ib bio hl units 2/7

building block of nucleic acid

nucleotide

what is nucleotide composed of

phosphate group, pentose sugar, nitrogenous base

what bases does DNA contain

adenine, guanine, cytosine, thymine

what bases does RNA contain

adenine, guanine, cytosine, uracil

is dna or rna single stranded

rna

is dna or rna double stranded

dna

what sugar does dna contian

deoxyribose

what sugar does rna contain

ribose

hershey and chase experiment

used radioisotopes to label T2 bacteriophage either internally or externally, determined which part of the virus contained the instructions for infection, realized only thing being transmitted between virus and bacterium is the stuff inside-genetic material makes up the virus

what does the condensation reaction form in the backbone of the dna

phosphodiester (covalent) bond between 3' carbon (OH) and 5' carbon(PO4)

which direction is the backbone of the dna assembled

5' to 3' direction - creates alternating phosphate/sugar backbone

how is the double strand of dna held together

hydrogen bonds

what direction is the double strand of dna formed in

anti parallel

purines (double ring structure) pair with

pyrimidines (single ring structure)

purines are

adenine and guanine

pyrimidines are

cytosine and thymine

adenine with

thymine

guanine with

cytosine

triple bond between which pair in dna

cytosine and guanine

double bond between which pair in dna

adenine with thymine

in formation of chromosomes, dna is supercoiled with several proteins that are called

histones

structures formed when dna is coiled with proteins in formation of a histone is called

nucleosomes

what do nucleosomes consist of

two molecules each of four histone proteins (an octomer)

why is dna attracted to histones?

dna is negatively charged

steps of making a chromosome

1) starts with histone
2) dna wraps around octomer
3) dna associated with octomer (protein) =nucleosomes
4) series of nucleosomes=chromosome
-fiber formed from groups of nucleosomes =chromatid
5)H1 histone locks spool in place, can't unwind
6) further histone association occurs outside nucleosome with connection of H1 histone protein

histone is

protein whose primary purpose is to associate itself with dna

octomer is

8 little histone proteins

how much of the human dna actually codes for proteins

less than 2%

what percentage of the dna is unique for every person

98%

what percentage is known as genes

2%

majority of dna is composed of what type of sequences

repetitive

what are the two types of dna repetitive sequences

HRS, STR

HRS (highly repetitive sequences)

unique, no coding function, 5-300 bases in length

STR (short tandem repeats)

(ex. GAGGAGGAGGAG) used for dna profiling, unique regions: polymorphisms ,2-5 bases in length, inherited

unique regions on STR are called

polymorphisms

how many places (loci) will have polymorphisms

13 - look at these to match sample tissues

how much of 2% helps to form the structure of the DNA around a centimeter-called structural dna

20%

what is necessary during cell division to double the quantity of DNA

replication of DNA

what does dna replication involve

enzymes, free nucleotides

what type of process is dna replication

semi-conservative

what experiment confirmed semi-conservative process

meselson stahl

what does semi-conservative process mean

when you make new pairs of DNA, you conserve half the strand into the new stand

5 steps to dna replication summary

1) unzipping dna strand
2) initiation of new strand
3) elongation of growing strand
4) the lagging strand
5) completion

step one of dna replication involves which enzyme

helicase bc it breaks down the hydrogen bonds between nitrogenous bases to expose these new bases to new pairs- unzips the dna (zipper starts at the replication fork) , identifies strands (depends on direction)

in dna replication how are new strands built (what direction)

5'-3' , so there there is an exposed 3' carbon, and bc of condensation reaction there is a hydroxl group on 3' end (can add another group and form water)

in dna replication what way is leading strand and what direction is new strand

leading is 3'-5' and new is 5' to 3'

what enzyme is involved in step two of dna replication

primase

what does primase do in step two of dna replication

adds a short sequence of RNA (5-10 nucleotides) called a primer at the replication fork, tells the action where to start

what enzyme is involved in step three of dna replication

dna polymerase III

what does dna polymerase III do in step three of dna replication

adds nucleotides in a 5' to 3' direction, nucleotides originate as dNTP molecules, two phosphate groups used as energy source to join nucleotide to complementary base, looks for primer, recognizes it and gets the complementary bases in 5'-3' direction

what enzymes are involved in step 4 of dna replication

primase, DNA pol III, dna ligase

replication occurs

continuously on parental strand

replication occurs in fragments called

ozaki fragments

DNA pol III adds

new dNTPs to the strand, waits until there are bases exposed, brings "chunks" together

in 4th step of dna replication, what does DNA ligase do

joins fragments brought by DNA pol III, once ozaki fragment is placed- joins two fragments together

what enzyme is involved in step 5 of dna replication

DNA pol I

what does DNA pol I do in 4th step of dna replication

removes the original RNA primer and replaces it with DNA nucleotides/bases (bc the primer is ran based) , spot checks for errors

what is transcription

process of synthesizing a complementary rna strand using dna as a template, copies stuff that is important, not transcribing the 2% anyways

what is rna used for in transcription

primary enzyme (RNAP), used to create the preRNA strand

transcription makes a single strand of rna that can

leave the cell and transmit the code

why does transcription only transcribe genes?

genes are the only things that mean anything

steps of transcription

1) rna poly searches dna strand for a coded region known as promoter
2) rna poly binds to promoter and begins to unzip 2 dna strands
3) rna poly also brings complementary NTPs to bind with only one of the DNA strands (known as the antisense strand)
4. transcription continues until the terminator is reached- indicates the completion of the transcription and causes the newly sequenced RNA to detach

diagramming in transcription uses a promoter called a

TATA box that tells RNA pol to bind there- will bind, break bases, and pulls in corresponding RNA nucleotides

strand used as a template in diagramming in transcription

antisense strand

other strand in diagramming in transcription is called

sense strand

sense strand in diagramming does what in transcription

gives the message

what is the terminator in diagramming in transcription

tells transcription to stop

rna strand in diagramming in transcription

same as the sense strand except all Ts are replaced by Us ( no thymine in RNA), this is the message but the sense strand is also the message

within protein coding regions in post-transcription modification there are stretches of non-coding DNA called what

introns

in post transcription modification the initial rna strand that is formed contains both

introns and exons (expressed sequences)

in post- transcription modification what are specialized enzymes that cut the non coding regions

splicosomes

what is added to the 5' end in post-transcription modification

cap (guanine)

what is added to the 3' end in post-transcription modification

poly -A tail (adenine)

why is the cap and the poly-a tail added to the new mRNA in post-transcription modification

provides some protection

every protein begins with what sequence (post-transcription modification)

AUG (won't start until this sequence is read)

CH3 is what group

methyl

appears that dna that is inactive is also what

highly methylated (meaning that methyl groups have been added) - like barr bodies

transcription factors

proteins that assist with gene expression by binding the RNA poly to the promoter

transcription activators

proteins which cause looping of dna to shorten the distance to the next promoter

repressors

proteins that bind to dna segments called silencers to block transcription

environment can also

play a role in a number of genes that are expressed (areas of pollution)

translation

the process by which a mRNA molecule is used to determine the sequences of amino acids found in a protein... takes place of ribosomes.... to be continued

ribosome consists of

two subunits (large and small)

each subunit of ribosome is composed of

rRNA and proteins, constructed in the nucleus

between the two subunits of a ribosome there are

binding sits for mRNA and three sites for the binding of tRNA ( A and P and E sites)

the A site between the two subunits of a ribosomes does what

holds the tRNA carrying the next amino acid

the P site between the two subunits of a ribosomes does what

holds the tRNA carrying the growing chain

the E site between the two subunits of a ribosome does what

site from which the tRNA has lost its amino acid and is discharged (e= exit)

all three types of rna work together to form

polypeptide

how is mra read

in a 5' to 3' direction as a series of codons (triplet bases)
1) first codon bases will enter on 5' end with GGG cap
2) looking for start codon - AUG
3) 64 possible combinations (4 RNA bases)
4) 20 amino acids
5) lots of redundancy - degenerate

the tRNA molecule will move...

sequentially through the three binding sites from A to P to E (exit)

tRNA or transfer RNA is

a nucleic acid with 5' to 3' end
3' end has a base sequence CCA which is where the amino acid will attach
folder "clover leaf" structure due to hydrogen bonds that occur between parts of the single strand
on one of the loops of clover there is an anticodon unique to each tRNA which will pair with specific mRNA codon
activated when amino acid is attached

four phases of translation

initiation, elongation, translocation, termination

initiation stage of translation begins with

start codon AUG which is found on 5' end of the mRNA

during initiation each codon will

attach to a particular tRNA molecule with the exception of the 3 stop codons (61 with amino acids), this attachment is facilitated by an enzyme specific to each amino acid and requires energy,

once the amino acid attaches to the tRNA in initiation of translation the structure is

activated and combines with the large ribosomal subunit and forms the translation initiation complex

elongation

more tRNAs will bring amino acids to the mRNA ribosomal complex, elongation factors provide assistance in joining tRNAs to the mRNA at the A site, the initiator tRNA moves to the P site and peptide bonds are formed between amino acids

translocation in translation begins when

during elongation

what is translocation

the movement of one tRNA from one site to another adding the amino acid to the growing chain, as the tRNA moves from the A site to the Psite it transfers the polypeptide chain to the new tRNA which enters exposed A site

when does termination begin

with one of the three stop codons