UNIT 3 - Genetic Instructions

nucleotides

1. 5 carbon sugar (on 2’ carbon)

2. bases

3. one or more phosphate groups

purines

• double-ring structures

  • adenine and guanine

pyrimidines

• single-ring structures

  • thymine and cytosine

  • uracil for RNA

nucleoside

• combination of sugar and base

phosphodiester bond

covalent bond that connects one nucleotide to the next

• C - O - P - O - C linkage

parts of a eukaryotic transcription unit (a gene) in order from upstream to downstream

1. a promoter containing a TATA box

2. transcription start site

3. transcribed region

4. terminator downstream of the coding region

RNA polymerase

• unwinds DNA

• reads DNA template from 3' to 5'

• quaternary protein complex 

• catalyzes the addition of nucleotide triphosphate to the 3'OH of the growing chain

downstream

towards the 3' end of the RNA/DNA coding strand and 5' end of the DNA template

upstream

towards the 5' end of the RNA/DNA coding strand and 3' end of the DNA template

terminator

part of the gene where RNA Polymerase is released

gene

sequence of DNA including promoter, coding region, and terminator

• codes for protein

promoter

• sequence of the DNA double helix that binds transcription factors to control gene expression

• points out the exact spot and location where RNA polymerase must attach

transcription factor

protein that binds to a regulatory region of DNA to control gene expression

ribosomal RNA (rRNA)

found in all ribosomes and is essential for translation

transfer RNA (tRNA)

carries individual amino acids to the ribosomes in translation

transcription unit

• sequences of DNA that produces a RNA transcript

open reading frame

between the start and stop codons

+1 site

transcription start site (bacterial)

transcription in prokaryotes

1. initiation of transcription happens at the promoter sequence

2. a sigma factor protein binds to the promoter (-10 and -35 box)

   1. helps recruit RNA polymerase to bind

3. the first base that serves as the template to transcribe into RNA is called the +1 site

transcription in eukaryotes

1. initiation of transcription happens at the promoter sequence (TATA box)

2. TATA binding protein and general transcription factor are proteins that assemble at the promoter

   1. help RNA polymerase bind and promote transcription

   2. basal transcription complex

3. regulatory transcription factors

   1. activators & repressors bind to DNA sequences and regulate transcription

exons

expressed regions = code for amino acids

introns

intervening sequences = do not code for anything

splicing

introns must be cut out or the resulting RNA will contain extra bases that do not code for amino acids

splice junctions

sequences between exons & introns that are cut sites

splice variants

more than one type of protein can be made from a single gene coding for an mRNA

5’ untranslated region

upstream of start codon

3’ untranslated region

downstream of stop codon

what does it mean by the genetic code is redundant?

more than one codon codes for an amino acid

wobble effect

some tRNAs recognize more than one codon because they tolerate mismatches in the 3rd position of the codon

genetic code

describes what codons on mRNA match the anticodons on tRNAs to determine which amino acids get added to the protein sequence

general transcription factors

bind to core promoter regions on DNA to help recruit RNA polymerase and form the pre-initiation complex required to start transcription

environment

the conditons an organism experiences

genotype

the hereditary (genetic) info within an organism’s genome

phenotype

the resulting expression of the genotype within an organism resulting in observable traits

mutation

a change in the genotype relative to the wild-type sequence

wild-type

a reference defined as the “non-mutant” genotype in the gene of interest

mutant

an organism with a changed genotype relative to the wild-type sequence usually in a specific location in the DNA

point mutations

change in a single base in the DNA, resulting in a difference base pair

synonymous (silent) mutation

changes a codon but not the resulting amino acid

nonsynonymous (missense) mutation

changes a codon and results in a different amino acid in the protein

nonsense mutations

creates a new stop codon → truncated protein

insertion/deletion mutations

frameshift mutations → changes the reading frame of mRNA

major & minor grooves

• uneven outside contours of DNA

• important because proteins that interact with DNA often recognize a particular sequence of bases by making contact with the bases by the grooves

base stacking

• contributes to the stability of the double helix

• interactions between the bases in the same strand

• occurs bc of the nonpolar flat surfaces of the base tend to aggregate away from water and stack on top of each other as tightly as possible

sigma factor

• promoter recognition in bacteria

transcriptional activator protein

binds to a specific DNA sequence known as an enhancer

elongation

primary transcript

RNA transcript that comes off the template DNA strand and contains the complement of every base that was transcribed from the DNA template

polycistronic mRNA

molecules of mRNA that code for multiple proteins

RNA processing

primary transcript → finished mRNA

1. additional of the 5’cap

2. polyadenylation: addition of poly(A) tail at the 3’ end

3. RNA splicing: joining exons and removing introns

alternative splicing

• primary transcripts from the same gene can be spliced in different ways to yield different mRNAs → different protein products

• differs in whether a particular exons is or isnt removed from the primary transcript

aminoacyl tRNA synthetases

connect specific amino acids to specific tRNA molecules

• therefore directly responsible for actually translating the codon sequence in a nucleic acid to a specific amino acid in a polypeptide chain

reading frames

different ways of parsing the string into codons

gene expression

series of processes by which DNA is transcribed in RNA and RNA is translated into protein

transcriptional gene expression

turn transcription off/on and change how much mRNA is made

translational

control amount of protein made by changing mRNA stability

post-translational

control protein activity by post-translation modifications & degradation (enzyme binding)

zero/no gene expression

due to a mutation, no possiblity of gene expression

basal gene expression

very low “background” level of gene expression from random RNA polyermase binding to a promoter

low expression

detectable above background gene expression, but not abundant

high expression

transcription is occuring rapidly, many transcripts are being made, RNA polymerase recruitment to the promoter is strong

constitutive gene expression

gene expression is always on, but could be high (tRNA or rRNA) or low (Lacl or MalT)

differential gene expression

gene expression is regulated to be up or down depending on the developmental environmental conditions (or both)

label the DNA of a prokaryote

1. promoter, with -35 and -10 box

2. transcription start site (+1)

3. start codon

4. stop codon

5. terminator sequence

5’ coding strand 3’

3’ template strand 5’

label the mRNA of a prokaryote

1. 5’ untranslated region:

   1. ribosomal binding site

2. start codon

3. stop codon

4. 3’ untranslated region:

   1. hairpin loop

label the DNA of a eukaryote

1. promoter, TATA box

2. transcription start site

3. start codon

4. exons and introns

5. stop codon

6. terminator sequence

coding strand

template strand

label the mRNA of a eukaryote

1. 5’ untranslated region

   1. 5’ cap

   2. ribosomal binding site

2. start codon

3. exons/introns

4. 3’ untranslated region

   1. poly A tail

hotspots

sites that are especially mutable

germ cells

haploid gametes or the diploid cells that give rise to them

somatic cells

any cell excluding reproductive cell

• rate of mutation greater than in germ cells

polymorphism

common genetic differences in a population

single-nucleotide polymorphism

a difference between two sequences at a single nucleotide position

transposable elements/transposons

movable DNA sequences that can insert themselves into a gene

gene regulation

ways in which cells control gene expression

• when, where, and how much

gene regulation/expression of constituitve genes

1. promoter “strength”

   1. how effectively RNA pol & transcription factors bind to the promoter

   2. mRNA half life

      1. affects how quickly the mRNA is degraded after its made, and longer mRNA lasts, the more protein copies can be translated

operon

a set of coding sequences for related proteins all sharing the same promoter and terminator

operator region

region of DNA where a regulatory protein binds

• can overlap with promoter, upstream of it, or downstream of it

catabolic operons

• produce proteins that are involved in the catabolism (breakdown) of the signal molecule

  • eg. mal and lac operons

anabolic operons

produce proteins that are involved in the synthesis (anabolism) of the signal molecule

• eg. arginine operon

signal molecule

presence determines whether the operons are expressed at high levels

inducers

when present, the lac and mal operons are expressed at high levels (operons turned ON)

lac operon

• contains three genes: lacZ, lacY, and lacA

lacZ gene

produces protein beta-glactosidase

lacY gene

transports protein that transport lactose into the cell

negative regulation

1. repressor protein binds

2. no RNA polymerase binds

3. no transcription

postive regulation

1. activator protein binds

2. RNA polymerase binds

3. transcription

mal operon

malP and malQ

• weak promoter

malT

regulatory protein

• involved in the regulation of the malPQ operon

• constitutively expressed

beta-galactosidase

enzyme that breaks down lactose inside E-coli cells

lacI gene

regulatory protein

• constitutively expressed

• lacI protein is a repressor

• can bind to the operator and prevents/blocks RNA polymerase from binding