BioChemistry Flashcards
What are the structural proteins
Collagen Elastin Keratin Actin Tubulin
Motor Proteins
Capable of force generation through a conformational change. Include myosin, kinesin, and dyenin
Binding Proteins
Bind a specific substrate, either to sequester it in the body or hold its concentration at a steady state
Cell Adhesion Molecules
Binds cells to other cells or surfaces.
Include cadherins, integrins, and selectins
Antibodies
Target a specific antigen (may be a protein on surface of a pathogen or toxin)
Enzyme linked receptors
Participate in cell signaling through extracellular ligand bonding and initiation of second messenger cascades
G protein-coupled receptors
Have a membrane bound protein associated with a trimeric G protein. Also initiate second messenger systems
Trioses
3 carbon sugar
Tetroses
4 carbon sugars
Aldoses
Sugars with aldehydes as their most oxidized group
Ketoses
Sugars with ketones as their most oxidized group
D-Sugars
Sugars with the highest numbered chiral carbon with the -OH group on the right
L-Sugars
Sugars with the highest numbered chiral carbon with the -OH group on the left
Enantiomers
D and L forms of the same sugar
Diastereomers
Differ at at least one but not all chiral carbons
Epimers
Differ at exactly one chiral carbon
Anomers
A subtype of epimers that differ at the anomeric carbon
Anomeric Carbon
The new chiral center formed in ring closure; the carbon containing the carbonyl in the straight chain form
Alpha Anomers
Have the -OH on the anomeric carbon trans to the free CH2OH group
Beta Anomers
Have the -OH on the anomeric carbons cis to the free CH2OH group
Glycoside formation
Basis for building complex carbohydrates and requires the anomeric carbon to link to another sugar
Deoxy sugars
Sugars with an -H replacing an -OH group
Cellulose
Main structural component of plant cell walls, main source of fiber in human diet
Starches
Main energy storage forms for plants
amylose and amylopectin
Glycogen
Major energy storage form for animals
Nucleotides
Contain 5 carbon sugar bonded to nitrogenous base
Nucleotides in DNA
Contain deoxyribose
Nucleotides in RNA
Contain ribose
Types of nucleotides (5)
Adenine (A) Cytosine (C) Guanine (G) Thymine (T) Uracil (U)
Watson Crick Model
DNA backbone is composed of alternating sugar and phosphate groups
Read 5’ to 3’
Watson Crick Model
Two strands with antiparallel polarity, wound into double helix
Purines pair with pyrimidines
Purines
A and G
Pyrimidines
U, T, C
Chargaff’s Rules
Purines and Pyrimidines are equal in number in a DNA molecule.
A=T
G=C
DNA Replication
Prokaryotes vs. Eukaryotes (Nuclei)
Prokaryotic Cells: One per chromosome Helicase Single stranded DNA binding protein Primase DNA polymerase 3 DNA polymerase 1 (replacement of RNA with DNA) DNA Ligase (joining of okazaki fragments) DNA topoisomerases
Eukaryotic Cells: Multiple per chromasome Helicase Single stranded DNA binding protein Primase DNA polymerase RNase DNA polymerase DNA ligase DNA topoisomerase Telomerase
DNA polymerase
Synthesizes new DNA strands, reading the template DNA 3’ to 5’ and synthesizing the strand to 5’ to 3’
Leading Strand
Requires only one primer and can the be synthesized continuously
Lagging Strand
Requires many primers and is synthesized in discrete fragments called okazaki fragments
Recombinant DNA
DNA composed of nucleotides from 2 different sources
DNA Cloning
Introduces a fragment of DNA into vector plasmid. A restriction enzyme cuts both the plasmid and fragment leaving both with sticky ends which can bind
Hybridization
Joining of complementary base pair sequences
Polymer Chain Reaction (PCR)
An automated process by which millions of copies of DNA sequence can be created from a very small sample by hybridization
Southern blotting
Can be used to detect the presence and quantity of various DNA strands in a sample
Central Dogma
DNA>RNA>Proteins
Initiation Code
AUG
Termination Codes
UAA, UGA, UAG
Redundancy and Wobble
Allow mutations to occur without affecting the protein
Silent Mutations
No effect on protein synthesis
Nonsense Mutations
Produce a premature stop codon
Missense Mutations
Produce a codon that codes for a different amino acid
Frameshift Mutations
Result from nucleotide addition or deletion and change the reading frame of subsequent codons
Messenger RNA (mRNA)
Carries the message from DNA in nucleus via transcription of the gene, travels into cytoplasm to be translated
Transfer RNA (tRNA)
Brings in amino acids; recognizes the codon on the mRNA using its anticodon
Ribosomal RNA (rRNA)
Makes up much of the ribosome, enzymatically active
Steps of Transcription
1) Helicase and topoisomerase unwind DNA double helix
2) RNA polymerase 2 binds to TATA box within promoter region of a gene
3) HnRNA synthesized from DNA template (antisense) strand
Post-transcriptional Modifications
1) 7-methylguanylate triphospahe cap added to 5’ end
2) Polyadenosyl (poly-A) tail added to 3’ end
3) Splicing done by spliceosome; introns removed exons ligated together
Translation
Occurs at ribosome
3 stages: initiation, elongation, termination
Post-translational Modifications
Folding by chaperones
Formation of quaternary structure
Cleavage of proteins or signal sequences
Covalent addition of other biomolecules
Operons
Inducible or repressible clusters of genes transcribed as a single mRNA
Transcription Factors
Search for promoter and enhancer regions in the DNA
Promoters
Within 25 base pairs of the transcription start site
Enhancers
More than 25 base pairs away from transcription start site
Osmotic Pressure
The pressure applied to a pure solvent to prevent osmosis and is related to concentration of the solution
Osmotic Pressure equation
II=iMRT
Passive Transport
Does not require ATP bc molecule is moving down concentration gradient.
Or from area of higher concentration to lower concentration
Types of Passive Transport
Osmosis
Simple Diffusion
Facilitated Diffusion
Simple Diffusion
Does not require transporter
Small nonpolar molecules move from an area of high concentration to low concentration until equilibrium is reached
Osmosis
Diffusion of water across a selectively permeable membrane
Facilitated Diffusion
Uses transport proteins to move impermeable solutes across the cell membrane
Active Transport
Requires energy (ATP) or existing favorable ion gradient
Endocytosis & Exocytosis
Methods of engulfing material into cells or releasing material to the exterior of cells. Both via cell membrane
Pinocytosis
The ingestion of liquid into the cell from vesicles and formed from the cell membrane
Phagocytosis
Ingestion of solid material
Glycolysis
Occurs in the cytoplasm of all cells
Doesn’t require oxygen
Yields 2 ATP per glucose
Glucokinase
Important enzyme of glycolysis
Present in pancreatic Beta-islet cells as part of the glucose sensor and is responsive to insulin in the liver
Hexokinase
Important enzyme of glycolysis
Traps glucose
Phosphofructokinase 1 (PFK-1)
PFK-1
Rate limiting step
Phosphofructokinase 2 (PFK-2)
Produces F2, 6-BP, which activates PFK-1
Glyceraldehyde-3-phosphate dehydrogenase
Produces NADH
3-phosphoglycerate Kinase and Pyruvate Kinase
Perform substrate level phosphorylation
Pyruvate Dehydrogenase
Converts pyruvate to acetyl-CoA
Stimulated by insulin and inhibited y acetyl-CoA
Citric Acid Cycle AKA krebs Cycle
Takes place in mitochondrial matrix
Purpose to oxidize acetyl-CoA to CO2 and generate high energy electron carriers (NADH & FADH2) and GTP
Krebs Cycle nmemonic
Citrate is krebs special substrate for making oxaloacetate
Citrate Iscitrate Alpha Ketoglutarate succinyl-CoA succinate Fumarate malate oxaloacetate
