GN 311 Exam 4 Studying

Alkaptonuria

1902, a build-up of homogentisic acid in cartilage, urine, skin and nails
-can lead to joint problems, heart valve problems, hearing loss
-suggested relationship between genotype and protein
-absence of homogentisate activity

PKU (phenylketonuria)

leads to accumulation of phenylpyruvic acid in the brain

Albinism

inability to produce melanin pigment, causing vision problems
-recessive disorder

metabolic pathways

stepwise series of reactions
-if there is a mutation in a gene coding for a particular enzyme, a metabolic block occurs

Beadle and Tatum

one gene one enzyme hypothesis

Auxotroph

requires some chemical for growth- won't grow on minimal media

Prototroph

will grow on minimal media since it is capable of synthesizing all other nutrients that it needs for growth

cystic fibrosis

mutation in a structural protein, causing mucus accumulation in lungs

sickle cell anemia

defective hemoglobin molecule has one amino acid substitution (GAG to GUG)
-cells dont get enough oxygen since His cannot bind as well

Somatic mutations

occur in non-reproductive cells and passed to new cells through mitosis, creating a clone of cells having the mutant gene

Germline mutations

mutation in a cell that produces gametes, passed to one half members of next generation

mutations can cause

loss of function or gain of function

point mutations

substitution of one base for another

transition mutation

purine to purine or pyrimidine to pyrimidine

transversion mutation

purine to pyrimidine or vice versa

Missense (nonsynonymous)

changes the amino acid (may alter protein function or protein is nonfunctional)

Nonsense

changes the amino acid to a stop codon

Silent (synonymous)

codes for the same amino acid

readthrough

stop codon is changed to a codon that codes for amino acid resulting in a longer protein

reverse mutations

mutant phenotype to wild type phenotype

intragenic mutation

within the same gene as mutation being suppresed

intergenic

occurs in a different gene (eg. Mutation in anticodon of tRNA reverses effects of initial mutation)

intergenic suppressor mutation

occurs in a gene other than the one bearing the original mutation, alters translation
-produces an individual that has both the original and suppressor mutation, but wild type phenotype

spontaneous point mutations

occur under normal conditions

Depurination

removes a purine base from a nucleotide at either G or A bases, results in apurinic site (missing purine)

Deamination of Cytosine

results in Uracil. Causes GC to AT transition, remove amino group

Wobble Base Pairing

mispairing due to flexibility in helix, results in transitions after replication, causing replication errors
-2 rounds of replication are needed to alter both strands of the DNA

5-bromouracil

normally pairs with adenine, but can also pair with guanine
-may become incorporated into DNA in place of thymine during replication, producing an incorporation error. it may mispair with guanine in the next round of replication, then pair with cytosine leading to a permanent mutation.
-if it pairs with adenine, no replicated errors occur

2-aminopurine

normally pairs with thymine, but can also pair with cytosine

Base analogs mispair more frequently than normal bases

-requires round of replication to incorporate base analog
-requires 2 more rounds of replication to obtain complete transition

oxidating agents

damage DNA and cause mutations
-oxidative rxn converts guanine into 8-oxyguanine, pairing with adenine instead of cytosine during replication
-the adenine may pair with normal thymine during the next round of replication causing GC to TA transversions

inter calculating agents

may produce mutations by sandwiching themselves between adjacent DNA, distorting the 3D helix

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

supressor mutation (+ -)

cancel each other out

Triple mutation (+++) or (---)

shifts back into frame

Strand slippage

can cause frameshift mutation
-newly synthesized strand loops out, resulting in the addition of one nucleotide on the new strand
-template strand loops out, resulting in omission of one nucleotide on the new strand

unequal crossing over

Misalignment of the two DNA molecules during crossing over, resulting in one DNA molecule with an insertion and the other with a deletion

Fragile X Syndrome

Extra copies of a trinucleotide repeat (CGG) on the X chromosome, can cause severe intellectual disability

X rays can cause chromosome breakage

caused by breaking phosphodiester bonds
-X rays can also damage bases and cause point mutations

UV Light

can cause pyrimidine dimer formation (mainly Thymine dimers)
-distort the double helix and inhibit replication

Xeroderma pigmentosum

human disorder where a repair mechanism is defective. Results in tumors on skin surface
-due to faulty nucleotide excision repair of thymine dimers

Transposable genetic elements

-can move from one site to another site
-can move to a different chromosome
-can alter phenotypes when they move by disrupting a gene or regulatory area

Ac (activator)

transposable element with functional transposase

Ds (dissociation)

does not contain a functional transposase gene (deletion) so it requires the AC transposase to move

replicative transposition

(copy and paste), uses transposes to move a copy

nonreplicative transposition

(cut and paste), uses transposes to move the original transposon and inset into a new site
-Ac-Ds in maize

retrotransposons

uses reverse transcriptase to create DNA from element's RNA

Transposable element insertion

mechanism for insertion

1. Staggered cuts made in target sequence
2. Transposable element (insertion sequence) inserted into target
3. Gaps filled in by DNA polymerase and nicks sealed

Purpose of transposons

Arabidopsis: Regulate plant growth
Humans: Antibody formation
Drosophila: Telomerase enzyme not present, ends of chromosome have transposon type sequences… similar to telomerase
Bacterial Genes can move between chromosome and plasmids with transposons, once drug resistant, can spread to other bacterial species

Direct repair

does not replace altered nucleotides but, instead, changes them back into their original (correct) structures
-one enzyme recognizes mutation and fixes by itself
-in bacteria--> photo reactive repair, enzyme photolyase absorbs light and clips dimer
-repairs pyrimidine dimer

methyltransferase

restores correct form to incorrectly methylated guanine bases
-removes methyl group

proofreading during replication

-Correction of errors in base pairing made DURING replication by DNA polymerase
-DNA polymerase stalls replication
-Exonuclease from the DNA polymerase removes incorrect nucleotide and then DNA polymerase insets the correct nucleotide

mismatch repair

The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides. In E.coli, methylation distinguishes old DNA from new DNA. Just after replication the new strand is not yet methylated unlike the old strand
-repairs replication errors including misfired bases and strand slippage

mismatch repair proteins

recognize abnormal helical structure and identify the incorrect base

exonucleases

remove an area of the new strand from the methylated sequence to the mismatch

DNA polymerase

fills in the gap and ligase seals the nick. Does not remove lesions (damaged DNA)

Nucleotide Excision Repair (NER)

Repairs bulky lesions that alter/distort double helix
-strands of DNA are separated and held apart by SSBPs
-enzyme cleaves sugar phosphate bonds on both sides of lesion removing several nucleotides including the defective area
-DNA polymerase fills the gap and DNA ligase seals nick

Base Excision Repair (BER)

removes modified bases
-glycoslysases recognize and remove defective bases resulting in an AP Site
-then AP endonuclease cleaves the phosphodiester bond next to the missing base (causes a nick) and then removes the rest of the nucleotide
-DNA polymerase fills in the gap and DNA ligase seals the nick

homologous recombination repair

• Uses the sister chromatid to repair the break
• Uses the many of the same enzymes as homologous recombination in meiosis
  • BRCA1, BRCA2
  -repairs double strand breaks

nonhomologous end joining

A quick-and-dirty mechanism for repairing double-strand breaks in DNA that involves quickly bringing together, trimming, and rejoining the two broken ends

results in a loss of information at the site of repair.
-often leads to translocations, deletions, and insertions

translesion DNA polymerases

-specialized polymerases that can bypass lesions on the DNA during replication
-these polymerases often make errors
-these polymerases allow replication to proceed at the cost of introducing mutations

Structural genes

encode proteins that are used in metabolism or biosynthesis or that play a structural role in the cell

regulatory genes

Encode products that interact with other sequences and affect the transcription a/o translation of these sequences

regulatory elements

DNA sequences that are not transcribed but play a role in regulating other nucleotide sequences

domain

a discrete structural and functional region of a protein

constitutive

expressed all the time

motifs

simple structures that can fit into the major groove of the DNA double helix

helix-turn-helix

two alpha helices connected by a turn- common in bacteria

zinc finger

a loop of amino acids containing a zinc ion- eukaryotes

leucine zipper

basic arms bind the DNA, not the zipper- eukaryotes

Rapid turn ON or rapid turn OFF

Provides the ability to respond rapidly to sudden changes

Sequential Gene Expression

cascades of gene expression that turn on in order- these are frequently cyclical

constitutive expression/ housekeeping genes

Continuously expressed under normal conditions - always ON such as rRNA and tRNA genes

Positive control

Regulator protein (activator) binds to DNA to stimulate transcription

negative control

Regulator protein (Repressor) binds to DNA to prevent transcription

inducible control

Transcription is normally off and is turned on when a small molecule binds the regulatory protein

repressible control

Transcription is normally on and is turned off when a small molecule binds the regulatory protein

operon

a group of structural genes plus sequences that control transcription

Lactose

broken down into galactose and glucose with the enzyme beta-galactosidase

Regulatory gene

lacI- codes for repressor

Promoter

lacP- binds RNA polymerase to allow transcription

Operator

lacO- interacts with repressor

structural genes of lac operon

-lacZ: B-galactosidase
-lacY: permease
-lacA: transacetylase

polycistronic mRNA

is produced during transcription. this is translated into the three separate products

normal operation of the lac operon

-Lactose absent: the regulator protein (a repressor) binds to the operator and inhibits transcription
-lactose present: some of it is converted into allolactose, which binds to the regulator protein making it inactive, and cannot bind to the operator so transcription occurs

The lac operon in E. coli

is negative inducible

mutations of lac operon

cis acting: action of an element affects only the genes adjacent to it
trans acting: diffusible product is produced, the mutant gene does not have to be adjacent to the other genes to affect them

regulatory gene

I+ : normal repressor
I- : repressor cannot bind operator due to repressors bad binding site
Is : repressor cannot bind allolactase (s= super repressor)

operator

Oc : constitutive operator, operator cannot bind to repressor

promoter

P- : promoter cannot bind to RNA polymerase

Z-, Y-, and A-

result in defective enzymes

Glucose presence

if it is present, cAMP in cells go down

if absent, cAMP in cells go up

Catabolite repression

System of gene control in some bacterial operons in which glucose is used preferentially and the metabolism of other sugars is repressed in the presence of glucose.

CAP

required for activation of lac operon

glucose available energy source=

lac operon off

positive inducible control of the lac operon

-when glucose levels is high: levels of cAMP are low, so transcription rate is low
-when glucose levels are low: levels of cAMP are high and readily binds CAP, so high rate of transcription

tryptophan operon

-negative control: regulatory molecule binds to the DNA to turn genes OFF
-repressible system: repressor myst interact with a co-repressor (trp in this case) and then the repressor- co-repressor complex can bind to the DNA to turn off the operon

Allosteric action

small molecule makes conformational change in repressor
-a change occurs in the conformation of the repressor when it binds to trp