BIO 4

DNA is inside

the nucleus

Chromosomes

human genome containing 46 chromosomes arranged in 23 pairs

Chromosomes are made of

DNA proteins (histones) packed together

genomes

complete set of genetic information

double-helix

two polynucleotide strands, twist about one another

strands are antiparallel

sugar phosphate backbone

Bases extend towards

middle of the helix

complementary base pairing

base hydrogen bond with another

A pairs with T (2 hydrogen bonds)

G pairs with C (3 hydrogen bonds

A with T has how many hydrogen bonds

2

G with C has how many hydrogen bonds

3

one molecule of DNA corresponds to

1 chromosome (two strands together)

5 prime carbon

where a phosphate ends

DNA is the same

throughout the body, it only depends on which parts of the DNA is getting expressed

DNA replication (simple)

making a copy of the DNA in a cell

DNA replication (complex)

connecting nucleotides to form a long chain of DNA according to the template

each strand can serve as a template for the formation of a new, complementary strand

complementary nature of DNA double helix is important in replication

semi conservation of DNA replication

unwind and unzip DNA

old strand serves as a template

complementary nucleotides are added to form a new strand

result of replication of DNA

parent (old) strand serves as template

two daughter helices that are identical to parent helix and to each other

each daughter helix contains one old strand and one new strand

what catalyzes the polymerization of nucleotides

DNA polymerase

catalyzes the addition of nucleotides to existing 3 OH groups-requires primers

DNA synthesis proceeds

in the 5 to 3 direction ONLY

primers

short RNA starters are synthesized by primase (an RNA polymerase)

prokaryotes

single origin of replication

eukaryote

multiple points of origin

leading strand synthesis

continuous (5)

lagging strand synthesis

discontinuous (3)

topoisomerase

relieves twisting forces

the target of antibiotics and anticancer agent

helicase

opens double helix

DNA is opened, unwound, and primed by

primase, topoisomerase, and helicase

primase

synthesizes RNA primer

DNA polymerase 3, in 5 to 3 directions, synthesizing leading strands

DNA lagging strand and DNA polymerase 3

DNA polymerase synthesizes first an Okazaki fragment and then another fragment as more template DNA is exposed

DNA polymerase 1

removes ribonucleotides of primer, replaces them with deoxyribonucleotides

DNA ligase

closes gap in sugar-phosphate backbone after DNA polymerase 1

Chromosome shortening (simple)

ends (telomeres) could shorten because of a problem with lagging strand synthesis

mismatched bases

errors may be made during synthesis

what can damage bases

UV light/ radiation damages nucleotides ‘light damage’

UV light induces covalent bonds between adjacent thymine’s forming a dimer

telomeres

ends of linear chromosomes

chromosome shortening (complex)

lagging strand is missing the end (cannot copy the end)

telomere shortening is a sign of aging (both cells and individual)

telomerase (made of RNA and protein) replicates the end chromosome

special cells turn on telomerase to keep dividing (stem cells, immune cells, cancer cells)

Copy mistakes and proofreading

DNA polymerase can repair mismatched bases after replication (mismatch repair)

felt through a ‘bump’ from mismatched pair

light repair

photolyase uses light energy to break covalent bonds between thymine dimers (reverse of above reaction)

new sunscreens/skin creams claim that they can do this

nucleotide excision repair

remove and fix damaged or wrong nucleotides (bases)

xeroderma pigmentosum- forms skin cancers from being unable to repair

genes

units of genetic information (DNA) that carry instructions for building polypeptides (proteins) or functional RNA molecules along with regulatory sequences

Gene Expression

process of converting archived information (DNA sequences) into molecules (proteins) that actually do things in cells

protein production

messenger RNA serves as

intermediary between genes and proteins

central dogma of molecular biology

by Francis Crick ‘the central dogma of molecular biology’

summary of the flow of information in cells

codes for RNA molecules that do not function as mRNA and are not translated into proteins

transfer RNA (tRNA)

ribosomal RNA (rRNA)

transfer RNA

interpreter molecules, transfers amino acids to the ribosomes

ribosomal RNA

components of ribosomes

information is not always in one direction

information flows from RNA back to DNA (retroviruses)

transcription

DNA to mRNA

complementary base pairing rules

process by which messenger RNA (mRNA) is made from a DNA template

translation

mRNA to protein

uses genetic code

Process by which proteins and peptides are synthesized from mRNA

genetic code

rules that specify the relationship between nucleotide sequence and an amino acid sequence

4 nucleotide bases specify into

20 amino acids

there is a 3 base code to ensure that there is enough

triplet code

each amino acids is coded for by a group of three bases

codon

group of three bases that specifies a particular amino acid

start codon

identifies the site at which protein synthesis should start

there is only one

stop codons

signify that protein synthesis is complete

there are multiple

the codon table

(type of dictionary) to translate mRNA sequences to amino acid sequences

redundant- more than one triplet may specify the same amino acid

unambiguous- each codon has only one meaning

conservative- first two bases of codons that specify same amino acid are usually identical

universal- same genetic code is used by all living things

mutation

any permanent change in an organism’s DNA

effects depend on location of mutation

point mutation

replacement of one nucleotide with another

silent mutation

does not alter amino acid sequence

missense (substitution) mutation

changes one amino acid to another

nonsense mutation

changes codon for an amino acid to STOP codon- polypeptide chain is too short thus non functional protein

base insertion or deletion (frameshift mutation)

alter reading frame of mRNA triplets

affects all codons positioned after site of insertion or deletion

results in non-functional protein

missense mutation example

red blood cells becoming sickle cell from one amino acid change

transcription only occurs on a

gene (not all DNA sequences are transcribed)

called a transcription unit

RNA polymerase travels along DNA template strands from

3’ to 5’ (RNA is going 5’ to 3’)

only one serves as a template for RNA, the other one is called coding strand

3 steps in transcription

initiation

elongation

termination

where RNA polymerase begins transcribing

by binding at a promoter

starts copying at +1 site

initiation

promoter

transcription factors or sigma factors

promoter

part of DNA, initiation site of transcription

short sequence of DNA that facilitates binding of RNA polymerase, enabled transcription of downstream genes

acts as ‘initiate transcription here’ signal

transcription factors or sigma factors

proteins

binds to promoter region of DNA

recruit RNA polymerase 2

initiation in prokaryotes

sigma factors (transcription factors in bacteria) binds to promoter

initiation in eukaryotes

basal transcription factor binds to promoter, and regulatory transcription factor binds to enhancer

together they recruit RNA polymerase

RNA polymerase

opens the helix, transcription begins, does not need a primer

copying starts at +1 site

elongation

sigma factor/transcription factor is released

RNA polymerase moves along RNA 3 to 5 synthesizing RNA in the 5 to 3 direction

termination in prokaryotes

transcription stops when RNA polymerase reaches a termination sequence (code for RNA that forms a hairpin)

termination in eukaryotes

transcription termination is triggered at poly(A) signal sequence

a tail of hundreds of A is added to the mRNA

in prokaryotes, transcription and translation are

tightly coupled

what has to happen to RNA transcription before translation

alteration of 5’ and 3’ ends

splicing out of introns

mRNA processing

in eukaryotes

mRNA transcription that is released from RNA polymerase is not ready to be translated it must first be processed

occurs in the nucleus before mRNA is exported to the cytoplasm for translation

addition of the 5’ cap

addition of the 3’ poly(A) tail

removal of introns

5’ cap

composed of modified guanine nucleotide

serves as a recognition signal for translation machinery (ribosome)

3’ poly(A) tail

composed of 100-250 adenine nucleotides

facilitates transport out of nucleus

protects mRNA message from degradation in the cytoplasm

eukaryotic genes contain

noncoding regions

exons

expressive (coding) regions

introns

intervening (noncoding) regions

removal of introns

RNA splicing is catalyzed by small nuclear RNAs and small nuclear ribonucleoproteins snRNAs and snRNPs

forms a multiprotein complex called a spliceosome

products of transcription

messenger RNA (mRNA)

transfer RNA (tRNA)

ribosomal RNA (rRNA)

other non-coding RNAs

other non-coding RNAs

mostly regulate gene expression

translation

process by which proteins and peptides are synthesized from mRNA

done by ribosomes

uses transfer RNA as interpreter molecules

tRNA structure

made of 80 nucleotides from RNA that was transcribed from DNA

all are not alike

differences from tRNAs

anti-codons: pairing with codons

anti-codon sequences

anti-codon sequence determines what amino acid gets attached on top of tRNA

charged tRNA

a tRNA bound to an amino acid

called aminoacyl-tRNA

aminoacyl-tRNA synthetases ‘match maker’ (simple)

matchers correct amino acid to correct tRNA

aminoacyl-tRNA synthetases ‘match maker’ (complex)

each aminoacyl-tRNA synthetase is specific for one amino acid and all the tRNAs that correspond to that amino acid

the enzyme uses ATP to attach (charge) correct amino acid to 3’ end of correct RNA

synthetase reads identity features on the tRNA (anticodon/other recognition sites) to ensure accuracy

process ensures tRNA delivers to the ribosome carries the correct amino acid for its anticodon

ribosome

site of protein synthesis

composed of ribosomal RNA and proteins

ribosomal small subunit

holds mRNA in place

ribosomal large subunit

has 3 binding sites for tRNAs, contains active sites for peptide bond information

Ribosomal A (aminoacyl or arriving) site

holds incoming tRNA with attached amino acids

Ribosomal P (peptide) site

holds the tRNA with growing polypeptide attached

Ribosomal E (exit) site

holds tRNA that will exit, amino acid no longer attached

translation initaitaion

mRNA binds to small subunit of ribosome

initiator aminoacyl tRNA binds to start codon

large subunit of ribosome binds completing ribosome complex