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| What does Biochemistry study? |
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Definition
The chemistry of biological systems and their components:
- Structure (Proteins and DNA)
- Functions (Enzymes and DNA Replication)
- Systems and Processes (Cell Metabolism, Respiration) |
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| What are the main types of biological molecules? |
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Definition
- Amino Acids
- Fatty Acids
- Carbohydrates
- Nucleic Acids |
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Definition
Proteins.
- Half Amine, half carboxylic acid.
- R group changes depending on the a.a.
- ca. 20 a.a.s. found in biological systems
- Corresponding to 20 different R groups. |
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Formed by the dehydration reaction of two amino acids. Forms an Amide.
Amide bonds are very strong, making proteins very resilient.
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Definition
•Large polymers of amino acids
–Amino acids in tandem, held together by peptide bonds
Proteins are different from each other based on their aa sequence
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How many 8 aa proteins can you have?
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Definition
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•Protein: Primary Structure
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Definition
| –Refers to the sequence in a chain of amino acids |
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| Protein: Secondary Structure |
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Definition
–Within a protein, atoms attract each other, interact via hydrogen bonding.
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Three possible secondary structures
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Definition
•Alpha Helix
Beta Sheets
Random Coils (no structure)
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Definition
•Rigid conformation
Very stable
The R groups all project outward
–Prevents bumping into each other
–Helices interact with others through their R groups
–Always right handed
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Definition
•Chains arrange themselves in parallel strands
Flat structure
R groups oriented up/down
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Protein: Tertiary Structure
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Definition
–Refers to the 3D structure and/or shape of any given protein
Aggregation of helices, sheets and random coils
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Protein: Quaternary Structure
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Definition
–Refers to the structure and shape of
Two or more domains within a protein
Two or more proteins
…As well as the nature of the interaction between them
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Term
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Definition
•When a protein is first made in the cell, it “folds” to obtain its intended structure.
Other proteins called Chaperone Proteins sometimes assist in protein folding.
In order for a protein to have the correct function, it must have the correct shape/structure
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Term
| Protein Misfolding: Alzheimers |
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Definition
–Amyloid-b Protein
When amyloid misfolds, it is not soluble, and thus, it deposits
Increased deposition of amyloid is linked to increased neuronal death…
…which in turn leads to increased memory loss
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Term
| Protein Misfolding: Prions and Mad Cow Disease |
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Definition
–A prion is a protein that folds incorrectly and, as a result, loses it’s ability to function
Usually, prions will be proteins involved in brain function
Also, a prion is an “infectious” protein
It helps other proteins like it misfold as well!!
So then you have a lot of one protein that does not function
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Term
Protein Catalysts: Enzymes
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Definition
•Biological entities(proteins) that “catalyze” reactions.
A catalyst is a chemical that speeds up a reactionwithout itself being consumed.
The catalyst interacts with the chemicals and even reacts, but it is regenerated at the end of the reaction.
Enzymes mediates nearly all the reactions in the cell/body.
There is an enzyme for virtually every chemical transformation possible in the cell
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Definition
•Studies of enzymes
Most enzymes are named according to the reaction they carry out PLUS suffix: -ase
Examples of enzymes and their function:
–a-amilase: breaks down starch into glucose faster than sulfuric acid
–Alcohol Dehydrogenase: Converts ethanol into acetaldehyde
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Enzyme Classification - List
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| Functional Group Transfer |
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Definition
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Definition
| Eliminations (Products are often double bonds) |
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Definition
| Change one enantiomer to another |
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Definition
| Form hard-to-make bonds using ATP |
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| Important Characteristics of Enzymes |
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Definition
–They work under mild conditions whereas chemical catalysts do not.
•Body T°, atmospheric pressure, neutral pH.
–Very Specific (Stereospecific)
•Enzymes are very good at recognizing the shape of their substrates (reactants) and/or products ONLY.
–Higher reaction rates
•Enzymes carry out reactions occur much faster (106-1012 faster)
–Capacity for Regulation
•Enzymes can be chemically modified to be slowed down or sped up based on need.
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Term
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Definition
• - Important for maintenance of structure and shape of the cell.
–Keeping the cytoplasm together
•Actin
•Microtubules
•Collagen (hair)
–Generally found in aggregates.
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Definition
• - The most prevalent structural protein in the cell
–Its aggregates from actin rods
–The rods aggregate to form thin filaments
–The filaments have direction (polarity)
•It needs ATP, the energy currency of the cell, in order to be assembled
•Has important roles in muscle contraction, cell motility, cell division and cytokinesis etc.
•Thin filaments of actin are essentially the highways of the cell.
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Definition
• - The protein that composes them is b-tubulin
•Similar to Actin filaments but much bigger
•Also needs ATP for assembly
•Continually grow on one end and shrink on the other
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Definition
• - Pick up and deliver:
–Molecules
–DNA/RNA
–Other proteins
•Myosin is one of the more famous ones.
–Involved in muscle contraction
–Several types of Myosins (~20)
–All Interact with Actin
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Definition
•Thin Filaments are made of Actin
Thick Filaments are made of Myosin
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Definition
• - Structure
–Head/Binding Domain
–Light Chains
–Cargo Binding Domains
•Involved in Vesicular Transport
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Definition
•Big, varied group of biological molecules
Can be extracted from cells and tissues
Most of them are non-polar in nature
–Do not dissolve in water
Some have very complex structures
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Term
| What do nutrients function as in the body? |
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Definition
•Like starch, lipids function as nutrient storage in the body
–Starch is short term storage
–Lipids/Fats are long term storage
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Term
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Definition
Steroids, Prostaglandins and Terpenes
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Definition
•Most basic lipid you can find
–A long alkane chain with a carboxylic acid functional group at the end
•Fatty: Alkane (hydrophobic)
•Acid: Carboxylic Acid (hydrophilic)
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Definition
•Fatty acid esters of glycerol
•Triglycerides occur when all three -OH have been esterified
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| What is a Triglyceride if it is solid at room temperature? |
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Definition
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| What is a Triglyceride if it is liquid at room temperature? |
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Definition
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Saturated (Alkanes)
Unsaturated (Alkenes) |
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| Triglycerides - Saturated |
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Definition
–The longer the chain, the higher the m.p.
–At lower T°, it will be solid
–Grease, Animal fats
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| Triglycerides - Unsaturated |
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Definition
–The more double bonds it has, the lower the m.p.
–At lower T°, it will be liquid
–Vegetable Oils, Margarine, Butter
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| Triglycerides - Saturated vs. Unsaturated |
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Definition
–Unsaturated
•More soluble in water due to double bonds
•Easier to break down in metabolic processes
–Implications in Medicine
•Aneurisms
•Blood Clots
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Definition
Complex polycyclic molecules found in all plants and animals
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Definition
–Hormones (most commonly associated)
–Emulsifiers
–Membrane steroids
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Definition
•Initially isolated from the prostate
•Also present in minute quantities in all fluids
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| Prostaglandins - Function |
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Definition
– - Nervous system
–Blood pressure
–Blood clotting
–Inflammatory responses
–Digestive system
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| How are prostaglandins different from steroids? |
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Definition
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Definition
•Diverse family of compounds
–All have carbon skeletons derived from isoprene
–Isoprene units can be modified to give a large variety of terpenes
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Term
| Terpenes - Classification |
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Definition
•If 10C = monoterpene
•If 15C = sesquiterpene (sesqui = 1.5)
•If 20C = diterpene
•If 30C = triterpenes
•If 40C = carotenes
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Definition
Saponification is addition of strong base and water to release the fatty acids from the triglyceride
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Definition
•Object (chemical, bacterium, virus) that is foreign to the body/organism.
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Definition
•Organism or agent capable of causing disease.
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•Phagocytic cell used in the elimination of pathogens.
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Literally, “toxicity to cells”. Refers to the ability of a cell to kill a pathogen/antigen
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Definition
Cell suicide. All cells have this process of self-destruction encoded in their genetic makeup.
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Studies the function of the immune system in health and disease.
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Definition
–Physical Barriers
Innate Immunity
Adaptive Immunity
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Definition
•First line of defense
–Prevent the entrance of the virus and you don’t have to worry about fighting it
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–Targets any foreignonents without regard for its identity.
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–Phagocytic cells (cell eating)
•Neutrophils
•Monocytes and Macrophages
•Natural Killer (NK) cells
•Eosinophils
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Definition
Target foreign and infected cells
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| How natural killer cells work? |
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Definition
NK finds a cell and recognizes it as infected/foreign Releases proteins in the vicinity of the target cell: Perforin and Granzyme
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Makes pores in cell membrane
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Definition
•invades the cell induces apoptosis (cell suicide)
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Definition
•Specific to pathogens
•Activated by the innate immune system
•Its key characteristic is Memory:
–It recognizes previous invaders
–Develops stronger responses known, recurrent pathogens
–Immune system prepares itself for future infections
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Term
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Definition
•The type of cell used in the adaptive immune system
Produced in the bone marrow and reside mostly in the blood and the lymphatic system.
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Term
| Major types of Lymphocytes |
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Definition
–B cells (humoral response: antibodies)
–T cells (cell-mediated response: macrophages)
•T cells and B cells are indistinguishable until they are activated by an antigen.
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Term
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Definition
| Naive Stage, Effector Stage, and Memory Stage |
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Definition
–Cells are matured but have not encountered an antigen.
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Definition
–Have been activated by an antigen, multiply in great numbers, and are involved in eliminating it.
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–After infection is eliminated, number of cells decrease, but a few remain in case the same infection reoccurs (memory)
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| Secreted by B-Cells. Many different kinds, so it can find the right shape to bind to the antigen. Then it makes a bunch of that shape, and recognizes it later. Antibodies act as flags. |
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| T-Cells: Cell mediated response |
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Definition
–Activation of antigen-specific T-cells
–Activation of macrophages and natural killer (NK) cells
–Secrete chemical signals (cytokines) that recruit innate immune system
Basically: Macrophage - eating instead of antibodies
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Term
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Definition
•Cytotoxic: A cell that has phagocytic activity. That is, it is involved in killing foreign cells.
•Helper: No phagocytic activity. Activate and direct cytotoxic cells.
•Regulatory: Suppress the cytotoxic response once the infection has been overcome.
•Memory: a cell that has been activated and used in an immune response. It contains the antibodies and receptors used to recognize the given infection. If the infection reoccurs the immune response will be swifter and stronger.
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Definition
Gays are majority
Women 20%
MSM 38% |
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Definition
•
–RNA:
–Reverse Transcriptase:
–HIV Integrase:
–Viral Protease:
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Definition
| Stores the information for HIV proteins |
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Definition
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| Integrates DNA into host's DNA |
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–As all enzymes are made together, protease cuts them into individual units
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| ART. Reverse transcriptase inhibitors. HIV can develop resistance to this |
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Definition
•Vomiting
•Nausea
•Erratic Sleeping
•Abnormal Fat Distribution
•Abnormal Metabolism
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–Inhibit the protease from cutting proteins into their functional structure
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–Block the HIV protein to prevent it from interacting with CD4 to prevent infection
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