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BIO211: Genes Molecules & Cells > Final Exam > Flashcards

Final Exam Flashcards

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Organic Chemistry 101 flashcards
1
Q

Covalent Bonds

A

The strongest bond in which atoms share an electron

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2
Q

Noncovalent Bonds

A

A bond in which no sharing of electrons takes place

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3
Q

Ionic Bonds

A

Ionic bonds form between two or more atoms by the transfer of one or more electrons between atom

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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

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5
Q

Hydrophobic Forces

A

The attraction between water-hating/repelling forces. Will not interact with water, will clump together.

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6
Q

Hydrophilic

A

The attraction between water-loving forces. Will hydrogen bond, will interact with water

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7
Q

Lipid

A

A group of molecules usually composed of fatty acids that are insoluble in water

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8
Q

Structure of a Lipid

A

Glycerol and fatty acid tail

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9
Q

Saturated Fatty Acid

A

All single bonds in the hydrocarbon

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10
Q

Unsaturated Fatty Acid

A

1 or more double bonds in the hydrocarbon that create a kink

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11
Q

Phospholipid Structure

A

Phosphate, glycerol, and fatty acid

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12
Q

4 Nucleotides in DNA

A

Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)

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13
Q

Pyrimidines

A

Cytosine and Thymine. Consists of one ring in its structure

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14
Q

Purines

A

Adenine and Guanine. Consists of two rings in its structure

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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

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16
Q

Amino Acid Group

A

Carboxyl group, amino group, and side chain “R” (different for each amino acid)

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17
Q

How many different amino acid side chains are there?

A

20 different side chains

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18
Q

Non-Polar Amino Acids

A

Glycine, Alanine, Valine, Cysteine, Proline, Leucine, Isoleucine, Methionine, Tryptophan, Phenylalanine

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19
Q

Polar Amino Acids

A

Serine, Threonine, Tyrosine, Asparagine, Glutamine

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20
Q

Negatively Charged Amino Acids

A

Aspartic Acid, Glutamic Acid

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21
Q

Positively Charged Amino Acids

A

Lysine, Arginine, Histidine

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22
Q

Gene

A

A unit of information that codes for a protein

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23
Q

Peptide Bond

A

Covalent bond that links amino acids

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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.

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25
Q

Redundancy

A

Multiple codons for the same amino acid

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26
Q

Mutation

A

A change in the DNA sequence, even just 1 letter, could lead to a different amino acid.

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27
Q

Lipid Nanoparticle (LNP)

A

A lipid ball where RNA is packaged inside. Made of lipids, cholesterol, and mRNA

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28
Q

mRNA Vaccine

A

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.

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29
Q

Cationic Lipids

A

Positively charged lipid. The positively charged headgroups repel. The repelling creates a sharp cone shape that can create holes in the membrane

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30
Q

Endocytosis

A

In to a cell

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31
Q

Exocytosis

A

Out of a cell

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32
Q

Membrane Permeability

A

The ability to diffuse through a cell membrane. Depends on molecule size and properties.

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33
Q

What molecules can pass through the cell membrane? Which can’t?

A

Small, nonpolar molecules CAN pass. Large, polar molecules and ions CANNOT pass

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34
Q

Unsaturated and Saturated Fatty Acid Tails in the Cell Membrane

A

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.

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35
Q

Translation

A

From RNA to Protein

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36
Q

Steps of Translation

A
  1. Initiation
  2. Elongation
  3. Termination
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37
Q

Components of a Protein

A
  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)
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38
Q

tRNA

A

RNA molecule that base pairs that mRNA

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39
Q

Ribosome

A

Site of translation that harnesses and provides energy to link amino acids

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40
Q

Initiation of Translation

A
  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
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41
Q

Trafficking

A

Intentional movement of molecules in cells

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42
Q

Proteasome

A

Unfolds and degrades proteins

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43
Q

Rough ER

A
  1. Translation on ribosome occurs
  2. Protein folding and modification (glycosylation)
  3. Quality control (proteasome)
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44
Q

Glycosylation

A

The attachment of carbohydrate side chains and sugars to the backbone of a protein

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45
Q

Vesicles

A

Transport organelles that transport proteins to different parts of the cell

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46
Q

Smooth ER

A
  1. No ribosomes of protein productions
  2. Makes lipids, phospholipids, cholesterol, and steroids (Contains enzymes to make these molecules)
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47
Q

Golgi Apparatus

A
  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
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48
Q

Lysosome

A

Large vesicles with digestive enzymes that break down molecules, organelles, and pathogens

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49
Q

Secretory Pathway

A

Ribosomes, Rough ER, Vesicles to Golgi, Golgi Apparatus

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50
Q

Vacuoles

A

Large, long-term storage compartment

51
Q

What makes up the endomembrane system?

A
  1. ER (Rough & Smooth)
  2. Golgi Apparatus
  3. Lysosomes
  4. Vacuoles
52
Q

Phosphorylation

A

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
Q

Why can serine, tyrosine, and threonine be phosphorylated?

A

They are polar molecules so they have an OH group on their side chain.

54
Q

3-Classes of Receptors

A
  1. Enzyme Coupled Receptors (Phosphorylation)
  2. G-protein coupled (GPCR)
  3. Ion-Channel Coupled
55
Q

Internal Signaling Domain

A

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
Q

Transmembrane Domain

A

Domain that passes through the membrane and holds the protein embedded. Usually made up of non-polar amino acids and hydrophobic proteins

57
Q

Ligand Binding Domain

A

The domain on the outer surface of the cell binds the ligand signal. Usually composed of charged proteins

58
Q

Types of Cell Communication

A
  1. Contact-Dependent
  2. Paracrine
  3. Synaptic
  4. Endocrine
59
Q

Contact-Dependent Signaling

A

Cells communicate by direct physical contact. Requires cells to be in close proximity to one another

60
Q

Paracrine Signaling

A

Involves the release of signaling factors. Act locally on nearby target cells, not through the bloodstream

61
Q

Synaptic Signaling

A

Specialized form of paracrine signaling that occurs at synapses.

62
Q

Endocrine Signaling

A

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
Q

Cytotoxic T Cell

A

Recognizes and kills infected cells

64
Q

Helper T Cell

A

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
Q

B Cell

A

Binds to the BCR (B Cell Receptor). Produces antibodies.

66
Q

Cytokines

A

Signaling molecules used by immune system to stimulate a response

67
Q

Antibodies

A

Protein complex used to recognize pathogen, signal for destruction

68
Q

Signal Transduction

A

Can change gene expression by turning genes on/off

69
Q

Transcription Factors

A

Proteins that help find genes and impact expression

70
Q

Karyotype

A

Spread of chromosomes that allows you to see abnormalities

71
Q

Chromosomes

A

Densley packaged DNA and protein

72
Q

Translocations

A

Pieces of DNA from different chromosomes. Chromosomes break off and pair incorrectly

73
Q

Exons

A

Pieces of RNA that stay in mRNA

74
Q

Introns

A

Pieces of RNA that are removed

75
Q

Splicing

A

Process that removes introns and links exons

76
Q

Promoter

A

DNA sequence that attracts transcription machinery

77
Q

Transcriptional Start Site (TSS)

A

Where transcription begins

78
Q

Terminator

A

DNA sequence that ends transcription

79
Q

RNA Polymerase

A

Collection of proteins that execute transcription. RNA Polymerase II is the most common. Sits down on the promoter region

80
Q

TATA Box

A

Complex that initiates the process of transcription. Directs the transcription machinery to the correct start site

81
Q

Transcription Machinery/Factors

A

TBP and TAF bring in and load RNA polymerase

82
Q

TBP (TATA Binding Proteins)

A

Protein that binds to the TATA box to begin transcription

83
Q

TAF (TBP Associated Factors)

A

Protein that is brought in by TBP to assist in the start of transcription

84
Q

Coding Strand

A

Has gene sequence and ORF

85
Q

Template Strand

A

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
Q

Basal Gene Expression

A

The simplest and default form in which a protein of mRNA is expressed

87
Q

Enhancer

A

DNA elements that up-regulate basal transcription

88
Q

Up-Regulation

A

Turn up level of expression

89
Q

Down-Regulation

A

Turn down level of expression

90
Q

Parts of the Human Body with High Gene Expression

A

Tissues and parts of their body that actively perform their functions often have high gene expression. Example: heart, liver, kidney

91
Q

Parts of the Human Body with Low Gene Expression

A

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
Q

Where are enhancers located?

A

Can be very close to the promoter OR very far. Can be upstream or downstream

93
Q

Repressor

A

DNA elements that down-regulate basal transcription

94
Q

What are the two different mechanisms of enhancers?

A
  1. Looping Mechanism
  2. DNA Packing Mechanism
95
Q

Looping Mechanism

A

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
Q

DNA Packing Mechanism

A

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
Q

Demethylases

A

Remove DNA Methylation

98
Q

Acetyltransferases

A

Add acetyl marks to histones

99
Q

Methyltransferases

A

Add DNA methylation

100
Q

Deacetylases

A

Remove acetyl marks on the histones

101
Q

Negative Feedback Regulation

A

End product inhibits the system

102
Q

Positive Feedback Regulation

A

End product promotes the system

103
Q

Histone Modification

A

Chemical mark added to the histone tail

104
Q

Acetylation

A

Opens up chromatin (Euchromatin)

105
Q

Methylation

A

Tightly packs chromatin (Heterochromatin)

106
Q

Epigenetic Code

A

Indicates where an epigenetic mark is. Example: H3K14ac: Histone 3, Lysine 14, Acetyl Mark

107
Q

Phosphomutant

A

Convert non-phosphorylatable amino acid (Serine to Alanine)

108
Q

Phosphomimetic

A

Convert to amino acid that mimics a phosphate group (Serine to any negatively charged amino acid)

109
Q

Potency

A

Ability to differentiate

110
Q

Cell Differentiation

A

Ability to self-renew and differentiate into different cell types

111
Q

Mechanical Work

A

Movement within cell or cell itself. (Myosin motor, kinesin motor, dynamic microtubules)

112
Q

Transport Work

A

Import/Export molecules. (Channel proteins, endo/exocytosis

113
Q

Chemical Work

A

Promote chemical reactions. (Kinases, methylases, ribosome)

114
Q

Passive Transport

A

The movement of materials through the cell membrane without using energy (diffusion)

115
Q

Active Transport

A

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
Q

Sodium-Potassium Pump

A

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
Q

Enzymes

A

Biological catalysts. Aid or speed up chemical reactions. Help reduce the amount of ATP needed in a reaction

118
Q

Examples of enzymes

A

Kinases, polymerases, ribosome, components in spliceosome

119
Q

Activation Energy

A

Energy needed to start a reaction

120
Q

Barrier

A

Need to invest energy (ATP) to get over barrier to start a reaction. Enzymes reduce activation energy barrier

121
Q

Cellular Respiration

A

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
Q

Mitochondria Function in Cellular Respiration

A

Mitochondria are crucial for cellular respiration, acting as the powerhouses of the cell by generating ATP through aerobic processes

123
Q

2 spaces of Mitochondria

A

Matrix and Inner-Membrane Space

124
Q
A

BIO211: Genes Molecules & Cells (1 decks)

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