DNA replication, mRNA processing and protein synthesis

Nucleotide

monomer of nucleic acids; contains a deoxyribose sugar, one or more phosphate groups, and a nitrogenous base

Deoxyribose

A five-carbon sugar that is a component of DNA nucleotides

Nitrogenous Base

An organic base that contains nitrogen, such as a purine or pyrimidine; a subunit of a nucleotide in DNA and RNA

Double Helix

Two strands of nucleotides wound about each other; structure of DNA

Chromatin

Protein-DNA complex that serves as the chromosomes' building material

Chromosome

structure within the nucleus that comprises chromatin that contains DNA and protien, the hereditary material

Leading Strand

Strand that is synthesized continuously in the 5'-3' direction, which is synthesized in the direction of the replication fork

Lagging Strand

during replication, the strand that is replicated and contains Okazaki Fragment and away from the replication fork

Primase

Enzyme that synthesizes the RNA primer; the primer is needed for DNA pol to start synthesis of a new DNA strand

Helicase

During replication, this enzyme helps to open up the DNA helix by breaking the hydrogen bonds

Okazaki Fragment

The short segment of DNA synthesized discontinuously in small segments in the 3' to 5' direction by DNA polymerase

DNA pol III

-Primary enzyme complex required for prokaryote DNA replication
-Using parental DNA as a template, synthesizes a new DNA strand by adding nucleotides to an RNA primer or a pre-existing DNA strand

Ligase

An enzyme that connects two fragments of DNA to make a single fragment as DNA pol III can't connect a nucleotide to a 5' end

DNA pol I

Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides (from a 3' to 5' end and ligase connects it fully)

Telomeres

DNA at the end of linear chromosomes that do not code for anything; designed to be cut off

Replication Bubble

-The region at which the DNA was unwound and the DNA strands are being replicated

Origin of Replication

Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides (AUG that codes for met and is the start codon)

Telomerase

enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends

Point Mutation

-A mutation that affects a single base

RNA primer

short segment of RNA used to initiate synthesis of a new strand of DNA during replication

Proofreading

function of DNA pol in which it reads the newly added base before adding the next one

-DNA pol Epsilon does this in eukaryotes to correct any errors that occur during DNA replication, ensuring high fidelity in the process.

The significance of Griffiths transformation experiment as well as the experiment carried out by Hershey and Chase

1928

Griffith discovered bacterial transformation, where external DNA is taken uo by a cell, thereby changing its morphology and phsiology.

r strain= not disease causing

s strain= disease causing

so bascialy Griffith injectied s strain into mice and they died. the he injected the r they didn't die. In another experiment, he injected mice with heat-killed s-strain and they survived. In the third experiment, amixtute of a live r strain and a heat killed s strain were injected. the mice died. Describe the process of protein synthesis

Base pairing in nucleic acids (A - T and C - G)

Purines → A & G (2 carbon-nitrogen ring)
Pyrimidines → T & C (1 carbon-nitrogen ring)
-One purine and pyrimidine make up a pair
-Base pair held together by hydrogen bonds
-2 purines = too large
-2 pyrimidines = too small

Antiparallel nature of DNA (3’ and 5’) as well as its basic structure

-DNA's 2 strands are going in opposite directions, one in 3' to 5' end and the other is the opposite
-Called 3' and 5' ends, bc of the carbon numbering at the end of DNA strands. So the 3' end has carbon #3 as the one at the end
-3' end has hydroxyl group attached (-OH)
Made of Nucleotides which are made of:
-Sugar-phosphate backbone (deoxyribose)
-Phosphate group (attached to the 5' end)
-Nitrogen bases (a, t, g, c)
-A and G are purines (2 carbon-nitrogn rings)
-T and C are pyrimidines (1 carbon-nitrogen ring)
-One purine and one pyrimidines make up a base pair

Role of each enzyme in replication of DNA

Prokaryotes

Helicase → Opens up the DNA helix, creating replication forks
Single strand binding protiens (SSB) →
Topoisomerase → Prevents super coiling by cutting a strand and putting it back tg
Primase → synthesizes RNA primer from the 5' to 3' end, sliding along the 3' to 5' end, complementary to the leading DNA strand
DNA pol
-DNA pol I → Removes primer RNA using exonuclease activity and places down nucleotides
-DNA pol III → Binds with the primase to add nucleoides from the 3' to 5' end
Ligase → seals the remaining gaps between the nucleotides after DNA pol I

Eukaryotes
Helicase → Opens up the DNA helix, creating replication forks
Topoisomerases → Prevents super coiling by cutting a strand and putting it back tg
Telomerase → Makes telomeres at the end of chromosomes
Primer → synthesizes RNA primer from the 5' to 3' end, sliding along the 3' to 5' end, complementary to the leading DNA strand
DNA pol
-DNA α (alpha) → Initiates DNA replication by synthesizing short RNA primers by working with primase
-Replicated leading and lagging strand, but hands over the rest to another DNA pol.
-DNA β (beta) → Involved in DNA repair
-Not involved in DNA replication
-DNA δ (delta) → Main pol for lagging strand
-Helps fill gaps after RNA primer removal
-Proofreading ability
-DNA ε (epsilon) → Main pol for leading strand
-Strong proofreading ability
Ligase → seals the remaining gaps between the nucleotides after DNA pol I

Describe the process of replication, including the production of leading and lagging strands. (see class notes on this) We are using the example from prokaryotes.

-Single origin of replication, proceeds in both directions creating a replication bubble
-Helicase unwinds the DNA double helix at the replication fork
-Single-strand binding proteins (SSBs) stabilizes the unwound strands
-Topoisomerase relieves super coiling tension
-Primase lays down RNA primer to provide a starting point of DNA pol III
-Leading strand is synthesized in the 5' to 3' direction towards the replication fork
-DNA pol III adds nucleotides continuously after the primer
-Lagging strand is synthesized in the opposite direction and is not continuous
-Forms short fragments called Okazaki fragments bc the primase has to wait till the DNA strand gets longer
-Each fragment begins with RNA primer and DNA pol III extends the fragments
-DNA pol I remove primer and adds nucleotides there
-Ligase connects the Okazaki fragments together
-Replication stops when forks reach termination sites

Why telomers exist and the function of telomerase

Why → designed to be cut off- not coded for anything

Function → designed to not code for any DNA. Without them, you would lose important information every time your. cells divide

DNA repair (see notes and use 14.6 as a resource)

-UV rays can make pyrimidine dimer (where it breaks the DNA nucleotides covalent bonds)
-p53 is activated and recruits enzymes (one is names NUCLEASE)
-it cuts the DNA on each side of the dimer and removes the DNA containing the dimer
-DNA pol synthezises new DNA to repair hole and ligase finalizes it

Protein synthesis

terms to know

Ribosome

cellular structure that carries out protein synthesis

mRNA

-Messenger RNA
-Type of RNA that carries information from DNA to ribosomes during protein synthesis/ transcription
-Complementary to the coding strand of DNA, replacing thymine for uracil

tRNA

-Transfer RNA
-Type of RNA that brings amino acids to the ribosomes during translation

Transcription

-Process through which pre-mRNA forms on a template of DNA using RNA polymerase in the nucleus. pre-mRNA is then spliced and brought to a ribosome in the cytoplasm.

Translation

-In the cytoplasm, where the ribosome reads the mRNA and makes tRNA with the amino acid attached to it, creating a polypeptide.

-The process where ribosomes, in the cytoplasm, synthesize proteins by decoding mRNA into a sequence of amino acids with the help of tRNA

Amino Acid

-Protein monomer
-Has a central carbon or alpha carbon to which an amino group, a carboxyl group, a hydrogen, and an R group or side chain is attached
-The R group is different for all 20 common amino acids

Gene

-A segment of DNA on a chromosome that codes for a specific trait or protien

RNA polymerase

-Enzyme similar to DNA polymerase that binds to the DNA and separates the DNA strands during transcription and makes the pre-mRNA by reading the coding strand of DNA

Codon

A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid, -AUG is the start codon and other sequences are the stop codon.

Anticodon

-A group of three bases on a tRNA molecule that are complementary to an mRNA codon

Complementary Strand

A strand of DNA whose sequence of bases can pair (according to base pairing rules) with the sequence of bases found in a DNA strand (A with T/U) (G with C)

Coding Strand

-The strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine

Start Codon

-Codon that signals the ribosomes to begin translation; codes for the first amino acid in a protein
-AUG → methionine

Stop Codon

UAA, UAG, UGA

-Codon that signals to ribosomes to stop translation

Degeneracy

-Describes that a given amino acid can be encoded by more than one nucleotide triplet; the code is degenerate, but not ambiguous

Exon

-Sequence present in protein-coding mRNA after completion of pre-mRNA splicing
-Parts of the segment of RNA that code for a specific protein

Intron

-Non-protein-coding intervening sequences that are spliced from mRNA during processing

Spliceosomes

-An enzyme that assist in the editing of mRNA during RNA splicing

Be able to describe what is meant by "the genetic code," and the near universality of the code among all living things

-The genetic code is the set of rules by which the information encoded in DNA is translated into proteins
-Determines how sequences of three nucleotides (codons) specify particular amino acids during protein synthesis
-Each amino acid is coded using a 3 nucleotide sequence (AUG is for met.)
-Redundancy (degeneracy) → Most amino acids can be coded for using multiple different codons
-There are stops and start codons → AUG (start), UAA, UGA, UAG (stop)

-Genetic code is almost the same in every organism, from bacteria to humans
-This suggests a common evolutionary origin/ancestor
-Some exceptions like mitochondria
-Universal genetic code allows for genetic engineering advances

Explain the central dogma in biology

-Describes the central flow of genetic information within a biological system
-introduced by Francis Crick in 1958
-it states that information flows in 1 direction
-DNA → RNA (transcription) (DNA's genetic code is used to make mRNA)
-RNA → Protein (translation) (mRNA is used to make the amino acids for protein)

Be able to construct a strand of mRNA using a DNA template and then make a chain of amino acids using the mRNA codon table (which will be given on the test)

Processing of pre-mRNA in eukaryotes (cap, tail, splicing)

-pre-mRNA undergoes processing steps before becoming mature RNA for translation

-The 5' end is capped with a modified guanine nucleotide (7-methylguanosine), capped in the beginning of transcription
-To protect the mRNA from degration and help the ribosome recognize it and bind to it for translation

-A Poly-A Tail is added to the 3' end. It's a long strand of Adenine nucleotides
-Enhances mRNA stability

-pre-mRNA contains coding and non-coding regions called exons and introns
-Exons code for the specific protein, while Introns do not
-Enzymes called spliceosomes remove introns and join the exons together
-snURP's (Small Nuclear Ribonuclear Proteins) are in spliceosomes to do this
-each snURP recognizes a specific sequences of the pre-mRNA to help the spliceosome to accurately cut out the introns and join the exons tg
-introns are spliced and released as lariat structures and degraded

-No snURP = defective gene expression

Be able to explain how humans, with 20,000 genes, can make 100,000 proteins

Alternate mRNA splicing
-A single gene can make multiple mRNA transcripts/code for multiple proteins by rearranging exons during splicing
-editing to the mRNA can be different depending on the signal the cell receives
-EX: Troponin T gene as many splicing patterns leading to different isoforms

Gene regulation and expression variability
-Genes are expressed differently depending on the cell type, tissue etc.
-The same gene might code for different proteins with different roles in different cells

Protein complex formation
-Some proteins assemble into multiunit complex's

ESSAY → Describe the process of protein synthesis