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biochem review from First Aid and Kaplan

What is the structure of Chromatin? It is negatively charged DNA that loops twice around a histone octamer to form a nucleosome bead.
What is unique about H1 histone protein? H1 is the only histone that is not in the nucleosome core.
What is the function of H1 histone? H1 ties nucleosomes together in a string.
When does DNA condense to form mitotic chromosomes? DNA condenses during mitosis
What is heterochromatin Condensed, transcriptionally inactive DNA. Think: " HeteroChromatin= Highly Condensed"
What is Euchromatin Less condensed, transcriptionally active Think: "Eu= true, truly transcribed"
What are the 4 nucleotides? Adenine, Thymine, Guanine, Cytosine
What are the purines? A and G, Think: "PURe As Gold: PURines"
What are the pyrimidines? C and T, Think: CUT the Py(pie): PYrimidines
Which nucleotides have two rings in their structure? Purines
Which nucleotides have one ring in their structure? Pyrimidines
What is special about Guanine? it has a ketone
What is special about Thymine? It has a methyl group attached. Think: "THYmine has a meTHYl" It is also found in DNA
What is special about Cytosine? Deamination of cytosine makes Uracil
Where is Uracil found RNA
Which has a stronger bond: G-C or A-T? G-C because it has 3 H bonds. The more G-C bonds a DNA stand contains the higher the melting point of the strand.
What are the amino acids necessary for purine synthesis? Glycine, Aspartate, Glutamine
What makes up a nucleoside? base + ribosome
What makes up a nucleotide? base + ribosome + phosphate, linked by a 3'-5' phosphodiester bond
How are purines made de novo? purines are made from IMP precursor
How are pyrimidines made de novo? Pyrimidines are made from orotate precursor with PRPP added later
What is made first: ribonucleotides or deoxyribonucleotides? Ribonucleotides are synthesized first and are converted to deoxyribonucleotides by RIBONUCLEOTIDE REDUCTASE
The conversion of PRPP to IMP (AMP and GMP) requires what? Glycine, Aspartate, Glutamine and THF
Conversion of Carbamoyl phosphate to Orotic Acid (precursor of pyrimidines) requires what? Aspartate
What enzyme is required to convert dUMP to dTMP? Thymidylate synthase
What enzyme is required to convert DHF to THF? Dihydrofolate reductase
What is DNA transition? Substitution of a purine for a purine or a a pyrimidine for a pyrimidine. Think: "TransItion = Identical type"
What is DNA transversion Substituting a purine for pyrimidine. Think: "TransVersion = conVersion between types"
Features/Characteristics of the Genetic Code? The genetic code is: - unambiguous - Degenerate/Redundant - Commaless, nonoverlapping - Universal
What does it mean to say that the genetic code is unambiguous? Each codon specifies only 1 amino acid
What does it mean to say that the genetic code is degenerate/redundant? More than 1 codon may code for the same amino acid
What is the only amino acid that is coded by only one codon? Methionine is encoded by only one codon (AUG)
What does it mean to say that the genetic code is Commaless, nonoverlapping? DNA is read from a fixed starting point as a continuous sequence of bases. However some viruses are an exception.
What does it mean to say that the genetic code is universal? Genetic code is conserved throughout evolution. Exceptions include mitochondria, archaebacteria, Mycoplasma, and some yeasts.
What is a silent mutation It is a mutation that produces the same amino acid and is often due to a base change in the 3rd position of the codon. Due to tRNA wobble
What is a Missense mutation? mutation that results in a different amino acid being produced.
What is a Nonsense mutation? mutation that results in the production of an early STOP codon. Think: "STOP the NONSENSE"
What is a Frameshift mutation? a mutation that causes a misreading of all nucleotides downstream, usually resulting in a truncated, nonfunctional protein.
Which is the most severe DNA mutation? What is the least severe? Most severe = Nonsense Least Severe = silent
What do single stranded binding proteins do? Prevent strands from reannealing
What does DNA topoisomerases do? create a nick in the helix to relieve supercoils created during replication
Primase makes an RNA primer on which DNA polymerase III can initiate replication
DNA polymerase III only found in prokaryotes only. Functions to elongate leading strand by adding deoxynucleotides to the 3' end. Elongates lagging strand until it reaches primer of preceding fragment. 3'-5' exonuclease activity profreads each added nucleotide
DNA polymerase I prokaryotic only, degrades RNA primer and fills in the gap with DNA. DNA polymerase I excises RNA primer with 5'-3' exonuclease
DNA ligase Seals
Nucleotide excision repair Specific endonucleases release the oligonucleotide-containing damaged bases; DNA polymerase and ligase fill and reseal the gap
Base excision repair Specific glycosylases recognize and remove damaged bases, AP endonuclease cuts DNA at apyrimidinic site, empty sugar is removed and the gap is filled and resealed.
Mismatch repair Unmethylated, newly synthesized string is recognized, mismatched nucleotides are removed and the gap is filled and resealed
Nonhomologous end joining Brings together 2 ends of DNA fragments. no requirement for homology
mRNA longest type of mRNA, start codon = AUG, stop codon = UGA, UAA, UAG, made by RNA polymerase II
rRNA most abundant type, made by RNA polymerase I
tRNA smallest type, 75-90 nucleotides long, secondary structure is cloverleaf form made by RNA polymerase III
Promotor region site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus (AT rich upstream sequence with TATA and CAAT boxes)
Mutation in promotor region commonly causes: dramatic decrease in amount of gene transcribed
Enhancer region stretch of DNA that alters gene expression by binding transcription factors
Silencer region site where negative regulators (repressors) bind
Eukaryotic RNA polymerases RNA polymerase I makes rRNA RNA polymerase II makes mRNA as well as opens DNA at promoter site RNA polymerase III makes tRNA RNA polymerase has no proof-reading functions but can initiate chains
RNA processing Occurs in nucleus. After transcription: 1) capping on 5' end 2) polyadenylation on 3' end 3) Splicing out of introns Initial transcript is called heterogeneous nuclear RNA (hnRNA) Capped and tailed transcript is called mRNA
Exons contain actual genetic information coding for protein, different exons can be combined by alternative splicing to make unique proteins in different tissues
Introns intervening noncoding segments of DNA
tRNA wobble accurate base pairing is required only in the 1st two nucleotide positioning of an mRNA codon, so codons differing in the 3rd 'wobble' position may code for the same tRNA/amino acid
Steps of protein synthesis Initiation, elongation, termination
Proteasomal degradation attachment of ubiquitin to defective proteins to tag them for breakdown
CDK cell cycle regulator Cyclin dependent kinase, constitutive and inactive
Cyclins cell cycle regulator Regulatory proteins that control cell cycle events, phase specific, activate CDKs
Cyclin-CDK complexes must be both activated and inactivated for cell cycle to progress
Tumor suppressors Rb and p53 normally inhibit G1 to S progression, mutations in these genes result in unrestrained growth
Permanent Cell type remains in G0, regenerates from stem cells, Ex of permanent cell types: neurons, skeletal, cardiac muscle and RBCs
Stable (quiescent) cell type Enter G1 from G0 when stimulated to grow Ex of stable cell types: Hepatocytes, lymphocytes
Labile cell type Never go into G0, divide rapidly with a short G1 Ex: Bone marrow, gut epithelium, skin, hair follicle
Rough Endoplasmic Reticulum (RER) site of synthesis of secretory proteins and of N-linked oligosaccharide addition to many proteins. Nissl bodies in neurons synthesize enzymes and peptide neurotransmitters
Smooth endoplasmic Reticulum (SER) site of steroid synthesis and detoxification of drugs and poisons
Where is there a high concentration of RER Mucus-secreting goblet cells of the small intestine and antibody secreting plasma cells
Where is there a high concentration of SER liver hepatocytes and steriod hormone producing cells of the adrenal cortex
Golgi Apparatus function 1) distrubution center of proteins and lipids from ER to plasma membrane, lysosomes and secretory vesicles 2) Modifies N-oligosaccharides on aspariagine 3) Adds O-Oliogosaccharides to serine and threonine 4) addition of mannose-6-phosphate to specific lys
I cell disease inherited lysosomal storage disorder, failure of addition of mannose-6-phosphate to lysosome proteins
Microtubule cylindrical structure composed of a helical array of polymerized dimers of alpha and beta tubulin, each dimer has 2 GTP bound. Grows slowly and collapses quickly
molecular motor proteins transport cellular cargo toward opposite end of microtubular tracks Dynein = retrograde to microtubule Kinesin = anterograde to microtubule
Cilia Structure 9+2 arrangement of microtubules Axonemal dynein- ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets
Cytoskeletal elements actin, mysoin, microtubules, intermediate filaments
Actin and Myosin found in microvilli,involved in muscle contraction, cytokinesis, adhering junctions
Microtubules Cilia, flagella, mitotic spindle, neurons, centrioles
Intermediate Filaments Vimentin, desmin, cytokeratin, glail fibrillary acid proteins (GFAP), neurofilaments
Plasma membrane composition Asymmetric fluid bilayer, contains cholesterol, phospholipids, sphingolipids, glycolipids and proteins High cholesterol or long saturated fatty acid content leads to increased melting temp and decreased fluidity
Vitemtin Stain Immunohistochemical stain for Connective tissue
Desmin Stain Immunohistochemical stain for muscle
Cytokeratin Stain Immunohistochemical stain for epithelial cells
GFAP stain Immunohistochemical stain for Neuroglia
Neurofilaments stain Immunohistochemical stain for Neurons
Sodium Pump Na-K ATPase is located in the plasma membrane with ATP site on cytoplasmic side. For each ATP consumed, 3 Na go out and 2 K come in. During cycle, pump is phosphorylated
Collagen most abundant protein in the human body, extensively modified, organizes and strengthens extracellular matrix
Type 1 Collagen most common type, found in the Bone, Skin, Tendon, dentin, fascia, cornea, late wound repair
Type 2 Collagen Cartilage(including hyaline), vitreous body, nucleus pulposus
Type 3 Collagen Reticulin, skin, blood vessels, uterus, fetal tissue, granulation tissue
Type 4 Collagen Basement membrane or basal lamina
Vitamin C is required for what part of collagen synthesis Its needed for hydroxylation of specific proline and lysine residues
Ehlers-Danlos Syndrome Faulty collagen synthesis causing: hyperextensible skin, tendency to bleed, hypermobile joints. There are 6 types and inheritance and severity vary depending on the type. May be addociated with joint dislocation, berry aneurysm, organ rupture.
What type of collagen is most often affected in Elhers-Danlos Syndrome Type 3 collagen
Osteogenesis Imperfecta aka Brittle Bone Disease, most common form is autosomal Dominant with abnormal Type 1 collagen. Sx: multiple fractures, blue sclerae, hearing loss, dental imperfections
Alports Syndrome due to a variety of gene defects resulting in abnormal type 4 collagen, most common is X linked recessive. Sx: progressive hereditary nephritis, deafness, ocular disturbances
Elastin stretchy protein within lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava. rich in proline and gylcine, broken down by elastase which is normally inhibited by alpha 1 antitrypsin
Marfans syndrome caused by a defect in fibrillin
Emphysema can be caused by alpha 1 antitrypsin deficiency resulting in excess elastase activity
Created by: 44106594



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