BIOS 220 Exam 2 (Key Words)

Peptide Bonds

Holds amino acids together

Primary Structure

Amino Acids

Secondary Structure

Alpha Helices/Beta-pleated sheets, amino acids

Tertiary Structure

Hydrophobic Interactions, Hydrogen Bonds, Ionic Bonds, Covalent Disulfide Bridges

Quarternary Structure

Held together by the same non-covalent forces and disulfide bonds that stabilize tertiary structures

Molecular Chaperones

Cellular structure that helps properly fold some proteins

Central Dogma

DNA —→ mRNA (transcription) ——→ Proteins (translation)

Genotype

an individual's complete set of genetic material or the specific genetic makeup (DNA sequence) at a particular location or locus on chromosomes

Phenotype

physical traits that are a product of the proteins produced

Exceptions

1) Many genes code for RNA molecules

2) These other RNAs preform important functions in the cell

3) Sometimes information flows in the opposite direction

Genetic Code (contains)

• Rules that specify the relationship between a sequence of nucleotide bases in DNA or RNA

• Corresponding sequence of amino acids in protein

Sense Codon

• Group of three bases

• Specifies a particular amino acid

Start Codon

AUG

Stop Codons

UGA, UAA, UAG

Computer Model

shows the three-dimensional structure

Ribbon Model

emphasizes the internal regions of base pairing

Flattened Cloverleaf Model

shows pairing between complementary nucleotides

Anticodon

compromised of three bases and interacts with a codon in mRNA

Properties of the Code

Redundant

Wobble Pairing

Allows for one type of tRNA to pair with more than one synonymous codon on mRNA

Unambigous

One codon never codes for more than one amino acid

Non-overlapping

Codons are read one at a time; any single nucleotide isn’t part of more than one codon

Universal

all codons that specify the same amino acids in all organisms with a few minor exceptions

Conservative

the first 2 bases are identical when multiple codons specify the same amino acid

Through wobble, a single —— can pair with more than one ——

anticodon, codon

Mutation

• any permenant change in an organism’s DNA

• a modification in a cell’s information archive

• a change in its genotype

• able to create new alleles

Point mutation

results from a single base change

Chromosome-level mutations

• are larger in scale

• often nresults from the addition or deletion of chromosomes from the individual’s karyotype

Mutation’s Effects on organisms

• Mutations fall into one of these categories

• Most mutations are neutral or slightly deterious

• Some mutations aren’t in coding regions but can still affect phenotype by affecting gene expression

Machinery (translation)

ribosomes

Polyribosomes

an mRNA with many ribosomes attached

Posttranslational Modifications

proteins (prokaryotes and eukaryotes) that often undergo modifications after translation and before the protien becomes active

Chemical modification

methylation, acetylation, phosphorylation, etc.

Cleavage

Amino acids are sometimes removed

Folding assistance

molecular chaperones are proteins that help the nascent polypeptide fold into its optimal confirmation for activity

Operon

a stretch of DNA containing a cluster of genes that are transcribed together from a single promoter

Promoter

DNA sequence required for transcription to initiate via binding of RNA polymerase

Promoter

RNA sequence required for transcription to initiate via the binding of RNA polymerase

Structural Genes

Genes that encode proteins involved in a common process, and that are important for cell function

Operator

DNA sequence downstream of promoter, to which a regulator protein can bind and prevent movement of the RNA polymerase from the promoter to transcribe the structural genes

Regulator

a protein coded by a regulator gene, that binds the operator and controls transcription of the structural genes

Once an operon is transcribed

a polycistronic message is produced

Cistron

a section of DNA or RNA that codes for a specific protein

Polycistron

an mRNA that encodes for more than one protein

Repressor

blocks transcription

Activator

activates transcription

Positive control

The regulator protein binds to the operon and is required to activate expression of the operon (ACTIVATOR)

Negative Control

The regulator protein binds to te operon and represses transcription (REPRESSOR)

Inducible

Operon is normally OFF and can be induced or turned ON for transcription

Repressible

Operon is normally ON and can be repressed or turned OFF for transcription

Negative inducible operon

with active repressor, transcription is off/substrate makes the repressor inactive, transcription is on

Negative repressible operon

with inactive repressor, transcription is on/product makes the repressor active, transcription is off

Positive inducible operon

with iactive activator, transcription is off/substrate makes activator active, transcription is on

Positive repressible operon

with active activator, transcription is on/product makes the activator inactive, transcription is off

Negative

means a REPRESSOR binds operator

Positive

means an ACTIVATOR binds upstream activation DNA sequence

Inducible

transcription becomes on

Repressible

transcription becomes off