What are intranucleolar and perinucleolar chromatin?
part of the nucleolus -- DNA protein
What are nucleoli?
What are the functions of the nucleolus?
biogenesis of ribosomes -- different sub-units of RNA are arranged, indirect role in protein synthesis, nucleolar DNA responsible for resynthesis of daughter nucleoli at the end of cell division
What are the functions of the nucleus?
command center, contains DNA -- contain genes, control reproduction, control heredity, control moment by moment functions of all cells, DNA → (transcription) → RNA → (translation) → proteins
What are the two types of protein in the nucleus?
structural and dynamic
What is a gene?
segment of DNA that determines the sequence of amino acids in a protein
What are the functions of genes?
the biological unit of heredity, located at a definite locus on a particular chromosome, determines the characteristics of a species as a whole and of the individuals within it, gives order and the protein executes it
How many genes are in a cell?
about 100,000 genes in the DNA of every cell
What is a mitochondria genome?
a single circular DNA
What is a nuclear genome?
consists of multiple DNA molecules dispersed among a haploid set of chromosomes
What is genome size determined by?
the total number of base-paired nucleotides, or base pairs in the DNA molecule
How many base pairs are found in the human nuclear genome?
3 billion base pairs
What is the make up of DNA?
made of chemical subunits -- nucleotides
What are the three components of DNA?
phosphate group, deoxyribose, nitrogenous base
What is the sugar of DNA?
What are the four nitrogenous bases of DNA?
adenine, cytosine, guanine, thymine
What are the purine nitrogenous bases?
adenine and guanine
What are the pyrimidine nitrogenous bases?
cytosine and thymine
Which nitrogenous bases have double rings?
purines (adenine and guanine)
Which nitrogenous bases have single rings?
pyrimidine (cytosine and thymine)
What are the paired nitrogenous bases in DNA?
adenine and thymine, cytosine and guanine
What forms the helical strands of DNA?
phosphoric acid and deoxyribose
How many hydrogen bonds between adenine and thymine?
2 H bonds
How many hydrogen bonds between cytosine and guanine?
3 H bonds
Where is RNA mostly found?
What are the chemical subunits of RNA?
What are the three components of DNA?
phosphate group, ribose, nitrogenous base
What are the four nitrogenous bases of RNA?
adenine, guanine , cytosine, and uracil
Is RNA single or double stranded?
single, if folds back on itself to form a hair pin loop like structure -- some of it forms a double helix
What are ribosomes?
cytoplasmic organelles containing several kinds of RNAs and tons of proteins
Where are ribosomes found?
found in all cells except RBCs, platelets, and sperm
Which cell type has fewer ribosomes, prokaryotic or eukaryotic?
What are the types of ribosomes?
free and membrane bound
What are the functions of ribosomes?
guide the synthesis of protein, central role in protein synthesis, provide sites for orientation of mRNA, tRNA, and the AA, promote the biochemistry of translation
What are the ribosome binding sites?
mRNA site, A site, P site, E site
Describe the mRNA binding site on ribosomes:
located in the small sub-unit in the ribosome -- for binding with mRNA
Describe the A binding site on ribosomes:
for binding with aminoacyl tRNA -- brings in new AA during translation -- large sub-unit
Describe the P binding site on ribosomes:
binding with peptidyl tRNA -- carries the growing polypeptide chain -- large sub-unit
Describe the E binding site on ribosomes:
behind the P site -- transiently binding with the outgoing tRNA after it has left its AA -- large sub-unit
When does replication of DNA occur?
occurs in the nucleus during the S phase of interphase -- replicates the cell (DNA --> DNA)
Where does transcription occur?
in the nucleus
When does transcription occur?
during all phases of the cell cycle (DNA --> RNA)
What is translation?
RNA --> protein, decodes the genetic message
Where does translation occur?
When does translation occur?
during all phases of the cell cycle
What are the functions of the genetic code?
coded in terms of linear sequence of bases in the DNA, linear base sequence of mRNA carries the genetic information copied from DNA during transcription, this is the translated into a sequence of amino acids during protein synthesis at the ribosome
What is the genetic language?
What is a codon?
series of 3 adjacent bases in one stand of DNA or RNA coding for a specific AA
How many codons are possible?
What are the stop codons?
UAA, UAG, UGA
What are the start codons?
What are the 3 elements of a typical protein-coding gene?
core promoter, proximal control elements, transcription unit
What is a template strand?
strand of DNA that serves as the template for mRNA
What is the coding strand?
the nontemplate strand, not involved in transcription
What is the DNA promoter site?
a series of nucleotides that have specific affinity for RNA polymerase
What happens when RNA polymerase binds with the DNA promoter site?
the operon is activated
What type of cell less accessible to activation & transcription?
What catalyzes the transcription of DNA?
RNA polymerase II
Describe the function of RNA polymerase II:
can glide along the DNA and search for a site of initiation -- promoter
What are transcription factors?
some bind to DNA before the polymerase enzyme can bind to the promoter -- binding to the promoter site triggers unwinding of DNA double helix and the initiation of the transcription process
What happens when hydrogen bonds between the complementary base pairs?
unwinding of the DNA
What is formed between the bases of the free ribonucleotide triphosphates and the bases in the sense strand?
temporary hydrogen bonds
How does the RNA chain grow?
from 5' to 3' (anti-parallel to the DNA)
What are the two functions of RNA polymerase?
links one ribonucleotides with the next, cleaves off 2 phosphates from each ribonucleotide triphosphate
When does elongation of the RNA stop?
when the polymerase transcribes a special sequence -- termination signal -- polymerase releases both the DNA template and the new RNA strand
What are the two types of termination signals in prokaryotic cells?
protein called rho factor, short GC-rich sequence followed by several U bases near the 3' end of the mRNA(this causes the RNA to fold into a hairpin loop)
Which strand of DNA is copied?
How fast is DNA copied?
20-50 nucleotides per sec
What is the error frequency in DNA transcription?
1 wrong for every 10,000 copied
How is mRNA degraded in prokaryotic cells?
enzymatic ally within 1-3 minutes of synthesis
How long does synthesis take in eukaryotic cells?
synthesis may take hours because transcription occurs in the nucleus and the mRNAs are transported to the cytoplasm for translation
What is the sequence of transcription in eukaryotic cells?
3 RNA polymerases -- RNA polymerase II transcribes the genes to make mRNA to be translated into proteins, polymerase I -- in the nucleoli -- makes the large ribosomal RNAs, polymerase II -- in the nucleoplasm -- synthesizes tRNAs and the 5S rRNA, heterogenous nuclear RNA (hnRNA) -- variety of the sizes, the 3 polymerase enzymes recognize different start signals on the DNA: I and II recognize sequences upstream for transcription, III recognizes specific gene regulatory protein that binds to a sequence downstream
What do RNA polymerase enzymes I and II recognize?
sequences upstream form transcription
What does RNA polymerase enzyme III recognize?
specific gene regulatory protein that binds to a sequence downstream
Describe RNA polymerase enzyme I:
-- in the nucleoli -- makes the large ribosomal RNAs
Describe RNA polymerase enzyme II:
in the nucleoplasm -- synthesizes tRNAs and the 5S rRNA (heterogenous nuclear RNA (hnRNA) -- variety of the sizes)
Describe RNA polymerase enzyme III:
recognize different start signals on the DNA
What modifications occur before hnRNA leaves the nucleus as mRNA?
1. 5' end of the RNA is capped by guanylyl transferase (the cap has a guanosine residue linked to a triphosphate at the 5' end -- defines the eukaryotic translational start site, protein synthesis will start at whatever AUG codon is nearest to the 5' cap and proceed by decoding mRNA until a stop codon is encountered, 5' cap may protect the mRNA from degradation by nucleases that attack RNA at the 5' end) 2. transcript destined to become an mRNA receives poly(A) tail at a special signal sequence -- AAU, AAA sequence at its 3' end to complete the primary RNA transcript (signal sequence signals where the poly(A) tail should be added, done by poly(A) polymerase enzyme without needing the DNA template)
What are introns?
intervening sequences -- long stretches of DNA in between gene fragments in eukaryotic cells
What structures are rare in prokaryotes, uncommon in lower eukaryotes, and abundant in higher eukaryotes?
What is the function of introns?
protect the integrity of the genes in gene families from elimination thru unequal crossing over, act as regulatory elements in the transcription of genes, hasten the evolution of new and potentially useful proteins
What are extrons?
they flank the introns in the coding sequence
What are spliceosomes?
assemble on introns of the primary RNA transcript
What are spliceosomes made of?
small nuclear ribonucleic-proteins (snurps) , snurps cut out the introns during mRNA processing
Describe the structure of tRNA:
adaptor molecule that carries the amino acid, a 3' end with the amino acid, the 5' end with a phosphate group, 3 loops -- T-C loop, DHU loop, and the anticodon loop, an amino acid helix
What is the role of tRNA in protein synthesis?
recognizes the enzyme aminoacyl synthetase -- responsible for attaching the specific amino acid to it, carries the amino acid in the form of aminoacyl tRNA to the ribosome, interacts with mRNA codons to translate the genetic message and place the amino acids in the correct sequence in the polypeptide chain, binds the growing polypeptide chain to the ribosome
What is the function of the wobble position?
has the base inosine (unusual), permits flexibility in the pairing between the 3rd base of the mRNA codon and the complementary base in the anticodon, inosine can pair with U, C, or A, permits the use of fewer tRNAs for some amino acids than the number of codons that specify those amino acids
What is the anti-codon of 3'CGG5'?
What strand is used when you copy DNA to mRNA?
What is an anticodon?
the specific 3-base sequence in tRNA that pairs up with a specific codon in mRNA
What is the role of the anticodon in translation?
"mates" up with the codons of the amino acids of the mRNA for protein synthesis
What are the four processes of protein synthesis?
activation, initiation, elongation, and termination
Describe the activation process of protein synthesis:
free AA in the cytoplasm combine with the respective tRNAs
What is required for the activation process of protein synthesis?
AA, tRNA, ATP, Mg, specific aminoacyl synthetase
Describe the initiation process of protein synthesis:
ribosomal subunits, mRNA, and the first aminoacyl tRNA form an initiation complex in the cytoplasm
What is required for the initiation process of protein synthesis?
Describe the termination process of protein synthesis:
ribosomal subunits, mRNA, and completed polypeptide chain dissociate
What is required for the termination process of protein synthesis?
one of three stop codons (UAA, UAG, UGA), GPT, release factor (RF1, RF2, RF3)
What are the four steps to protein assembly?
transcription, activation, initiation, and translation
Describe transcription step of protein assembly:
synthesis of DNA to mRNA in nucleus, - mRNA is modified and processed, passed from the nucleus to the cytoplasm where the 5' end binds to a ribosome (part of initiation)
Describe activation step of protein assembly:
free AA combine with corresponding tRNAs in the cytoplasm
Describe initiation and translation step of protein assembly:
3-base anticodon in tRNAs pair with corresponding codons in mRNA attached to the ribosome
Describe the translation step of protein assembly:
elongation of protein chain by peptide bond formation between adjacent AAs attached to tRNAs
What two things happen after the translation step of protein assembly?
termination of the protein chain when a stop codon reaches the A site, modifications of the new protein
***Assume that you have a gene 99 bases long. Due to mutation, three bases were deleted. Also, as the protein was being synthesized, the amino acid methionine was cleaved off during co-translational modification process. The protein synthesis was not interrupted and went on as usual. The completed polypeptide has how many amino acids in it?
30 amino acids. For a 99-base long DNA there will be 33 codons as each codon is a triplet of bases. consider the following: Methionine was deleted, so -1 one more amino acid. No amino acid for stop codon. This means that your hypothetical mRNA will fetch you 30 amino acids in your protein.
***33 codons should fetch you how many amino acids when such a mRNA is translated?
***If 3 bases were deleted due to mutation, how many amino acids will be wiped out from the protein?
***Transcribe the gene from following strand of DNA to make a mRNA: 3'... GGC TAC AAA TGA CCA ATT CGT...5'
5'... AUG UUU ACU GGU UAA ... 3'
*** What will be the anticodons in the tRNA of the second and third codons of your mRNA in 5'... AUG UUU ACU GGU UAA ... 3'?
***The second and the third tRNAs in 5'... AUG UUU ACU GGU UAA ... 3' will pick up which amino acids BEFORE they translate the mRNA?
Phenylalanine and threonine respectively. Since the genetic codon table you have consists of DNA and mRNA codons only, what you have to do is to look at the corresponding mRNA for a given tRNA anticodon, and find the amino acid for that mRNA codon form the table.
***Assuming that all mRNA codons have been translated, the completed polypeptide will have how many amino acids in it? (5'... AUG UUU ACU GGU UAA ... 3')
***Modification of the mRNA involves:
Modification of a primary mRNA transcript involves adding GGG cap at the 5' end and a poly A tail at the 3'end. a mRNA processsing involves removing intron copies and splicing exon copies. The question is about modification and not processing.
***Which one doesn't belong in the process of chemical carcinogenesis?
amplification. Chemical carcinogenesis hypothesis states that it involves 3 stages: induction, promotion, and progression. Some chemicals act as inducers, others as promoters. Still others act as both inducers and promoters. Progression is the progression of the cancerous growth.
***What are the six types of tumors describe in the notes?
Arises in epithelical tissue (e.g., gut, skin and glandular tissue).
***What is sarcoma?
Originates in connective tissue (e.g., bone, and muscle).
***What is lymphoma?
Arises in lymphatic tissue (e.g., lymph nodes)
***What is lipoma?
Originates in adipose tissue.
***What is leukemia?
Refers to proliferation of leucocytes.
***What is melanoma?
Refers to heavily pigmented tumor of skin.
***What are oncogenes?
viral genes that when activated, can induce uncontrolled cell division that may lead to cancer
***how many cancer causing oncogenes have been found?
***What do we call normal cellular genes that closely resemble oncogenes?
***How do oncogenes become expressed?
mutations of the oncogenes,translocation of oncogenes to other chromosomal sites where their expression increases, loss of tumor suppressing genes
***What are the two major types of mutation?
Point or longer segment
***What is point mutation?
involve a single nucleotide. Can be (a) Transition, in which one purine or pyrimidine is replaced by another. OR (b) Transversions, in which a purine is replaced by a pyrimidine or vice versa. Chemicals such as hydroxylamine can induce transition.
***What is silent mutation?
Silent mutation changes the third position in the codon. Leaves the amino acid sequence unchanged, resulting in the production of a normal protein.
***What are the types of point mutation?
silent, missense, nonsense, frameshift
***What is missense mutation?
Changes the first or second position in the codon, which changes the meaning of the codon; since the altered codon codes for a different amino acid.
***What is nonsense mutation?
Occurs when a codon for an amino acid is mutated into a stop codon, which leads to the production of a shorter protein
***What is frameshift mutation?
Occurs when a single base is added or deleted from a codon. This causes a misreading of the genetic message downstream of the mutation, producing an incorrect protein from then on.
***What are the types of long segment mutation?
deletions, translocations, insertions
***What is deletion mutation?
deletion of whole genes
***What is translocation mutation?
Translocation of a DNA segment from its normal location in the genome to another place in the same chromosome or a different one
***What is insertion mutation?
Insertions of long segments of DNA into another gene
***What are some DNA stop codons?
ATT, ATC, ACT
***What are some stop codons in mRNA?
UGA, UAG, UAA
***What can the anticodon CGI pair with in tRNA?
GCU, GCC, GCA (I can pair with U, C, or A)
***What direction is mRNA translated in?
***What does the biding of RNA polymerase to DNA require?
***What portion of a gene contains a TATA box, CAAT box, GC box, and enhancer base sequence?
***What assembles at editosomes and connects the mRNA transcript if it is different from the corresponding gene?
***What is a portion of DNA, TAC at the 3' end to ATC at the 5' end?
***What is the process of copying the DNA to make two identical DNA's?
***What is the transmission of genetic code from a gene to an mRNA?
***What is the process of decoding the genetic message in mRNA?
***What is the sequence of bases in DNA that determines the sequence of mRNA?
***What type of mutation would change GAA to GUA, changing glutamine to valine?
***What type of mutation would change UUA to UAA, changing leucine to a stop codon?
***Where does elongation of protein synthesis occur?
the A site of the ribosome
***Which RNA decodes the message during translation?