5

adenine

thymine

guanine

cytosine

dna bases

adenine

guanine

purines

thymine

cytosine

pyrimidines

bonds between sugar and phosphates

phosphodiester

bonds between bases

hydrogen

adenine pairs with

thymine

guanine pairs with

cytosine

bases are bound to

sugars

bases are bound to sugar by ___ bond

covalent

sugar in dna

deoxyribose

sugar in rna

ribose

every DNA double helix = hybrid; one strand of “old” DNA bound to one strand of newly synthesized DNA

semiconservative replication

helicase, unwinds DNA molecule, breaks hydrogen bonds between bases \n

SSBP bind to each strand, keep them from reforming double helix \n

Topoisomerase produce breaks in DNA molecule to relieve the stress of unwinding, then repair breaks

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DNA polymerases build new \n complementary strand (add new nucleotides \n to the 3’ end, pair with old DNA) \n

DNA polymerase can not start the process; primer of RNA nucleotides is first built for complementary strand. \n

primase adds RNA nucleotides, then DNA polymerase can take over, keep building complementary strand. \n

primer is replaced by DNA nucleotides

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DNA polymerase builds new complementary strand from 5’ end to 3’, adding nucleotides to the 3’ end = leading strand \n

other strand also needs to be replicated; can only build new strands by adding to 3’ end \n

other strand = lagging strand, built in short stretches going from

short strands being built = Okazaki fragments \n

DNA ligase join Okazaki fragments

replication steps

5’ end to 3’ - adding nucleotides to 3’ end

direction of building complementary pair

which enzyme unwinds DNA molecule, breaks hydrogen bonds between base pairs

helicase

Which enzyme binds to each strand, keeps them from reforming double helix

SSBP

Which enzyme produces breaks in DNA molecule to relieve stress of unwinding, also repair the breaks?

Topoisomerase

Which enzyme builds new complementary strand by adding new DNA nucleotides to the 3’ end, which pair with old DNA?

DNA polymerase

Which enzyme joins Okazaki fragments on the lagging strand?

DNA ligase

Which enzyme adds the RNA bases which start the new strands?

Primase

Which enzyme provides a starting point or DNA synthesis?

Primer

built from the 5’ end to 3’, adding nucleotides to the 3’ end

leading strand

built in short stretches going from 5’ to 3’

lagging strand

short strands built (built in short stretches, 5’ to 3’)

Okazaki fragments

special nucleotide sequence

postpone erosion of genes near ends of DNA molecules

telomers

build telomers

embryos, cancer cells have high telomerase activity

telomerases

3’-TAGC-5’ would pair with

5’-ATCG-3’

monomer of protein

amino acid

what bond holds amino acids together

peptide

single-stranded

RNA

double-stranded

DNA

sugar = ribose

RNA

sugar = deoxyribose

DNA

bases = CGAU

RNA

bases = CGAT

DNA

messenger

transfer

ribosomal

small nuclear

signal recognition particle

RNA types

CARRIES INFORMATION for making protein from nucleus to cytosol

mRNA

carries information for making protein FROM nucleus TO cytosol

tRNA

catalyzes formation of peptide bonds between amino acids

rRNA

processing pre-RNA, splicing mRNA

snRNA

directs ribosome to RER

SRP

what enzyme synthesizes RNA

RNA polymerase

what structure assembles polypeptide chains

ribosome

ribosomes: what it’s made of

proteins and rRNA

ribosomes: how many subunits

2

ribosomes: binding sites

P, A, E

site that holds tRNA that carries growing POLYPEPTIDE chain \n

P

site holds tRNA that carries next AMINO ACID to be ADDED to the chain

A

EXIT site where discharged tRNAs leave the ribosome

E

which subunit of ribosome is catalytic

large

mRNA binds the small subunit of ribosome \n

beginning of the coding region of mRNA is AUG \n

tRNA with anticodon UAC has methionine attached \n

tRNA with met attached binds to P site of ribosomes; requires energy in the form of GTP \n

Large subunit joins the small subunit

A tRNA with next amino acid comes into tA site, requires GTP for energy \n

Amino acids are bound by peptide bond \n

Now ribosome moves so free tRNA is at E site and tRNA with polypeptide chain moves is at the P site (translocation); requires GTP \n

free tRNA exits ribosome \n

end of the coding region will have a stop codon that signals end of polypeptide chain

\
No tRNA binds to this codon, instead a release factor binds, requires GTP for energy \n

polypeptide chain is released

translation steps

what powers translation

GTP

binding to P site

coming into A site

moving to E site

binding of release factor

GTP required

transcription & translation are coupled

no nucleus

bacterial mRNA not modified; used immediately

protein synthesis in prokaryotes

Folding, either spontaneously or with the aid of chaperone proteins \n

Proteolysis – some polypeptide chains are cut into smaller chains \n

Glycosylation – sugars are added to some proteins, some of these sugar chains are important to “address” the protein \n

Phosphorylation – Protein Kinases phosphorylate proteins to activate them \n

Methionine is often removed

post-translational modifications

5’ end receives a modified nucleotide 5’ cap

The 3’ end gets a poly-A tai

post-transcriptional modifications

post-transcriptional modifications: introns removed, exons joined

RNA splicing

Which DNA strand is read to make RNA

template

if DNA sequence was 3’-ATCG-5’ then the complementary mRNA sequence would be

5’-UAGC-3’

where does RNA polymerase first bind to DNA

promotor

which process produces RNA

transcription

what is added to 5’ side of new RNA

methylated cap

which are removed from RNA

introns

areas of gene that are noncoding

introns

coding areas of gene

exons

set of three nucleotides on mRNA that is code for correct amino acid

codon

set of three nucleotides on tRNA that match up with mRNA

anticodon

what molecules are produced in transcription

RNA

first tRNA (carrying MET) enters to this site

P

rest of tRNAs (2-?) enters to this site

A

what molecules are produced in translation

proteins, polypeptide chains

If the mRNA sequence isAUG CCC AAG UAA then the amino acid sequence is

which of the following processes occur in nucleus

DNA replication, transcription

inducible vs repressible: catabolic pathway operons

inducible

inducible vs repressible: anabolic pathway operons

repressible

inducible vs repressible: synthesis induced by chemical signal

inducible

inducible vs repressible:  synthesis repressed by high levels of end product

repressible

inducible vs repressible:  usually off

inducible

inducible vs repressible: usually on

repressible

makes the gene express and synthesize proteins

positive gene regulation

represses gene expression

negative gene regulation

activator of transcription

CAP

When glucose is scarce, CAP is activated by binding with cAMP

\
CAP attaches to lac operon promoter; increases affinity of RNA polymerase

\
Accelerates transcription

\
When glucose levels increase, CAP detaches from lac operon

\
Transcription returns to normal state

positive control of lac operon

helps regulate other operons that encode enzymes used in catabolic pathways

CAP

Proteins that regulat transcription in eukaryoyes

\
Thousands; both repressors and enhancers

transcription factors

upstream from genes

determines start point of transcription

TATA box

\
* How long a mRNA remains active is important
* Bacterial mRNA has short half life; minutes
* Eukaryotic mRNA undergoes post transcriptional modification
* Can remain active for hours

gene expression controlled post-transcriptionally

\
* Ubiquitin is added to proteins?
* Marks for destruction
* Proteasomes bind to protein molecules, degrade them

gene expression controlled post-translationally

differences in cell types (multicellular eukaryocytes)

gene expression

differential gene expression

expression of different genes by cells with same genome

differences observed in cell types

\
* Determines anterior vs posterior
* Encode for cytoplasmic determinants that initially establish the axes of the body of Drosophila
* Also called egg-polarity genes; control orientation of egg and consequently the fly
* Bicoid - front half of body; nanos affects back half

maternal effect genes

maternal effect gene origin?

oocyte

when maternal effect genes appear

during oogenesis

prior to fertilization

encode factors (e.g., RNA) that are present in the oocyte and required for early embryonic development

maternal effect gene effect

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* Embryo DNA produces mRNA
* Establish pattern of segments
* Code for the body segments and pattern of organism

segmentation genes

three types of segmentation genes

gap, pair-rule, segment polarity

refine broad regions set by maternal genes into more defined regions along A/P axis

gap gene

Divide embryo into seven zone

pair-rule gene

finish defining the embryonic segments

segment polarity gene

\
* Code mainly for transcription factors; development plan for the segments
* Highly conserved region that codes for DNA binding domain in transcription factors
* Contain “homeodomain”
* Control pattern formation in late embryo, larva, adult stages

homeotic gene