DNA Replication

Mismatch repair

when other enzymes remove and replace incorrectly paired nucleotides resulting from replication errors

Replicated errors are permanent

mutations on daughter DNA molecules that are continuously passed on

A small few mutations can cause

beneficial genetic variation that natural selection operates on during evolution, possibly leading to a new species.

repeated rounds of replication produce

shorter and shorter DNA molecules with uneven ends

Telomere

special nucleotide sequences at the ends of eu. chromosomal DNA. No genes; DNA acts as a buffer zone that protects the organism's genes (Doesn't prevent erosion, postpones it)

Bacterial chromosome

the main component of a bacteria's genome. One double-stranded, circular DNA molecules that is associated with a small amount of protein

Eukaryotic chromosome

one linear DNA molecule associated with a large amount of protein

Chromatin

the complex of eukaryotic DNA and proteins that is packed in the nucleus

Heterochromatin

tightly compacted DNA that is inaccessible to the machinery responsible for transcribing the genetic info encoded in the DNA (The genes are not expressed)

Euchromatin

loosely packed DNA that is accessible to replication processes so the genes can be transcribed

Histones

proteins that are responsible for the first level of DNA packing in chromatin.

Nucleosome

the basic unit of DNA packaging, consisting of DNA wound twice around a protein core of eight histones and "linker" DNA in between each nucleosome.

Helicase

enzyme that untwists the double helix at the replication forks, making the parental strands available as templates

DNA polymerase I

enzyme that removes primers and replaces them with DNA nucleotides

DNA polymerase III

enzyme that adds DNA nucleotides to the RNA primer 3' end, then continues to add DNA that is complementary to the parental DNA template

Primase

enzyme that synthesizes RNA primers

DNA ligase

enzyme that joins the sugar-phosphate backbones of Okazaki fragments into a continuous DNA strand

Nuclease

enzyme that cuts out DNA segments that are damaged

Telomerase

enzyme that catalyzes the lengthening of telomeres in eu. germ cells, restoring their original length and compensating for the shortening that occurs during replication.

leading strand

the new complementary strand synthesized continuously along the template strand toward the replication fork (5' -

lagging strand

a discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' -

Okazaki fragment

the segments of the lagging strand

when DNA pol I and III work on Okazaki fragments

gaps are left behind

on leading strands only _______ primer is required on lagging strands, each Okazaki fragment is ___________

one

primed separately

nucleotides are chemically reactive because of their ________. _________ join monomers together, ______________

triphosphate tails (unstable - charge)

dehydration reactions

catalyzed by DNA polymerase (2 P groups are lost as pyrophosphates)

hydrolysis of pyrophosphate can be energy coupled with

exergonic reactions driving the polymerization reaction

Frederick Griffith (1928)

Discovered transformation (experiment showed living nonpathogenic bacteria could be transformed into pathogenic bacteria and reproduce bc of unknown substance in heat-killed pathogenic cells)

primer

the initial complementary nucleotide chain produced during DNA synthesis made of RNA. Synthesized by the enzyme primase

virus

DNA (or RNA) enclosed by a protective coat (protein). Reproduction requires infecting and taking over the cell's metabolic machinery

Hershey & Chase

Discovered DNA was genetic material (radioactivity experiment)

Protein tracer: sulfur

DNA tracer: phosphorus (found inside cell)

Chargaff's Rules

1. DNA base compositions vary by species

2. A-T, G-C ratios are equal

Watson & Crick

Made semiconservative replication model (1 parent, 1 daughter strand)

Meselson & Stahl experiment (light and hybrid DNA supported semicon. model)

bases are specifically in purine and pyrimidine pairs bc

it is the only combination that results in a uniform diameter for the double helix

A-T hydrogen bonds

2 bonds

G-C hydrogen bonds

3 bonds

origins of replication

particular sites where the replication of chromosomal DNA begins and have specific nucleotide sequences that are recognized by proteins

replication fork

a y-shaped region at each end of a replication bubble where parental strands of DNA are unwound

Nucleic acid hybridization

the base pairing of one strand of a nucleic acid to a complementary sequence on another strand.

Plasmid

small circular DNA molecules in bacteria that are replicated separately. Has a small number of genes Can be used to clone DNA - researchers take plasmids and insert foreign DNA

Recombinant DNA molecule

a molecule containing DNA from two different sources, very often different species

Cloning vector

a DNA molecule that can carry foreign DNA into a cell and be replicated there. (Ex:) Plasmids

Restriction enzymes (restriction endonucleases)

enzymes that cut DNA molecules at a limited number of specific locations. Helpful in cloning and genetic engineering.

may cut the sugar-phosphate backbones in the two DNA strands in a staggered manner = double stranded restriction fragments with at least one single stranded end called sticky ends

Restriction site

the short, specific DNA sequence that restriction enzymes recognize so both DNA strands are cut at precise points within the site

Restriction fragments

sections of DNA molecules resulting from cuts by a restriction enzyme

Sticky end

short, single-stranded extensions that can form hydrogen-bonded base pairs (hybridize) with complementary sticky ends on any other DNA molecules cut with the same enzyme.

DNA ligase can make bonds permanent when it catalyzes the formation of covalent bonds that close up the backbones

Polymerase chain reaction (PCR)

a technique that amplifies any specific segment (target sequence) in a DNA sample within a test tube

3-step cycle:

1. Denature DNA

2. hybridization of DNA

3. DNA polymerase extends primers

DNA sequencing

using the principle of complementary base pairing to determine the gene's complete nucleotide sequence after it is cloned.

Cas9 protein

a bacterial nuclease used to cut double-stranded DNA molecules. Acts with "guide RNA" made from the CRISPR region of the bacteria genome.

Gene expression

the process by which DNA directs the synthesis of proteins (or, in some cases, just RNAs). Two stages: transcription and translation

Archibald Garrod (1902)

suggested genes dictate phenotypes through enzymes, proteins that catalyze specific chemical reactions in the cell. Symptoms of inherited diseases reflect an inability to make a particular enzyme.

Beadle and Edward Tatum

caused a mutation in one allele and directly deduce the function of the wild-type gene each cell type was unable to synthesize a particular essential nutrient in the minimal medium, but could grow on the complete medium

Minimal medium

the culture containing minimal nutrients for growth of wild-type cells

Complete medium

the culture containing all nutrients needed for growth, including any that a mutant cell can't synthesize.

one gene-one polypeptide hypothesis.

Each polypeptide is specified by its own gene

Revised version of Beadle and Tatum's hypothesis

DNA vs RNA

DNA: deoxyribose sugar, thymine, double strand

RNA: ribose sugar, uracil, single strand

transcription

the synthesis of RNA using information in the DNA. Information, like a gene's protein-building instructions, is "rewritten" from the template DNA to the complementary RNA.

Messenger RNA (mRNA)

a complementary sequence of RNA that is a transcript of a gene's protein-building instructions and carries the info to the cell's protein-synthesizing machinery.

Translation

the synthesis of a polypeptide using the info in mRNA. The nucleotide sequence is "translated" into the amino acids of a polypeptide. Takes place in the ribosomes.

Lack of compartmentalization in bacteria

allows translation to begin while transcription is in progress

Compartmentalization in eukaryotes

separate transcription (nucleus) and translation (cytoplasm) mRNA must leave the nucleus and have to be modified to produce the final, functional mRNA.

Primary transcript/pre-mRNA

the initial product of the transcription of a protein-coding eukaryotic gene that is further processed into finished RNA.

Triplet code

genetic instructions for a polypeptide chain are written in the DNA as a series of nonoverlapping, three-nucleotide words that is transcribed into a complementary series of nonoverlapping, three-nucleotide words in mRNA. The mRNA is translated into amino acids.

Template strand

the one of the two strands of DNA that is transcribed, serving as a template

Codon

the mRNA (or nontemplate DNA) nucleotide triplets, customarily written in the 5' - 3’ direction

3 codons that do not code for amino acids are

"stop" signals, or termination codons, marking the end of translation

codon AUG has two functions

1. code for the amino acid Methionine

2. functions as a "start" signal, or initiation codon

some codons

code for the same amino acid, only differing in their third base.

Reading frame

reading codons in the correct groupings in order to extract the intended message.

the genetic code is nearly

universal (codes for the same amino acids in almost every organism.)

Gives evidence to support that all organisms had a common ancestor very early on

RNA polymerase

an enzyme that pulls the DNA strands apart and joins together RNA nucleotides complementary to the DNA template strand in the 5' -

Promoter

the DNA sequence where RNA polymerase attaches and initiates transcription

Terminator (bacteria)

the sequence that signals the end of transcription

Transcription unit

the stretch of DNA downstream from the promoter that is transcribed in an RNA molecule

3 stages of transcription

1. Initiation

2. Elongation

3. Termination

Start point

inside the promoter of a gene. The nucleotide where RNA synthesis actually begins.

Transcription factor

in eukaryotes, a collection of proteins that mediate the bind of RNA polymerase and the initiation of transcription.

Transcription initiation complex

the whole complex of transcription factors and RNA polymerase II bound to a promoter.

TATA box

a crucial promoter DNA sequence in eukaryotes that transcription factors must bind to before RNA pol II can bind to the factors and create an initiation complex.

termination (bacteria)

Transcription proceeds through a terminator sequence in the DNA, causing the polymerase to detach from the DNA and release the transcript

termination (eukaryotes)

RNA pol II transcribes the DNA called the polyadenylation signal sequence, which specifies a polyadenylation signal (AAUAAA) in the pre-mRNA

This signal is immediately bound by certain proteins in the nucleus that cut the RNA transcript free from the polymerase, releasing the pre-mRNA to be processed

RNA processing

enzymes in the eukaryotic nucleus modify pre-mRNA in specific ways before the genetic message is dispatched to the cytoplasm.

5' cap

a modified form of a guanine (G) nucleotide added on to the 5' end (synthesized first) after transcription of the first 20-40 molecules.

poly-A tail

50-250 adenine (A) nucleotides added to the 3' end by an enzyme.

Function of cap & poly-A tail

facilitate the export of mature mRNA from the nucleus, protect the mRNA from degradation by hydrolytic enzymes, and help ribosomes attach to the 5' end of the mRNA in the cytoplasm

Untranslated regions (UTRs)

either 5' or 3' end parts of the mRNA that will not be translated into protein, but have other functions, like ribosome binding

RNA splicing

a stage of RNA processing in eukaryotic nuclei where large portions of RNA are removed and the remaining portions are reconnected.

Introns (intervening sequences)

the non coding segments of nucleic acids that lie between coding regions. Cut out and do not leave the nucleus

Exons (expressed sequences)

regions of nucleic acids that are eventually expressed, usually by being translated into amino acid sequences. Joined together and leaves the nucleus.

Alternative RNA splicing

a single gene can encode more than one kind of polypeptide due to the presence of introns in genes, depending on which segments are treated as exons during processing

Spliceosome

a large complex made of proteins and small RNAs that removes introns by binding to several short nucleotide sequences along the intron

Ribozymes

RNA molecules that function as enzymes. Proved not all biological catalysts are proteins

Some RNA splicing can happen without proteins or additional RNA molecules...

instead the RNA intron functions as a ribozyme and catalyzes its own excision

enzyme properties of RNA

1. Single stranded

2. RNA base functional groups

3. RNA can hydrogen bond with other nucleic acids

Transfer RNA (tRNA)

brings/transfers amino acids from the cytoplasmic pool of amino acids to a growing polypeptide being made by the ribosome. "Translates" the message in a series of codons along an mRNA molecule

Anticodon

a nucleotide triplet that can base-pair with the complementary codon on mRNA and corresponds with a certain amino acid

tRNA can be used

repeatedly by picking up its amino acid in the cytosol, bringing it to the polypeptide made in the ribosome, and leaving to pick up another of the same amino acid.

Aminoacyl-tRNA synthetases

a family of enzymes that ensures tRNA matches up with the correct amino acid specified by mRNA codons. 20 synthetases, 20 amino acids.

First instance of molecular recognition

1. Synthetase active sites fit only a specific combination of amino acid (attachment end) and tRNA (anticodon)

2. Catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the hydrolysis of ATP, resulting in aminoacyl tRNA (charged tRNA)

3. Aminoacyl tRNA is released from the enzyme and is then available to deliver its amino acid to the polypeptide chain on a ribosome

Second instance of molecular recognition

1. Pairing of the tRNA anticodon with the appropriate mRNA codon

2. Some tRNAs can bind to more than one codon because of the rules for base pairing between the third nucleotide base of a codon and the corresponding base of a tRNA anticodon

Wobble

the flexible base pairing between some tRNA anticodons and mRNA codons.

Explains why synonymous codons for an amino acid most often differ in their third nucleotide base but not other bases