gene expression external

nucleotides

repeating unit of DNA. bases = A, T (or uracil = U), C, G

DNA is antiparallel - sugar phosphate backbones run in opposite directions

genes and proteins

codes a protein (polypeptides made from a series of amino acids)

20 different amino acids and the order determines the protein structure - attraction and repulsions between non-adjacent amino acids results in 3D folding of polypeptides chain into specific shapes

proteins perform body functions

protein synthesis

process in which proteins are constructed from individual amino acids

RNA

ribonucleic acid - uses ribose sugar, starts out in nucleus but travels out to deliver message (difference from DNA)

kinds of RNA

mRNA = messenger RNA - job is to carry message based of DNA

tRNA = transfer RNA - job is to transfer the message

rRNA = ribosomal RNA - job is to help with making proteins and ribosomes

analogy about cake

DNA = grandma’s precious recipe book

ribosomes = your kitchen at your house

RNA = copy of one recipe

protein = ‘cake’ or meal

amino acids = ingredients

transcription full process

process in which information from gene in DNA strand is copied into a new molecule of messenger RNA (mRNA)

mRNA is complementary strand to the template strand (that provides template) of the DNA → other DNA strand is coding strand

CODING STRAND IS THE SAME CODE AS THE MRNA

gene is switched on, RNA polymerase attaches to the start of the gene. polymerase moves along the DNA, making a strand of messenger RNA out of free bases in the nucleus

before mRNA can be used as a template for protein production, it must be processed - removing and adding sections of RNA.

mRNA the moves out of nucleus into cytoplasm

promoter and terminator

promoter - section of gene where RNA polymerase binds

terminator - section of DNA telling enzyme to stop

transcription factors

many proteins are not needed in all cells or not needed all the time

sometimes a repressor will present to prevent the RNA polymerase from triggering the protein

activators

transcription factors help initiate transcription by helping polymerase bind to the gene

transcription

step 1 - RNA polymerase binds to promoter (section of DNA telling enzyme where to start)

step 2 - RNA nucleotides bind with DNA to create strand of mRNA. enzyme stops transcription when it reaches the terminator region

step 3 - mRNA detaches from DNA

step 4 - mRNA travels out of nucleus, exiting through nuclear pore

step 5 - mRNA arrives at ribosomes, ready to make proteins

notes

note 1 - coding strand remains on site of transcription to increase durability of DNA and prevent DNA from being damaged

note 2 - DNA doesn’t leave nucleus as it is a very large molecule containing all genes for organism, so therefore can only survive in nucleus

note 3 - when gene is switched off, enzyme cannot bind to promoter

translation - second phase

translation occurs within ribosomes, mRNA is used to create protein with correct amino acid sequence

mRNA read by ribosomes, tRNA brings in specific amino acids to build protein

process - mRNA is read three bases at a time. each three bases (codon) code one amino acid. e.g. AUG = methionine

ribosomes use codons to join the correct amino acids together, tRNA assists by bringing the correct amino acid to the growing polypeptide

codons, different kinds of codons

codon = three consecutive bases on mRNA coding amino acid. codons are complementary to DNA triplets (opposite of triplets)

start codon = establish start of translation (AUG = start codon)

stop codon = translation terminated/stopped (UAA, UAG, UGA = stop codon)

degeneracy

20 amino acids and 64 codons → know as degeneracy when two or more codons can specify the same amino acid

tRNA functions

molecule that transports the correct amino acids to ribosomes VIA binding tRNA to anti codons via complementary base pairing

note section 2

note 1 - tRNA anticodons will have a specific amino acid that they code to

note 2 - ribosome moves along mRNA to read codons (3 pairs at a time)

translation in more detail

when ribosomes reads AUG start codon, polypeptide chain begins

codons and anti codons temporarily bind to join amino acids

translation ends when stop codon is reached

polypeptides fold into 3D shape to form proteins

various video notes

mRNA doesn’t copy entire stands of DNA, only the parts it wants - only 2% of DNA codes proteins, most does nothing

ribosomes are made of proteins and RNA - ribosomal RNA

amino acids form peptide bonds to link together

STOP codons do not code for amino acids, they just let ribosomes know when to stop the peptide chain

kinds of mutations

substitution - one DNA base is replaced with another

insertion - one new base is added to the DNA

deletion - one base removed from DNA

mutations must occur in protein section of DNA to affect protein synthesis

substitution

may lead to no change if bases switched still code for the same protein e.g. CAA and CAT code val → silent mutation

more likely to occur in 2nd or 3rd letter of gene substitutions

if letter changed changes amino acid, this may alter structure/function of the protein → missense mutation (conservative = swapped amino acid for similar one, non - conservative = swapped for amino acid with very different properties)

if protein is cut short because base change codes stop codon, most likely non-functioning protein → nonsense mutation

frameshift mutations

insertion or deletion of base

ALL codons/triplets after mutation are affected → will likely code for new amino acid

this has significant and serious effects on protein’s shape (which will likely code for stop early)

inversion

section of DNA is inverted end to end

factors affecting mutation = mutagens

external = radiation (UV, x-ray), chemicals (cigarette smoke, nitrate preservatives)

internal = DNA replication issues during interphase, chromosome mutation (extra genes are duplicated)

also deletion where genes are cut out or insertion where broke chromosome section is reversed

chromosomes are vulnerable during meiosis

interesting fact - everyday, a section of DNA in your cells gets damaged. specialized enzymes can help repair some of those issues

enzyme

special protein speeding up chemical reactions

substrate

a reactant molecule binding to activate site of enzyme → enzyme helps accelerate reaction of substrate

catalyst

substance lowering the activation energy so reactions can happen faster

product

end result of reaction

metabolic pathway

a series of enzyme controlled chemical reactions, initial substrate is modified by the first enzyme to form a product, becoming a substrate for the next reaction acted on by another enzyme (until a final product is reached). once surplus of final product is made, end product goes back to inhibit the first enzyme from producing more

→ this process is essential for producing and breaking down many compounds in the cell

protein synthesis helps code enzymes

understanding metabolic pathways

names next to arrows = enzymes

first name = first substrate

last name = final product

mutations in metabolic pathways

if mutation occurs, substrate with build up and become toxic. in this diagram, B is building up and becoming toxic

genome

all genes combined = codes for an entire organism

phenotype and environmental impact

identical twins both coded for ‘being tall’ - one who didn’t eat/sleep as much would not be as tall.

most traits are influenced by lots of different environmental factors AND genes (note = so many different genes because of so many different proteins)

evolution and natural selection

beneficial mutation = more likely to survive (natural selection)

evolution = inheritance of certain characteristics in a population over multiple generations could lead to change in the whole species

ways environments affect proteins

certain environmental factors can switch genes on or off (transcribe or not transcribe them)

environmental conditions existing internally or externally can both effect phenotype (genotype unable to be expressed if environment works against it)

environment changes substance in cell (example - different amounts of initial substrates present in cell mean metabolic pathways may occur differently)

environment changes protein (enzyme) (example - can stop enzyme from functioning, meaning chemical reaction can no longer take place because it cannot be catalyzed in cell so specific substance cannot be made, affecting genotype)