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Exam 1 Flash Cards
Terms From 1st Syllabus
158
Biochemistry
Graduate
11/03/2010

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Term
Bases
Definition
Purine - double ring structure, Adenine and Guanine
Pyrimidines - single ring structures, Cytosine, Uracil and Thymine
Term
Deoxyribonucleotides
Definition
Sugar (deoxyribose), base (purine or pyrimidine) and phosphate groups
Term
Purines
Definition
Adenine and Guanine, double ring structure
Term
Pyrimidines
Definition
Cytosine, Uracil and Thymine, single ring structure
Term
Polynucleotides
Definition
Polymer of nucleotide monomers
Term
DNA Structure
Definition
Nucleotides linked by a phosphodiester bridge between the 5' and 3' C's of adjacent sugar groups (forming sugar-phosphate backbone)
There is a 5' end and 3' end
Term
Supercoiling
Definition
Folding back where one double strand passes over another double strand
Regular DNA is relaxed
Term
Topoisomerase
Definition
Enzymes that change DNA topology
Type I - Cleave 1 strand of DNA, swivel and reseal the DNA
Type II - Cleave both strands (generating a transient dbl strand break), pass a segment of DNA through the break and reseal the DNA
Term
DNA Gyrase
Definition
Uses energy in the form of ATP to introduce negative supercoils into DNA to make it easier to separate strands of the double helix
Term
Topoisomerase Inhibitors
Definition
Interfering with topoisomerase causes supercoils to build up downstream of the replication fork
Creates tension and stops replication, transcription or repair, anything that needs DNA unwinding
Term
Camptothecin
Definition
Plant alkaloid that blocks intermediate formed by Topo I and used in treating various types of cancers
Term
(+) Supercoiling
Definition
Hardest to separate
Supercoiled in a positive direction
Term
(-) Supercoiling
Definition
Easiest to separate
Supercoiled in a negative direction
Favors transcription
Term
Genome Size
Definition
H. Sapiens - 3 bil bps, 2.5 mil coding capacity, 25k genes
E. Coli - 4 mil bps, 3.4k coding capacity, 4 k genes
Term
Genome Organization
Definition
LINES/SINES for interspersed sequences of repetitive DNA
1.5% of DNA is exons that code for proteins
Term
Complexity
Definition
Indicates total length of different sequences present in a particular genome

More complex organisms have higher number of bps in general
However, some simple organisms have more DNA than humans but have more DNA than needed
Rel btwn complexity of an organism and number of bps becomes obscured as we move up evolutionary tree
Term
Cot Analysis
Definition
Analysis using the kinetics of DNA hybridizationto study the sequences that are in the genome

Value is directly proportional to sequence complexity
Term
DNA Melting
Definition
When heated the H bonds break, DNA becomes single stranded
Term
DNA Hybridization
Definition
1 - Shear DNA into few hundred fragments
2 - Melt DNA by boiling it near 90 degrees
3 - Incubate DNA 10-20 degrees below melting period to reform the double helix
4 - Can measure the rate of hybrid formation, which is depending on the concentration of complimentary strands
Term
Histone
Definition
Major structural chrom. proteins
1 - small 118-236 AAs, 13-26 kDa
2 - rich in (+) charged basic AAs (Arg/Lys) that can interact w/polyanionic backbone of DNA
3 - 5 main Classes based on AA sequence: H4, H5, H2A, H2B and H1 in a 2:2:2:2:1 ratio
4 - Subject to numerous post-translational modifications - targets of regulatory pathways
Term
Nucleosome
Definition
Fundamental repeating unit of eukaryotic chromatin organization
Octamer containing
Term
Chromatin
Definition
30-nm fiber composed of nucleosomes folded into a zig-zag/solenoid structure or a beads on a string form
Term
Chromosome
Definition
Contains genes, centromeres, telomeres and origins of DNA replication
Term
Centromere
Definition
Sequences that assure correct partitioning of chrom.s during mitosis
Interact w/proteins that segregate chrom.s
Roughly 1 mil bps in length, contain repetitive satellite DNA
Term
Telomere
Definition
Repeated sequences at the end of chrom.s for protection
Term
Coding Capacity
Definition
Tot # bps / (Avg AA per prot * 3)
Maximum number of avg-sized proteins that could be encoded by a genome
Term
3 Variables Determining DNA Melting Temp
Definition
Length - For sequences less than 100 bps the longer the length the more stable it is and has a higher melting point, after 100 bps length is negligible

Mismatches - In very short duplexes mismatches increase instability and lower the melting point

G+C content - GC rich DNA has a higher melting point because they contain 3 H bonds instead of 2 like AT bases
Term
Kinetic Components of Eukaryotic Genomes
Definition
Non-repetitive - unique, coding sequences that have the highest Cot # b/c they're the most complex

Middle-repetitive - Has some repetitive sequences, Cot # falls in the middle

Highly-repetitive - Contains the most amount of repetitive DNA and has the lowest Cot #
Term
Amino Acids
Definition
Building Blocks of Protein
20 kinds
Contain an amine/carboxylic group, H and a side chain
Have a chiral center (except Gly)
Optically active, in L formation
Term
Glycine
Definition
Smallest side chain (one H)
Extremely flexible
Found in flexible parts of proteins or in tight turns
Achiral
Term
Proline
Definition
Side chain attaches to backbone to form ring
Extremely rigid and constrains flexibility of protein backbone
Found in tight turns
Term
Aliphatic
Definition
Ala - Leu - Ile - Val
Hydrophobic and found in the interior of proteins
Ile and Val are beta branched -> sterically hinders free rotation and imposes structural constraints on peptide backbone
Term
Aromatic
Definition
Phe - Tyr - Trp
Bulky, planar and largely hydrophobic
Tyr and Trp amphiphilic and can make H bonds b/c O and N in reangs
Term
Sulfur-containing
Definition
Met - Cys
Largly hydrophobic, Cys is weakly acidic
Met initiates protein synthesis
Thiol on Cys can make disulfide bonds, which is important for tertiary and quaternary structural stabalization
Term
Acidic
Definition
Asp - Glu
End with carboxylic acid
Found on exterior of proteins
pKa around 4 in aqueous solutions
Negatively charged at neutral pH
Make good ionic bonds
Term
Basic
Definition
Arg - Lys - His
N containing groups in side chains that can be protonated
Side chain pKa values vary
His side chain has a pKa around neutral level so it makes a good buffer and is ideal for enzymes that catalyze rxns with proton transfer steps
Arg and Lys are positively charged at a neutral pH and can make good ionic bonds
Term
Polar
Definition
Asn - Gln - Ser - Thr
Hydrophilic uncharged side chains with terminal amines (Asn/Gln) or hydroxyls (Ser/Thr)
Involved in H bonding interactions
Term
Functional Groups
Definition
8 groups that the amino acids are divided into depending on the physical properties of their side chains
Term
Peptide Bonds
Definition
Formed by condensation rxns
Polymerization of amino acids
formed between the amine side of one amino acid and the carboxyl side of another amino acid
Term
Peptide Groups
Definition
Six atoms closest to the peptide bond lying in the same plane
Includes: carbonyl carbon with its oxygen, two a-carbons and the amine nitrogen with its hydrogen
Together form a linked sequence to form the polypeptide backbone
Term
Protein Primary Structure
Definition
Just the sequence of amino acids without folding
Term
Protein Fold
Definition
Adjacent planar peptide groups can rotate around each a-carbon and alter backbone conformation
Primary - AA chain, no folding
Secondary - Beta sheets and alpha helices
Tertiary - Disulfide bonds
Quaternary - Joining of subunits
Term
Protein Misfolding Disease
Definition
Mutations cause misfolding in proteins and this can cause diseases
Primary Amyloidosis
Alzheimer's Disease
Huntington's Disease
Term
Noncovalent Bonds
Definition
Includes ionic, hydrogen and van der Waals bonding
Term
Ionic Bonding
Definition
Attraction of a cation to an anion
Seen between an acidic and basic amino acids
Small metal cations or inorganic anions interact with charged side chains to stabilize protein conformations
Term
Hydrogen Bonding
Definition
Equal or unequal sharing of a proton between a weakly acidic donor group and a weakly basic acceptor group that contains an electron lone-pair
Side chain hydroxide or amide could share a proton with a carbonyl oxygen
critical in secondary structure stabalization
Term
van der Waals Bonding
Definition
Mutual attraction that two uncharged atoms feel when they approach each other
Caused by synchronization of electron clouds
Weakest but plays a role in packed interior of proteins where side-chains come into close proximity
Major type of binding observed between aliphatic side chains
Term
Hydrophobic Effect
Definition
Enormously important in stabilizing tertiary and quaternary structures
Tendency for hydrophobic molecules to minimize contact with water by packing together into oily globules
Term
Disulfide Bond
Definition
Covalent bond formed between terminal S between Cys-Cys
Oxidation reaction needing oxygen
Term
DNA Polymerase
Definition
Adds base pairs to DNA in a 5'->3' direction and also has exonuclease functions
Term
Exonucleolytic Proof Reading
Definition
Removes incorrect bases when they are improperly paired
Pol.s stall due to improper pairing and change shape so that the end of the growing strand is inserted into the active site and clips the incorrect base
Term
Fidelity of DNA Replication
Definition
5'->3' polymerization (10^-5) - makes mistakes b/c variant forms of nucleotidesimproperly base pair and get incorporated
3'->5' Exonuclease (10^-2) -> When enzyme stalls b/c improper base pairing it fixes it
Mismatch repair (10^-2) -> Corrects most of mismatched base pairs not repaired by exonucleolytic proofreading

All repair processes bring total fidelity to 10^-9
Term
Primase
Definition
RNA Polymerase that primes DNA synthesis by synthesizing a short complementary RNA strand
Term
Helicase
Definition
Involved in unwinding the DNA by using ATP
Term
Single Stranded DNA-binding Protein
Definition
Specifically binds single-stranded DNA to stabilize the single strands and protect it from forming stem-loops or being degraded by nucleases
Term
Leading Strand
Definition
Synthesized continuously by adding bases in a 5' to 3' direction
Term
Lagging Strand
Definition
Synthesized discontinuously with the generation of many small Okazaki fragments
Term
Replication Origins
Definition
Where replication begins
One in Prokaryotes
Multiple in Eukaryotes to decrease replication time
Term
Reverse Transcriptase
Definition
Creates DNA copy from RNA parent strand
Used by viruses that use RNA as the genetic material
Term
Mutation
Definition
Substitutions (transitions: pu->pu, py->py; transversions py->pu, pu->py)

Deletions of 1 or more bps

Insertions of 1 or more bps
Term
DNA Repair
Definition
1- Recognize damaged region by an endonuclease that makes an incision
2 - Exonuclease removes DNA adjacent to the damaged base on the damaged strand only
3 - Gap filled in by DNA polymerase
4 - Nick is sealed by DNA ligase
Term
Thymine Dimer
Definition
Cyclobutyl linkage of adjacent thymines often resulting from UV damage
Term
Mismatch Repair
Definition
Occurs soon after DNA has been replication
Exonuclease that removes DNA recognizes new (unmethylated) DNA and removes newly synthesized DNA
Corrects mismatched bases incorporated during DNA replication
Term
Xeroderma Pigmentosum
Definition
Example of a DNA repair deficiency
Results from an inability to remove and repair thymine:thymine dimers
Presents as dry skin in infancy, which atrophies, corneal ulcers, abnormal coloration of the skin and skin cancers
Tumors can appear and metastasize
Term
Lynch Syndrome
Definition
Mutation in genes encoding the human counterparts of genes that are in the mismatch repair pathway
Causes a predisposition to colon cancer
Affects 1/200 people
Term
HNPCC
Definition
Hereditary Nonpolyposis Colon Cancer - caused by DNA repair deficiency in humans
Also known as Lynch syndrome
Term
Polymerase I
Definition
Enzyme that participates in DNA replication
5'->3' DNA pol activity, adding bases
3'->5' exonuclease activity that mediates proofreading (reverse)
5'->3' exonuclease activity mediating nick translation during DNA repair (forward)
Term
Polymerase III
Definition
Does most of the work in new DNA polymerization
3'->5' exonuclease activity for editing during chromosomal replication
Term
Recombinant DNA
Definition
Form of artificial DNA created by combining two or more sequences that would not normally occur together through gene splicing
Term
Restriction Enzymes
Definition
Cleave "non-self" DNA at specific base sequences
Recognize palindromic sequences and cleave phosphodiester bonds in specific places
Term
Vectors
Definition
Vehicle used to transfer genetic material to a target cell
Term
Plasmids
Definition
Small circular DNA molecules found in bacteria used for cloning with a defined set of restriction sites to allow them to be manipulated
Term
Polymerase Chain Reaction
Definition
DNA sequence amplification using 2 oligonucleotide primers that flank fragment one would like to amplify
Use the 5' of the A end and the 5' of the B end
Term
Oligonucleotide Hybridization
Definition
Can hybridize and form a stable duplex with complementary sequences
Measure melting curves, mismatches are less stable
Term
Southern-Blot
Definition
Radioactive cloned DNA produced with dNTP and DNA pol
Labeled fragments used as probes to detect specific genes that have been electrophoresed and transferred to a filter
Term
Northern-Blot
Definition
Electrophoresing RNA using radiolabeled DNA "probe"
Term
DNA Sequencing
Definition
Different methods for determining order of the nucleotide bases in DNA
Use chain termination and amplification/cloning
Term
Microarray
Definition
Chips with thousands of oligonucleotides synthesized with photoactivated DNA synthetic rxns and photomasks
Chips used to analyze whether DNA forms stable DNA duplexes
Chips can be used to determine whether genes are expressed in cells or tissue using reverse transcriptase on mRNA and hybridizing it to the chip
Term
Polonies
Definition
Amplified population of DNA fragments to different locations of solid support
Use reversible fluorescent ddNTPs and fluorescent detectors to determine short segments
Can perform high-throughput sequencing so a high density of polonies can be sequenced and find the sequence to many different DNA fragments simultaneously
Term
Secondary Structure
Definition
Local conformation of its backbone, or main chain
Helices and sheets
Term
a-helix
Definition
PP chain twisted by same amount about each of its alpha-C atoms and assumes a helical conformation
Counterclockwise w/3.6 residues/turn with a linear distance of 5.4 A
H bond forms between main chain carbonyl O of Nth helical residue and the main chain amine of the (N+4)th helical residue
Term
B-sheet
Definition
All-trans peptide bondsadopt a rough planar geometry with H bonds forming between backbone carbonyls and backbone amines on adjacent strands
Neighboring hydrogen-bonded pp chains run in opposite directions
Have rippled or pleated appearance w/two residues repeating at a distance of 7A
Term
Tertiary Structure
Definition
Helices and sheets joined by nonrepetitive loop segments or coils
Not necessarily flexible as a random coil but instead are held rigidly in place as the backbone of an a-helix
Term
Amphipathic Helix or Sheet
Definition
Helix - Has h+ and h- sides because side chains of the (n+3)th and (n+7)th chains stick out the same directions to make a unified side
Sheet - alternating h+/h- residues that form one side as h+ and the other side as h-
Term
Structural Motifs
Definition
Certain combos of 2nd structural elements
Zn-finger: Beta-turn-helix structure, binds Zn through Cys and His side chains
EF-hand
Ankyrin-repeat
Beta-Barrels
Term
Protein Domains
Definition
Independently functional units of proteins that can serve their own purposes in the protein
Coiled-coil: forms basis of many structural proteins found in the cell, fibrous tissue and for functional proteins
Term
Quaternary structure
Definition
Spatial arrangement of many polypeptide chains in subunits in a single protein
Term
Structure/function Relationship
Definition
Example: Hb in a puckered form cannot bind oxygen but when it changes conformation to the planar structure it can bind oxygen better
Term
Ion Channel
Definition
Transmembrane proteins that form ion conducting pores through lipid bilayer so that h+ ions can pass through the h- center of the bilayer
Term
Ion Selectivity
Definition
Permits the flux of specific ions into or out of the cell based on structure of the channel
Term
Protein Dynamics
Definition
Proteins have various levels of structure and motions depending on their environment and binding
Term
Intramolecular Motions
Definition
Proteins not merely rigid bodies, can move
Atomic fluctuations - rapid vibrations
Collective Motions - breathing, coordinated vibrations of groups of covalently linked atoms
Triggered conformational changes - in response to ligand binding or other environmental change, can involve individual side chains to entire polypeptide subunits
Term
Allostery
Definition
Structural changes because of the binding of a ligand at one site altering the binding of another ligand at a distant site
Term
Cooperative Binding
Definition
Example: one Hb heme group binds one oxygen, conformation of the protein changes so that it's easier for the next oxygen to bind and then easier after that
Term
Ion Channel Gating
Definition
Proteins that undergo structural changes to convert between conducting and nonconducting conformations including activation, deactivation, inactivation and desensitization
Term
Native Conformation
Definition
Energy stabilizing this tertiary/quaternary structure coming mainly from noncovalent interactions where the protein folds into rapidly after synthesis
Term
Denaturation
Definition
Unfolding of proteins due to heat, pH, detergents, miscible organic componds or salts/urea/guanidine
Term
Protein Stability
Definition
Maintained by polypeptide interactions started by primary structure of the amino acids
Can go awry with substitutions: h- for h+, Gly to non-Gly, Non-Pro to Pro or Glu to Arg
Term
Protein Turnover
Definition
Balance between protein synthesis and protein degradation
Term
Dominant Negative Inhibition
Definition
Ability of mutant proteins to adversely affect the activity of wild type proteins
Term
Protein Aggregation
Definition
Collection of mis-folded proteins
Responsible for many degenerative diseases
Basically amyloidosis
Term
Fibril
Definition
Made of numerous closely packed B-sheets that make up amyloid deposits
Term
Amyloid
Definition
Deposits formed by proteins or protein fragments folded in a nonnative conformation that can be extracellular (plaques in Alzheimer's disease) or intracellular (Lewy bodies in Parkinson's disease)
Term
Transcription
Definition
Process of copying DNA to RNA
Term
Coding Strand
Definition
Contains the same sequence as the new RNA strand
Contains the gene that will be synthesized
Not actually transcribed
Term
Template Strand
Definition
Strand actually being transcribed
Serves as template for transcription
Term
Open Reading Frame
Definition
DNA corresponding to protein sequence is coding region with an ORF
Term
Promotor
Definition
DNA sequence that directs RNA pol to starting point of a gene within 250 bps
Around 75 and 90 bps upstream are activating sequences (promoter elements)
Term
Enhancer
Definition
DNA sequences that increase the activity of promoters
Can be found within proximal promotors or several kbps away
Cannot promote initiation alone
Term
Transcriptional activator
Definition
DNA-binding protein that regulates one or more gene by increasing rate of transcription
Term
TATA Element
Definition
Core promotor element
Found around 30 Nuc.s upstream of the initiator
Term
B-Thalassemias
Definition
Thalassemis: group of hereditary anemias resulting from an imbalance in the synthesis of alpha/beta chains of hemoglobin
Caused by point mutations impairing synthesis of beta chain
Found between 90 and 31 bp within TATA box
Mutations reduce or eliminate binding of transcriptional activators or TBP and reduce mRNA synthesis
Not dom (-) because only reduces amount of Thalassemias, some still gets made
Term
General Transcription Factor
Definition
Protein transcription factors involved in formation of pre-initiation complex and bind with RNA pol II to single-stranded DNA gene template to read it
Term
Coactivator
Definition
Protein that increases gene expression by binding to an activator that contains a DNA binding domain
Can't bind DNA alone
Term
Co-Repressor
Definition
Decreases gene activity by binding to a transcription factor which contains a DNA binding domain
Can't bind DNA alone
Term
Constitutive Promotor
Definition
Always bound by transcriptional activators
Promote genes that must be expressed in all cells at all times
Term
Inducible Promotor
Definition
Bound by transcriptional activators and activated in response to cellular conditions
Protein factors bind only under specific circumstances
Term
Chromatin
Definition
Combination of DNA, histone and other proteins that make up chromosomes
Compacted form of DNA
Term
Nucleosome
Definition
Basic unit of DNA packaging
DNA wrapped twice around a histone octet
Term
Histone Acetylation
Definition
Causes transcriptional activation by having causing the DNA strands to disassociate from the histones
Term
DNA Binding Domain
Definition
Protein domain containing at least one motif that recognizes double or single stranded DNA
Term
Transcriptional Activation Domain
Definition
Domain of a protein that interact with transcriptional apparatus that activate transcription
May be glutamine rich, proline rich or acidic
Term
Nuclear Receptor
Definition
Proteins found within cells responsible for sensing steroid and thyroid hormones and work with other proteins to regulate the expression of specific genes
Term
Steroid Hormone Receptor
Definition
Term
Protein PHosphorylation
Definition
Term
Regulated Proteolysis
Definition
Term
LIgand
Definition
Term
Intracellular Localization
Definition
Term
Histone Acetylase
Definition
Term
Histone Deacetylase
Definition
Term
DNA Methylation
Definition
Term
CpG
Definition
Term
RNA Splicing
Definition
Term
Primary Transcript
Definition
Term
Exon
Definition
Term
Intron
Definition
Term
Spliceosome
Definition
Term
snRNA
Definition
Term
snRNP
Definition
Term
Splice Site
Definition
Term
Alternative Splicing
Definition
Term
5' 7-Methyl Guanosine Cap
Definition
Term
Polyadenylation
Definition
Term
5' UTR
Definition
Term
3' UTR
Definition
Term
Message Decay
Definition
Term
miRNA
Definition
Regulates stability and translation of specific mRNAs
Term
PCR
Definition
Term
Real-time PCR
Definition
Term
Quantitative PCR
Definition
Term
Mutation Detection
Definition
Term
Viral Load
Definition
Term
Molecular Diagnosis
Definition
Term
Hybridization Probes
Definition
Term
Factor V Leiden Mutation
Definition
Term
HIV-1 Drug Resistance Mutation
Definition
Term
K-RAS Mutation Analysis
Definition
Term
EGFR Pathway
Definition
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