*BIOLOGY 1345*

*Helicase*

unzips/opens DNA

Chargaff showed

that the proportion of A and T, G and C are the same, so they bind together. A (30.9%) T (29.4%) G (19.9%) C (19.8%)

Describing DNA

the antiparallel structure of the double helix affects replication DNA polymerases add nucleotides only to the free 3' end of a growing strand; therefore, a new *DNA strand can elongate only in the 5' to 3' direction*

Okazaki fragments

the lagging strand is synthesized as a series of segments called *Okazaki fragments*, which are joined together by *DNA ligase*

Replicating the Ends of DNA Molecules

the usual replication machinery provides *no way to complete the 5' ends*, so repeated rounds of replication *produce shorter DNA molecules* with uneven ends -the ends of our molecules keep getting shorter and shorter each round of replication

Elongation (gene to protein)

1) codon recognition 2) peptide bond formation 3) translocation

error rate

after proofreading repair is low but not zero

Translation Termination (when it reaches a stop codon) (gene to protein)

(there is no tRNA molecule that has a top anticodon, it has a release factor (similar, but no amino acid attached to it))

nucleotide excision repair

(when have mismatch pair) -a nuclease cuts out and replaces damaged stretches of DNA

Replication (gene to protein)

*Prokaryotes* -small, circular genomes -single origin of replication -DNA is not packed tightly and has fewer associated proteins *Eukaryotes* -long linear genomes -multiple origins of replication -DNA wrapped in histone proteins

gene parts

-*promoter*: controls how often & how much of that gene is synthesized -*transcription unit*: section of the gene that is copied into an RNA molecule

3 stages of Translation (gene to protein)

1) initiation 2) elongation 3) termination energy is required in some steps (endergonic)

origins of replication in eukaryotic cell

1) replication begins at specific sites where the two parental strands separate and form replication bubbles 2) the bubbles expand laterally, as DNA replication proceeds in both directions 3) eventually, the replication bubbles fuse, and synthesis of the daughter strands is complete

DNA polymerase

-can only replicate DNA in the 5' to 3' direction -DNA polymerase can only extend an available 3' -OH end -It needs a primer

Topoisomerase

-cuts the DNA & reattaches it -keeps process smooth (keep it from knotting up) -helps keeping tension from occurring down stream (relieves overwinding strain ahead of replication forks by breaking, swiveling, and rejoining DNA strands)

Ribosomes (gene to protein) (rRNA)

-facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis -2 ribosomal subunits (large and small) that are made of proteins and ribosomal RNA (rRNA) -rRNA is a ribozyme (catalyst)

*Primase*

-lays down a primer -the enzyme that lays down an RNA primer at the 5' end -DNA polymerase can then add new nucleotides to the free 3' end

genes

-not all genes encode proteins -one gene can make more than one protein -some genes only code for RNA

gene to protein in eukaryotic cell locations

-transcription and RNA processing: nucleus -translation: in cytoplasm (DNA never leaves nucleus)

3 stages of transcription (gene to protein)

1) *Initiation*: RNA polymerase binds to promoter region & starts the synthesizes of RNA molecule (rate limiting step) 2) *Elongation*: running down template strand (RNA polymerase moves along the gene extending the RNA chain) 3) *Termination*: reaches a stop signal & stops (transcription ends and the RNA transcript and RNA polymerase are released)

Accurate translation requires two steps (gene to protein)

1) a correct match between a tRNA and an amino acid, done by an enzyme: aminoacyl-tRNA synthetase (binds to the tRNA & the proper amino acid & attaches it) 2) a correct match between the tRNA anticodon and an mRNA codon

Missense mutations (substitution)

still code for an amino acid, but not the correct animo acid (sickle-cell disease)

Protein has how many monomers?

20

What would be the anticodon to the codon 5' AUG 3'?

3' UAC 5'

if the DNA sequence of a gene read 3' TCA 5', what would be the anticodon to the codon of the mRNA transcript?

3' UCA 5'

If 15% of DNA is adenine, what % is guanine?

35%

DNA has how many monomers?

4

What is important piece of information did Chargaff's rule provide in the deciphering of DNAA structure?

A pairs with T C pairs with G

chromosomes contains

DNA and protein

DNA damage

DNA can be damaged by exposure to harmful chemicals or physical agents such as cigarette smoke & x-rays; it can also undergo spontaneous changes

Transcription (gene to protein)

DNA to RNA -RNA is made in the 5' to 3' direction using the 3' to 5' DNA strand as template

Ribosome (gene to protein)

E: exit P: polypeptide, tRNA is going to reside here, (it has a polypeptide chain growing off of it) A: new amino acid coming in

Alteration of mRNA ends (gene to protein)

Each end of pre-mRNA molecule is modified in a particular way -the 5' end receives a modified nucleotide *5' cap* (pre-mRNA molecule in eukaryotic cells) -the 3' end gets a *poly-A tail* These modification share several functions -they ca seem to facilitate the export of mRNA to the cytoplasm -they protect mRNA from hydrolytic enzymes (from being chopped up) -they help ribosomes attach to the 5' end ^to start translation

(1) Nucleosomes

Histone attaching -wrap DNA around it, to bind it

What is the precise nature of the genetic material that is transferred into the bacteria and changes it's pathogenicity?

It is DNA

Why 'nucleic acids'?

So called because they are found within the nucleus of cells

DNA backbone

sugar/phospate -phosphodiester bond (covalent bond)

Eukaryotic cell transcription (gene to protein)

TATA box -requires a bunch of other proteins to bind before the RNA polymerase can begin

gene to protein in prokaryotic cell locations

all stages (transcription/translation) in cytoplasm (no nucleus)

U replaces T

U & A bind G & C bind

the molecule associated with an anticodon is

tRNA

Transformation

a change in genotype and phenotype due to assimilation of foreign DNA (somehow the trait of being pathogenetic, being able to infect hosts, was transferred from the dead S strain over to the R strain) -picking up DNA from the dead cells & incorporating it to their genome

Insertions and Deletions

are additions or losses of nucleotide pairs in a gene -these mutations have a disastrous effect on the resulting protein more often than substitutions do -insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation (silent, missense, nonsense) -an insertion or deletion usually causes a frameshift which means they normally don't cause silent mutations, but rather missense or nonsense mutations

Processing Eukaryotic mRNA (gene to protein)

before it can be used to produce protein, pre-mRNA must be processed

Single-stand binding proteins

binds to and stabilizes single-stranded DNA until it is used as a template -helps strands stay apart

DNA polymerase ("Hand" Model)

brings in appropriate base that will match to the next nucleotide on the template stand and then it attaches it to OH on the 3 prime end

multiple RNA polymerases (gene to protein)

can bind to a gene and transcribe it producing large quantities of mRNA which can then be translated

RNA polymerase (gene to protein)

catalyze the assembly of RNA nucleotides into an RNA strand -opens up DNA, attaches itself & synthesizes the mRNA molecule

Nonsense mutations (substitution)

change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein

DNA polymerase can

check and correct its work

*DNA ligase*

close them (okazaki fragments) off -sealing fragments together -joins Okazaki fragments of lagging strand; on leading strand, joins 3' end of DNA that replaces primer to rest of leading strand DNA -seals gaps up

mRNA

copy of the gene we just made

polysomes/polyribosomes (gene to protein)

each mRNA molecule can have several ribosomes bind to it

Complementary

each strand always match up to specifics -A & T -G & C

Hershey and Chase concluded

that DNA, not protein, is the heredity material

Semiconservative replication

each strand comes apart, acts as a template strand & a new strand is made to each old strand -our two new molecules have half new DNA and old DNA (THE ONE IN OUR DNA)

A bacterial cell (gene to protein)

ensures a streamlined process by coupling transcription and translation bacteria can have translation occur before transcription is eve finished (can not happen in eukaryotic cells)

*Primase*

enzyme that lays down the primer that is necessary for polymerase to be able to add the nucleotides

exons (gene to protein)

expressed, usually translated into amino acid sequences

RNA polymerase needs a primer to initiate production of mRNA

false

wobble (gene to protein)

flexible pairing at the third base of a codon, and allows some tRNAs to bind to more than one codon

The Flow of Genetic Information (gene to protein)

genes found in DNA -the information content of genes is in the specific sequences of nucleotides -proteins are the links between genotype and phenotype -*gene expression*, the process by which DNA directions protein synthesis, includes two stages: transcription and translation

codon

group of 3 nucleotides, always red together -must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced

charges t-RNA (gene to protein)

has its amino acid attached to it

Silent mutations (substitution)

have no effect on the amino acid produced by a codon b/c of redundancy in the genetic code

DNA

heredity material

The bases in DNA pair up by forming

hydrogen bonds

Termination of Transcription (gene to protein)

in bacteria: the polymerase stops transcription at the and of *the terminator* and the mRNA can be translated without further modification in eukaryotes: it is more complicated and the mRNA has to be modified before it can translated to protein

genetic code

is redundant: several codons that may code for same amino acid -not ambiguous: same codon will always give you the same amino acid -is universal: does not matter what you are (fly, anime, plant, fish, bacteria) the codons signal for the same animo acid

Discontinuous DNA synthesis

lagging stand

Continuous DNA synthesis

leading strand, 5' to 3'

the molecule associated with a codon is

mRNA

Translation (gene to protein)

mRNA to protein

alternative splicing (gene to protein)

many pre-mRNAs are processed by reactions that join exons in different combinations (*alternative splicing*) to produce different mRNAs from a single gene -consequently, the number of different proteins an organism can produce is much greater than its number of genes -one gene can code for many several different proteins, has to do with how our cells splice exons and introns

Mutation that causes sickle-cell disease?

missense

polypeptide chain are (gene to protein)

modified after translation or targeted to specific sites in the cell (some) (can go to ER & golgi apparatus) -polypeptide synthesis always begins in the cytosol -synthesis finishes in the cytosol unless the polypeptide signals the ribosomes to attach to the ER -polypeptides destined for the ER or for secretion are marked by a signal peptide (ribosomes are identical and can switch from free to bound)

tRNA

needed for translation -wind into four double-helical segments, forming a cloverleaf pattern when viewed in a 2 dimension -*anticodon*: the three-nucleotide segments that base pairs with a codon in mRNAs (reads the codon in the mRNA) -the other end links the amino acid corresponding to the anticodon

Transcription of Non-Protein-Coding Genes (gene to protein)

non-protein-coding genes that encode ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) are not translated

introns (gene to protein)

noncoding regions (prokaryotes do not have it)

The DNA in the nucleus is organized by being wrapped around histone proteins in a 'beads-on-a-string' structure known as a:

nucleosome

telomeres

parts that get shorter -do not code for anything important -no genes in our regions is this a problem for prokaryotes? no, b/c their DNA is circular

sequence changes may become

permanent and can be passed on to the next generation, if it occurs on gametes -these changes (mutations) are the source of genetic variation upon which natural selection operates 99% of the time mutations are neutral

mRNA splicing (gene to protein)

occurs in the nucleus, removes introns from pre-mRNAs and joins exons together

mismatch repair

of DNA, repair enzymes correct errors in base pairing (ex: A binds to C)

point mutation

one nucleotide that has been changed

Template strand (gene to protein)

only reading, RNA

In the double helix which of the following is correct?

pyrimidines bond with purines

*DNA Polymerase 1*

removes that primer & adds correct nucleotides -Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides

Nucleotide-pair substitution

replaces one nucleotide and its partner with another pair of nucleotides

rRNA

ribosomal

Initiation (gene to protein)

ribosome, mRNA, first tRNA come together 1) small ribosomal subunit binds to mRNA 2) large ribosomal subunit completes the initiation complex

Anti-parallel

runs 5'3, 3'5

in eukaryotes, RNA polymerase 3 (gene to protein)

transcribes tRNA genes and the gene for one of the four rRNAs and *RNA polymerase 1* transcribes the genes for the three other rRNAs -promoters for these genes are specialized for the correct RNA polymerase type -in bacteria, only a single RNA polymerase the exists, and it transcribes all types of genes

The production of RNA from DNA is called

transcription

The production of protein from RNA is called

translation

DNA polymers 3

using parental DNA as a template, synthesized new DNA strand by adding nucleotides to an RNA primer to a pre-existing DNA strand