl binds to the start codon
3. the large ribosomal subunits bind and complete the complex