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113 Cards in this Set

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Adenine
Derivative of Purine. One of 4 basic building blocks of DNA. Binds to Thymine
Antiparallel
DNA is antiparallel, strands run in different directions. 5' - 3' and 3'-5'
Central Dogma
The idea that genetic information flows from DNA -> DNA , DNA -> RNA, and RNA -> Protein

(Replication, Transcription, Translation)
Chargaff's Rules
1. A=T, G=C
2. Same in both strands
cytosine 
Derivative of Pyrimidine, One of 4 basic building blocks of DNA. Binds to Guanine
deoxyribonucleic acid (DNA)
Anti parallel Double-helix, made of ATGC, Contains code for all genetic info.
DNA replication 
Genetic info flowing from DNA->DNA. Creates identical DNA strand copy.
genotype
The genetic makeup of an organism. Determines its physical trait.
guanine
Derivative of Purine. One of 4 basic building blocks of DNA. Binds to Cytosine
messenger RNA (mRNA)
Major component of translation. Takes genetic code to ribosome for amino acid production
nucleic acid
linear chains of nucleotides
nucleoside 
formed from Pyrimidine bases and Purine bases bond with Deoxyribose sugar
nucleotide 
Formed by adding a phosphate to a nucleoside. Building block of nucleic acid.
phenotype 
An organism's physical traits.
purine 
Base compound for Adenine and Guanine
pyrimidine 
Base compound for Thymine and Cytosine
ribosome 
Protein sythetic factory. form Amino acids/ polypeptides
ribonucleic acid (RNA) 
Single strand of genetic info. Made of AUGC. U = Uracil
thymine 
Derived from pyrimidine. building block of DNA. Binds with Adenine
transcription 
going from DNA ->RNA
transfer RNA (tRNA) 
Carries amino acids to ribosomes to create polypeptide chains
Avery, MacLeod, McCarty,
proved "biological specificity" of Nucleic acids. continued work of Griffith
translation 
RNA - > Amino Acid (Polypeptide)
uracil 
Derivative of pyrimidine, replaces Thymine in RNA.
Mendel
3 laws of inheritance

1. Independent assortment = Traits inherited separately of each other
2. Independent Segregation - genes can be different or same. 1 allele from each parent
3. Dominance = 1 allele dominant, 1 allele recessive. 3:1 ration. (Dominant = tall, recessive = short, 3 tall 1 short)
Miescher
First discovered DNA, called it Nuclein.
Garrod, Beadle, Tatum
Garrod first showed Genotype determines Phenotype.

Beadle, Tatum proved this theory, also hypothesized 1 gene, 1 polypeptide.
 Levene
Discovered 4 bases of DNA, ATGC
Todd
proved 3' to 5' directionality and terminus'
Griffith
first hint at DNA being genetic material, with mice and R&S colonies
Chargaff,
Chargaffs rules, 1. A=T, G=C
Hershey, Chase
Proved that phages transfered DNA.
Franklin, Wilkins
Discovered A-DNA and B-DNA by using x-ray crystallography. Lead to discovery of DNA structure.
Watson, Crick
proposed DNA as double stranded helix.
affinity chromatography 
exploits a proteins ability to bind ligands. attaches ligands to beads, pours bacteria through, some proteins bind to the ligands, helps determine which proteins are present.
α‐helix 
2' structure of polypeptide. H-bonds on inside give structure and regularity.
amino acid 
basic building block of polypeptides.
β‐strand 
makes up β‐sheet. fully extended region of peptide chain
β‐turn 
Connects α-helix and β‐strand. allows polypeptide to change to direction. gives super secondary structure
β‐sheet (antiparallel, parallel) 
Multiple β‐strands make up sheet.

Antiparallel = sheets run opposite direction

Parallel = sheets run same direction.
column chromatography 
separates proteins by repeatedly partitioning through columns of beads Then analyzes with a UV monitor.
denatured state 
protein is denatured after excessive heat or chemical agents. Weak non-covalent bonds are broken. made up of random conformations.
disulfide bond 
Disulfide bonds are created during the synthesis of cystine. Aids in tertiary structure.
electrophoresis 
protein sample applied to one end of gel plate, electrode to the other end. Pulls certain proteins further down field based on their isoelectric pH.
gel filtration 
Separates proteins by size. Uses special beads that capture smaller proteins, and let large pass by.
hydrogen bond 
non-covalent. only between NOF and H. H bonds between AT and GC help stabilize DNA. 2' and 3' structures as well.
hydrophobic interactions 
Water molecules surround hydrophobic amino acids. Seen in 3' 4' protein structures
hydrophobicity 
tendency of molecules to aggregate in water.
ion‐exchange chromatography 
Uses electrostaic interactions to separate proteins. Charged beads attract certain proteins.
ionic bond 
Stabilize 3' structure. can be disrupted by pH
molecular chaperone 
attach to hydrophobic regions of polypeptides. can help fold polypeptide chains.
molecular exclusion chromatography 
same as gel filtration
peptide 
Amino acids bonded together create a peptide
peptide bonds 
Amide bond that links amino acids, forms peptides or polypeptides.
peptidylprolyl cis‐trans isomerase 
changes cis and trans peptide bonds. accelerates protein folding
tertiary structure 
3d structure. contains multiple super secondary structures. can be a protein
polypeptide 
long chain of >1 amino acids
primary structure 
1 linear chain of amino acids. (Polypeptide)
protein 
3' or 4' structure. made of different regions and sometimes >1 pp chain
protein disulfide isomerase 
PDI corrects sulfide bonds in proteins. Enzyme. process not known.
quaternary structure 
>1 pp chain makes up a protein. not all proteins are 4'
residue 
Amino acids once linked together by peptide bonds are called residues
secondary structure 
has folding patterns ( a-helix, b-sheets) in single pp chain
van der Waals interactions 
assist in folding. polar and non polars react. can attract and repel.
substrate 
molecule that en enzyme is catalyzing
hypervariable region 
small region in IgG. Important contributor to antigen binding specificity.
Bohr effect 
Decrease in pH or increase in Co2 causes hemoglobin to release oxygen.
immunoglobulin G (IgG) 
4' protein. In immune system. has 12 domains. and 4 pp chains. 2 light 2 heavy.
cooperativity 
communication between the 4 heme groups that allows hemoglobin to gain and lose oxygen.
induced fit mechanism 
Enzyme changes shape to fit substrate
domain 
region in large pp chain. often has certain function. Fold might occur.
light chain 
short pp chain of a 4' structure protein
energy of activation 
energy needed to start/complete enzyme reaction
lock and key mechanism 
active site fits perfectly to substrate
allosteric site, allosteric effectors 
Allosteric effector = small molecule that binds to a protein and cause a change in its function.

Allosteric site = binding to sites other than active sites.
enzyme 
catalyst that speeds up metabolic processes
myoglobin 
3' structure = oxygen storage system in muscle. Single heme group stores oxygen.
enzyme‐substrate complex 
Molecule while Enzyme and substrate are bonded, during reaction.
sickle cell anemia 
-Causes Hemoglobin to fail at binding oxygen.
- Difference in regular cell and sickle cell is a single Amino acid change.

Malaria is resistant to sickled cells.
heavy chain 
Long pp chain. part of 4' structure protein.
variable region 
in IgG, where antigens bind
hemoglobin 
Hemoglobin - 4' = oxygen transport system in blood. 4 subunits = 4 heme groups
quaternary structure 
>1 pp chain making up a protein. can have domains. not required.
A‐DNA 
Right handed helix, discovered by franklin, very rare
palindrome 
(dyad symmetry) aka inverted repeats = reads the same forwards and backwards
In DNA
B‐DNA 
Most common. Right handed DNA, Watson and crick
plasmid 
Small, circular, self replicating DNA molecule
base‐stacking 
Stabilizes DNA structure.
DNA gyrase 
Introduces negative supercoils to counteract positive supercoiling that helicase may create. in bacteria.
stem‐loop structure 
(Hairpin) Spacer in palindrome cause the loop. Bases aren't complimentary in loop, cant bind to each other.
renaturation 
Re-annealing, complimentary single strands come together.
cruciform structure 
caused by inverted repeats, H bonds between bases of same strands
single‐strand DNA binding protein (SSB) 
Bind to single stranded DNA after helicase seperates and prevents strands from re-annealing
supercoil 
when double helix is wound around itself. This changes the conformation. ( Topology)
helicase 
Enzyme that separates the strands of the DNA double helix.

4' structure, homohexamer, one strand goes through middle.

Requires energy!
topoisomer 
otherwise identical DNA molecules with different degrees of supercoiling.
topoisomerase (Type I, Type II) 
- these enzymes introduce a brief or tansient cleavage of the DNA backone, PDE. 3' structure.

- type I = transient single stranded dna breaks. no ATP required.

- type II =transient double stranded dna breaks. Requires ATP
melting temperature 
-Tm= melting temp, point at which the DNA strands are 1/2 seperated,(1/2 denatured)
nicked circular DNA 
Phosphodiester backbone has "nick" or missing piece in it. Cannot supercoil.
interphase 
Phase of cell's life where DNA RNA and Proteins are synthesized. ~90% of its life is spent in this phase
metaphase 
Spindles attached to kinetochores of chromatids. Chromatids move towards middle of cell
beads on a string 
DNA winds around a 8 histone complex like beads on a string to produce a nucleosome. DNA between histones is known as linker DNA
nucleoid 
Super condensed complex of proteins and DNA in Bacteria
euchromatin 
Less condensed form of chromatin in Eukaryotic cell. This is transcribed
30‐nm fiber 
Nucleosome arrangement, Zig Zag or Solenoid model.

Zig Zag = nucleosomes on alternating sides

Solenoid = nucleosomes on same side
chromatin 
condensed nucleoprotein complex.
SMC protein 
Structural Maintenance of Proteins
heterochromatin 
More condensed form of chromatin in Eukaryotic cell. This is NOT transcribed
nucleosome 
Beads on a string, 8 histone complex wrapped in DNA
scaffold model 
when 30nm chromatin fiber binds to protein scaffold to make loops
histone 
family of proteins that interact with DNA binding ( Beads on a string)
telomere 
Chromosome ends. essential for stability of chromosome.
nick 
deletion of a bond in DNA