Biochemistry Flashcards
4 elements of protein structure
Primary- linear amino acid sequence
Secondary- alpha helices and beta-pleated sheets
Tertiary- Folding protein into 3 dimensional shape
Quaternary- multisubunit protein complex
Enzymes are characterized by
Specificity, high rate of activity, affinity for their specific substrate (Km), and the maximal rate of reaction when substrate is present in excess concentration (Vmax)
Coenzymes
Most vitamins and certain metals act as coenzymes that facilitate enzyme catalytic activity
Carbohydrates are stored as
glycogen in the liver and muscle
DNA and RNA 3 main components
Purine or pyrimidine base molecule, sugar, phosphoric acid molecule
Protein synthesis occurs
on the ribosome where mRNA carries the message and directs the order of AA in the protein, tRNA delivers each amino acid per code, and rRNA catalyzes the assembly of amino acids into protein
4 major biomolecules
carbohydrates, amino acids, fatty acids, nucleotides
Biomolecules are building blocks for
polysaccharides, lipids, proteins, and polynucleotides
Proteins
Form the structural backbone of cells and tissues and are responsible for enzymatic reactions, membrane transport, hormonal regulation, immune system, and transmission of cell to cell messages
All amino acids contain
An amino group and a carboxylic acid group and fall into 2 large groupings (primary and secondary amines)
Primary amine
nitrogen atom has only one bond to the carbon
Secondary amine
Nitrogen atom is bonded to two carbon atoms
Basic amino acids
Lysine, arginine, and histidine
Acidic amino acids
Glutamate and aspartate
9 essential amino acids
histine, leucine, isoleucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine
AA of the urea cycle
Urea cycle- conversion of ammonia to urea
arginine, ornithine, and citrulline
Urea cycle
Conversion of ammonia to urea
Main pathway for excretion of nitrogen waste product from protein metabolism. Coordinated in the cytoplasm and mitochondria of the cell.
Peptide bond
formed between two AA and is the primary element of peptide and protein structure.
Formed in the ribosome
In bond formation direction, loses water, in bond hydrolysis direction gains water
Sickle cell anemia
SNP replacing glutamic acid with valine
No post-translational modification of which AA have been identified?
Ala, Gly, Ile, or Val
Composition of carbohydrates
Carbon, hydrogen, and oxygen
During fasting, glycogen can be
hydrolyzed to release glucose and maintain blood sugar levels
ABO human blood types
Specific glycosylation of cell surface proteins (glycoproteins) as well as the same specific glycosylation of membrane lipids is the base of human blood groups.
Lipids include
fatty acids, cholesterol, essential vitamins, and glycerides
Long chain fatty acids/ phospholipids are precursors for
prostaglandins and leukotrienes
Difference between a nucleoside and a nucleotide
Nucleoside- deoxyribose and nitrogenous base pair (AT or CG)
Nucleotide- one to three phosphate groups are added
Exons
Sections of DNA that carry specific genes
Introns
Sections of DNA that carry no genetic information
Enzymes
Basically catalysts, assist in chemical reactions but are not consumed in the reaction. Accelerate the chemistry of getting from a substrate to a product.
Accomplish this by lowering the activation energy.
Key elements of enzyme-assisted reactions
Specificity- only one or a limited number of closely related substrates
Acceleration- Reaction occurs manifold over what would normally occur
Stearic or induced fit
The active site of an enzyme is spatially configured to accept only one substrate configuration or a very limited number. This model involves molecular size, orientation or reactive groups, ionic and hydrogen bonding, and possibly movement of the enzyme protein backbone. This model has replaced the original lock and key model of enzyme activity.
How do enzymes accomplish their goals? Many explanations exist, but they fall into the following basic categories:
Stearic or induced fit
Localized chemistry
Transition state
An enzyme without its cofactor is an
Apoenzyme or apoprotein
Niacin
Can be converted into 2 coenzymes- NAD and NADP
Cofactors
Coenzymes that are metals
Fat soluble vitamins
A, D, E, K
Deficiency associated with Vitamin A
Night blindness
Deficiency associated with vitamin D
Rickets
Deficiency associated with B2 or B3
Pellagra
Deficiency associated with B1/thiamine
Beriberi
First order reaction
Substrate goes to product without interaction of another molecule, except the enzyme
V=ds/dt=ks
Glycolysis
Carbohydrate metabolism
30-32 moles ATP per mole of glucose
Gluconeogenesis
Glucose can be synthesized from noncarbohydrate precursors predominantly in the liver
Precursor molecules to glucose
Lactate, pyruvate, glycerol, and keto-acids
Ketone bodies
Acetoacetate, beta-hydroxybutyrate, and acetone
Concentrations can rise in ketosis or ketoacidosis
Brain and heart use ketone bodies as a direct energy source through reconversion to acetyl-coa
Propionyl vs acetyl-CoA
If the original fatty acid molecule contains an even number of carbons, then acetyl-CoA is the only product. If the fatty acid chain contains an odd number of carbons, then the terminal product is propionyl-CoA.
Cause of DNA damage, missing base
Removal or purine nucleotides by heat or acid
Cause of DNA damage, altered base
Alkylating agents, ionizing radiation
Cause of DNA damage, wrong base
Deamination
Cause of DNA damage, deletion or insertion
Intercalating chemicals
Cause of DNA damage, cyclobutyl dimer
UV irradiation
Cause of DNA damage, strand breaks
Ionizing radiation, chemicals
Cause of DNA damage, strand-cross linking
Chemicals
