CELL 120 Unit 3

Central Dogma of Biology

DNA -> RNA -> Protein. DNA encodes RNA in the nucleus, RNA leaves the nucleus and RNA encodes polypeptides in the cytoplasm at the ribosome

bidirectional replication

DNA strands unwind, begins outward from the two replication forks, continues in both directions

Hurwitz and Furth

Discovered RNA polymerase, which transcribes RNA. Discovered in a blunt force experiment.

Avery experiment

Follow up on Griffith experiment. Found out that DNA was the transforming factor when they used enzymes to break it down; discovered that DNA stores and transmits genetic information from 1 generation of bacteria to the next.

Base pairing in DNA

occurs through hydrogen bonding, C-G (3 hydrogen bonds) A-T (2 hydrogen bonds). Less reactive than RNA b/c H instead of OH on 2' carbon.

subunits

one gene one enzyme explanation is a little bit simplified. In some cases, multiple genes code or polypeptides that combine to form one enzyme

Beadle and Tatum experiment

one gene one enzyme hypothesis. If a gene is mutated or defective- will affect the protein

3 parts of nucleic acids

phosphate group, pentose (5-C) sugar, Nitrogenous bases

polysaccharide

polymer (glycogen)

macromolecules

polymers- large molecules that are made up of smaller molecules or monomers

termination of translation

polypeptide freed from ribosome when stop codon reached. Synthesis is from N-terminus to C-terminus

open reading frame in translation

portion of DNA that corresponds to the part of the RNA that encodes the translated

exons in eukaryotes

portion of gene that codes for amino acids. processing involves "capping" at 5' end and poly-A tail at 3' end

Structures that determine shape and function

primary, secondary, tertiary, quaternary structures

Level that determines protein shape and function

primary- all levels affects function but primary starts it

nitrogenous bases

purines and pyrimidines

dispersive replication

replication results in both original and new DNA dispersed among the two daughter strands

tertiary structure

secondary structures and other coiled regions fold into 3-D shapes. This is when a polypeptide may become functional protein. Defines quaternary

DNA replication can be

semiconservative, conservative, dispersive

primary structure

sequence of amino acids, linear sequence, and defines secondary structure

okazaki fragment

short sequences of DNA nucleotides which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication.

types of DNA mutations

silent, missense, nonsense, frameshift

DNA

storage molecule of genetic information in all organisms except some viruses. Double stranded and antiparallel. Reads 3'-5'. Base-pairing occurs between antiparallel strands.

leading strand

strand that is getting read for replication

chirality

structure and its mirror image are not identical. Molecules are chiral- lift or right handed- amino acids are chiral

polysaccharides (polymer)

sugar subunits (monomer)

A site

tRNA enters

RNA primer

that serves as a starting point for DNA synthesis. Required for DNA replication-enzymes that catalyze this process

Non-template strand

the strand of DNA that is not transcribed into RNA during transcription. Coding; sense strand.

treatment 4 of Griffith's experiment

control: injected living R and heat killed type S bacteria into mouse living type R cells have been transformed into virulent type S cells by a substance form the heat killed type S cells

Treatment 1 of Griffith's experiment

control: injected living S bacteria into mouse Conclusion: type S cells are virulent

Treatment 2 of Griffith's experiment

control: injected living type R bacteria into mouse conclusion: type R cells are benign

"heat-killing" bacteria

denatures proteins, but DNA is still intact

Replication

double stranded and replicated in nucleus. Before cells divide, they need to double the amount of DNA so resulting daughter cells contain correct amount of DNA.

DNA polymerase 3

duplication of the chromosal DNA

ligase

joins the okazaki fragments and DNA synthesized after replacing the RNA primer

protocol for hershey and chase experiment

label protein of DNA of bacteriophages, let bacteriophages infect bacteria, remove "ghosts" from outside of bacteria see what the bacteriophages injected protein or DNA.

translation =

mRNA > polypeptide

DNA replication

1. DNA is unwound (5'-3' top, with 3-5' bottom- anti parallel) breaking the hydrogen bonds between nitrogenous bases 2. RNA primers are inserted- primase (protein that acts like an enzyme) lays down the RNA primer. Lays down a shorter version of RNA on top of parts of the DNA with its opposite 3. DNA synthesized 5'-3'- mixes DNA and RNA together 4. DNA is unwound (leading and lagging strand) 5. more RNA primers are inserted 6. DNA replication continues 7. DNA replication continues, primers are removed, fragments are joined- okazaki fragments

translation at the ribosome

3 Sites E, P, A

tRNA is read

3'-5'

DNA is read

5'-3'

mRNA is read

5'-3'

nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

aminoacyl-tRNA synthetase

An enzyme that joins each amino acid to the correct tRNA. Amino acid is activated by the covalent binding of AMP and pyrophosphate is released. Correct tRNA binds to synthetase, and amino acid is covalently attached and AMP is released. The charged tRNA is released. Protein loads amino acids onto tRNA, then used at the ribosome to translate a mRNA transcirpt into amino acids

DNA repair mechanisms

Any of several processes by which enzymes repair DNA damage. DNA polymerase 1 & 3- proofread and correct point mutations during replication

Nirenberg and Leder experiment

Made codons in a "soup" applying product rule. Codon probability: proportion (normalizing the data) the probability is compared to 1.00

semiconservative replication

Method of DNA replication in which parental strands separate, act as templates, and produce molecules of DNA with one parental DNA strand and one new DNA strand - how DNA actually replicates

basic (alkaline)

R groups attract H+ ions out of solution

hydrophobic

R groups do not interact with water- associated with membranes

aromatic

R groups have ring structures

hydrophilic

R groups interact readily with water

Acidic

R groups lose H+ ions to solution

3 polymerases in eukaryotic transcription

RNA polymerase 1 - makes large rRNA transcripts RNA polymerase 2- makes mRNA transcripts RNA polymerase 3- makes tRNA and small rRna transcripts

Pentose (5-C) sugar

Ribose (in RNA) and deoxyribose (in DNA)

Key components of Avery experiment

S-strain bacteria; virulent R-strain bacteria; non-virulent DNA from S strain bacteria DNase= enzyme that "chews up" all DNA present RNase= enzyme that "chews up" all RNA present Protease= enzyme that "chews up" protein

template strand

The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript. anti-coding, non-sense strand. 3'-5'

Thymine Dimer formation

Ultraviolet exposure can commonly result in DNA damage. Which causes a mutation.

Biochemical pathway

a gene code for protein that has a function in the cell.

purines

adenine (A) and guanine (G)

4 deoxyribonucleotides

adenine, guanine, cytosine, thymine. Doesn't have 2 prime hydroxyl group (H not OH-)

4 ribonucleotides

adenine, guanine, cytosine, uracil- have 2 prime hydroxyl group (OH-)

silent mutation

alters a base but does not change the amino acid

protein or polypeptide (polymer)

amino acid subunits (monomer)

Initiation of translation

mRNA is attached to a subunit of the ribosome, the first codon is always AUG. tRNA binds to start codon of mRNA. Large ribosomal subunit binds

translation continued

mRNA sequence "interpreted" 5'-3' RNA message is "translated" by tRNAs (complementary recognition sequences or anticodons, are read 3'-5')

transcription orientation

mRNA sythesized 5'-3'. Made off the template strand of DNA- exact copy of non-template strand.

monosaccharide

monomer (glucose)

Nucleic Acid (polymer)

monomers are nucleotides. Formed from condensation/dehydration reactions. Building blocks of nucleic acids- DNA and RNA

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

introns in eukaryotes

not in prokaryotes. are spliced out in the mRNA processing- there until transcription

Griffith's experiment

an experiment carried out by Griffith using the heat-killed bacteria in mice to discover that a factor in heat-killed, disease-causing bacteria can "transform" harmless bacteria into ones that can cause disease

topoisomerase/gyrase

any of a class of enzyme that reduce supercoiling in DNA by breaking and rejoining one or both strands of the DNA molecules

Single stranded binding protein

binds to single-stranded regions of DNA

How genes work

biochemical pathway, and subunits

phosphodiester bond

bond formed in nucleic acid synthesis

amino acids

building blocks of proteins

DNA + proteins =

chromosomes. if RNA transcription is happening

Hershey-Chase Experiment

confirmed that DNA is the genetic material because only radiolabeled DNA could be found in bacteriophage-infected bacteria

sulfur

containing

Treatment 3 of Griffith's experiment

control: injected heat killed type S bacteria into mouse conclusion: heat killed type S cells are benign

nucleic acid (polymer)

nucleotide subunits (monomer) RNA: Ribonucleotide subunits DNA: deoxyribonucleotide subunits

DNA is located in

nucleus

missense mutation

A base-pair substitution that results in a codon that codes for a different amino acid.

conservative replication

Conservative replication is a theoretical method of replication where the original strands of DNA are left intact and two new strands are formed bonded together.

pyrimidines

Cytosine (C), Uracil, (U) and thymine (T)

Initiation of bacterial transcription prokaryotes

Initiation: promotor functions as recognition site for sigma factor. RNA polymerase is bound to sigma factor, causing it to bind to promotor. Elongation/synthesis of RNA transcript: sigma factor is released, and RNA polymerase slides along the DNA is an open complex to synthesize RNA Termination: RNA polymerase reaches the terminator, it and the RNA transcript dissociates from the DNA

Helicase

enzymes that bind and may even remodel nucleic acid or nucleic acid protein complexes

E site

exit site

polymerization

formation of a polymer from monomers- occurs through dehydration (condensation) reaction and hydrolysis reaction

formation of polypeptides

formed though condensation reactions, forms peptide bond. In polypeptide chain- letter code- and synthesized from N-terminus to C-terminus

lagging strand

has the same DNA as the leading strand but is not used in replication -just chillin

secondary structure

hydrogen form to alpha-helices and B-pleated sheets. Defines tertiary structure

types of amino acid categories

hydrophobic, hydrophilic, basic (alkaline), Acidic, Sulfur, aromatic

DNA polymerase 1

to fill DNA gaps that arise during DNA replication, repair and recombination

transcription

to make a written copy of, to transfer (data) from one recording form to another-DNA is transcribed

translation

to turn into one's own or another language. To transfer or turn from one set of symbols to another- RNA is translated

Quaternary structure

two or more polypeptides join together to form a functional protein

Initiation of Eukaryotic Transcription

variable promotors bind to DNA "TATA" box at -30. The "TATA" signals to promotor. 3 RNA polymerases

dehydration (condensation reaction)

water is formed in the creation of bonds

hydrolysis reaction

water is used up in breaking up bonds

P site

where the new amino acids are connected to the polypeptide chain

Ribosome

where translation occurs- rough ER- made up of a small and large subunit