BIOL 107: EXAM 1
104 Cards in this Set
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Watson and Crick
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- Reported DNA in 1953
- won nobel prize in 1962 and shared it with Wilkens
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Nucleotide structure
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Nitrogenous base
5 C Sugar
Phosphate group
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Phosphate group
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One phosphorous atom bonded to 4 Hydrogen atoms
Negatively charged
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the connection between each nucleotide is a ...
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Phosphodiester bond
(phosphorous and 2 oxygens chemically bonded)
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3 Pyrimidines
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Cytosine
Thymine (DNA)- ethyl group
Uracil (RNA)- no ethyl group
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Characteristics of a pyrimidine
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6 membered ring that contains two nitrogen atoms
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Characteristic of a Purine
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hexagon+ pentagon combination
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2 Purines
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Adenine- N off the ring
Guanine- O off the ring
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Sugars
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DNA (deoxyribose) - H at 2' position
RNA (ribose) - OH at 2' position
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Chargaffs Rules
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%A = %T
%C = %G
%C+%T= 50%
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Watson and Crick model
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-Right handed double helix (from Rosaland Franklins X-ray)
-Sugar phosphate backbone outside
-Bases inside
-10 base pairs per turn
-strands are antiparallel
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Base pairing
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A with T - forms 2 H bonds
G with C- forms 3 H bonds
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Macromolecules
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-Polymers formed from monomers-> great diversity
- fats and lipids are not polymers
- important for living organisms
- synthesis and breakdown, carried out with help of an enzyme
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Synthesis/Dehydration of macromolecules
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Water is formed as a product for H and OH coming together
New bond created
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Breakdown/ Hydrolysis of a macromolecule
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Where H2O is added, breaking the bond into H and OH
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Enzymes
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accelerates chemical reactions but are not consumed by the reaction
- usually always a protein
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Proteins
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consist of C,H,O,N and S
- monomer repeat unit is an amino acid
- polymer state is a polypeptide
- can be found in folded structures
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Lipase
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enzyme that hydrolyzes ester bonds in phospholipids and triacylglycerides
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Amino Acids
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- 20 diff. AAs
- a carbon (central C connected to 4 diff. groups)
-4 groups (amino, carboxyl, hydrogen, R group)
- 19/20 naturally occurring
- Proline R group is attached to the N to create a 5 membered ring structure
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Amino Group
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N and 2-3 Hydrogens attached
- acts as a base (accepts a H and becomes + charged)
- at physiological pH (7) it is in a charged state with extra proton and +1 charge
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Carboxyl group
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-COOH
- OH group can act like a weak acid and give up a proton to solvent
- related to ketones and aldehydes
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Carbonyl group at physiological pH
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pH 7.2 in blood, carbonyl groups are deprotonated- they have a neg. charge associated with them
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Nonpolar amino acids
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Have R groups that are hydrophobic
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Polar amino acids
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Hydrophillic and have polar side chains
- second class
- interact with water through H bonding
- N and Q don't have side chains w/ acid/base properties b/c of carboxyl group
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Charged amino acids
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- electronically charged side chain, hydrophilic
- acidic AA have carboxylic side chains that deprotonate in aq. media near ph 2.7 (neg. charged)
- basis AA have side chains that are protonated at physiological pH and are + charged
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Polypeptide formation
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- occurs by dehydration reaction
- b/n carboxyl and amino
- loss of H20 forms C-N known as a peptide bond
-performed by ribosome
- analyze starting at N-terminus to C- terminus
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structure-function relationship of polypeptides
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not all polypeptides are proteins, must be folded to be a functional protein
structure dictates protein function
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Primary Structure
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determine shape and function, relies on covalent bonds
- list of AAs from N- to C- terminus
- single chain with peptide bonds
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Secondary structure
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- interactions b/n backbone groups
- H bonds
- a helix and b pleated sheets
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Tertiary
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- interactions b/n R groups, not backbone of atoms
- 3D arrangement of secondary structures
- bonds include H, disulfide bridge, ionic bond, and Hydrophobic interactions
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Quaternary structures
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- interactions b/n 2 or more polypeptides
- same interactions/bonds as tertiary
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AA polymerize to form protein....
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a covalent bond forms b/n the amino group of one nucleotide and the carboxylic acid of the second
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Genes
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carry the information that encodes the traits that were observed in an organism
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chromosomes
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the chemical structures that contain genes, these are the molecules passed from parent to offspring during reproduction
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Griffiths experiment
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- early 20th century
- studied bacterial strains that cause pneumonia
- R strain- pathogenic (virulent), small and rough texture
- S strain- non-pathogenic (non-virulent), larger and smooth coat of polysaccharides
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Griffiths 3 control reactions to experiment
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1. S cells into mice- died
2. R cells into mice- lived
3. heat treated S cells to make them non-living and observed the mice lived
* mixed heat killed S cells and living R cells and observed the mice died and pulled out living S cells
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Griffiths conclusion
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something in the heat killed S strain converted the live R strain to the pathogenic strain- a transforming substance
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Averys experiment- filtrate (1944)
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- new technology to hydrolyze biomolecules
- Started with S strain and generated filtrate of macronutrients
- complex sugars, fats, nucleic acids, and proteins
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Averys experiment- outcome
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treated 5 identical batches with one of 5 enzymes (RNase, DNase, Protease, Lipase, Carboase) and applied it to R strain bacteria
Outcome- DNase was the only one that transformed the nature of the S strain filtrate to
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Transformation (general facts)
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- uptake of DNA from environment
- single circular chromosome
- occurs when cell is stressed due to low nutrient density/ challenging agents
- 1% or less are competent (ability to take up exogenous DNA)
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gene expression
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creation of polypeptides from genes encoded in DNA- based chromosome
- DNA transcribed into mRNA
- mRNA translated into protein
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Location of transcription and translation in prokaryotes
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both processes occur in the cytoplasm
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transcription and translation location in eukaryotes
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transcription occurs in the nucleus, translation occurs in the cytoplasm
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Central Dogma
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information flows from chromosome (DNA) -> RNA (mRNA) -> protein
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Triplet code
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4x4x4=64
only combination that codes for all 20 amino acids
singlet 4 =4
doublet 4x4=16 not enough
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codon
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3 nucleotides that specify one amino acid
ex. UGG= Trp
Exist in both DNA and RNA
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Redundancy in genetic code
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- more than one code for an AA
- written as 5'-XYZ-3'
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Start and stop codon
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start- start of the encoded protein sequence, usually AUG
stop- usually 3 at stopping point- UAA, UAG, UGA
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Template strand of transcription
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Hydrogen bond with incoming nucleotide pairs in RNA polymerase during synthesis
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Coding strand of transcription
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- same sequence as mRNA product
- DNA sequence is ACGT instead of mRNA with ACDU
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3 stages of transcription
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initiation
elongation
termination
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Initiation
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- transcription begins at promoter
- promoter recognized by transcription factors and TATA box
- RNA polymerase begins to synthesize mRNA using the DNA template strand
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Elongation
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-RNA polymerase reads 3'-5' but writes 5'-3'
- doesn't require a primer
- uses nucleoside triphosphate as substrates
- writes AGCU but reads AGCT
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Termination
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- RNA polymerase dissociates from the chromosome and releases the mRNA
- folds into a pair pin
- prok. involves termination sequences
- euk. are associated with RNA processing
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mRNA in prokaryotes
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- chromosomes and ribosomes in cytoplasm
- translation and transcription occur simultaneously in cytoplasm
- mRNA translated into protein as soon as it is made
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mRNA in eukaryotes
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-mRNA made in nucleus, ribosomes in cytoplasm
- transcription and translation can't occur at the same time
- mRNA transported from the nucleus to the cytoplasm
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mRNA processing in eukaryotes
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- pre-mRNA (in humans, plants, and yeast) is made during transcription
- pre-mRNA modified into mRNA in nucleus
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RNA processing in eukaryotes
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5' end capping- add. of a methylated guanine (protects the end)
3' end capping- add. of poly A tail
UTR- untranslated regions, one next to 5' cap, the other next to 3' tail
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Function of cap and tail
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1. mRNA translation
2. mRNA export from nucleus, no export of cap or tail are missing- Quality control
3. mRNA stability in cytoplasm- when poly A tail degrades, the mRNA is removed from the cell through hydrolysis
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RNA splicing in eukaryotes
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- removes "intervening" sequences (Introns), not protein coding
- unites "exported" seq. (Exons) b/c protein coding
- this produces mature protein coding seq. in translation
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RNA splicing
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- branch site in an intron is a specific RNA seq. 5'-UGA or UAA
- branch site attacks the donor site at the 5' end of the intron, creates lariat structure
- 3' end of upstream exon attacks the acceptor site in the nearest intron
- connects 2 eons and leads to release of intron which is…
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Gel electrophoresis of RNA
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- focus on size and length
- neg. charge at wells, pos. at far end due to neg. charge of phosphate group in RNA
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importance of gene regulation in eukaryotes
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-contain control elements
- seq. that regulate transcription, upstream of promoter
- enhancer region, independent transcription binding sites, upstream of the gene
- proximal control elements close to 5' end to contain multiple transcription factor binding sites
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General Transcription factors
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used for all protein-coding genes, recruits RNA polymerase
- bind to proximal control elements of almost all genes
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specific
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used for a set of protein-coding genes
- req. for high levels of transcription
- both DNA and other regions that bind to proteins
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Transcription activation facts
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-occur over long distances
-DNA bending proteins assist- enhancer and proximal control regions neighbor
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order of transcription activation
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1. activator (tr. factors that increase gene expression) bind to the enhancer region of the gene
2. general tr. factors bind to proximal control region
3. mediator proteins- bind to both the activators at the enhancers and the general transcription factor at the proximal control region
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transcription repressors
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-repressors bind to sequences in the enhancer region called silencers to turn off gene transcription
- DNA bending proteins & mediator proteins are needed
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Cell differentiation
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activators and repressors differentiate cells with the same genomic DNA
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RNA interference (RNAi) (discovery)
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Fire & Mello- RNA silence-gene expression in eukaryotes, won the nobel prize
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Translation is RNA mediated
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mRNA
rRNA
tRNA
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What does tRNA do in transcription
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brings specific AA to ribosome and inserts the AA into the growing polypeptide chain if the correct codon is found in mRNA
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tRNA features
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- clover leaf structure- base pairs stabilize structure
- folds further into L shape
- anticodon: base pairs with mRNA codon
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tRNA charging
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-AA attached to the opp. end of the tRNA from the anticodon (3' end)
- only one type of AA is attached to each tRNA= makes tRNA charged when bound
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function of ribosome (general)
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-rRNA plays a catalytic role = protein synthesis
- ribosomal proteins hold rRNA, mRNA, and tRNA in place to carry out protein synthesis
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specific functions of ribosome
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1. bind to mRNA to read codon w/ high specificity
2. bind ot tRNA so mRNA is read w/o errors
3. catalyze peptide bond formation b/n incoming AAs and the growing polypeptide chain
4. ribosome must move along the mRNA so it can read each codon in order
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subunits of ribosome
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large- has all tRNA binding sites
small- contains mRNA binding site
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Binding site of ribosome (large subunit)
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A site
P site- peptidyl
E site
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general steps of translation
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initiation: protein synthesis
elongation: adds AA to generate a longer polypeptide chain
termination: ends protein synthesis when all of the coding region is read
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Initiation of translation in prokaryotes
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-small subunit binds mRNA
- use ribosome binding sequence so the start codon is lined up with the start site of translation
- initiator tRNA binds start codon (AUG), charged with AA Met
- large subunit joins small subunit, initiator tRNA is at P site
- energy from conversion of GTP to…
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Initiation of translation in eukaryotes
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-only a single protein coding region
- loading or ribosome occurs at the 5' cap of mRNA
- scans mRNA toward the 3' end till it reached the 1st 5' AUG seq.
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Advantages of Prokaryote translation
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anywhere there is a ribosome binding sequence, the following protein can be synthesized, bacteria can increase expression of related genes
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Elongation of translation
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1. recognition of mRNA codon in the A site by nuclease pairing to the correct charged tRNA
2. form. of peptide bond b/n the amino group of the new AA and the c-terminus of the growing peptide chain
3. translocation of the newest tRNA from the A site to the P site (5'-3')
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Codon recognition of elongation in translation
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aa-tRNA binds A site
tRNA anticodon base paires to the mRNA codon present in the A site
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Translocation in elongation of translation
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-peptidyl- tRNA moves from A to P site
- empty tRNA moves from E site- gets released
- new mRNA codon is exposed at A site, ready for new aa-tRNA
- cycle is repeated until a stop codon enters the A site
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Peptide bond formation in elongation of translation
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- bond b/n new AA at A site and polypeptide at P site
- transfers polypeptides to A site
- catalyzed by RNA
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Termination
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-release factors bind stop codon in A site- cause hydrolysis that releases polypeptide
- subunits can dissociate
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Protein misfolding diseases
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-Scrapie
- Parkinsons Disease
- Alzheimers
- Transthyretein
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Mad cow disease
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introduction of one misfolded protein can stimulate the production of misfiled copies
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Chaperonin proteins in the cell
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1. unfolded polypeptide enter the cylinder from one end
2. cap attaches- cylinder changes shape, creating hydrophillic enviro. for folding
3. cap comes off and folded protein released
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Gel electropheresis, studying proteins in primary structure
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- GE separate proteins by size instead of nucleic acids
- SDS-PAGE gel used
- protein size measured by molecular weight in kiloDaltons
- proteins are unfolded by "SDS" before ran through the gel- must be primary structure
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mutations are...
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changes in the DNA sequence that give rise to new alleles and can be passed down
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Point mutation
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a change in one base pair
ex. THE CAT
SHE CAT
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sickle cell anemia
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a point mutation, red blood cells clump and clog the vessels
Causes changes in the 6th AA of the primary structure = changes in quaternary structure
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3 types of point mutations
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- substitution
- insertion
- deletion
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substitution mutation
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genes found in 2 individuals differ at one location
ex. GGAG
GGGG
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Insertion mutation
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one copy of a gene will have more nucleobases as compared to the wild type sequence
ex. CTGGA
CTGTGAGA
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Deletion mutation
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opposite of insertion, a gene is missing one or more nucleobases
ex. CTGGAG
CTAG, GG missing
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Silent
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a type of substitution
- no change in the amino acid
- changes happen at the 3rd base of a codon
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Missense mutations
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change in the AA
- changes at 1st/2nd codon
- sickle cell anemia
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nonsense mutations
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-changes to a stop codon
- neg. mutation because a truncated protein will be produced
- shortened polypeptide is not functional
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How do mutations arise
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- spont. changes in DNA- chromosome
- induced changes due to mutagens (UV light or ionizing radiation)
- polyaromatic hydrocarbons cause mutation (in cigarette smoke)
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Frameshift mutation
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change in nucleotide # not in a multiple of 3
- mRNA changes which creates a new protein sequence
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Non-frameshift mutations
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change in nucleotide # in multiple of 3
- entire codons lost/gained
- resulting protein will be shorter/longer by a total of N/3
- N = # nucleobases added/lost
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BIOL 107: EXAM 1