Final Exam Flashcards
1
Q
Covalent Bonds
A
The strongest bond in which atoms share an electron
2
Q
Noncovalent Bonds
A
A bond in which no sharing of electrons takes place
3
Q
Ionic Bonds
A
Ionic bonds form between two or more atoms by the transfer of one or more electrons between atom
4
Q
Hydrogen Bonds
A
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
5
Q
Hydrophobic Forces
A
The attraction between water-hating/repelling forces. Will not interact with water, will clump together.
6
Q
Hydrophilic
A
The attraction between water-loving forces. Will hydrogen bond, will interact with water
7
Q
Lipid
A
A group of molecules usually composed of fatty acids that are insoluble in water
8
Q
Structure of a Lipid
A
Glycerol and fatty acid tail
9
Q
Saturated Fatty Acid
A
All single bonds in the hydrocarbon
10
Q
Unsaturated Fatty Acid
A
1 or more double bonds in the hydrocarbon that create a kink
11
Q
Phospholipid Structure
A
Phosphate, glycerol, and fatty acid
12
Q
4 Nucleotides in DNA
A
Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)
13
Q
Pyrimidines
A
Cytosine and Thymine. Consists of one ring in its structure
14
Q
Purines
A
Adenine and Guanine. Consists of two rings in its structure
15
Q
Compare and Contrast DNA/RNA
A
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
16
Q
Amino Acid Group
A
Carboxyl group, amino group, and side chain “R” (different for each amino acid)
17
Q
How many different amino acid side chains are there?
A
20 different side chains
18
Q
Non-Polar Amino Acids
A
Glycine, Alanine, Valine, Cysteine, Proline, Leucine, Isoleucine, Methionine, Tryptophan, Phenylalanine
19
Q
Polar Amino Acids
A
Serine, Threonine, Tyrosine, Asparagine, Glutamine
20
Q
Negatively Charged Amino Acids
A
Aspartic Acid, Glutamic Acid
21
Q
Positively Charged Amino Acids
A
Lysine, Arginine, Histidine
22
Q
Gene
A
A unit of information that codes for a protein
23
Q
Peptide Bond
A
Covalent bond that links amino acids
24
Q
Polymerization
A
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.
25
Redundancy
Multiple codons for the same amino acid
26
Mutation
A change in the DNA sequence, even just 1 letter, could lead to a different amino acid.
27
Lipid Nanoparticle (LNP)
A lipid ball where RNA is packaged inside. Made of lipids, cholesterol, and mRNA
28
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.
29
Cationic Lipids
Positively charged lipid. The positively charged headgroups repel. The repelling creates a sharp cone shape that can create holes in the membrane
30
Endocytosis
In to a cell
31
Exocytosis
Out of a cell
32
Membrane Permeability
The ability to diffuse through a cell membrane. Depends on molecule size and properties.
33
What molecules can pass through the cell membrane? Which can't?
Small, nonpolar molecules CAN pass. Large, polar molecules and ions CANNOT pass
34
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.
35
Translation
From RNA to Protein
36
Steps of Translation
1. Initiation
2. Elongation
3. Termination
37
Components of a Protein
1. 5' Cap (Methyl guanine of 5' end of RNA)
2. Poly-A Tail (100-200 adenines of 3' end of RNA)
3. Open Reading Frame (ORF)
4. 5' UTR and 3' UTR (Before and after ORF)
38
tRNA
RNA molecule that base pairs that mRNA
39
Ribosome
Site of translation that harnesses and provides energy to link amino acids
40
Initiation of Translation
1. 5' cap recruits ribosome to mRNA
2. Scans 5' to 3' looking for AUG
3. Once found AUG, large ribosome sits down on mRNA, forming the A, P, and E sites
4. Large ribosome moves 5' to 3' on mRNA
5. 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
6. 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
41
Trafficking
Intentional movement of molecules in cells
42
Proteasome
Unfolds and degrades proteins
43
Rough ER
1. Translation on ribosome occurs
2. Protein folding and modification (glycosylation)
3. Quality control (proteasome)
44
Glycosylation
The attachment of carbohydrate side chains and sugars to the backbone of a protein
45
Vesicles
Transport organelles that transport proteins to different parts of the cell
46
Smooth ER
1. No ribosomes of protein productions
2. Makes lipids, phospholipids, cholesterol, and steroids (Contains enzymes to make these molecules)
47
Golgi Apparatus
1. Receive, refine, modify, and distribute molecules.
2. Series of stacks called cisterna (different functions in each). Uses vesicles to sort and ship proteins
3. Example ^: Sugar or phosphate groups may be removed or attached
48
Lysosome
Large vesicles with digestive enzymes that break down molecules, organelles, and pathogens
49
Secretory Pathway
Ribosomes, Rough ER, Vesicles to Golgi, Golgi Apparatus
50
Vacuoles
Large, long-term storage compartment
51
What makes up the endomembrane system?
1. ER (Rough & Smooth)
2. Golgi Apparatus
3. Lysosomes
4. Vacuoles
52
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)
53
Why can serine, tyrosine, and threonine be phosphorylated?
They are polar molecules so they have an OH group on their side chain.
54
3-Classes of Receptors
1. Enzyme Coupled Receptors (Phosphorylation)
2. G-protein coupled (GPCR)
3. Ion-Channel Coupled
55
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
56
Transmembrane Domain
Domain that passes through the membrane and holds the protein embedded. Usually made up of non-polar amino acids and hydrophobic proteins
57
Ligand Binding Domain
The domain on the outer surface of the cell binds the ligand signal. Usually composed of charged proteins
58
Types of Cell Communication
1. Contact-Dependent
2. Paracrine
3. Synaptic
4. Endocrine
59
Contact-Dependent Signaling
Cells communicate by direct physical contact. Requires cells to be in close proximity to one another
60
Paracrine Signaling
Involves the release of signaling factors. Act locally on nearby target cells, not through the bloodstream
61
Synaptic Signaling
Specialized form of paracrine signaling that occurs at synapses.
62
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
63
Cytotoxic T Cell
Recognizes and kills infected cells
64
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
65
B Cell
Binds to the BCR (B Cell Receptor). Produces antibodies.
66
Cytokines
Signaling molecules used by immune system to stimulate a response
67
Antibodies
Protein complex used to recognize pathogen, signal for destruction
68
Signal Transduction
Can change gene expression by turning genes on/off
69
Transcription Factors
Proteins that help find genes and impact expression
70
Karyotype
Spread of chromosomes that allows you to see abnormalities
71
Chromosomes
Densley packaged DNA and protein
72
Translocations
Pieces of DNA from different chromosomes. Chromosomes break off and pair incorrectly
73
Exons
Pieces of RNA that stay in mRNA
74
Introns
Pieces of RNA that are removed
75
Splicing
Process that removes introns and links exons
76
Promoter
DNA sequence that attracts transcription machinery
77
Transcriptional Start Site (TSS)
Where transcription begins
78
Terminator
DNA sequence that ends transcription
79
RNA Polymerase
Collection of proteins that execute transcription. RNA Polymerase II is the most common. Sits down on the promoter region
80
TATA Box
Complex that initiates the process of transcription. Directs the transcription machinery to the correct start site
81
Transcription Machinery/Factors
TBP and TAF bring in and load RNA polymerase
82
TBP (TATA Binding Proteins)
Protein that binds to the TATA box to begin transcription
83
TAF (TBP Associated Factors)
Protein that is brought in by TBP to assist in the start of transcription
84
Coding Strand
Has gene sequence and ORF
85
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)
86
Basal Gene Expression
The simplest and default form in which a protein of mRNA is expressed
87
Enhancer
DNA elements that up-regulate basal transcription
88
Up-Regulation
Turn up level of expression
89
Down-Regulation
Turn down level of expression
90
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
91
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)
92
Where are enhancers located?
Can be very close to the promoter OR very far. Can be upstream or downstream
93
Repressor
DNA elements that down-regulate basal transcription
94
What are the two different mechanisms of enhancers?
1. Looping Mechanism
2. DNA Packing Mechanism
95
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
96
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.
97
Demethylases
Remove DNA Methylation
98
Acetyltransferases
Add acetyl marks to histones
99
Methyltransferases
Add DNA methylation
100
Deacetylases
Remove acetyl marks on the histones
101
Negative Feedback Regulation
End product inhibits the system
102
Positive Feedback Regulation
End product promotes the system
103
Histone Modification
Chemical mark added to the histone tail
104
Acetylation
Opens up chromatin (Euchromatin)
105
Methylation
Tightly packs chromatin (Heterochromatin)
106
Epigenetic Code
Indicates where an epigenetic mark is. Example: H3K14ac: Histone 3, Lysine 14, Acetyl Mark
107
Phosphomutant
Convert non-phosphorylatable amino acid (Serine to Alanine)
108
Phosphomimetic
Convert to amino acid that mimics a phosphate group (Serine to any negatively charged amino acid)
109
Potency
Ability to differentiate
110
Cell Differentiation
Ability to self-renew and differentiate into different cell types
111
Mechanical Work
Movement within cell or cell itself. (Myosin motor, kinesin motor, dynamic microtubules)
112
Transport Work
Import/Export molecules. (Channel proteins, endo/exocytosis
113
Chemical Work
Promote chemical reactions. (Kinases, methylases, ribosome)
114
Passive Transport
The movement of materials through the cell membrane without using energy (diffusion)
115
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
116
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
117
Enzymes
Biological catalysts. Aid or speed up chemical reactions. Help reduce the amount of ATP needed in a reaction
118
Examples of enzymes
Kinases, polymerases, ribosome, components in spliceosome
119
Activation Energy
Energy needed to start a reaction
120
Barrier
Need to invest energy (ATP) to get over barrier to start a reaction. Enzymes reduce activation energy barrier
121
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.
122
Mitochondria Function in Cellular Respiration
Mitochondria are crucial for cellular respiration, acting as the powerhouses of the cell by generating ATP through aerobic processes
123
2 spaces of Mitochondria
Matrix and Inner-Membrane Space
124
