bio- exam 2

macromolecules

huge compared to atoms, play an important role in life

four classes of macromolecules

• carbohydrates

• lipids

• proteins

• nucleic acids

how are macromolecules made

carbs, proteins, nucleic acids made from combining small pieces into larger pieces

monomers

small pieces that make up carbs, proteins, nucleic acids

polymers

repeated pieces of monomers

how are polymers built

chemical reactions are used to build the bonds between monomers to form polymers

dehydration

• used to join monomers and build polymers

• remove a water molecule from monomers

hydrolysis

• used to break down polymers

• split water molecules

nucleic acids

macromolecules that store info and play key roles in evolution and life

where is DNA stored

• nucleus in eukaryotic cells

  • nucleoid in prokaryotic cells

where can RNA be found in eukaryotes

both inside and outside the nucleus

what are nucleic acids made of

polymers made of monomers called nucleotides

what are nucleotides made of

• 5 carbon sugar (pentose)

• nitrogen- containing base (nitrogenous base)

• 1 to 3 phosphate groups

sugar in DNA

deoxyribose

sugar in RNA

ribose

purines

nitrogenous bases with 2 carbon rings

• adenine and guanine in both

pyrimidines

nitrogenous bases with 1 carbon ring

• cytosine and thymine in DNA

  • cytosine and uracil in RNA

phosphodiester bond

chemical bond that holds together nucleotides

how do DNA strands run

antiparallel

• ex. two land road

is RNA double or single stranded

can be found as both

type of RNA that forms many secondary structures/ loops

Ribosomal RNA

type of RNA that forms some secondary structures

tRNA

can RNA self replicate

yes

RNA world hypothesis

• RNA can store info and act like an enzyme

• capable of self- replication

  • these traits of RNA are used to support RNA as the first genetic material

where can DNA be found in our cells

• nucleus

• mitochondria

Frederick Griffith

• 2 strains of pneumonia, tested to kill mice

Oswald Avery

treated bacteria with different enzymes, mixed material together

(expanded on Griffith’s experiment)

transformation

griffith and avery proved that DNA is the material that was able to transform the virus

(occurs when bacteria or other organisms incorporate foreign DNA into their cells)

martha chase and alfred hershey

• worked with bacteriophages

  • viruses of bacteria

• phage T2, knew it had both DNA and proteins (capsid)

• infected bacteria to produce more viruses

• infected E. Coli w diff groups of T2

• found that protein stayed with the phage and DNA entered the cells

• DNA was transmitted to E. Coli and was responsible for making new phages, not proteins

Edwin Chargaff’s Rules

• % A = % T, % C = % G

• DNA base composition varies between species

Rosalind Franklin

• died from complication w ovarian cancer bc of how much radiation she worked with

• her work was critical to understand the structure of DNA

Watson and Crick’s Double Helix

• nitrogenous bases on the inside

• sugar (deoxyribose) connected to them

• phosphate groups on the backbone

building block for DNA

nucleotides

• includes nitrogenous base, sugar, phosphate group

nucleosides

nitrogenous base and sugar found in nucleotides

semiconservative model of DNA replication

each daughter DNA strand has one copy of the parental DNA strand

conservative model DNA replication

two parental strands come apart, serve as a template, and then rejoin

dispersive model DNA replication

each strand contains DNA from parents and daughter molecules

Matthew Meselson and Franklin Stahl

• grew e coli containing heavy isotope nitrogen

• transferred to a lighter isotope and separated by mass

• second replication was separated into one more dense and one less dense group, supported the semiconservative replication

where does DNA replication start

origins of replication

(where two DNA strands pull apart from each other)

replication fork

Y-shaped area at each end where replication takes place

how does replication move

in both directions

what does the origins of replication form

replication bubble

replication bubble

enzyme called helicase unwinds the double stranded DNA at each replication fork

topoisomerase

relieves pressure on DNA ahead of the fork by breaking, swiveling, and rejoining strands

binds to the single DNA strands inside the replication bubble and keeps them from rejoining

single stranded binding proteins

begins replication

primase makes an RNA primer

• adds RNA nucleotides one at a time 5’ to 3’ direction

• only 5-10 nucleotides long

adds new nucleotides once RNA primer is in place

DNA polymerase III

deoxyribonucleoside triphosphates (dNTPs)

new nucleotides in the form of ATP, GTP, TTP, and CTP

DNA polymerase

• sliding clamp goes around DNA strand and holds in place

• grips strand and adds dNTPs

combines new nucleotides to the RNA primer or other nucleotides

dehydration reaction

what end are new nucleotides always added to

3’ end

replicated continuously, needs only 1 RNA primer

leading strand

composed of several fragments each started from its own RNA primer

lagging strand

okazaki fragment

fragments that compose the lagging strand

removes the RNA nucleotides and replaces them with DNA

DNA polymerase I

glues the okazaki fragments together

DNA ligase

catalyzes the breaking of hydrogen bonds between base pairs to open the double helix

helicase

stabilizes single-stranded DNA

single-strand DNA-binding proteins

breaks and rejoins the DNA double helix to relieve twisting forces caused by the opening of the helix

topoisomerase

catalyzes the synthesis of the RNA primer

primase

extends the leading strand

DNA polymerase III

holds DNA polymerase in place during strand extension

sliding clamp

catalyzes the synthesis of the RNA primer on an okazaki fragment

primase

extends an okazaki fragment

DNA polymerase III

holds DNA polymerase in place during strand extension

sliding clamp

removes the RNA primer and replaces it with DNA

DNA polymerase I

catalyzes the joining of Okazaki fragments into a continuous strand

DNA ligase

proofread newly made DNA

DNA polymerases

mismatch repair of DNA

repair enzymes correct errors in base pairing

nuclease cuts out and replaces damaged stretches of DNA

nucleotide excision repair

error rate after proofreading

low, but not zero

create problems for the linear DNA of eukaryotic chromosomes

limitations of DNA polymerase

telomeres

special nucleotide sequences at the ends of eukaryotic chromosomal DNA molecules that postpone the erosion of genes near the ends of DNA molecules

special enzyme that adds bases to the end of linear chromosomes

telomerase

• corresponds to the DNA bases

  • has its own RNA molecule

where is telomerase often found in humans

cells that produce gametes

PCR

polymerase chain reaction

denaturation (PCR)

separates two strands of DNA

annealing (PCR)

attaches primers to DNA

extension (PCR)

synthesizes complementary DNA strand from dNTPs, starting at primer

an unusual, heat-stable DNA polymerase that is key to PCR

Taq polymerase

eukaryotic genomes short DNA sequences

short tandem repeats, cary in repeat numbers among individuals

Beadle and Tatum

• bread mold, used x-ray to cause cells to mutate

• ended up with several mutants that could not survive on minimal media and needed additional amino acids

Srb and Horowitz

• determined the biochemical pathway of arginine synthesis in N. Crassa and found 3 classes of mutants

• determined that each class of mutant carried out one step in the metabolic pathway

one gene- one enzyme hypothesis

• some genes encode for nonenzyme proteins

• some genes encode for a subunit of a protein

• some genes encode functional RNA molecules

  • tRNA, rRNA, microRNAs

occurs in the nucleus and produces mRNA

transcription

occurs in ribosomes and makes a polypeptide chain

translation

two main parts of the process of going from DNA to a protein

transcription and translation

DNA to RNA to proteins

central dogma

each of these encodes for one amino acid

codon

DNA triplet code on the nontemplate strand

codons

stop codons

UAA, UGA, UAG

start codon

AUG

first amino acid for every polypeptide chain

AUG

changes in the genetic information of a cell

mutations

changes in just one nucleotide pair of a gene

point mutations

can lead to the production of an abnormal protein

change of a single nucleotide in a DNA template strand

single nucleotide-pair substitutions

replace one nucleotide with another

(point mutation)

3rd codon position

wobble position

missense mutations

still code for an amino acid, but not the correct one

change an amino acid into a stop codon and usually leads to a nonfunctional protein

nonsense mutations