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Exam 1 Flashcards

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1
Q

What is the Central Dogma

A

DNA to mRNA to Protein

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2
Q

Common Characteristics of Cells

A

1) Central Dogma
2) Cells are self-replicating

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3
Q

Name and type of building blocks for DNA

A

Nucleotides A- T and G-C

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4
Q

Name and type of building blocks of mRNA

A

Nucleotides A-U and G-C

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5
Q

What are the building blocks of proteins

A

Amino acids

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6
Q

What is the process called when you go from DNA to mRNA

A

Transcription

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7
Q

What is the process called when you go from mRNA to Protein

A

Translation

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8
Q

What is cell theory?

A

all living cells are formed by growth and division of living cells

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9
Q

What is a gene?

A

The portion of DNA (Chromosomes) that codes for one functional protein

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10
Q

What is the genome?

A

Is the full set of all the genes to produce proteins

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11
Q

What function do genes serve in the cell?

A

They provide instruction for form, function, and behavior of cells by coding protein products

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12
Q

What does gene expression mean?

A

When a gene is transcribed and translated

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13
Q

Describe what differential gene expression is.

A

all cells contain the entire genome but only specific genes are expressed to produce the specific protein that the cell needs to perform its function

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14
Q

What use did Light microscopy have?

A

Good for defining nucleus, cell boundary, and cytoplasm

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15
Q

What limitations did light microscopy have?

A

-Required very thin sections
-not capable of visualizing the smallest cell structures

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16
Q

What is the use of Electron Microscopy

A

Beams of electrons are used to visualize very small cellular structures

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17
Q

Transmission Electron Microscopy (TEM)

A

-Electrons transmitted through thin sections of a specimen
-Good for internal structure

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18
Q

Scanning Electron Microscopy (SEM)

A

-Electrons scattered off the surface of the sample
Ability to determine the surface of structures and details

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19
Q

The Tree of Life Has Which Domains?

A

Bacteria, Archaea, Eukaryotes

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20
Q

What are the Differences and similarities between Prokaryotes and Eukaryotes?

A

Pro
-no nucleus
-no organelles
-Bacteria and Archaea

Euk
-Nucleus
-Organelles
-Plants, Animals, Fungi, and Protists

Shared
-Plasma Membrane (PM)
-Macromolecules

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21
Q

All cells are descendants of?

A

A common prokaryotic ancestral cell

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22
Q

Describe Charectisritcs of Prokaryotes.

A

-Variety of shapes (eg. spherical, rod, spiral)
-Often have a cell wall outside of PM (tough and protective coat)
-No nucleus single internal compartment with DNA and cytoplasm
-quick replication (20mins)
-often single cellular
-present in almost all habitats with varied biochemistry
-Some prok are photosynthetic others need an organic source for energy and production of energy

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23
Q

List of Organelles of Eukaryotic Cells.

A

Mitochondria
Golgi Apparatus
Endoplasmic reticulum (soft and rough)
lysosomes
ribosomes
peroxisomes nucleus
chloroplast

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24
Q

Function of Mitochondria.

A

production of ATP via aerobic respiration

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25
Q

Function of Golgi Apparatus.

A

sorts new proteins

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26
Q

Function of Soft ER.

A

synthesizes lipids, hormones, and some proteins

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27
Q

Function of Rough ER.

A

Protein Processing

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28
Q

Function of Lysosomes.

A

Breaks down unwanted material

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29
Q

Function of Peroxisomes.

A

Detoxify

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30
Q

Function of Nucleus.

A

Genome/DNA resides (transcription)

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31
Q

Function of Ribosomes.

A

mRNA->Protein (translation)

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32
Q

Endocytosis

A

invagination of PM, forming a vesicle and pinching off to bring substances into the cell

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33
Q

Exocytosis

A

the phospholipids in the wall of the vesicle fuse with the phospholipid of the PM open up and content is released to the extracellular fluid

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34
Q

Cytosol

A

gel-like fluid in which organelles are suspended ( water with dissolved proteins) eg. enzymes that carry out biological rxn -> glycolytic enzymes

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35
Q

Cytoplasm

A

cytosol and organelles beside the nucleus

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36
Q

Cytoskeleton

A

a network of protein filaments( actin , mircrotublues , intermiediate)

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37
Q

actin filaments

A

microfilaments (smallest) involved in cell movement

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38
Q

microtubules

A

composed of tubulin subunits( largest)
-structure for cellular extension
-organizing chromosomes during cell division (spindle apparatus)
-important in vesicle trafficking

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39
Q

Intermediate filaments

A

Intermediate in size and are involved in the strengthening of cellular structures ( eg. keratin in nails)

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40
Q

What are some model organisms?

A

Escherichia Coli( E.coli)- Prokaytoic cells that serve as bacterial species
Saccharomyces cerevisiae: Brewers yeast Eukaryotic cell
Plants: Arabidopsis
Animals: C.Elegans, Drosophila, mice, tilapia

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41
Q

Why do we use model organisms?

A

reproduce quickly, genetic manipulation, unicellular/multicellular, and transparent species.

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42
Q

atomic number

A

refers to the number of protons an atom has in its nucleus

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43
Q

atomic weight

A

is equal to the number of protons + neutrons ( each weighs about 1 amu)

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44
Q

neutral atom

A

equal number of protons and neutrons

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45
Q

isotopes

A

are atoms of the same element ( same atomic number, same protons) with different numbers of neutrons

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46
Q

Why do atoms bond with each other ?

A

atoms are most stable when the outermost shell contains full electrons. atoms will bond with other atoms to achieve stability

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47
Q

Covalent bonds

A

two atoms share a pair of elctrons

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48
Q

polar covalent bonds

A

Sharing of a pair of electrons unequally between 2 atoms
eg. O bonded with H and N bonded with H

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49
Q

In aqueous solutions which type of bond is the strongest by order?

A

Covalent bonds
Ionic Bonds
Hydrogen Bonds
Van Der Waals

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50
Q

Ions

A

an atom that completely gained or lost electrons

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51
Q

Cations

A

(+) eg Na+ lost and electron

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52
Q

anions

A

(-) eg Cl- gained an electron

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53
Q

Ionic bond

A

form when a cation is attracted to an anion (+-)
eg. Na+Cl-(Strong bond in a vacuum but weaker in water)

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54
Q

Hydrogen Bond

A

When 2 polar molecules ( or different regions of the same molecule) are attracted to each other: a hydrogen bond forms between (+) of one molecule and (-) ( relatively weak)

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55
Q

Hydrophilic

A

a substance that is ionic, polar covalent bonds “charged”
they love water.

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56
Q

Hydrophobic

A

a substance that tends to be non-charged, molecules with nonpolar covalent bonds don’t interact with water. ( eg. long chains or hydrocarbons due to similar electronegativity)

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57
Q

Van der Waals forces

A

they’re nonspecific interactions resulting from the distribution of electrons
- they occur in all types of molecules including nonpolar molecules and are relatively weak.

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58
Q

Acids

A

Substances that release protons when dissolved in water
H+= Proton

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59
Q

pH scale range

A

1-14

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60
Q

Pure water pH level

A

7

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61
Q

Why is it important to maintain constant pH in biological molecules?

A

Molecules are sensitive to change in pH ( structure and function)

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62
Q

What are organic compounds?

A

Molecules that contain carbon except CO2

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63
Q

What is a functional group?

A

common arrangements of atoms

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64
Q

mono-

A

one eg. monomer

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65
Q

di-

A

dimer eg. dimer

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66
Q

oligo-

A

A few eg. oligomer

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67
Q

poly-

A

many eg. polymer

68
Q

Monomer of protein

A

amino acids

69
Q

Monomer of carbohydrates

A

monosaccharides ( simple sugars)

70
Q

Monomer of Lipids

A

possible “ faty acids+glycerol”

71
Q

Monomer of nucleotides

A

Nucleotide ( ATGCU)

72
Q

What is a Carbohydrate?

A

A molecule that gives Energy and Structure is usually composed of
( CH2O) they tend to form a ring structure.

73
Q

What is an isomer?

A

Same chemical formula but different structures eg. glucose and fructose.

74
Q

Disaccharides

A

2 monosaccharides reacting to come together

75
Q

Anabolic Reaction

A

a reaction that makes larger molecules composed of smaller molecules

76
Q

Catabolic Reaction

A

breaking down bigger molecules into smaller ones

77
Q

What is a condensation/dehydration reaction

A

Water is removed during the reaction ( H from one monosaccharide and OH from the second Monosaccharide)

78
Q

What type of bond is formed between monosaccharides?

A

glycoside linkage

79
Q

Types of Disaccharides.

A

Maltose: Glucose + Glucose
Lactose: Galactose + Glucose
Sucrose: Glucose + Fructose

80
Q

Types of polysaccharides of Glucose.

A

Cellulose
glycogen
starch

81
Q

Cellulose

A

Structure of plant cell wall

82
Q

Glycogen

A

Energy storage polymer, found in muscles and liver of animals

83
Q

Starch

A

Energy storage polymer in plants.

84
Q

What is a lipid?

A

“fats” water-insoluble molecules

85
Q

Fatty acid

A

the common component of lipids that is made up of hydrocarbons with carboxyl groups at the end

86
Q

Saturated Fatty acids

A

only single bonds between all C’s in the chain therefore max hydrogen and carbon bonds.

87
Q

Unsaturated Fatty acids

A

at least 1 double bond between adjacent C’s in the chain, double bonds cause a bend in the chain and can disrupt van der Walls forces ( contributes to fluidity)

88
Q

Glycerol- Triglycerol/triglyceride

A

Glycerol with 3 fatty acids ( neutral fats) is very good for energy storage and exists in animal fats and plant fats

89
Q

Phospholipids

A

glycerol with 2 fatty acids and a phosphate group linked to another hydrophilic / charged group

90
Q

amphipathic

A

has both charged ( hydrophilic) regions and uncharged (hydrophobic) regions

91
Q

What is the main use for Phospholipids

A

They serve as the cell membrane and their ability to act a a bilayer creates those walls.

92
Q

Chololestorol

A

steroid, polysoprenoids

93
Q

Glycolipid

A

monosaccharide linked to a lipid

94
Q

Amino acid

A

the monomer of proteins composed of 20 different a.a that are present in a cellular context

95
Q

What is a.a that are acid ( charged)

A

aspartic acid
glutamic acid

96
Q

What is a.a that is basic ( charged)

A

lysine
arginine
histidine

97
Q

What is a.a that is polar ( uncharged)

A

asparagine
glutamine
serine
threonine
tyrosine

98
Q

What is a.a that is nonpolar ( uncharged)

A

alanine
Valine
leucine
isoleucine
proline
phenylalanine
methionine
tryptophan
glycine
cysteine

99
Q

What group of amino acids are hydrophilic?

A

Charged: Acid and Basic
Uncharged Polar

100
Q

What group of amino acids are hydrophobic

A

nonpolar/uncharged side chains

101
Q

peptide bond

A

forms between adjacent a.a through a condensation synthesis reaction. happens between C of the COOH group of a.a and the N of the amino group of the next a.a

102
Q

polypeptide/peptide

A

shorter chain of amino acid( less than 50 a.a)

103
Q

protein

A

larger chain of a.a folded into its functional protein

104
Q

What are the ends of a protein called

A

N ( amino terminus)
C ( Carboxly terminus)

105
Q

Nucleotides

A

monomers of nucleic acids, DNA, and RNA
-they also can be used for energy and cell signaling

106
Q

What is the general structure of a nucleotide?

A

Phosphate, Sugar, Base

107
Q

What sugar is involved in nucleotides?

A

5 C’s ribose(RNA) and deoxyribose(DNA) .
the difference lies in the 2’ carbon lacking an OH

108
Q

What are the two types of bases in nucleotides?

A

Pyrimidines
Purines

109
Q

Pyrimidines

A

One six-membered ring
Uracil (U, RNA only)
Cytosine (C, Both)
Thymine (T, DNA only)

110
Q

Purines

A

5-membered ring fused to the 6-membered ring
Adenine ( A, Both)
Guanine ( G, Both)

111
Q

What is the role of the Phosphate group in nucleotides?

A

-nucleotides used to produce chains of DNA or RNA have one phosphate
-nucleotides used for other purposes may have 2 or 3 phosphates
eg. AMP, ADP, ATP, GMP, GTP

112
Q

What characteristic allows proteins to carry out their job?

A

each protein has a special 3-D conformation

113
Q

What leads to protein folding? In tertiary structures

A

it is due to noncovalent interactions between atoms of the backbone as well as side chains (eg. H-bonds, Other electrostatic interactions, van der Walls)

114
Q

What role do hydrophobic forces play in determining shape?

A

nonpolar side chains tend to cluster in the interior of a protein

115
Q

What type of fold conformation due proteins take and what determines that shape?

A

Lowest Energy, and specific amino acids in the polypeptide chain.

116
Q

Primary Structure of Proteins

A

refers to the order of amino acids in the polypeptide chain

117
Q

Chaperon Proteins ( Chaperoins)

A

heat shock proteins (HSP), help other proteins fold into the proper configuration

118
Q

Proteins come in a variety of shapes and sizes such as?

A

size of 50-2000

119
Q

common folding patterns

A

alpha helix
Beta sheets
(secondary structure)

120
Q

What interactions lead to secondary structure?

A

occur between the N-H and C=O in backbone

121
Q

alpha helix

A

polypeptide turns around itself-> forms a rigid cylinder

122
Q

what bonds form in alpha helix?

A

H-bond is made with the H of amino group and O of carboxyl of 4th a.a down the chain

123
Q

Beta sheets (pleated)

A

hydrogen bonds forming between the amino and carboxyl groups of different a.a in segments of the polypeptide chain that lie side by side

124
Q

What directions do beta sheets face?

A

can have parallel and antiparallel configurations.

125
Q

Tertiary Structure

A

The Full 3-D conformation formed by the entire polypeptide folding and looping Often involves side chain-to-side chain interactions (noncovalent and hydrophobic)

126
Q

Quaternary structure

A

if a protein exists and functions as a complex of more than one polypeptide chain ( subunits) how those subunits fit together is the quaternary structure.

127
Q

Domain

A

A region of a polypeptide with a specific function ( folded into a compact and stable structure)

128
Q

Subunit

A

separate polypeptide chain that comes together and binds with another polypeptide subunit to form a fully functional protein.

129
Q

What are the characteristics of proteins with multiple subunits?

A

-specific binding of subunits together ( quaternary structure)
-subunits can be the same or different
-The number of subunits can vary

130
Q

Protein Structure can be stabilized by?

A

disulfide bonds formed between nonadjacent cysteine residues

131
Q

True or False proteins have regions and domains that are highly conserved.

A

True

132
Q

Proteins are broken down into families, Give some examples.

A

serine protease
kinase
phosphates
^(all enzymes)

133
Q

serine protease

A

cleave peptide bonds of proteins

134
Q

kinase

A

phosphorylate other proteins

135
Q

phosphatases

A

dephosphorylate other proteins

136
Q

Protein Function

A

all proteins work by binding to another molecule ( binding is specific)

137
Q

Ligand

A

any substance that is specifically bound to a protein

138
Q

Given the protein name the Ligand
Enzyme
Antibodies
Receptor

A

substrate
antigen
Chemical Signal: Nuerotransmiter or hormone

139
Q

Binding site

A

the region/domain that associates with a ligand ( usually consisting of a cavity composed of specific a.a)

140
Q

antibodies

A

The immune system produces Immunoglobin in response to foreign pathogens( viruses, bacteria, etc.).

141
Q

What do antibodies bind to?

A

antigens ( target molecules on the pathogen)

142
Q

What are the 4 subunits of the antibody

A

2 heavy chains
2 light chains
hypervariable domain (bind the antigen)

143
Q

What allows for variation of antibodies?

A

Humans can make billions of different antibodies because of the hypervariable domain.

144
Q

How does an antigen neutralize antigens?

A

mechanism like aggragetaion of antigens

145
Q

Enzyme

A

biological catalyst
reduces the activation energy to increase the role of biochemical reactions

146
Q

Describe the process of enzymes doing work.

A

-Enzymes bind to one or more substrate molecules and form the enzyme-substrate complex
(reaction occurs)
-Enzyme -Product Complex
( product dissociates)
Enzyme and Product

147
Q

What happens to the enzyme at the end of the reaction?

A

The Enzyme is not consumed so it’s ready to bind to more substrates

148
Q

Rate of reaction

A

(conversion of substrate to product)

149
Q

affinity

A

how tightly an enzyme interacts with its substrate

150
Q

what role do noncovalent interactions play between substrate and enzyme

A

more -> higher affinity
less -> lower affinity

151
Q

Describe how to set up an experimental design to measure the reaction rate and affinity of enzyme-substrate interactions.

A

-a known and constant amount of enzyme is added to each of a series of test tubes.
-the same amount of enzyme in each tube
-add to the tubes known and increasing concentrations 0->uM
-after this measure the rate of the reaction ( either substrate consumption or product formation)

152
Q

Michaels Menton plot

A

the plot of the rate of reaction vs substrate concentration

153
Q

Km

A

-Michaels constant
-Relative measure of affinity
-substrate concentration at 1/2 Vmax
-the lower the Km higher the affinity

154
Q

line weaver Burk plot

A

reciprocal of each side of the equation

155
Q

What does b represent in Burks plot

A

y-intercept = 1/Vmax

156
Q

what does the m represent in the Burks’s plot

A

slope= (Km/Vmax)

157
Q

Co-factors/Co-enzymes

A

additional helper ions for molecules that facilitate enzymatic reactions

158
Q

enzyme modulation

A

enzymes can be inhibited or activated

159
Q

allosteric enzymes

A

regulatory molecules bind to sites on the enzyme other than the active site that modulates activity

160
Q

In what ways do cells control protein function?

A

-Regulating gene expression
-Controlling catalytic activity
-Controlling degradation
-Formation of Protein complex

161
Q

Regulation of gene expression for protein control.

A

upregulating and downregulating levels of protein via regulation of gene expression

162
Q

Regulating catalytic activity

A

-other molecules often regulate enzymes
-feedback, allosteric, phosphorylation, kinases.

163
Q

feedback inhibitor

A

an enzyme acting early in a pathway is inhibited by a product produced later in the pathway.

164
Q

What types of interactions are occuring with allosteric molecules?

A

often noncovalent interactions

165
Q

What types of interactions are occuring with phosphorylates and kinases?

A

covalent interactions

166
Q

Controlling degradation involves?

A

tagging a protein with ubiquitin( small peptide) flags it for destruction

167
Q

Formation of protein complexes

A

-To complete a complicated task assemblages of more than 1 protein often rely on a timed sequence of ATP or GTP hydrolysis
-scaffolding proteins help protein complexes assemblage

Cell Bio (3 decks)

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