Final Exam Flashcards
Covalent Bonds
The strongest bond in which atoms share an electron
Noncovalent Bonds
A bond in which no sharing of electrons takes place
Ionic Bonds
Ionic bonds form between two or more atoms by the transfer of one or more electrons between atom
Hydrogen Bonds
A special type of bond in which a hydrogen atom is covalently bonded to a very electronegative atom such as a N, O, or F atom
Hydrophobic Forces
The attraction between water-hating/repelling forces. Will not interact with water, will clump together.
Hydrophilic
The attraction between water-loving forces. Will hydrogen bond, will interact with water
Lipid
A group of molecules usually composed of fatty acids that are insoluble in water
Structure of a Lipid
Glycerol and fatty acid tail
Saturated Fatty Acid
All single bonds in the hydrocarbon
Unsaturated Fatty Acid
1 or more double bonds in the hydrocarbon that create a kink
Phospholipid Structure
Phosphate, glycerol, and fatty acid
4 Nucleotides in DNA
Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)
Pyrimidines
Cytosine and Thymine. Consists of one ring in its structure
Purines
Adenine and Guanine. Consists of two rings in its structure
Compare and Contrast DNA/RNA
RNA: Less stable, transient molecule, usually single helix. Uracil instead of Thymine
DNA: More stable (lack of 2’ OH group), stays in nucleus, usually double helix. Thymine instead of Uracil
Amino Acid Group
Carboxyl group, amino group, and side chain “R” (different for each amino acid)
How many different amino acid side chains are there?
20 different side chains
Non-Polar Amino Acids
Glycine, Alanine, Valine, Cysteine, Proline, Leucine, Isoleucine, Methionine, Tryptophan, Phenylalanine
Polar Amino Acids
Serine, Threonine, Tyrosine, Asparagine, Glutamine
Negatively Charged Amino Acids
Aspartic Acid, Glutamic Acid
Positively Charged Amino Acids
Lysine, Arginine, Histidine
Gene
A unit of information that codes for a protein
Peptide Bond
Covalent bond that links amino acids
Polymerization
Carboxyl group and amino group interact to form a polymer. When an amino acid is added to the C-terminus, a dehydration reaction occurs and the polymer is formed.
Redundancy
Multiple codons for the same amino acid
Mutation
A change in the DNA sequence, even just 1 letter, could lead to a different amino acid.
Lipid Nanoparticle (LNP)
A lipid ball where RNA is packaged inside. Made of lipids, cholesterol, and mRNA
mRNA Vaccine
Injected into the body through a lipid nanoparticle. The LNP endocytoses into the cell into the endosome. The cationic lipids within the LNP can break holes in the endosome and release mRNA in the cytoplasm. Once RNA is released, our immune system can translate it into protein and create antibodies to fight and recognize virus in the future.
Cationic Lipids
Positively charged lipid. The positively charged headgroups repel. The repelling creates a sharp cone shape that can create holes in the membrane
Endocytosis
In to a cell
Exocytosis
Out of a cell
Membrane Permeability
The ability to diffuse through a cell membrane. Depends on molecule size and properties.
What molecules can pass through the cell membrane? Which can’t?
Small, nonpolar molecules CAN pass. Large, polar molecules and ions CANNOT pass
Unsaturated and Saturated Fatty Acid Tails in the Cell Membrane
Saturated Tails: straight, tight packing
Unsaturated Tails: kink, looser packing.
Since unsaturated tails can’t pack as tightly, diffusion happens more rapidly because it is easier for things to pass through.
Translation
From RNA to Protein
Steps of Translation
- Initiation
- Elongation
- Termination
Components of a Protein
- 5’ Cap (Methyl guanine of 5’ end of RNA)
- Poly-A Tail (100-200 adenines of 3’ end of RNA)
- Open Reading Frame (ORF)
- 5’ UTR and 3’ UTR (Before and after ORF)
tRNA
RNA molecule that base pairs that mRNA
Ribosome
Site of translation that harnesses and provides energy to link amino acids
Initiation of Translation
- 5’ cap recruits ribosome to mRNA
- Scans 5’ to 3’ looking for AUG
- Once found AUG, large ribosome sits down on mRNA, forming the A, P, and E sites
- Large ribosome moves 5’ to 3’ on mRNA
- tRNA brings in amino acid and adds to the growing peptide chain. Ribosome shifts to the right and tRNA is situated in the P-site and the other tRNAs exit through the E site
- When the ribosome hits a stop codon, termination occurs. Proteins enter the A site and break open the ribsome and the last tRNA with the polypeptide chain is in the P-site. It never exits through the E site and a protein is formed
Trafficking
Intentional movement of molecules in cells
Proteasome
Unfolds and degrades proteins
Rough ER
- Translation on ribosome occurs
- Protein folding and modification (glycosylation)
- Quality control (proteasome)
Glycosylation
The attachment of carbohydrate side chains and sugars to the backbone of a protein
Vesicles
Transport organelles that transport proteins to different parts of the cell
Smooth ER
- No ribosomes of protein productions
- Makes lipids, phospholipids, cholesterol, and steroids (Contains enzymes to make these molecules)
Golgi Apparatus
- Receive, refine, modify, and distribute molecules.
- Series of stacks called cisterna (different functions in each). Uses vesicles to sort and ship proteins
- Example ^: Sugar or phosphate groups may be removed or attached
Lysosome
Large vesicles with digestive enzymes that break down molecules, organelles, and pathogens
Secretory Pathway
Ribosomes, Rough ER, Vesicles to Golgi, Golgi Apparatus
Vacuoles
Large, long-term storage compartment
What makes up the endomembrane system?
- ER (Rough & Smooth)
- Golgi Apparatus
- Lysosomes
- Vacuoles
Phosphorylation
The addition of a phosphate group to one or more sites on a protein. The phosphate group links to one of the three amino acids that have an OH group (Serine, Tyrosine, and Threonine)
Why can serine, tyrosine, and threonine be phosphorylated?
They are polar molecules so they have an OH group on their side chain.
3-Classes of Receptors
- Enzyme Coupled Receptors (Phosphorylation)
- G-protein coupled (GPCR)
- Ion-Channel Coupled
Internal Signaling Domain
Domain on the inside of the cell that changes shape and chemistry. Usually composed of polar amino acids that can be involved phosphorylated or interact with hydrophilic inside of the membrane
Transmembrane Domain
Domain that passes through the membrane and holds the protein embedded. Usually made up of non-polar amino acids and hydrophobic proteins
Ligand Binding Domain
The domain on the outer surface of the cell binds the ligand signal. Usually composed of charged proteins
Types of Cell Communication
- Contact-Dependent
- Paracrine
- Synaptic
- Endocrine
Contact-Dependent Signaling
Cells communicate by direct physical contact. Requires cells to be in close proximity to one another
Paracrine Signaling
Involves the release of signaling factors. Act locally on nearby target cells, not through the bloodstream
Synaptic Signaling
Specialized form of paracrine signaling that occurs at synapses.
Endocrine Signaling
Involves the release of hormones into the bloodstream through endocrine cells. These hormones travel through the bloodstream to reach distant target cells and their receptors
Cytotoxic T Cell
Recognizes and kills infected cells
Helper T Cell
Binds on to the TCR (T Cell Receptor). Signals for B cells to produce antibodies. When binds to the antigen-MHC II complex, it secretes cytokines to stimulate other immune cells
B Cell
Binds to the BCR (B Cell Receptor). Produces antibodies.
Cytokines
Signaling molecules used by immune system to stimulate a response
Antibodies
Protein complex used to recognize pathogen, signal for destruction
Signal Transduction
Can change gene expression by turning genes on/off
Transcription Factors
Proteins that help find genes and impact expression
Karyotype
Spread of chromosomes that allows you to see abnormalities
Chromosomes
Densley packaged DNA and protein
Translocations
Pieces of DNA from different chromosomes. Chromosomes break off and pair incorrectly
Exons
Pieces of RNA that stay in mRNA
Introns
Pieces of RNA that are removed
Splicing
Process that removes introns and links exons
Promoter
DNA sequence that attracts transcription machinery
Transcriptional Start Site (TSS)
Where transcription begins
Terminator
DNA sequence that ends transcription
RNA Polymerase
Collection of proteins that execute transcription. RNA Polymerase II is the most common. Sits down on the promoter region
TATA Box
Complex that initiates the process of transcription. Directs the transcription machinery to the correct start site
Transcription Machinery/Factors
TBP and TAF bring in and load RNA polymerase
TBP (TATA Binding Proteins)
Protein that binds to the TATA box to begin transcription
TAF (TBP Associated Factors)
Protein that is brought in by TBP to assist in the start of transcription
Coding Strand
Has gene sequence and ORF
Template Strand
Used as a template in transcription. RNA polymerase uses it as a template to recreate the gene sequence in mRNA (replace T with U)
Basal Gene Expression
The simplest and default form in which a protein of mRNA is expressed
Enhancer
DNA elements that up-regulate basal transcription
Up-Regulation
Turn up level of expression
Down-Regulation
Turn down level of expression
Parts of the Human Body with High Gene Expression
Tissues and parts of their body that actively perform their functions often have high gene expression. Example: heart, liver, kidney
Parts of the Human Body with Low Gene Expression
Cells with highly specialized functions may have low gene expression because they only express the genes necessary for their specific functions. Example: brain cells (don’t want brain constantly functioning because can lead to impaired function if everything is activated at once)
Where are enhancers located?
Can be very close to the promoter OR very far. Can be upstream or downstream
Repressor
DNA elements that down-regulate basal transcription
What are the two different mechanisms of enhancers?
- Looping Mechanism
- DNA Packing Mechanism
Looping Mechanism
The enhancer physically interacts with the promoter region of the gene. This interaction is facilitated by the bending and looping of the DNA. Looping allows the enhancers to come in close proximity to the promoter region which up-regulates gene expression. Repressors can prevent looping by blocking RNA Pol II from the promoter which blocks transcription
DNA Packing Mechanism
Repressors create heterochromatin whereas activators disrupt heterochromatin. In heterochromatin, the DNA is tightly wound around histone proteins, forming a highly condensed structure. This tight packing makes it difficult for the transcriptional machinery, including RNA polymerase and other transcription factors, to access the DNA and initiate transcription.
Demethylases
Remove DNA Methylation
Acetyltransferases
Add acetyl marks to histones
Methyltransferases
Add DNA methylation
Deacetylases
Remove acetyl marks on the histones
Negative Feedback Regulation
End product inhibits the system
Positive Feedback Regulation
End product promotes the system
Histone Modification
Chemical mark added to the histone tail
Acetylation
Opens up chromatin (Euchromatin)
Methylation
Tightly packs chromatin (Heterochromatin)
Epigenetic Code
Indicates where an epigenetic mark is. Example: H3K14ac: Histone 3, Lysine 14, Acetyl Mark
Phosphomutant
Convert non-phosphorylatable amino acid (Serine to Alanine)
Phosphomimetic
Convert to amino acid that mimics a phosphate group (Serine to any negatively charged amino acid)
Potency
Ability to differentiate
Cell Differentiation
Ability to self-renew and differentiate into different cell types
Mechanical Work
Movement within cell or cell itself. (Myosin motor, kinesin motor, dynamic microtubules)
Transport Work
Import/Export molecules. (Channel proteins, endo/exocytosis
Chemical Work
Promote chemical reactions. (Kinases, methylases, ribosome)
Passive Transport
The movement of materials through the cell membrane without using energy (diffusion)
Active Transport
The movement of materials through the cell membrane using energy through a pump or channel protein. Creates a gradient. Higher concentration on one side of the membrane
Sodium-Potassium Pump
A protein in the cell membrane that actively transports sodium (Na+) out of the cell and potassium (K+) into the cell. ATP transfers its phosphate group to the protein which changes the protein’s shape. The shape change allows the protein to open intracellularly to put Na+ outside the cell and K+ into the cell
Enzymes
Biological catalysts. Aid or speed up chemical reactions. Help reduce the amount of ATP needed in a reaction
Examples of enzymes
Kinases, polymerases, ribosome, components in spliceosome
Activation Energy
Energy needed to start a reaction
Barrier
Need to invest energy (ATP) to get over barrier to start a reaction. Enzymes reduce activation energy barrier
Cellular Respiration
Process cells use to obtain energy through 3 major steps (Glycolysis, Citric Acid Cycle, Electron Transport Chain). Converts glucose to ATP. Inputs glucose and gets ATP as an output.
Mitochondria Function in Cellular Respiration
Mitochondria are crucial for cellular respiration, acting as the powerhouses of the cell by generating ATP through aerobic processes
2 spaces of Mitochondria
Matrix and Inner-Membrane Space
