DNA and Protein Synthesis

DNA

deoxyribonucleic acid

copy of entire DNA sequence in almost every cell with exception of RBC

holds our genetic info

DNA structure

made of organic molecules= nucleotides

nucleotides

one of structural components or building blocks of DNA= made of 5- carbon sugars, phosphate group, nitrogenous base

3 parts of nucleotide

phosphate group, pentose sugar, nitrogenous bases

how many carbons should pentose sugar have

5 carbons

when numbering carbons=

always move clockwise from oxygen

on right hand side= always number first carbon (ALWAYS location of base)

c2= ALWAYS a hydrogen below the carbon

c5= ALWAYS have phosphate

they can face 2 directions

backbone of DNA: to form DNA strand=

nucleotides are linked into chains while alternating phosphate and sugar groups= these phosphate groups make up backbone of a DNA chain

rungs of DNA

4 types of nitrogenous bases= Adenine, thymine, guanine, cytosine

G+C= 3 H+ bonds

A+T= 2 H+ bonds

nucleotides attached tog=

form 2 long strands that spiral to create double helix structure

base pairs

erwin chargraff analyzed base pair composition and saw : % of A= % of T and same with G+C

means theres same amount of A and T and same amount of G+C = shows they pair with one another

DNA sequencing

determining order of nucleotides within a gene

order/ sequencing of bases determines what biological instructions are contained in strand of DNA

nucleotides can be joined tog in any order= any sequence of bases is possible

to form strand of DNA=

nucleotides linked into chains with alternating phosphate and sugar groups (first one then other then back to first)

hydrogen bonds

complete ladder and are responsible for holding double helix together

differences in # of H+ bonds ensues bases link together correctly and create a dif in strength between 2 sets

what do the arrangement of nitrogenous base pairs and the H+ bonds between pairs allow?

lets DNA molecules replicate in sections

DNA essentially unzips along the H+ bonds in sections of 50 nucleotide groups at a time

why is DNA referred to as double helix?

cuz of its helical (spiral) structure

antiparallel strands

2 strands of DNA r said to run anti-parallel to each other= run in opposite directions to each other = 5prime- 3prime and 3prime- 5prime on bottom

gene

instructions for life encoded on these=life determined by genes

contains a code

section of DNA used to express a certain trait

coded DNA instructions that control production of proteins

can be several thousand base pairs long or into millions

RNA

DNA’s other molecule

ribonucleic acid

copies genetic info and uses to make functional proteins

• Made in the nucleus

• Found in the nucleus and cytoplasm

• Functions at ribosomes in the cytoplasm

Amino Acids

sets of 3 bases

code for 21 dif amino acids

produce ALL proteins in our body

scientists involved with dna

• Watson & Crick

  • Proposed the double helix model

  • DNA strands are antiparallel

  • Complementary base pairing explains replication

• Rosalind Franklin

  • Used X-ray diffraction

  • Showed DNA is helical with a consistent width

  • Her data supported the double helix model

• Hershey & Chase

  • Used bacteriophages

  • DNA enters the cell, protein does not

  • Concluded DNA is the genetic material

• Chargaff

  • Base pairing rules

  • A = T, C = G

  • Base ratios differ between species

dna functionv

• Stores genetic information

• Instructions for making proteins

• Controls cell activities through protein production

• Replicates so genetic information is passed to new cells

• Determines traits of an organism

pyrmidines

organic compounds composed of carbon, nitrogen, hydrogen, oxygen

small single ringed structures

structure provides stability and allows them to stack tightly with larger purines in DNA

needed by body made internally through process= de nuvo synthesis

since each strand used to make another= complemantary strands= if u seperate the two= rules of base pairing would allow u to reconstruct base sequence of other strand

purines

adenine and guanine both purines

organic molecules

double ring structures

made of carbon and nitrogen atoms and hydrogen molecules giving them chemical stability

human body gets from foods like meats, red meats, certain seafoods (anchiove, sardines,etc)

body breaks purines down= uric acid = dissolves in blood= passes through kidneys= leaves through urine

if body produces too much uric acid…

kidneys cant get rid of it= builds up in blood

if uric levels stay high for too long= sharp crystals of uric acid can form in joints and tissues= produces arthritis called gout

replication occurs…

location where the double helix seperates and replication occurs

asymmetric

“parts go together”

chemical polarity is seperation of electrical charges so a molecules has a negatively and positively charged end

nucleotides= asymmetric and NOT IDENTICAL on both sides

always linked into “head to tail
fashion= entire DNA strand has chemical polarity

which direction is dna strand always built in

5”-3”

to get protein…

need a molecule related to DNA= RNA

RNA molecules

contain coded info for making proteins

its the protein that determines the traits we see

1 job in cell= make proteins

RNA pt 2

polymer molecules made of subunits= monomers= amino acids

made of 1 or more nucleotides

single stranged

each strand of RNA…

can be thought of as a chain with a nucleotide at each chain link

each nucleotide in RNA…

made of sugar, base phosphate,

what change in RNA makes it more unstable and prone to degredation

sugar (ribose instead of DEOXYRIBOSE)- 5 carbon sugar (pentose) with a OH at carbon 2

what happens when U is replaced with T from DNA strand to RNA?

will create a new sequence that will allow the info to leave the nucleus, move into cytosol, enter a ribosome and create a code for protein

whats another reason that RNA is able to leave the nucleus?

cuz adenine now pairs with uracil

protein synthesis

process of making a protein from a single amino acids

involves 2 dif processes= transcription and translation

assembly of amino acids into proteins is controlled by RNA

protein

an organic molecule ( made of carbon) \ of many amino acids

perform many functions; catalyzing metabolic reactions, dna replication, responding to stimuli, providing structure to cells/ organisms and transporting molecules from 1 location to another

3 types of RNA

allow proteins to occur:

1. messenger RNA (mRNA)

2. ribosomal RNA (rRNA)

3. transfer RNA (tRNA)

RNA polymerase

helps to build mRNA strand

reads/ moves in 3”-5” and builds 5”-3”

unzips DNA and zips back together

builds backbone

matches base pairs (complimentary)

checks work

rezips DNA strand

uses 1 strand of DNA as template to assemble nucleotides into a strand of RNA

antiparallel to template strand

strand is now= SINGLE AND IS mRNA

mRNA (not a protein)

one single strand

messenger

complimentary to DNA strand of a gene

made of segment= codon

constructed of codon triplets needed to select correct amino acids

codon

3 nucleotides

instructions needed to make a protein

removes genetic infro from nucleus=into cytosol of cell where it meets with ribosomes (rRNA)

rRNA

it is a location

where proteins r made

r=ribosomal

genetic info removed from nucleus= moves through nuclear pores = will float around until it meets a ribosome

*ribosome in a cell= protein builder

*ribosome in a cell=

protein builder

amino acids form…

polypeptide chain=beginning of a protein

polypeptide chain=

will stay inside ribosome until fully constructed

when is polypeptide chain called a protein

when its released from ribosome and hits the “stop” codon/ message

what do the sequence of nucleotide bases that make up mRNA strand serve as

instructions for order amino acids should be joined together to produce polypeptide chain (string of A.A)

then ribosome reads instructions

tRNA

once mRNA strand left nucleus= it finds a ribosome= now ready for A.A to be brought in

transfers more amino acids to ribosomes for protein synthesis

structure of tRNA

folded structure with 3 hairpin loops that form the shape of a 3-leaf clover

bottom loop contains= sequence called anticodon

anticodon= will be complementary to codon that is found on mRNA strand

hairpin has a directional value= top of hairpin structure (on the 3”) each tRNA has 1 A.A attached

structure of tRNA

1.) when the right tRNA moves into ribosomes it lines up with codon on mRNA strand and lets go off A.A it was carrying

2.) the A.A is then released and attached to a growing chain of A.A at top of ribosome

3.) string of A.A being built= polypeptide chain (peptide chain)

transcription

process of creating an mRNA strand from DNA strand

this is where the DNA strand acts as a template

DNA strand= template strand

uracil is utilized= change in the code signals to the cell that this strand can leave the nucleus

at beginning of transcription and process kinda =

RNA helicase going to seperate strand of DNA

when building RNA= theres codon sections in DNA template that tells enzyme RNA Polymerase where to start making an mRNA strand= these called promoters

promoters

as u move through transcribing (reading strand of DNA to build RNA) there also codon signals to tell RNA polymerase to stop/ terminate

RNA editing

many mRNA molecules require some editing before they are ready to go into action and leave the nucleus

pre mRNA vs mature mRNA

before edits in nucleus vs after edits into cytosol into ribosome

introns

dna sequences not involved in coding for proteins

exons

kept and “expressed” in synthesis of proteins

before mRNA can deliver the message to ribosome=

introns are removed from sequence and exons are spliced together to make mRNA

DNA (gene) transcription= pre mRNA= (splicing into)= mRNA

in some genes more than 90% of pre-mRNA is destroyed, and never appears in mRNA

once mRNA transcribed = moved from DNA in nucleus and released into cytosol

translation

begins mRNA molecule in cytosol finds and moves into a ribosome

translation also includes building of polypeptide chain by the RNA molecule

ribosome binds new tRNA molecules and A.A as it moves as long mRNA

at the ribosome= RNA’s message is translated into a specific protein

2 types of ribosomes in cell

free= produce proteins used by cell= these also structures used to build new proteins

bound= produce proteins that r transported out of cell

role of tRNA in translation

in an addition to an A.A, each tRNA molecule has 3 unpaired bases= these bases called the anti codon, and are complementary to the mRNA codon

(anticodon for AUG is UAC)

ribosome breaks the bonds between the tRNA and A.A= this allows the A.A to join the polypeptide chain and allows the tRNA molecule to leave ribosome where it is free to pick up another A.A in the cell

translation, transcription memorize

transcribe in town (nucleus) , translate on road (cytosol “travel to make proteins”)

mRNA part 2

like an assembly line worker who attaches one another, ribosome breaks the bonds between the tRNA and the A.A = allows the A.A to join the polypeptide chain and allows the tRNA molecule the ribosome, where it is free to pick up another A.A in the cell

before built, how does RNA “know” where to start and stop in making the RNA copy of DNA?

as mRNA strand moves into ribosome, rRNA enzyme begin to read the strand looking for start codon: AUG

1. polypeptide chain will continue to grow until the ribosome reaches on of stop codons

2. when ribosome reaches one of stop codons= it releases the newly formed polypeptide= it folds and we call it a protein

3. this is END OF TRANSLATION

proteins made=

joining amino acids into long chains = polypeptide chains=make a protein

what do we ALWAYS do to find the A.A on a codon chart?

read mRNA strand

gene mutations

mutations that produce changes in a single gene

point mutations

large category of mutations that describe a change in a single nucleotide if DNA = “Scale mutations” also called

involving changes in ONE or FEW nucleotides cuz they occur at SINGLE point in DNA sequence

happen in specific location

does NOT affect rest of the strand

can include Substitute mutations

substitute mutations

one base changed to another

a change in codon can change an A.A and cause a small change in the protein produced

a substitution could….

1. change a codon that encodes a dif A.A and cause a small change in a protein

2. change a codon to one that encodes the same A.A and causes no change in the protein produced= silent mutation

3. change an A.A coding codon to a “stop” codon and creates and incomplete protein= can have serious effects since incomplete protein probs wont function

substitution of a base can result in dif types of mutations:

• silent

• missense

• nonsense

silent mutations

change in nucleotide has no effect on polypeptide product

missense mutations

a new A.A takes the previous A.A’s place= changes the protein being created

resulting protein= unable to function properly

(sickle cell anemia)

nonsense mutations

substitution causes this by changing codon for A.A into a premature stop codon

no function polypeptide will be produced from this gene

frameshift mutations

since protein- coding DNA into codons 3 bases long, insertions and deletions can alter a gene so that its message is no longer correctly passed

when insertions/ deletions shift the whole “reading frame” of genetic message

by shifting reading frame= frameshift mutations may change EVERY A.A that allows the point of the mutation

can alter a protein so that it is unable to perform its normal functions

a branch of a point mutation

though substitutions usually only affect a single A.A, frameshift can cause a ripple affect that can be dramatic

insertions

mutations in which extra base pairs inserted in a new place in DNA

the earlier in this sequence this occurs- the more altered the protein will be

ex. if 3 nucleotides inserted= it will add an additional A.A (rare)= most detrimental mutation cuz it will alter the A.A sequence

meaning the STOP codon maybe read at the incorrect time

if polypeptide chain too long/short = protein wont be functioning

deletions

mutations in which a base or a section of DNA is lost, or deleted