Molecules: Biochemistry Flashcards
(367 cards)
1
Q
Hydrogen bonding
A
intermolecular bonding between H and F, O, or N
2
Q
Hydrophobic molecule
A
Nonpolar molecules aggregate together away from water due to the strong cohesive hydrogen bonding between water molecules
3
Q
Hydrophilic molecule
A
Molecules or ionic compounds which dissolve easily in water because their negatively charged ends are attracted to the partial positive charge of water’s hydrogens while their positively charged ends are attracted to the partial negative charge of the oxygen
4
Q
Hydrolysis
A
A macromolecule is broken into two smaller molecules through the addition of water
5
Q
Dehydration
A
the reverse reaction of hydrolysis in which two molecules combine to form a larger molecule where water is formed as a byproduct
6
Q
ATP hydrolysis reaction
A
Water serves as a nucleophile and attacks the electrophilic phosphoanhydride bond between the beta and gamma phosphates of the ATP molecule. The freed gamma phosphate can then be used by a kinase to phosphorylate target proteins
7
Q
Fatty acids
A
building blocks for most complex lipids; composed of long chains of carbons (typically an even number) truncated at one end by a carboxylic acid which act as fuel for the body as they can serve as long term energy storage and their oxidation liberates large amounts of chemical energy
8
Q
Saturated fatty acid
A
possess only single carbon-carbon bonds
9
Q
Unsaturated fatty acid
A
posses one or more carbon-carbon double bonds
10
Q
Triacylglycerols (triglycerides)
A
also known as fats or oils; constructed from a 3 C backbone called glycerol which is attached to 3 fatty acid chains; their function is to store metabolic energy and provide thermal insulation and padding
11
Q
Adipocytes
A
fat cells whose cytoplasm contains almost nothing but triglycerides
12
Q
Phospholipids
A
class of lipids built from a glycerol backbone but a polar phosphate group replaces one of the fatty acids; polar head, nonpolar tail which makes them well suited as the major strucutural component of cell membranes
13
Q
Amphipathic
A
molecules that have a polar and nonpolar end ie. phopsholipid
14
Q
Sphingolipids
A
class of lipids which contain a long chain fatty acid and a polar head group but the backbone molecule is an amino alcohol called shingosine
15
Q
Phosphatids
A
class of lipids with a phosphatidic backbonde which is just another way of describing the glycerol backbone with a phosphate group attached
16
Q
Steroids
A
four-ringed structures which include some hormones, vitamin D, and cholesterol which regulate metabolic activities
17
Q
Terpenes
A
class of lipids that are often part of pigments in the body
18
Q
Waxes
A
class of lipids formed by an ester linkage between a long-chain alcohol and a long-chain fatty acid
19
Q
Vitamins
A
particular type of organic molecule that are essential, meaning they cannot be produced by the body
20
Q
Fat-soluble vitamins
A
are transported in the body along with the fats obtained from the diet and also assist in the absorption of these fats; ie. Vitamin A and D
21
Q
Eicosanoids
A
released from cell membranes as local hormones that regulate blood pressure, body temperature and smooth muscle contraction ie. prostaglandins
22
Q
Lipoprotein
A
a class of proteins which contain a lipid core surrounded by phospholipids and apoproteins so that they can transport insoluble lipids in hydrophilic medium such as blood
23
Q
Density of lipoproteins
A
when the ratio of protein to lipid is larger, the density of a lipoprotein is greater because proteins are more dense than lipids
24
Q
Carbohydrates
A
the high concentration of C-H bonds allows for the storage of large amounts of energy (about half that of lipids) with alochols present along the carbon chain; structure of Cn(H20)n
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Polysaccharides
long chains of monosaccharides formed by a dehydration reaction
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Monosaccharides
single sugar molecules which the tissue can use for energy when the hydrolysis of polysaccharides occurs
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Hexose
6 carbon carbohydrates ie. glucose and fructose
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Glycogen
a branched glucose polymer with alpha linkages which is found in all animal cells but especially in muscle and liver cells
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Glucose
hexose that can be oxidized to transfer its energy to ATP
30
Insulin
increases the rate of facilitated diffusion for glucose and other monosaccharides into cells
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Starch
polsysaccharade made up of a large number of glucose molecules which plants use instead of glycogen for long-term energy storage
32
Cellulose
polysaccharide made up of glucose connected by beta linkages which is used as structural material for cell wall rather than for energy storage ie. amylose and amylopectin
33
Digestion of alpha and beta linkages
Humans have enzymes to digest the alpha linkages of starch and glycogen but do not have enzymes to digest the beta linkages of cellulose
34
Nucleotides
molecules made up of a five carbon (pentose) sugar, a nitrogenous base, and a phosphate group which are involved in comprising the building blocks of every organism's genetic material and involved in the cell's use of energy
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Nucleosides
molecules consisting of a pentose sugar attached to a nitrogenous base
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Nucleic acid
polymer of nucleotides ie. DNA, RNA
37
Phosphodiester bond
In DNA/RNA, it is the linkage between the 3' C of one sugar molecule and the 5' carbon of another (attached to phosphate group)
38
sugar phosphate backbone
backbone of DNA/RNA where glucose molecules are interconnected by phosphodiester bonds
39
DNA
deoxyribonucleic acid; contains the 4 bases adenine, guanine, thymine, and cytosine
40
Purines
two-ring nitrogenous bases ie. A and G
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Pyrimidine
1 ring nitrogenous bases ie. C and T
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Watson-Crick model
known as B form of DNA where the two strans lie antiparallel to each other bound together by hydrogen bonds between nitrogenous bases forming a double-stranded structure
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Base pairing
hydrogen bonding between nitrogenous bases of DNA/RNA A-T/U and C-G
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Antiparallel strands
one strand of DNA runds 5' to 3' while its complementary stran runs 3' to 5'
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Strandedness of DNA and RNA
DNA is double stranded while RNA is usually single stranded
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base pairs (bp)
how the length of a DNA strand is measured
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Complementary strands
two strands of DNA/RNA whose bases are able to hydrogen bond with each other
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double helix
structure of DNA which contains two distinct grooves, the major and minor groove; each groove spirals once around the double helix every 10 base pairs
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Number of hydrogen bonds between A-T/U
2
50
Number of hydrogen bonds between C/G
3 which means that more energy is required to separated GC bonds
51
RNA
ribonucleic acid is identical to DNA except that C number 2 on the pentose has a hydroxyl group attached, it is almost always single stranded and it contains the pyrimidine uracil instead of thymine and is not confined to the nucleus like DNA
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ATP
adenosine triphosphate which is the main source of readily available energy for the cell
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Amino acids
building blocks of proteins which contain side groups of varying physical and chemical properties
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amide
an amine connected to a carbonyl carbon; creates a peptide bond which is formed via a dehydration reaction
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side chain of amino acid
also called R group; each amino acid differs only in its R group which is attached to the alpha carbon
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Categories of AA R groups
acidic, basic, polar, and nonpolar
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Chirality of AA
alpha carbon has 4 chemically distinct groups (except for glycine) meaning that it will be chiral and will rotate plane polarized light
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Glycine
Gly, G, nonpolar
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Alanine
Ala, A, nonpolar
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Valine
Val, V, nonpolar
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Leucine
Leu, L, nonpolar
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Isoleucine
Ile, I, nonpolar
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Phenyalanine
Phe, F, nonpolar, aromatic
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Tryptophan
Trp, W, nonpolar, aromatic
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Methionine
Met, M, nonpolar
66
Proline
Pro, P, nonpolar
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Serine
Ser, S, polar, hydroxyl group
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Threonine
Thr, T, polar, hydroxyl group
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Cysteine
Cys, C, polar, thiol group
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Asparagine
Asn, N, polar, amine group
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Tyrosine
Tyr, Y, polar, aromatic with hydroxyl group
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Glutamine
Gln, Q, polar, amide group
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Aspartic acid
Asp, D, acidic, carboxylic acid
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Glutamic acid
Glu, E, acidic, carboxylic acid
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Histidine
His, H, basic, aromatic
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Lysine
Lys, K, basic, amine group
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Arginine
Arg, R, basic, amine group
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Primary structure
the number and sequence of amino acids in a polypeptide
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Secondary structure
alpha helix or beta sheet which are reinforced by hydrogen bonds between the carbonyl oxygen of one amino acid and the hydrogen on the amino group of another
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Conformation of protein
shape of protein which is determined by its primary structure
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Tertiary Structure
the 3D shape formed by curls and folds of the peptide chain
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Forces that contribute to Tertiary Structure
1. Covalent disulfide bonds 2. electrostatic (ionic) interactions between acidic and basic side chains 3. hydrogen bonds 4. van der waals forces 5. hydrophobic bonding 6. kinks caused by proline
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Cystine
a dimer that is formed by covalent disulfide bonds between two cysteine amino acids on different parts of the chain
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Hydrophobic bonding
when side chains are pushed away from water toward the center of the protein
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Quarternary structure
when 2 or more polypeptides bind together
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Solvation layer
the solvent interface of any chemical compound or biomolecule that constitutes the solute; forces hydrophobic groups (if polar like water) into the inner area of the protein which is highly favorable because it allows a decrease in the size of the highly ordered solvation layer, increasing the entropy of the system
87
Denatured
when the native conformation is disrupted (losing most of its secondary, tertiary, and quaternary structure) so that it no longer functions
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Denaturing agent: Urea
disrupts hydrogen bonds
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Denaturing agent: Salt or change in pH
disrupts electrostatic bonds
90
Denaturing agent: mercaptoenthanol
disrupts disulfide bonds
91
Denaturing agent: organic solvents
disrupts hydrophobic bonds
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Denaturing agent: heat
disrupts all bonds
93
Cytochromes
proteins which require a prosthetic heme group in order to function ie. hemoglobin and the cytochromes of the ETC in the inner membrane of the mitochondria
94
Glycoproteins
proteins with carbohydrate groups attached and are a component of the plasma membrane and are generally more than 50% protein ie. AB antigens on red blood cells that determine an individual's blood type
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Proteoglycans
mixture of proteins and carbohydrates and consist of more than 50% carbohydrate ; major component of the extracellular matrix
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Two types of proteins
globular and structural
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Minerals
dissolved inorganic ions inside and outside the cell; by creating electrochemical gradients across membranes, they assist in the transport of substances entering and exiting the cell; can combine and solidify to give strength to a matrix, and can act as cofactors assisting enzyme or protein function
98
Enzymes
typically globular proteins which function as catalysts lowering the energy of activation for a biological reaction, thus increasing the rate of that reaction without altering the equilibrium of the reaction
99
Substrate
the reactant(s) upon which an enzyme works
100
Active site
the location on the enzyme where the substrate binds usually with numerous noncovalent bonds
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Enzyme-substrate complex
the enzyme and substrate bound together
102
Enzyme specificity
enzymes are designed to work only on a specific substrate or group of closely related substrates
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Lock and key model
the active site of the enzyme has a specific shape like a lock that only fits a specific substrate, the key
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Induced fit model
the shapes of both the enzyme and the substrate are altered upon binding which increases specificity and helps the reaction to proceed by destabilizing the substrate
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Saturation kinetics
as the relative concentration of substrate increases, the rate of the reaction also increases but to a lesser and lesser degree until Vmax has been achieved
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Vmax
the point at which the rate of the reaction cannot proceed any faster as all the enzymes are saturated
107
Turnover number/kcat
number of substrate molecules one active site can convert to product in a given unit of time when an enzyme solution is saturated; kcat = Vmax/[E]
108
Michaelis consant, Km
the substrate concentration at which the reaction rate is equal to 1/2 Vmax and indicates how highly concentrated the substrate must be to speed up the reaction
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Km trend
if a higher concentration of substrate is needed to achieve 1/2 Vmax (km) than it must have a lower affinity for the substrate (inversely proportional to intrinsic enzyme-substrate affinity)
110
Cofactor
a non-protein component (minerals or coenzymes) which an enzyme requires
111
Coenzymes
cofactors that are organic molecules (water soluble vitamins or their derivatives)
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Water-soluble vitamins
many serve as coenzymes
113
Shape of reaction rate vs pH
bell curve
114
Shape of reaction rate vs. temperature
bell curve skewed left
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Shape of reaction rate vs substrate concentration
gradually rises until it levels off at Vmax
116
4 Primary means of enzyme regulation
1. proteolytic cleavage 2. reversible covalent modification 3. control proteins 4. allosteric interactions
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Allosteric interactions
the modifiication of an enzyme's configuration through the binding of an activator or inhibitor at a specific binding site on the enzyme
118
zymogen (proenzyme)
an inactive form of an enzyme which becomes irreversibly activated when specific peptide bonds on zymogens are cleaved; activation may also be instigated by other enzymes or a change in environment (ie. pH)
119
Feedback inhibition
negative feedback; one of the products downstream in a reaction series comes back and inhibits the enzymatic activity of an earlier reaction
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Positive feedback
one of the products downstream in a reaction series comes back and activates the enzymatic activity of an earlier reaction
121
Allosteric regulation
regulation of enzymes caused by molecules that do not resemble the substrates of the enzymes that they inhibit and do not bind to the active site; instead, they bind to the enzyme and cause a conformational change
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Positiive cooperativity
increases in substrate concentration increase enzyme efficiency as well as the reaction rate as the first substrate changes the shape of the enzyme, allowing other substrates to bind more easily ie. hemoglobin and oxygen
123
Negative cooperativity
Increases in substrate concentration decrease enzyme effeciency as well as the reaction rate as the first substrate changes the shape of the enzyme so that it is more difficult for other substrates to bind
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Irreversible inhibitors
agents that bind irreversibly to enzymes and disrupt their function; typically via covalent bonds
125
Competitive inhibitors
compete with the substrate by binding reversibly with noncovalent bonds to the active site raising the apparent Km but not changing Vmax; can be overcome by increasing the concentration of substrate
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Uncompetitive inhibitors
bind at a site other than the active site but do not bind to the enzyme until it has associated with the substrate to form the enzyme-substrate complex; apparent Km decreases but Vmax is lowered because the substrate stays bound to the enzyme for a longer period of time
127
Mixed inhibitors
bind at a site other than the active site and bind to either the enzyme alone or the enzyme-substrate complex; depending on type either increase or decrease Km; lowers Vmax
128
Noncompetitive inhibitors
a special type of mixed inhibitors; bind just as readily to enzymes with a substrate as to those without to a spot other than the active site; cannot be overcome by excess substrate so they lower Vm
129
Competitive inhibition: Km and Vmax
Km increases, Vmax constant
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Noncompetitive inhibition: Km and Vmax
Vmax decreases, Km constant
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Oxidoreducatase
catalyze the transfer of electrons or hydrogen ions ie. oxidation-reduction reactions
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Transferase
catalyze reactions in which groups are transferred from one location to another
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Lyases
catalyze reactions in which functional groups are added to double bonds or conversely, double bonds are formed via the removal of functional groups
134
Isomerase
catalyze the transfer of groups within a molecule, with the effect of producing isomers
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Ligase
catalyze condensation reactions coupled with the hydrolysis of high energy molecules from ATP or some other nucleotide
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Synthase
the particular type of lyase that catalyzes the addition of one substrate to the double bond of a second substrate; does not require ATP
137
Synthetase
another name for ligase that require energy input from ATP or some other nucleotide
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Kinase
enzyme that phosphorlyates a molecule to activate or deactivate it
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Phosphatase
enzyme that dephosphorylates a molecule to activate or deactivate it
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Prostaglandin
lipids that act as hormones which bind with receptors intracellularly (since it is a hydrophobic hormone)
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Gene
nucleotide sequence that can code for a certain product or set of products; a unit of heredity that codes for a trait
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Genome
the complete sequence of nucleotides of the genetic material
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Central Dogma
DNA is transcribed to RNA which is translated to amino acids to form a protein
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Epigenome
encompasses all of the epigenetic changes that affect gene expression
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Histones
the sections of DNA that are not in use are wrapped tightly around globular proteins called histones; have basic functional groups that gives these proteins a net positive charge to attract negatively charged DNA strands and assist in wrapping porcess
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Nucleosome
eight histones wrapped in DNA
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Solenoid
nucleosomes wrapped into coils
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Supercoil
solenoids wrapped into coils f
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Chromatin
the entire DNA/protein complex; by mass about 1/3 DNA, 2/3 protien, and a small amount of RNA
150
Euchromatin
uncoiled DNA which is accessible to be transcribed
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Heterochromatin
tightly condensed DNA which is not accessible to be transcribed
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Single copy DNA
nucleotide sequences represented by only one copy of a nucleotide sequence and are associated with regions of euchromatin that are being actively transcribed
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Repetitive DNA
present in non-coding regions of DNA which has multiple consecutive copies of the same nucleotide sequence and remains tightly coiled in regions of heterochromatin
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DNA methylation
example of epigenetic regulation which involves the addition of an extra methyl group to particular cytosine residues; causes DNA to be wound more tightly causing these sections to not be transcribed; can be inherited
155
DNA acetylation
increases transcription
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non-coding RNA (ncRNA)
sections of RNA that do not code for protein products which contribute to the regulation of the chemical changes that affect chromatin structure
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Homologues
a chromosome and its partner chromosome which code for the same traits
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Diploid
any cell that contains homologous pairs of chromosomes
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Haploid
any cell that does not contain homologous pairs of chromosomes
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Polyploidy
when a a cell has more than 2 copies of homologous chromosomes
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Transcription
the process by which RNA is manufactured from a DNA template
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Translation
takes the nucleotide sequence of the RNA transcript and translates it into the language of amino acids, which are then strung together to form a functional protein
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Initiation (transcription)
a group of transcription factors identifies a promoter on the DNA strand, at the promoter the transcription factors assemble into a transcription initiation complex , RNA polymerase unzips the DNA double helix creating a transcription bubble
164
Transcription factors
DNA binding proteins
165
Promoter
a sequence of DNA nucleotides that designates a beginning point for transcription; help regulate where on the genome transcription can take place and how often certain sequences are transcribed
166
Consensus sequence
the most commonly found promoter nucleotide sequence recognized by a given species of RNA polymerase; variation from this sequence causes RNA polymerase to bond less tightly which leads to the associated genes being transcribed less frequently
167
Elongation (transcription)
RNA polymerase transcribes only 1 strand of the DNA nucleotide sequence into a complementary RNA nucleotide sequence; moves 3 to 5' but transcribes 5' to 3'
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Template/antisense strand
the transcribed strand of DNA
169
Coding/sense strand
non-transcribed DNA strand that protects its partner against degradation; complementary to template strand
170
Termination
the end of transcription which occurs when a specific sequence of nucleotides known as the termination sequence is reached
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Activators
bind to DNA close to the promoter to activate activity of RNA polymerase
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Repressor
bind to DNA cose to the promoter to repress activity of RNA polymerase
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Enhancer
short, non-coding regions of DNA found in eukaryotes; function similarly to activators but act at a much greater distance from the promoter
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Jacob-Monod model
model of prokaryotic genetic regulation; the genetic unit consists of the operator, promoter, and genes that contribute to a single prokaryotic mRNA (the operon)
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Lac operon
codes for enzymes that allow E.coli to import and metabolize lactose in the absence of glucose; activated when glucose is scarce and lactose is present; cAMP binds to and activates CAP which binds to a CAP site upstream of the lac promoter
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Catabolite activator protein (CAP
binds to a CAP site upstream of the promoter of the lac operon and activates it allowing for transcription and then translation of lac proteins ; example of positive control
177
Lac operator
located downstream of the promoter; when lactose is not present, a lac repressor protein binds to the operator site and prevents transcription of lac genes; ex. of gene repression; when lactose is available it binds to lac repressor protein making it unable to bind to operator and transcription occurs
178
Primary transcript
the initial RNA nucleotide sequence arrived at through transcription also called pre-mRNA or heterogeneous nuclear RNA, hnRNA
179
5' cap
post-transcription modification that serves as an attachment site in protein synthesis during translation and as a protection against degradation by exonucleases
180
poly-A tail
post-transcription modification that has been added to the 3'end which aids in the export of mature RNA to cytoplasm after splicing and serves a role in helping to initiate translation, also protects from degradation
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Splicing
post-transcriptional modification where portions of the primary transcript are excised and discarded
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Introns
non-coding regions of DNA, often excised through splicing
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Exons
coding regions of DNA that often become part of the mature mRNA
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snRNPs
small nuclear ribonucleoproteins; contains an assortment of proteins and snRNA; during the splicing proces, they act as a ribozyme and splicing occurs when snRNPS recognize nucleotide sequences at the end of introns and pull the ends of the introns together forming a lariat
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Ribozyme
an RNA molecule capable of catalyzing specific chemical reactions
186
Spliceosome
the complex formed from the association of the snRNPs and additional associate proteins; excises the introns and joins the ends of the exons together
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Alternative splicing
allows the cell to incorporate different variable coding sequences into the mature mRNA; different splicing patterns of the same gene can create different polypeptides
188
Degnerative genetic code
more than one series of 3 nucleotides may code for the same amino acid
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Codon
3 consecutive nucleotides on a strand of mRNA
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Stop/termination codons
UAA, UGA, UAG; signal an end to protein synthesis
191
Initiation codon
AUG; indicates where translation will begin; codes for methionine
192
Wobble pairing
flexibility in the bonding at the third base pair position in the codon and anticodon which explains why multiple codons can code for the same amino acid
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Ribosome
composed of a small subunit and large subunit both made up of rRNA where translation occurs
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Small/large subunits of ribosome
measured in terms of sedimentation coefficients in Svedberg units (S); 30S and 50S in prokaryotes (70S) and 40S and 60S in eukaryotes (80S)
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Nucleolus
manufactures ribosomes in eukaryotes
196
Initiation (translation)
with the help of initiation factors the 5' end of the mRNA attaches to the small subunit of a ribosome, a tRNA containg the 5' CAU 3' anticodon sequester the AA methionine and settles into the P site; this is the signal for the large subunit to join and form the initiation complex; most regulation of translation occurs during this step
197
Elongation (translation)
the ribosome slides down the mRNA strand one codon at a time in the 5' to 3' direction, a new AA ataches to A site, the C terminus of methionine attaches to N terminus of amino acid at A site by peptidyl transferase , ribosome shifts, tRNA carrying methionine moves to E site and peptide is now in P site
198
Termination (translation)
translation ends when the ribosome reaches a stop codon; when this happens, proteins known as release factors bind to the A site allowing a water molecule to add to the end of the polypeptide chain and the polypeptide is freed from the tRNA and ribosome , and the ribosome breaks up into its subunits to be reused later
199
Chaperones
proteins that assist in the folding process of polypepyides
200
Post-translational modification of proteins
these modifications are a mechanism for regulating gene expression by affecting which products ultimately become funciton; i/e adding sugar, lipid or phosphate groups , cleavage
201
Signal peptide
20 amino acid sequence near front of polypeptide that is recognized by SRP that carries the entire ribosome complex to a receptor protein on the ER, mitochondria, nucleus or other organelles
202
SRP
signal recognition particle
203
Where does translation occur?
begins on free-floating ribosomes in cytosol and may be directed to other organelles if it ocntains a signal peptide
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Semiconservative replication
because each copy contains 1 strand from the original DNA and the one newly synthesized strand
205
Origin of replication
replication does not begin at the end of the chromosome but toward the middle at a site called the origin of replication
206
Replication unit/ replicon
each chromosome of eukaryotic DNA is replicated in many discrete segments called replicons
207
DNA helicase
unwinds the double helix, separating the 2 strands
208
DNA polymerase
synthesizes the new DNA strans by pairing complementary free-floating deoxynucleotides with the sequence of nucleotides on the exposed strands of DNA; cannot initiate replication without a primer
209
Primase
an RNA polymerase that creates an RNA primer to initiate the strand
210
Single strand binding (SSB) tetramer proteins
aka helix destabilizer proteins; prevents the single strand in the loop from folding back on itself
211
Lagging strand
interrupted strand which is formed from a series of disconnected strands called Okazaki fragments
212
5 main steps of DNA replication
1. helicase unzips double helix 2. primase builds a primer 3. DNA polymerase assembles leading and lagging strands 4. RNAse H removes the primers 5. DNA ligase joins the Okazaki fragments together
213
DNA ligase
joins together neighboring Okazaki fragments to form a completed copy of double-stranded DNA helix
214
Telomere
repeated nucleotide units that the protect the ends of chromosomes; shortened by repeated rounds of replication , a condition that has been linked to aging and disease
215
Telomerase
catalyzes the lengthening of telomeres in eukaryotic organisms
216
Mitosis
a nuclear division without genetic change; it consists of a series of steps that organize and divide replicated chromosomes
217
Prophase
condensation of chromatin into chromosomes, centrioles move to opposite poles of the cell, nucleolus and nucleus disappear as nuclear envelope breaks down , spindle apparatus begins to form
218
Centromere
group of proteins that join together sister chromatids
219
Centrioles
located in centrosomes
220
Spindle apparatus
consists of astersm kinetochores, and spindle microtubules
221
Asters
microtubules radiating from the centrioles
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Spindle microtubules
connect the 2 centrioles
223
Kinetochore
a structure of protein and DNA located at the centromere of the joined chromatids of each chromosome; grows from centromere
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Metaphase
chromosomes align along the equator of the cell which ensures that they will be separated such that each daughter cell receives one of each chromosome
225
Anaphase
sister chromatids split at their attaching centromeres and segregate to opposite sides of the cell; shortening of kinectochores pull the sister chromatids apart and moves them toward opposite poles; cytokinesis may begin to occur
226
Disjunction
split of sister chromatids
227
Cytokinesis
the actual separation of the cellular cytoplasm due to constriction of microfilament around the center of the cell
228
Telophase
the nuclear membrane reforms, followed by the reformation of the nucleolus; chromosomes decondense ; cytokinesis continues
229
Mutation
any alteration in the genome that is not due to genetic recombination
230
Spontaneous mutation
occurring due to random errors in the natural process of replication and recombination
231
Induced mutation
occur due to mutagens
232
Mutagen
damage DNA and increase the frequency of mutation above the baseline frequency of spontaneous mutation
233
Gene mutation
alteration in the sequence of DNA nucleotides in a single gene
234
Chromosomal mutation
occurs when the the structure of a chromosome is changed
235
Somatic mutation
mutation in a somatic cell which is not passed to offspring
236
Point mutation
if a mutation changes a single nucleotide in a double strand of DNA ie. base substitution, addition, deletion
237
Transition mutation
a base substitution exchanging one purine for another purine and vice versa
238
Transversion mutation
a base subsitution exhanging one pyrimidine for a purine or vice versa
239
Base substitution mutation
results when one nucleotide is swapped for another during DNA replication
240
Addition mutation
inserting a new nucleotide into the sequence
241
Deletion mutation
deleting a nucleotide from the sequence
242
Silent mutation
type of neutral mutation in which the amino acid sequence is unchanged
243
Missense mutation
base substitution changes a codon, creating a missense codon which results in the translation of a different AA
244
Nonsense mutation
change to the nucleotide sequence creates a stop codon where none previously existed
245
Frameshift mutation
when the deletions or additions occur in multiples other than 3; changes the reading frame
246
Chromosomal deletion
portion of the the chromosome breaks or is lost during homologous recombination and/or crossing over events
247
Duplication
when a DNA fragment breaks free of one chromosome and incorporates into a homologous chromosome
248
Gene duplication/amplification
increase the amount of a gene's product
249
Translocation
when a segment of DNA from one chromosome is exchanged for a segment of DNA on another chromosome
250
Inversion
the orientation of a section of DNA is reversed on a chromosome
251
Transposons/transposable elements
DNA segments that excise themselves from a chromosome and reinsert themselves at another location
252
Proto-oncogenes
certain genes that stimulate normal growth in human cells
253
Oncogenes
genes that cause cancer
254
Carcinogens
mutagens that cause cancer
255
Tumor suppressor genes
help regulate normal cell growth ie. retinoblastoma nd p53 proteins which act at checkpoints during the cell cycle
256
Gametes
haploid reproductive cells
257
Meiosis I
separates homologus chromosomes to produce 2 haploid cells m each with one copy of the 23 chromosomes
258
Prophase I
homologous chromosomes line up alongside each other, matching their genes exactly and exchange DNA via crossing over leading to genetic recombination
259
Importance of genetic recombination
provides variation in the genetic makeup of gametes and their offspring
260
Tetrad
the side by side homologues exhibiting a total of 4 chromatids
261
Synaptonemal complex
the complex of 2 homolgous chromosomes zipped along each other where nucleotides are exchanged during crossing over
262
Chiasma
the point where 2 chromosomes are attached creating an X shape during crossing over
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Gene linkage
increases the likelihood that certain traits will be inherited together
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Gene mapping
determines the locations and relative distances of genes on chromosomes from the rates o single and double crossover events
265
Metaphase I
2 homologues remain attached and move to the metaphase plate
266
Anaphase I
homologous chromosomes each separate from their partner, independently assorting to create 2 haploid cells
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Telophase I
nuclear membrane may or may not reform and cytokinesis may or may not occur (although both do in humans)
268
Meiosis II
appears much like mitosis
269
Nondisjunction
if during anaphase I or II the centromere of any chromosome does not split
270
Primary nondisjunction
nondisjunction in anaphase I, one cell will have an extra chromosome and the other will be missing a chromosome
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Secondary nondisjunction
nondisjunction in anaphase II, one cell having one extra chromatid and the one cell lacking one chromatid
272
Gametogenesis
the production of gametes
273
Spermatogonium
undergoes mitosis to produce 2 diploid copies known as primary spermatocytes
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Spermatocytes
each undergo meiosis I to each become 2 spermatids
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Spermatid
undergo maturation (loses cytoplasm and gains a tail) to become a sperm
276
Oogonium
undergoes mitosis to produce 2 primary ooctyes but arrest at prophase I until puberty
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Primary oocyte
completes meiosis I producing a secondary oocyte (the other daughter cell receives no cytoplasm and is discarded which is called a polar body)
278
Secondary oocyte
completes meiosis II only when penetrated by a sperm during the act of fertilization, during meiosis II another polar body will be discarded; arrest at metaphase II and released at ovulation
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Ovum
matures from ootid after meiosis II
280
Zygote
results from the joining of the genetic material of the sperm and ovum
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Mendelian ratio
3:1 F2 generation of F1 x F1
282
Locus
position on chromosome
283
Allele
codes for a specific outcome in a particular trait
284
Wild type
the most common allele type for a certain trait within a population
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Genotype
individual's genetic makeup
286
Phenotype
expression of trait
287
Complete dominance
dominant allele masks expression of the recessive allele
288
Law of Segregation
alleles segregate independently of each other when forming gametes during meiosis so that any gamete is equally likely to possess any allele
289
Penetrance
the probability of a gene or allele being expressed if it is present ie. in complete dominance the penetrance of the dominant allele is 100%
290
Expressivity
measure of how much the genotype is expressed as a phenotype; the degree of expression of a trait
291
Incomplete dominance
when a heterozygous individual exhibits a phenotype that is intermediate between its homozygous counterparts
292
Co-dominant
if the heterozygote expresses both phenotypes ie. blood type
293
Law of Independent Assortment
genes located on separate chromosomes assort independently of each other, such that genes that code for distinct traits when located on separate chromosomes do not affect each other during gamete formation
294
Phenotypic ratio of dihybrid cross
9:3:3:1
295
Sex-linked
genes located on the sex chromosomes
296
Gene pool
total collection of all alleles in a population
297
Glycolysis
the breakdown of glucose into pyruvate; can occur with or without oxygen; occurs in cytosol of all living cells; energy input/six-carbon phase and energy output/three-carbon phase; produces a net total of 2 ATP and 2 NADH; rate -limiting step: synthesis of fructose 1,6 bisphosphate
298
Substrate-level phosphorylation
the phosphate group being donated to ADP is initially attached to another molecule and is transferred to DP by a kinase enzyme
299
Fermentation
anaerobic respiration (metabolism in absence of oxygen); includes glycolysis as well as the reduction of pyruvate to ethanol or lactic acid and the oxidation of NADH back to NAD+ (which allows glycolysis to continue)
300
Cori Cycle
lactic acid expelled from cells is transported through the blood to the liver, where it is oxidized back to pyruvate, this pyruvate is converted to glucose and can be sent back to other tissues to help produce ATP
301
Pentose phosphate pathway (PPP)
begins with G6P creates NADPH (to be used for anabolic functions) and some five carbon sugars like ribose for nucleotides; oxidative branch (production of NADPH); non-oxidative branch (five carbon sugar)
302
Glycogenesis
the storage of glycogen
303
Gluconeogenesis
synthesis of glucose from non-carbohydrate products such as proteins and lactic acid; reverse of glycolysis; occurs in liver
304
Beta-oxidation
factty acids oxidized to acetyl-CoA; occurs in mitochondrial matrix; first fatty acids are converted into acyl-CoA, at the expense of 1 ATP, along outer membrane of the mitochondrion, the acyl-CoA is then brought into the matrix where it is cleaved 2 carbons at a time to make acetyl-CoA; produces FADH2 and NADH for every 2 carbons taken from the original fatty acid
305
Ketogenesis
in mitochondria of liver cells, fatty acids are converted into a ketone body which can be shared with other organs for energy; occurs during a prolonged fast when the body is no longer able to synthesize sufficient glucose
306
Ketone bodies
acetone, acetoacetic acid and beta-hydroxybutyrate; spare glucose for the brain and RBCs by providing an alternative source of energy for other organs;
307
Lipoprotein
complex of lipid and protein produced primarily in the liver, intestines and adipocytes and are expelled from these cells via exocytosis
308
Chylomicrons
primary transport molecules that carry lipids from the intestines to the liver where they are repackaged into VLDLs or HDLs
309
Very low density lipoproteins (VLDL)
transport lipids such as triglycerides, phospholipids, and cholesterol from the liver to other parts of the body such as muscle and adipocytes
310
High density lipoproteins (HDL)
pick up stray fatty acids and trigylcerides from the periphery and bring them to the liver
311
Lipase
hydrolyzes triglycerides and releases free fatty acids into the bloodstream
312
Protein anabolism
occurs primarily during the fed state and should be associated with glycolysis, glycogenesis, and lipid storage
313
Protein catabolism
occurs primarily during the fasting state and should be associated with gluconeogenesis, glycogenolysis, beta oxidation, and ketone body synthesis
314
Insulin and glucose levels
insulin is released from the pancreas in response to increased blood glucose levels and promotes glycolysis in tissues, glycogenesis in liver and muscle, fatty acid synthesis in liver, and fatty acid storage in adipocytes; promotes ketogenesis in late starvation
315
Glucagon
released from the pancreas in response to decreased blood glucose levels and promotes glycogenolysis in the liver and muscle, gluconeogenesis in liver, fatty acid release in adipocytes and beta oxidation in almost all tissues
316
Epinephrine/cortisol and glucose levels
released in response to stress and promotes glycogenolysis, the removal of glucose from storage and gluconeogenesis
317
Oxidative phosphorylation
occurs when oxidation reactions provide the energy for phosphorylation; requires the presence of oxygen as a final electron acceptor
318
Citric acid cycle/TCA/Krebs Cycle
begins with acetyl CoA transferring 2 carbons to the 4 carbon oxaloacetate; 2 carbons are lost as CO2 and oxaloacetate is regenerated; each turn produces 1 ATP, 3 NADH and 1 FADH2 for a total of 2 ATP, 6 NADH, and 2 FADH2
319
Electron transport chain (ETC)
series of proteins that carries electrons from NADH to O2 ie. ubiquinone and cytochrome c; Complex I receives 2e- from NADH and pumps 4H+ across membrane, Complex II receives e-s from FADH2 and transfers them to a quinone carrier, Q to make QH2; Complex III receives the electrons from QH2 and transfers them to cytochrome c, resulting in movement of 4 H+ across membrane; complex IV removes the electrons from cytochrome c and transfers them to oxygen moving 2 H+ across the membrane
320
Proton-motive force
proton gradient from proteons being pumped into mitochondrial intermembrane space
321
ATP synthase
the protons diffuse back into mitochondrial membrane through ATP synthase generating ATP (chemiosmotic coupling)
322
NADH/ATP ratio
2 or 3 ATP per NADH molecule
323
FADH2/ ATP ratio
2 ATP per FADH2 molecule
324
Obesity
body index above 30
325
Type I diabetes
autoimmune disease where the immune system attacks the beta cells of the pancreas and as a result insulin levels are almost nonexistent
326
Type II diabetes
characterized by increasing resistance to action of insulin at the target cell
327
Separations
variety of lab techniques that use intermolecular forces to separate a mixture into its component parts
328
Extraction
separation technique based on solubility; inovles 2 immiscible layers, commonly an aqueous layer and a less dense organic layer; substance of interest is drained
329
Distillation
technique used to separate compounds that have significantly different boiling points; compound with lower boiling point will boil off first
330
Fractional distillation
more precise method of distillation that can be used to separate liquids whose boiling points are fairly close together; vapor is run through glass beads, allowing the compound with the higher boiling point to repeatedly condense and fall back into solution
331
Crystallization
pure substances form crystals more easily than impure substances; used to purify solid compounds; difficult to arrive at pure substance
332
Chromatography
separation of a mixture by passing it over or through a matrix that adsorbs different compounds more or less strongly according to their properties, ultimately altering the rate at which they lose contact with the matrix
333
Column chromatography
solution containing the mixture is dripped down a column containing the solid phase (polar); the more polar compounds in the mixture travel more slowly down the column, creating separate layers for each compound; compounds collected as elutes
334
High pressure liquid chromatography (HPLC)
column and solution use an appratus that puts the system under high pressure
335
Paper chromatography
a small portion of the sample to be separated is spotted onto paper; one end of the paper is then placed into a nonpolar solvent; the solvent moves up the paper via capillary action and dissolves the sample as it passes up; the polar components move more slowly because they are attracted to the polar paper
336
Rf factor
distance of component/distance of solvent line; nonpolar substances have Rf closer to 1
337
Thin-layer chromatography
similar to paper chromatography except that a coated glass or plastic plate is used instead of paper and the results are visualized via an iodine vapor chamber
338
Size-exclusion chromatography
molecules are separated by their size through gel filtration; larger molecules elute first as smaller molecules must navigate through pores on gel
339
Ion-exchange chromatograpy
molecules are separated based on their net surface charge; utlizies cationic or anionic exchangers that slow down the movement off charged molecules
340
Affinity chromatography
uses highly specfic interactions to slow down select molecules; receptor-ligand, enzyme-substrate, antigen-antibody
341
Gel electrophoresis
molecular mixture is placed in a gel and an electric field is applied; larger particles move more slowly in the agarose gel; because nucleic acids are negatively charged they migrate through the gel in response to the electric field
342
Southern blotting
tecnique used to identify target fragments of a known DNA sequence in a large population of DNA; 1. chop up DNA 2. use gel electrophoresis to spread out pieces 3. southern blot into a membrane 4. add a radioactive probe made from DNA/RNA 5. visualize
343
Northern blot
just like southern blot but identifies RNA fragments not DNA fragments
344
Western blot
used to detect a particular protein in a mixture of proteins; similar to Southern blot with regards to overall technique
345
Separation of enantiomers
use differences in crystallization or add stereospecefic enzyme that will react with only one enantiomer
346
Nuclear magnetic resonance spectroscopy
study of the interaction between atomic nuclei and radio waves; aldehyde: 9.5 ppm; carboxylic acid: 10-12 ppm; benzene: 8 ppm; alcohol: 1-5 ppm; methyl: <1 ppm
347
Splitting
caused by neighboring hydrogens that are not chemically equivalent; number of peaks = n +1 where n is the number of neighboring hydrogens that are not chemically equivalent
348
Chemical shift
the difference between the resonance frequency of the chemically shifted hydrogens and the resonance frequency of hydrogens on a reference compound
349
Integral trace
a line drawn above the peaks that rises each time it goes over a peak; the rise of the integral trace is proportional to the number of chemically equivalent hydrogens in peak beneath it
350
IR spectroscopy
reveals functional groups due to intramolecular vibrations and rotations; bond must have a ipole moment or no energy will be absorbed; carbonyl: 1700 cm-1; OH: broad dip 3200-3600; aldehyde: twin peaks 2800-3000; N-H: 3300 (small with no carbonyl and bumpy and large for amide)
351
Fingerprint region
complex vibrations that distinguish one compound from a similar compound are found in the 600 to 1400 cm-1 region
352
UV spectroscopy
detects conjugated systems
353
Mass spectometry
used to determine a compound's molecular weight
354
Molecular ion
the original molecule with one less electron created from mass spectrometry
355
Parent peak
peak made by the molecular ion
356
Base peak
peak with the most abundance
357
Nucleic acid hybridization
allow scientists to identify nucleotide sequences by binding a known sequence with an unknown sequence (DNA-DNA, DNA-RNA, RNA-RNA); can be used to find a particular gene in a gene library
358
Restriction enzymes
digest/cut nucelic acids only at certain nucleotide sequences along the chain (such sequences are called restriction sites or restriction sequences)
359
Gene cloning
accomplished either through bacteria and a cDNA library or through PCR
360
Vector
typically a plasmid or sometimes an infective virus with the gene of interest
361
cDNA
DNA produced from mRNA using reverse transcriptase
362
PCR
need primers, nucleotides, polymerase; 1. denature (heat) 2. anneal primers (cool) 3. polymerization repeat (heat)
363
Microarray/gene chip
compares the levels of mRNA between 2 cells and/or conditions `
364
Restriction fragment length polymorphism (RFLP)
human population is polymorphic at restriction sites thus it can be used to identify individuals
365
Single nucleotide polymorphisms (SNPs)
the genome of one human differs from the genome of another at about one nucleotide in every 1000; can identify individuals
366
Human gene therapy
involves genetic manipulation of an affected individual's DNA in which the defective allele is replaced by the wild type
367
Biometry
the use of statistical methods to understand biological data
