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38 Cards in this Set

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Molecular Control Mechanisms
Ligand
* any molecule/ion that binds to the surface of a binding site (protein) by other than covalent bonds
Ligand binding (due to)
1. oppositely charged ions or polarized groups
2. attractions between nonpolar regions
Facts about LIGANDS ...
* ligand SHAPE COMPLEMENTARY to the shape of the binding site
* binding site SPECIFIC for ion/molecule
* ligand has AFFINITY for binding site (high/tight, low/loose)
* per cent SATURATION of binding sites is related to ... (concentration of ligand, affinity, and competition)
Almost all cell function depends on ...
protein
REGULATION (alteration) of protein (binding-sites) can occur in WHAT ways?
2 Ways:

1. altering shape of binding site alters binding
2. regulating protein synthesis
altering shape of binding site alters binding ...
(temperature, acidity, etc.)
a. allosteric modulation
- binding of one ligand at (regulatory site) alters shape/activity at other binding site (functional site) for 2nd protein/ligand binding.
b. covalent modulation
- covalent bonding of charged groups to protein side chains alters electrical field/affinity of site
Example: protien kinases
protein + ATP ---protein kinase --> protein-PO4 + ADP
(substrate)(enzyme)(products)
regulating protein synthesis
FACTS
* different cells contain different proteins
* proteins are coded for in DNA
* all cells in body have identical DNA
* cells differ because only a portion of the total DNA is used by a cell for protein synthesis
* the sequence of nucleotides determines the amino acid order in a protein (primary structure)
* a gene is a portion of a DNA molecule
* human cells contain more than 30,000 - 40,000 genes
* another nucleic acid RNA is also involved in protein synthesis
Information for protein synthesis FLOWS ...
DNA (nucleus) ....
RNA (nucleus/cytoplasm) ...
protein (cytoplasm)
DNA
* double helix
* 2 polynucleotide chains
* each nucleotide contains one base
* adenine, thymine, cytosine, or guanine
* a sequence of 3 bases on DNA is called ... a CODE WORD (or TRIPLET)
* each triplet eventually codes for a particular amino acid in the protein being synthesized
AAA
TTT
CCC
ACC
CCT
triplets
"redundant" in relation to DNA
* in some cases several different triplets all code for the same amino acid
Aside from codes for amino acids, what other codes are in DNA?
* start code
- TAC
* termination code
- ATC, ATT, ACT
mRNA
messenger RNA does what?
carries the message (code) from DNA in nucleus to cytoplasm (where protein sybthesis occurs)
what is it called when mRNA is made from DNA?
transcription
Transcription
* in the DNA just ahead of the gene to be transcribed ther eis a sequence of nucleotides called the PROMOTER (only on sense strand)
* RNA POLYMERASE (enzyme) binds to the promoter (on the sense strand) catalyzing BOTH the unwinding of the DNA strand and the covalent binding of ribonucleotides in the formation of mRNA.
* RNA polymerase moves along strand causing HYDROGEN BONDS to form between DNA and complementary bases of mRNA
* mRNA formed is complementary to DNA
* a 3 base sequence in mRNA is a CODON
* NUCLEAR ENZYMES remove introns before mRNA diffuses out thru nuclear pores to cytoplasm and splice pieces back together
* designation of sequences of nucleotides as introns/exons is NOT FIXED for a given gene
CODE WORDS or TRIPLETS vs CODONS
CODE WORDS or TRIPLETS:
triple letter sets in DNA
CODONS:
triple letter sets in mRNA
NOT ALL NUCLEOTIDES TRANSCRIBED ...
into mRNA code for amino acids
EXONS
expression regions ... portions of nucleotides that CODE (10-25% of nucleotides)
INTRONS
intervening sequences... portions of nucleotides that DO NOT CODE (75-90% of nucleotides)
Transcription allows a single piece of DNA ...
to create more than one protein
Translation
* mRNA in the cytoplasm binds to a RIBOSOME (free or on ER)
* at ONE END tRNA combines with a CODON in mRNA, on the OTHER END it covalently bonds to a SPECIFIC AMINO ACID (bonding of amino acid catalyzed by aminoacyl-tRNA synthetase
* tRNA anticodon BASE PAIRS with mRNA codon (carrying with it amino acids bonded to other end of tRNA)
* PEPTIDYL TRANSFERASE (ribosomal enzyme) catalyzes the formation of PEPTIDE BONDS between the amino acids (brought by tRNA)
* after peptide bonds are formed between amino acids, tRNA is released from the ribosome (goes to get another amino acid)
* when termination codon is reached, the COMPLETED PROTEIN is released from ribosome
what specifies the ORDER of amino acids in the protein?
* it is the SEQUENCE OF CONDONS in mRNA that specifies the ORDER of amino acids in the protein
tRNA
* transfer RNA
* smallest type of RNA
* folds back on itself forming a 3 SIDED CLOVERLEAF
anticodon
the 3 base sequence (three letter group) in tRNA
a ribosome is WHAT physically?
* a ribosome is the physical structure in the cytoplasm on which proteins are synthesized
aminoacyl-tRNA synthetase
* aminoacyl-tRNA synthetase (enzyme) links specific amino acids to tRNA
What do RIBOSOMES contain ...
* ribosomes contain protein and 2 subunits of ribosomal RNA (rRNA)
DNA Replication
* both strands used
* entire strand replicated
* DNA polymerase
* DNA ligase
Protein synthesis
is a process that can be regulated by:
1. altering the rate of transcrition
2. altering combinations of exons
3. regulating stability of mRNA
4. regulating mRNA translation
depends on protein synthesis ...
body structure andfunction depends on protein synthesis

zygote (1 cell) -------> adult body (40 trillion cells)
many many cell divisions (mitoses)
Mitosis
cell division/replication
.... also involves DNA replication in a manner SIMILAR to mRNA formation needed for protein synthesis
Mitosis is what kind of replication?
semi-conservative replication (1/2 old and 1/2 new)
time for cell division varies:
... once in 24 hrs (rapidly dividing cell)
... NEVER in lifetime (muscle/nerve cells)
Cell Cycle:

Cell Division

Notable
* cell spends most time in interphase
* every cell in the body has the same genetic information
* cells are different because differt combinations of genes are active
* during the process of cell differetiation genes are activated or inhibited
* errors in base sequencing that occur during cell divisions are called MUTATIONS
Mutations (can)
1. cause no noticable change in a cells functioning
2. modify a cells functioning but still be compativle with cell growth/replication
3. lead to cell death
Cell Cycle
* Cell Division
1. Mitosis (nuclear division)
2. Cytokinesis (cytoplasmic division)
Cancer
* is a disease in which control mechanisms for cell replication do not work
Characteristics of Cancer Cells:
1. anaplasia
2. cell membrane changes
3. antigenic changes
4. biochemical changes
5. changes in karyotype
Mutation causes
* gene cloning
* recombinant DNA
* restriction enzymes