biology ch. 4

what does deoxyribose directly translate to?

lacking oxygen

what is a nucleoside

a combination of a sugar and base

what do nucleoside triphosphates do

they are the molecules that are used to form DNA and RNA

what is a phosphodiester bond

links the backbone of DNA together

what is a 5’ end and a 3’ end

5’ end is the end where the nucleotide at the top has a free 5’ of the sugar

then the 3’ end is the end where the nucleotide at the bottom has a free 3’ of the sugar

what gives the dna strand polartity

the phosphodiester linkages and the differences in the 5’ end v.s the 3’ end

are the strands in a double helix parallel

no, they are anti parallel, meaning the 3’ end of one strand is always opposite the 5’ end

dna is always built

5’ to 3’

what bonds hold nucleic bases together

hydrogen bonds

2 between A&T

3 between C&G

base stacking

the interactions between bases and the same strand of DNA. occurs bc the nonpolar, flat surfaces of the bases tend to group together away from water molecules and end up stacking on top of each other as tight as possible

DNA polymerase

makes the daughter stands of DNA from the parent strands

what unzips DNA

helicase

is and expressed gene turned on or off?

on

where do transciption and translation occur in prokaryotes? what about eukaryotes

the cytoplasm in prokaryotes, in eukaryotes the processes are spatially separated

whats so special about how eukaryotes transcribe and translate in different areas

it allows for additional levels of gene regulation no possible in prokaryotes

is the sequence of the bases on a single strand of dna regulated?

no, this allows for tons of diversity

are RNA molecules longer of shorter than DNA?

shorter

can RNA molecules fold

yes they can fold into complex 3D structures

at the begining of time what what the original nformation storage molecule?

RNA

is RNA a catalyst?

yuh

is RNA more or less stable than DNA?

less

RNA polymerase

builds RNA

what is the strand of DNA copied to make mRNA called?

the template strand

stages of transcription

initiation

elongation

termination

initiation stage of transcription

RNA polymerase and other proteins are attracted to double-stranded DNA, RNA polymerase is then binded to the promoter and DNA is opended up

elongation stage of transcription

successive nucleotides are added to the 3’ end of the growing RNA transcript as the RNA polymerase proceeds along the template strand

the actual process of the mrna being made

termination stage of transcription

the RNA polymerase encounters a sequence in the template strand that causes transcription to stop and the RNA transcript to be released

basically just when it stops

which what is the DNA read to make RNA and which way is the RNA built

they are made antiparallel to each other

DNA is read 3-5, RNA is built 5-3

what are the codes for stop and start regarding transcription in DNA

the promoter (start) and the terminator (end)

TATA box

its a promoter

A DNA sequence present in many promoters in eukaryotes and archaea that serves as a protein-binding site for a key general transcription factor.

sigma factor

A protein that associates with RNA polymerase that facilitates its binding to specific promoters.

recognizes the sequences in the promoter, directs the RNA polymerase to the start of the gene by binding to the promoter and opens the DNA

after this the sigma factor can fall off, it’s not needed for elongation, just initation

general transcription factors

A group of proteins that binds to the promoter of a gene whose combined action is necessary for transcription.

helps RNA polymerase to find the gene and say like “hey transcibe me!”

transcriptional activator protein

A protein that binds to an enhancer to enable transcription to begin.

gene specific, will determine if a gene is turned on or off. far upstream from the promoter

recruits mediator complex

enhancer

A specific DNA sequence located upstream, downstream, or within a gene that is necessary for transcription.

mediator complex

A complex of proteins that interacts with the Pol II complex and allows transcription to begin.

recruits rna polymerase

pol II

protein coding genes

what is the final thing that needs to happen before transcription is initiated

When the mediator complex and Pol II complex are in place

how does RNA polymerase work?

4^n

how many ways you can put nucleotides together

is RNA more or less flexible than DNA?

more, due to being single stranded

nucelotide vs nucleoside

nucleotide= phosphates

nucleoside= no phosphates

where does the energy come from to make rna

the RNA nucleotides have 3 phosphates, 2 are broken off when the RNA is synthesizes. the breaking of those phosphates creates energy

exon

protein coding reigion

intron

noncoding region

purpose of the 5’ cap and the 3’ tail

protection and facilitate translation

splicing

removal of introns

translocating

moving stuff around the cell

what is the 5’ cap made of

basically, a modified GTP that has been put on backwards

binding site for ribosomes for translations

what does splicing

splicsosomes, complex of proteins and small RNAs

is snRNA ever translated into proteins?

no

how many genes in a human cell

20000

how many proteins made from the genes in a cell

70000

types of RNA’s and their functions

informational: mRNA

functional: snRNA- small nuclear RNA

4 levels of protein structure

primary: the order of the amino acids

secondary: the coils and folds due to hydrogen bonds between atoms in the backbone

tertiary; interactions among the side chains of the protein and the exclusion of hydrophobic residues by water causing it to curl more

quaternary: interaction of multiple polypeptides to form a functional protein

2 types of secondary structure

alpha helix, beta sheets

what is denauturing of a protein? how does it happen?

protein unwinds, caused by change in PH, salt concentration, temperature,

denature= protein no longer work

chaperone proteins

help proteins fold properly and prevent inappropriate aggregation

what energy drives the reaction of transcription

GTP

what is the start codon

AUG

what is tRNA

the translator

helps carry the amino acids to the ribosomes

ribosomes structure

consist of 2 subunits

consist of 20-50 proteins and 1-3 rRNAs

3 binding sites for tRNA

Aminoacyl site

• Peptidyl site

• Exit site

anticodon of tRNA

pairs with a matching codon on mRNA

ex: if the mRNA is AUG the tRNA anticodon is UAC, it binds and brings methienine and brings it to the ribosome

three stages of translation

Initiation

• Elongation

• Termination

translation in eukaryotes

initiation factors bind to the 5’ cap then recruit the small subunit and the met-tRNA

small subunit moves 5’ to 3’ until the P site is centered over the first AUG

The ribosome large subunit then binds to the small subunit forming the complete enzyme

translation initiation in prokaryotes

The ribosome small subunit binds to an internal RNA

sequences known as the Shine-Delgarno sequence

• A met-tRNA binds to the P site and then the large

completes the initiation complex

• The ribosome moves to the next AUG on the mRNA

shine delgarni

the small ribosome subunit that binds to internal RNA sequences in prokaryotes

Monocistronic mRNA

Codes for one polypeptide

• Eukaryotes

Polycistronic mRNA

Codes for more than one polypeptide

• Prokaryotes

elongation

what are the binding sites on mRNA and what do they do

A= the new tRNA enters here and brings the next amino acid that matches the mRNA codon

P= carries the growing protein chain

E= the tRNA that has already dropped off its amino acid moves here and then it leaves the ribosome

how does termination of translation work?

polyribosomes

A number of ribosomes can translate a single mRNA

simultaneously, forming a polyribosome (or polysome)

a bunch of ribosomes translating the same mRNA at the same time for efficiency purposes

tRNA

Charging

Amino acids are

added to tRNAs by

highly specific and

accurate enzymes

called tRNA

synthetases

• Most cells have one

tRNA synthetase for

each amino acid

• Fidelity is extremely

importan

what does tRNA synthetase do?

makes sure the correct amino acid is bound to the right tRNA

what is the bond that holds a water molecules together?

polar covelant bonds

frederick griffith

did the virulent mouse experiment that showed dna transformation

nice bacteria + mouse= live

bad bacteria + mouse = die

killed bad bacteria + mouse= live

killed bad bacteria + nice bacteria= dead mouse

killed bad bacteria left behind its dna and gets recovered by the nice bacteria that copies it

showed dna is the genetic material because if the DNA of the bad bacteria was destroyed the mouse would live

3 parts of a nucleotide

phosphate group

sugar

nitrogenous base

pyrimidine always pairs with

a purine

What kind of bonds hold the two strands of DNA together?

hydrogen bonding

abreviation for any base

dNTP or NTP

nucleotide abbreviations

adenine dATP ATP

guanine dGTP GTP

cytosine dCTP CTP

thymine dTTP

uracil UTP

where does the energy used to bind nucleic acids come from

the energy stored in the nucleotide’s phosphate bonds

sigma factor

directs the RNA polymerase

to the start of the gene by binding to the

promoter and opens the DNA duplex

Energy to drive RNA

synthesis comes from

the hydrolysis of the

NTPs

spilcing

(removal of

introns)

which end of mRNA has the cap?

5’

Spliceosome

A

complex of proteins

and small RNAs that

splice the exons

togethers

what does alternative splicing do?

allows the cell to make more that one protein for each gene