General Biology Exam 4

As DNA replicates it will

produce errors

Replication

occurs extremely rapidly
-incorporates 1000 base pairs per second
-error in 1 base per million
-every time cells divide, there are 60,000 mutations

3 DNA repair mechanisms

1. Proofreading mechanism (DNA polymerase)
2. Mismatch repair (methylation)
3. Excision repair

Proofreading mechanism (DNA Polymerase)

happens during replication; DNA polymerase has the ability to proofread
-as bases are added, DNA polymerase will proofread the DNA
and make sure the correct base is added
-if polymerase recognizes an error, it will remove the base and
the correct one will be added

Mismatch repair (methylation)

happens right after DNA replication; if there is an incorrect base pairing, DNA polymerase 1 will repair it
-newly synthesized DNA will be scanned for mismatch DNA pairs
-this happens before the new strand is methylated
-allows for recognition between the old and new strand

Methylation

as DNA exists, methyl is added
-the new strand is not yet methylated, so it knows what to repair
-gets rid of mutation do it doesn't go to new generations

Excision repair

occurs throughout the life of a cell and happens anytime you have physical damage to a cell
-creates thymidine dimers
-no pairs to A (T-T)
-cells are constantly being inspected for DNA damage and
modified bases
-the regions will be removed
-DNA polymerase will repair the DNA
-DNA ligase will seal up the DNA strand
-individuals have mutated excision enzymes
*Xeroderma Pigmentosum

Xeroderma Pigmentosum

these individuals cannot go out into the sun; they need to be completely covered or they get severe burns

Polymerase Chain Reaction (PCR)

used to make multiple copies of DNA very rapidly
-can be used for:
*DNA analysis
*Genetic research
*Synthesize proteins
*Diagnose diseases
have a template of DNA that you will replicate

Thermophilic DNA Polymerase

heat it up and it still remains active
-doesn't destroy proteins

What is required for a polymerase chain reaction?

-dATP (C, G, T)
-Primer
-Template
-Heat and cool process (continuous)

Gene Expression

DNA is transcribed into mRNA
-mRNA will be translates into a polypeptide

Gene

a DNA sequence found at a particular location on a chromosome
-going to require molecular machinery to be expressed

Beadle and Tatum

experiments with bread mold
-haploid; mutations are seen easily
-if you alter a gene, you alter the phenotype
-alter expression of an enzyme

Mutagen

alters DNA, creates a mutation

Prototroph

wild type mold
-they will create mutagens that will fit the Arginine mold

Autotroph

mutant mold
-they will create mutagen that will fit the Arginine mold

Conclusion of Beadle and Tatum's experiment

one gene for each enzyme in the metabolic pathway
-sometimes enzymes have multiple subunits that are made by
different genes
*One polypeptide per gene
-all mutations have a problem with Arginine pathway
*Intermediates are formed along the pathway
-depending on which enzyme is mutates, it requires different
nutrients

DNA to RNA

transcription

RNA to polypeptide

translation

Transcription happens in the

nucleus

Translation happens in the

cytosol

RNA

-has ribose sugar
-generally single stranded
*Has double stranding situations
-has 1 base that is different
*Uracil not thymine
*AU

3 types of RNA

mRNA
t RNA
rRNA

mRNA

messenger RNA
-made through transcription in the nucleus
-will leave the nucleus
-serves as a template for making proteins/polypeptides in the
cytosol

tRNA

transfer RNA
-double stranded RNA
-used for translation
*Specifies amino acid to be incorporated

rRNA

ribosomal RNA
-produces ribosomes

Viral RNA

uses RNA to make RNA
-flu
-polio

Retroviruses

converts RNA core into DNA (reverse transcriptase)
-HIV
-HPV

Transcription (DNA-->RNA)

1. DNA template
-complementary base pairing (CG, AU)
2. Ribonucleoside Triphosphates
-substrates
*ATP, CTP, GTP, UTP
3. RNA polymerase
-to form RNA polymers
-one strand of DNA will be used as a template
*Double helix partially unwinds
*RNA strand will peel away from the template
*Portion of DNA used will rewind and mRNA will be released

Transcription steps

1. Initiation
2. Elongation
3. Termination

1. Begins at a promoter (Transcription Initiation)

-the ability for this promoter to bind depends on the gene
-promoters are variable
*Some will bind RNA polymerase easier

Promoter

special sequence of DNA that RNA polymerase can bind to

2. Elongation (Transcription)

-RNA polymerase unwinds the DNA 20 base pairs at a time
-the new RNA will elongate from 5' to 3' end
-antiparallel to the template

3. Termination (Transcription)

-there will be a sequence in the DNA that specifies termination
*At the end of the gene
-2 ways transcript can be released
*Transcript falls away from the DNA
*Require a helper protein to remove the transcript

Translation

-prokaryotes have no nucleus
*Translation can begin before transcription is done
-eukaryotes must complete transcription
*Modify RNA---> Leave nucleus
*Then translation can begin

mRNA processing

pre mRNA---> mature mRNA
-on the pre mRNA strand you have introns
*Remove introns located between exons
*Exons remain and will be expressed; joined
*Splicing^

Alternative splicing (mRNA processing)

joining different exons together to create a mature RNA

Spliceosome

removes introns from in-between exons

Poly a Tail

allows mRNA to leave the nucleus; binds at 3' end (necessary for transcription)

Guanine cap (G-Cap)

added to the mRNA, allowing it to bind to the ribosome

Universal genetic code

will determine which amino acids are used to make a protein
-relates DNA to RNA and ultimately to incorporating amino acids

Codon

mRNA is read in 3 bases segments
-there are 64 different codons
-code for 20 different amino acids

Start codons

AUG (specific methionine)

Stop codons

UAA, UAG, UGA

There will be amino acids that have

more than one codon

Each codon is assigned only

only 1 amino acid

Genetic code is represented in

mRNA

Wobble effect

you can have a modification in the third base of your codon, and it can be tolerated because often a change in the third base will still incorporate the same amino acid

Translation happens in the

cytosol

Translation requires

mRNA
tRNA
ribosome

There is a specific tRNA for

each of the 64 codons

tRNA will carry

an amino acid

tRNA has an anti-codon at

the midpoint which associates complementary to the mRNA codon

Each one of the tRNAs will have a specific aminoacyl-tRNA synthase

that will add the amino acid to the tRNA

Ribosomes are the

site of protein synthesis

2 subunits of ribosomes

1. small
2. large

Ribosomal subunits are separated until

they associate with mRNA when translation begins

Large Subunit (4 sites)

1. T site: where tRNA associates with ribosome
2. A site: tRNA anti-codon binds with mRNA codon
3. P site: tRNA adds amino acid to growing polypeptide chain
4. E site: exit site; tRNA enters E site just before it leaves ribosome

Small Subunit

will validate that the 3 base segments will match up between the mRNA codon and the tRNA anti-codon
-appropriate hydrogen bonding

Initiation (translation)

-translation begins when you form the initiation complex
-the enzyme involved is initiation factor
-the initiation complex will bind upstream of the actual reading frame and then slides along until it located AUG

Initiation complex

includes tRNA, AUG, ribosomal subunits, mRNA

Elongation

-incorporating amino acids and elongating the polypeptide chain
-the ribosome moves along from the 5'-->3' direction on the mRNA
-incorporating amino acids, you add to the carboxyl end
-the large subunit will catalyze 2 reactions
-tRNA is going to join, releases methionine
*Will dissociate from the ribosome
-the 2nd tRNA will slide to the P-site
*Has 2 amino acids (methionine and its own)
-the next tRNA will enter A-site and slide to P-site and a peptide bond will form between its amino acid and the growing polypeptide chain
-previous tRNA slides to E-site and leaves

2 reactions the large subunit catalyzes in elongation (translation)

1. break the bond between the tRNA (in the P-site) and its amino acid
2. forms the peptide bond between the amino acid and the growing peptide chain
-peptidyl transferase (helps form bond)

Elongation factor (enzyme)

helps tRNA leave the ribosome

Termination (translation)

-done translating; incorporates a water molecule but not on an amino acid (stop codon)
-you encounter a releasing factor that tells the ribosome the peptide is complete

When you have translation and want to make a lot of a protein you can assemble

a polysome

Polysome

when you have an mRNA molecule with more than one ribosome attached
-makes protein synthesis quicker
-make more proteins simultaneously

Once protein is translated it can have

additional modifications

Protein can be released into

the cytoplasm

A ribosome can begin translation then stall translation and relocate to the

rough endoplasmic reticulum
*Once the polypeptide chain and ribosome arrive at the rough
E.R. the polypeptide can be fed into the E.R. and translation will
continue

Ribosomes are associated with the

Rough E.R.

If proteins need to go to other places within a cell, they need a

localization signal

Localization signal

part of the amino acid sequence
-when the protein or polypeptide arrives at the organelle, the
signal allows it to enter the organelle

If a ribosome goes to the E.R. there will be a

signal recognition particle

Signal recognition particle

-it will bind to a signaling sequence and direct the ribosome to E.R. membrane
-the particle will then bind to a receptor
-as translation is occurring, the polypeptide is being fed into the lumen of the E.R.
-the signaling sequence is cleaved
-once translation is complete, the polypeptide is in the rough E.R.
-from the rough E.R. these proteins will be modified and packaged and put into the vesicles and fuse with golgi
-from the golgi the proteins are put into vesicles and secreted from the cells (exocytosis)

Once your protein is translated

you can have post transitional processing of proteins

Proteolysis

cleave the protein into smaller parts

Glycosylation

add sugars to proteins

Phosphorylation

add phosphate group to proteins

A mutation is

any change in DNA that is passed to daughter cells

2 types of cells in the body

-Somatic cells: all cells that are not gametes
-Germ Line cells: sex cells or gametes

Somatic cell mutation

it will not be passed on to offspring

Germ line cell mutation

a mutation in the gametes that will be passed to future generations

Visible (phenotypic) mutation

easily detectible; seen by the eye

Metabolic mutation

not readily detectible by sight

Silent mutation

codes for a functional protein

Loss of Function Protein

codes for a nonfunctional protein

Gain of Function Mutation

codes for a new protein function

Point mutation

mutation in a single base/gene

-silent mutation
-missense mutation
-nonsense mutation
-frame-shift mutation

Silent Mutation

does not change the amino acid that is incorporated (wobble effect)

Missense mutation

causes an amino acid substitution, reduces the function of the protein or disable the protein

Nonsense mutation

base substitution that changes a codon that would incorporate an amino acid to a stop/termination codon (stops translation entirely)

Frame- shift mutation

occurs when you insert or delete a base, will change the entire reading frame from that point on

Chromosomal mutation

changes the arrangement of chromosomal DNA

-deletion
-duplication
-inversion
-translocation

Deletion

the loss of a chromosomal segment

Duplication

duplicating a section of your chromosome

Inversion

occurs when a chromosomal segment breaks away and rejoins in an opposite orientation (inverted)

Translocation

when a portion of a chromosome breaks off and attaches to another chromosome (translocate)

Two ways mutations can occur

1. Spontaneous
2. Induced