Cell Bio 11425 Proteins & Cell Function PDF

# Proteins are the Workhorses of the Cell - Proteins are about 15% of a cell. - Proteins have a wide range of functions: - Enzymes - Storage - Motor - Transporters - Structural components - Signaling - Receptors - Gene expression regulators # Proteins are strings of...

# Proteins are the Workhorses of the Cell - Proteins are about 15% of a cell. - Proteins have a wide range of functions: - Enzymes - Storage - Motor - Transporters - Structural components - Signaling - Receptors - Gene expression regulators # Proteins are strings of amino acids - Every amino acid has an alpha carbon with four attached groups: 1. Aminogroup 2. Carboxylgroup 3. Hydrogen atom 4. R-group - Amino acids are linked by peptide bonds which are formed through condensation/dehydration reactions: - The carboxyl group of one amino acid reacts with the amino group of another which releases water. # Peptide bonds are Strong, Covalent bonds, making them more difficult to break w/o enzymatic intervention, thus stable enough for protein support - Polypeptide chains have polarity: one end with a free carboxyl group (C-terminus) with a negative charge and another with a free amino group (N-terminus) - positive # The Primary Structure of a Protein Refers to the Sequence of Amino Acids - The dictatis how the protein folds. ## Secondary Structure are formed through hydrogen bonds between atoms in the peptide Backbone - Partial negative charge on the carbonyl oxygen, a partial positive charge on the hydrogen atom. ## Alpha Helix: formed by twisting the chain causing hydrogen bonds to form between every fourth amino acids; side chains aren't involved so they extend out; Complete turn every 3.6 amino acids ## Beta Sheet: formed by laying peptide chains next to each other, with hydrogen bonds between the backlanes - can be parallel or antiparallel # Motifs are combanations of secondary structures. # There are 20 amino acids, each with distinct R groups - R groups vary in polarity, size, and other characteristics, such as the ability to take part in disulfide bonds (cysteine), act as helix breakers (proline), and act as phosphorylation sites (serine, threonine, tyrosine) - Some amino acids can have positive or negative charges depending on the pH of the environment. # Hydrogen bonds are crucial for folding (proteins) - Weak bonds between an electronegative atom (oxygen & nitrogen) & a hydrogen atom bound to another electronegative atom. - Leftover atoms from peptide bonds are crucial for hydrogen bond formation within the protein backbone. - Can be broken by water molecules (hydrophilic) - In alpha helixes, hydrogen bonds are protected from water by being buried in the core of the helix; R groups extend outward. # Families of Organic Molecules in Cells - There are four categories: 1. Sugar - Carbs 2. Amino Acids - Proteins 3. Fatty Acids - Lipids 4. Nucleotide - DNA/RNA - The most important molecule would be Amino Acids - This is because proteins are considered the workhorse of the cell, as it has multiple functions within the cell's structure/function. - Proteins also make up 15% of the chemicals in a cell which is half of all the chemicals (cells will have 10^15) - A cell is 70% of water. # Multiplicity of Protein Function - **Enzymes** - catalyze reactions. - **Structural Proteins** - provide mechanical support - **Transport Proteins** - moves molecules or ions in/out - **Motor Proteins** - provides motive force: moving wheels, vesicles, or mitochondria within the cell. - **Storage Proteins** - store small molecules & ions. - **Signal Proteins** - carry signals from cell to cell. - **Receptor Proteins** - receives transmitts signals to response machinery. - **Gene Regulatory Proteins** - actives & deactivates genes - **Special Purpose Proteins** - proteins with special proteins. - If you want to understand how a cell functions, you must understand proteins. # Families of Macromolecules in Cells - _aa-_aa-_aa-_aa - Amino acid - Folding (is folded) modified folded protein (is folding "wrong") - The arrow is so long as there are so many steps within folding to get to the fully folded protein - Destroy (when un-needed/damaged) to work even after modification # Amino Acid Structure - alpha-carbon - Amino group H₂N-C-COOH Carboxyl - R-side chain - R-group has 20 different side chains. - Carboxyl group is highly acidic so it is typically negatively charged. - Amino group is a weak acid so it will function as a base so it will act positively - pH 7 both COOH & H₂N will be ionized. # Amino Acids are Linked by Peptide Bonds - H-N-C-C-O-H + H-N-C-C-O-H == H₂O + H-N-C-C-N-C-C-O-H - R -R -R -R - H -H -H -H - Peptide bonds are strong, covalent bonds that bond two amino acids together leaving where is still an amino group on one end and a carboxyl on another. - You want these bonds so the protein will be able to stay together in order to do its function/so it won't break during folding. - Peptide bonds are formed through the loss of water - condensation/dehydration - What is left over are called leftover atoms & can later be used to form hydrogen bonds. - Peptides bonds have no rotation - more planar than anything. - Though the single bonds around the alpha carbon have rotation which is good for folding & how a protein folds. - The peptide backbone is never changing. - The Side Chains are different - Typically the + charge side chains interacts with the - charge part of water. - Primary Structure is the specific amino acid sequence that is determined by the nucleotide sequence of the encoding gene. # Polarity of Water - Due to the unequal pull of the hydrogens to oxygen - water is considered to be very polar - The partial charge will be the dipokl moment - A Hydrogen bond - an electronegative atom usually C or N (negatively charged) will form a bond with another electronegative atom with a H atom attached (positively charged). - Hydrogen bonds are weak & noncovalent & forms between alpha helixes & beta sheets. - δ+ ^O-H |||||||| N - N-H |||||||| O - Donor atom - Acceptor atom # Special Amino Acids - Histidine - has a pH of 6.6 so due to it being so close to seven it is able to be neutral, positive, or negative charge - Acidic Side Chains are 4.7 so nothing will be low that - Bases won't go above 10-12. - Proline - due to its ability to create kinks - this ability doesn't allow for it to form alpha helices. - Glycine - b/c of its very small size - also doesn't allow for alpha helix formation. - Cystine - can form disulfide bonds - think paper clip - as it is two cystine side chains being clipped together by this formation - helps maintain structure during folding. # Secondary Structure - Secondary structures are primarily made by hydrogen bond. - Which can come from the leftover atoms after peptide bond formation - **Alpha Helix:** - There are hydrogen bonds between every fourth amino acid: 1, 4, 2, 5, 3,6 - There is a complete turn every 3.6 amino acids. - Side chains are involved in the creation of alpha helices though if you don't have the right combo, they won't form. - Proline can't as due to the kinks it makes trying to reach the backbone, this means those leftover atoms used to form hydrogen bonds for alpha helices aren't in the correct position. - Glycine can't because it's so small it will also change the shape. - **Beta Sheets:** - Peptide backbones are layered against one another - creating sheets. - N - M - C - Like alpha helix, the side chains in beta sheets are protecting the non-covalent bonds. - Can be parallel or antiparallel. - **Parallel** - Separated by long stretches of the backbone - Only formed with adjacent regions - 10 or 14 atoms connecting them. - **Antiparallel:** - Formed from both adjacent & non-adjacent - 12 atoms connecting them. - With sheets, they can be rolled around to create pores.