>>ib bio i: the central dogma, transcription, & translation<<

if u r one of my irls i hope u kno this account is a societal criticism/post-ironic social experiment

phosphate group

a functional group consisting of a phosphorus atom covalently bonded to four oxygen atoms.

pentose sugar

a five-carbon sugar molecule found in nucleic acids.

nitrogenous base

an organic base that contains nitrogen, such as a purine or pyrimidine; a subunit of a nucleotide in dna and rna.

purines

adenine and guanine.

pyrimidine

cytosine, thymine, and uracil.

phosphodiester bond

the type of bond that links the nucleotides in dna or rna. joins the phosphate group of one nucleotide to the hydroxyl group on the sugar of another nucleotide.

ester bonds (dna)

the phosphate group is attached to the hydroxyl group (5') of one sugar molecule, and the 3' carbon atom of the adjacent sugar molecule.

nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base.

* the carbon atoms of the sugar are numbered with the phosphate marking the 5' (five prime) carbon end and the oh group marking the 3' (three prime) carbon end.

double helix

two strands of nucleotides wound about each other; structure of dna.

semiconservative model

the two strands of the parental molecule separate, and each function as a template for synthesis of a new, complementary strand.

* end result is two sets of dna, each with 1/2 "old" dna and 1/2 "new" dna.

conservative model

two parental strands reassociate after acting as templates for new strands thus restoring the parental double helix.

dispersive model

each strand of both daughter molecules contains a mixture of old and newly synthesized dna.

meselson and stahl

designed an experiment to determine which model was accurate.

* first, they grew a culture of bacteria in a broth containing n15, a heavy isotope of nitrogen.
* as the bacteria divided, they integrated the n15 into their dna, making it denser.
* then they transferred the bacteria to a broth with only n14.
* this experiment proved the semiconservative model.

dna helicase

an enzyme that untwists the double helix of dna at the replication forks.

* need atp to break hydrogen bonds between complementary base pairs.

dna polymerase

move along the template strand (in 5' to 3' direction) and adds new nucleotides following base pairing rules.

* brings nucleotides into position so hydrogen bonds can form with the template strand. it then links the nucleotide to the new strand of dna.

antiparallel strands

simply means that the dna strands are parallel to each other, but one is upside down.

* the ends of each sugar phosphate backbone are labelled with the number of the carbon atom in the last deoxyribose sugar molecule 3' or 5' accordingly.

nucleosome

made from dna and nine histone proteins; the first structure involved in the supercoiling of dna. dna will wrap around the histone core twice.

histone

eight of these make up the core of a nucleosome, with a ninth to complete the structure.

octameric histone core

h2a, h2b, h3, h4.

histone octamer

two each of h2a, h2b, h3, and h4 form the protein complex which dna wraps around.

histone h1

connects dna to the nucleosome core and connects adjacent cores together.

linker dna

stretch of dna separating two nucleosomes.

watson and crick 1953

figured out structure of dna was a double helix.

how much does a nucleosome shorten the dna by?

one meter of uncoiled dna shortens to eighteen centimeters when it is arranged into nucleosomes.

x-ray diffraction

process used by rosalind franklin to make images of dna that helped reveal the structure of dna. this process involves directing x-rays at a material and studying how the beam scatters.

* helped conclude that dna was helical and consisted of repeating patterns.

maurice wilkins

* was a british physicist who worked with franklin.
* he later won a nobel prize alongside watson and crick.

hershey and chase 1952

used viruses to provide evidence that dna was the molecule of heredity. essentially, they tagged the protein coats of some viruses with sulfur 35 and the dna of other viruses with phosphorous 32 and then infected bacteria with these viruses. since they found radioactive material (phosphorus 32) in the dna of the bacteria, they concluded that dna is the source of genetic material.

exons (coding sequences)

regions of dna encode for proteins, which are responsible for carrying out various functions.

satellite dna

tandemly repeating sequences of dna (e.g. str's) that are structural components of heterochromatin and centromeres that are commonly used for dna profiling.

telomeres

regions of repetitive dna at the end of a chromosome that protect against chromosomal deterioration during replication. they are repetitive sequences at the ends of chromosomes that serve to protect the dna during replication to prevent mutations.

introns

non-coding sequences within genes that are removed by rna splicing prior to the formation of mrna.

non-coding rna genes

codes for rna molecules that are not translated into protein; examples include genes for trna.

gene regulatory sequences

sequences that are involved in the process of transcription that include promoters, enhancers, and silencers.

repetitive sequences (non-coding sequences form between \___% and \___% of the total genome.

50% and 60%.

rna splicing

process by which the introns are removed from rna transcripts and the remaining exons are joined together to make mrna.

tandem repeats

short sequence of dna that are repeated a variable number of times between individuals. since individuals have varying numbers of each, combinations of repeats are unique to individuals and can be used in dna profiling.

dna profiling using tandem repeats can be used to...

* establish paternal lineage by studying the y-chromosome.
* establish maternal lineage by studying mitochondrial dna.
* identify individuals by forensic testing.

aspects of dna structure that suggest mechanisms for replication

* nitrogenous bases are hydrophobic and should face inwards.
* since tight packing is required, purines and pyrimidines must be paired in an 'upside down' way.
* cytosine and guanine from 3 h-bonds, which contributed to dna stability.

how many hydrogen bonds form between adenine and thymine?

two.

how many hydrogen bonds form between cytosine and guanine?

three.

origins of replication

site where the replication of a dna molecule begins, consisting of a specific sequence of nucleotides.

* bubbles enlarge in both directions since replication is bidirectional.

replication fork

a y-shaped point that results when the two strands of a dna double helix separate so that the dna molecule can be replicated.

difference between origins of replications in eukaryotes versus prokaryotes

eukaryotes have multiple and bacteria (prokaryotes) have just one; they will fuse together eventually in eukaryotes.

dna gyrase (topoisomerase)

releases the strain that develops ahead of helicase.

single stranded binding proteins

hold the dna strands apart so the template strands can be copied.

rna primer

short segment of rna used to initiate synthesis of a new strand of dna during replication.

primase

synthesizes rna primers, using the parental dna as a template.

* many primers will be made during the process of replication.

dna polymerase iii

adds nucleotides after the primers in the 5' to 3' direction.

dna polymerase i

remove the primer from the 5' end and replaces it with dna nucleotides.

leading strand

the dna strand which is produced continuously.

* this strand uses the 3' to 5' strand of the old dna as a template.

lagging strand

produced in fragments, which move in the opposite direction from the replication fork.

* called okazaki fragments.
* primer, primase, and dna polymerase is needed to begin each fragment.
* ligase connects the okazaki fragments to make a continuous dna strand.

dna ligase

a linking enzyme essential for dna replication; catalyzes the covalent bonding of the 3' end of a new dna fragment to the 5' end of a growing chain.

okazaki fragments

small fragments of dna produced on the lagging strand during dna replication, joined later by dna ligase to form a complete strand.

transcription

the process of creating an mrna copy of a dna sequence. this copy contains the code/instructions on how to make a protein.

* occurs in the nucleus.
* occurs in the 5' to 3' direction.

rna polymerase

* first attaches to a region of dna called a promoter.
* opens up a 'transcription bubble' of dna to be used as a template.
* uses one strand of dna as a template to assemble nucleotides into a complementary strand of rna.
* adds new nucleotides to the 3' end of the growing chain.

nucleoside triphosphates (ntps)

free nucleotides; the building blocks of rna and are also used as energy molecules, especially atp.

* rna polymerase covalently binds them in a reaction which releases the extra two phosphates.

sense strand (coding strand)

the dna strand with the same genetic code as the rna strand being produced.

antisense strand (template strand)

the strand that is complemented during transcription.

promoter

a short non-coding sequence of dna bases. rna polymerase binds to it, but does not actually transcribe it; it is located upstream of a gene and indicates to rna polymerase which strand is the sense strand and which is the antisense strand for the particular gene being copied. it is also used in gene regulation.

differences between rna resulting from transcription (that has the same sequence) and the target dna sequence

1\.) uracil instead of thymine.

2\.) ribose sugar instead of a deoxyribose sugar.

proteins are made in the

cytoplasm.

mrna leaves the nucleus through

nuclear pores.

terminator

a sequence of nucleotides which cause rna polymerase to detach from the dna once they are transcribed.

eukaryotic dna has non-coding regions within a gene called

introns.

pre-mrna

precursor mrna; the first strand of mrna produced by gene transcription that contains both introns and exons.

mature mrna

contains the spliced exons along with two extra additions:

* a 5' modified guanine methylated cap is added.
* a poly-a tail (50-250 adenine nucleotides) is added to the 3' end.
* the 5' cap and poly-a tail protect mature mrna from degradation in cytoplasm.

mrna splicing

involves removing introns from the mrna.

alternative splicing of mrna

* involves removing exons.
* by removing specific exons, you can form different polypeptides from a single gene sequence.

central dogma

theory that states that, in cells, information only flows from dna to rna to proteins.

* the process that occurs between dna and rna is transcription.
* the process that occurs between rna and proteins in translation.

codons

a three-nucleotide sequence of dna or mrna that specifies a particular amino acid or termination signal; the basic unit of the genetic code.

start/stop codons (punctuation signals)

* start: aug.
* stop: uaa, uag, uga.

sections of dna involved in transcription

promoter to transcription unit to terminator.

spliceosomes

in eukaryotes, a large, complex assembly of snrnps (small nuclear ribonucleoproteins) that catalyzes removal of introns from primary rna transcripts.

methylation

a biochemical process that influences behavior by suppressing gene activity and expression.

* genes that are more heavily methylated are not usually transcribed or expressed.

transcription factors

proteins that regulate transcription by assisting or prohibiting the binding of rna polymerase at the promoter region of a gene.

transcription activator

cause looping of dna, which results in a shorter distance between the activator and the promoter region of the gene. this will bring about gene expression.

silencers/repressors

repress/prevent the level of transcription initiation.

translation occurs in

ribosomes.

in translation, what role do ribosomes play?

they interpret the mrna sequence and synthesize polypeptide chains.

* they "read" each mrna codon and match it with a trna molecule.

ribosomes are made up of

a large subunit and a small subunit.

* ribosome subunits are made of rrna (ribosomal rna) and proteins.

difference between ribosomes in eukaryotes and ribosomes in prokaryotes

eukaryotes have larger ribosomes (80s) while prokaryotes have smaller ribosomes (70s).

where is mrna decoded?

in the space between the large and small subunits.

* in this space, there are binding sites for mrna and three sites for the binding of trna.

codons correspond to

an amino acid determined by the genetic code.

codon chart

* the bases of the codon correspond to an amino acid or a stop signal.
* some amino acids have multiple codons, while others have only one.
* sixty-four total possible codons.
* this code is universal.

each trna has two distinct sites

1\.) an anticodon, which is a three-base sequence complementary to the codon.

2\.) an amino acid that will be added to the polypeptide chain.

trna structure

* has a 5' and a 3' end.
* has a three-leaf clover shape.
* the 3' end is free and has the base sequence "cca." this is where amino acids attach.
* contains sections which are double stranded because of base pairing.
* loops are made of unpaired bases. one of these loops has an exposed anticodon.
* the anticodon is unique to each.
* unique enzymes attach amino acids to the correct one.

initiation (translation)

1\.) mrna binds to the small ribosomal subunit at the mrna binding site.

2\.) initiator trna molecule carrying methionine bind to the start codon "aug."

3\.) large ribosomal subunit binds to the small subunit.

where is the start codon located on an mrna strand?

the 5' end.

initiator trna

located in the "p" site of the ribosome.

what does the next codon after the start codon do?

it signals another trna to bind at the "a" site.

what kind of bond forms between the amino acids of the "p" and "a" sites of a ribosome?

a peptide bond.

elongation (translation)

1\.) ribosome translocates three bases along the mrna.

2\.) during translocation, the trna in the "p" site moves to the "e" site where it is released.

3\.) meanwhile, the trna originally in the "a" site is now at the "p" site, and a new trna can bring in the next amino acid at the open "a" site.

in what direction does elongation occur?

5' to 3' direction (ribosomal complex moves towards the 3' end of the mrna over time).

termination (translation)

* elongation continues until a stop codon is reached.
* when a stop codon is at the "a" site, a protein called release factor will fill the "a" site and break off the polypeptide chain from the trna in the "p" site.
* mrna detaches from the ribosome and all trnas detach as ribosomal complex is disassembled.

what can happen to proteins after they are produced during translation?

* after the polypeptide is released, the protein may go to a few different places.
* proteins produced by free ribosomes are primarily used within the cell.
* proteins produced by ribosomes bound to the endoplasmic reticulum are typically secreted from the cell or used in lysosomes.

primary structure

the sequence and number of amino acids in the polypeptide.

secondary structure

structures made by the hydrogen bonds formed between carboxyl groups and amino groups.

* alpha-helix.
* beta-pleated sheets.

alpha helix

a spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure.

* results from hydrogen bonds between every 4th amino acid between nh and co groups, the helix provides structural strength.

beta pleated sheet

one form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.

* results when adjacent regions between nh and co groups form hydrogen bonds and lay side by side.

tertiary structure

the further folding of the polypeptide stabilized by the interactions between "r" groups.