EK B1 Ch1 Biological molecules COPY Flashcards
1
Q
glycine
A
- smallest amino acid, contains a hydrogen atom as the side chain- contributes to the structure n function of proteins-necessary for the synthesis of heme, an iron-containg molecule required for hemoglobin function in red blood cells
2
Q
glutamate, and derivatives of amino acid tyrosine
A
- are important for signalng molecules in the brain and function as neurotransmitters
3
Q
glutamine and alanine
A
- required for metabolic pathways involved in nitrogen metabolism
4
Q
amphipathic molecules
A
polar and nonpolar chemical properties contained within the same moleculefatty acids - consist of carobxyl group (polar) attached to an end hydrocarbon chain (nonpolar)
5
Q
fatty acids in living cells primarily act…..
A
as components of plasma membrane lipids, which form a hydrophobic barrier separating the aqueous phases of the inside and outside of cells.
6
Q
saturated fatty acids
A
have NO C=C double bonds in hydrocarbon chain
7
Q
unsaturated fatty acids
A
have C=C double bonds
8
Q
phospholipids
A
The most abundant lipids in cell membranes are phospholipids, which generally contain a simple organic molecule attached to a negatively charged phosphoryl group and two fatty acids. Besides the plasma membrane, eukaryotic cells (plant and animal cells) contain a variety of intra- cellular membranes consisting of fatty acid–derived lipids. These include the nuclear membrane, the inner and outer mitochondrial and chloroplast membranes, and mem-branes associated with the endoplasmic reticulum and Golgi apparatus
9
Q
ATP levels…
A
ATP levels inthe cell are a measure of available energy because a large number of biochemical reactions depend on phosphoryl transfer energy made available from ATP hydrolysis.
10
Q
triacylglycerols
A
Another important function of fatty acids in eukaryotes is as a storage form of energy, which is made possible by their highly reduced state. Fatty acids yield chemical energy upon oxidation in mitochondria. Used for energy storage in this way, fatty acids are converted to triacylglycerols and sequestered in the adipose tissue of animal cells, whereas plants store triacylglycerols in seeds. Triacylglycerols are neutral (uncharged) lipids that contain three fatty acid esters covalently linked to glycerol. Lastly, fatty acids and fatty acid–derived molecules have recently been shown to be important signaling molecules that bind to nuclear receptor proteins. In this way, fatty acids regulate lipid and carbohydrate metabolism, inflammatory responses, and cell development.
11
Q
peptide bond
A
any of 20 different amino acids can be linked together by a covalent bond called a peptide bond (Figure 1.11). Polypeptide chains also have polarity, as they contain an amino group on one end and a carboxyl group on the other. Therefore, the number of octamer polypeptides that can theoretically be assembled with any one of the 20 amino acids at each position is a staggering 208, or 2.58 × 1010 different protein sequences. However, the actual number of different polypeptide sequences encountered biologically is much smaller than the theoretical number because not all combinations of amino acids have useful structural and functional properties due to differences in the size and chem- istry of their side chains.
12
Q
Chitin
A
-is another abundant carbohydrate polymer found in nature, is a major component in the exoskeletons of many invertebrates (insects and crustaceans) and in the cell walls of some types of fungi. Chitin consists of repeating N-acetylglucosamine units, a derivative of glucose, linked together by the same type of β(1→4) glycosidic bonds found in cellulose. Many types of bacteria contain the enzyme chitinase, which is able to cleave the β(1→4) glycosidic bond in chitin and thereby facilitate decomposition processes.
13
Q
The polysaccharides amylose and cellulose contain….
A
…..the same repeating unit of glucose,but differ in the structure of the glycosidic bond linking adjacent units (shown in red). p. 15 a. Amylose (starch) is a polymer of glucose containing α(1→4) glycosidic bonds between glucose units.b. Cellulose, contained in plant cell walls,is identical in composition to amylose; however, the glycosidic bonds between glucose units arein the β(1→4) configuration,and adjacent glucose residuesare rotated 180°.
14
Q
bacteria cell wall
A
The bacterial cell wall itself is coated with either a capsule or a slime layer that aids in enabling the bacterium to attach to other cells or solid surfaces.
15
Q
bacteria cytoplasm
A
The cytoplasm of the bacterial cell contains all of the enzymes required for cell metabolism, as well as the chromosome, which consists of DNA compacted with nucleic acid binding proteins to minimize its size.
16
Q
bacteria chromosome
A
The bacterial chromosome is circular and localized to a region in the cell called the nucleoid.
17
Q
bacteria cytoplasm
A
also contains proteins involved in cell division and the assembly of extracellular structures, such as flagella and pili, which are used for cell movement.
18
Q
bacteria plasmid
A
Many types of bacteria contain one or more circular DNA molecules called plasmids, which may encode genes involved in cell mating or antibiotic resistance. The plasmid replicates independently of the bacterial chromosome. Recombinant DNA methods make use of bacterial plasmids for gene cloning.
19
Q
what is the size of eukaryotic cells versus prokaryotic cells
A
Note that the diameter of eukaryotic cells is as large as ∼10–100 μm, whereas the diameter of prokaryotic cells is only ∼1 μm. so eukaryotic cells are 10-100 times larger than most bacteria
20
Q
Bacteria are prokaryotic cells with……
A
a cytosolic compartment surrounded by a plasma membrane that forms a barrier separating the cell from the environment. Most bacteria contain a single circular chromosome and move using flagellar structures or pili located on the outside of the cell.
21
Q
Animal cells differences/ what makes them special
A
Animal cells are a type of eukaryotic cell and contain numerous intracellular membrane-bound compartments, which create microenvironments for biochemical reactions. Membrane-bound organelles in all types of eukaryotic cells include mitochondria, lysosomes, and peroxisomes, which are subcellular sites for specific metabolic reactions. ** why they are on the outside**
22
Q
Plant cell differences/ what amkes them special
A
Plant cells are eukaryotic cells that contain chloroplasts, which convert light energy into chemical energy by the process of photosynthesis.Plant cells also contain large vacuoles, which are responsible for maintaining metabolite pools. The plasma membrane of plant cells is surrounded by a cell wall consisting of cellulose, which provides structural integrity to the plant.vacuoles are very large membrane bound**remember Both mitochondria and chloroplasts contain their own genomic DNA, which encodes pro- teins required for organelle function. ***
23
Q
chromatin (euk)
A
eukaryotic DNA is packaged with proteins to form a structure called chromatin that is contained within a membrane-bound region of the cell called the nucleous
24
Q
nucleolus
A
which is where ribosomes are assembled from ribosomal RNA and protein
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ribosomes
Ribosomes are large RNA–protein complexes that mediate proteins syntehsis in prokartyotic and eukartoic cells
26
ER
rough adn smooth--\> which are highly invaginated membrane structures that sequester ribosomes for protein synthesis.
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Golgi apparatus
is a membranous structure involved in protein translocation within the cell and in facilitating protein secretion at the plasma membrane.
28
mammalian macrophage cells
are protective cells in the immune system that seek out and destroy invading microorganisms or abnormal cells based on identification of foreign cell surface proteinsare immune cells in animals that engulf microorganisms such as bacteriaMicrophages use pseudopodia to recognize foreign or abnormal cells based on cell surface proteins
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endosymbiotic theory
proposes that eukaryotic cells evolved about 1.5 billion years ago as a result of large predatory cells engulfing aerobic bacteria, which eventually gave rise to mitochondria. The symbiotic bacteria were able to use O2 in the atmosphere as an electron acceptor in oxidation–reduction reactions, which provided a form of chemical energy for the synthesis of ATP. The predatory cells benefited from the extra ATP produced by the symbiotic bacteria, which in turn were rewarded with a nutrient-rich environment. Supportive evidence for the endosymbiotic theory comes from DNA sequence similarities between mitochondrial and bacterial genomes that have been analyzed using computational methods.
30
liver
metabolic control center
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skeletal muscle
mechanical work and glucose homeostasis
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intestines
nutrient absorption
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adipose tissue
energy storage and hormonal signaling
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kidneys
water, nitrogen, and electrolyte balance
35
How does the molecule glucose fit into the seven hierarchical levelsthat define the chemical basis of life on Earth?
Glucose is a biomolecule that contains three of the most abundant elements in living systems: carbon, oxygen, and hydrogen. Amylose and cellulose are polymers of glucose, and glucose biosynthesis is maintained by highly regulated metabolic pathways. Glucose is the primary component of plant cell walls and can be stored for energy needs in plant and animal cells in the form of starch and glycogen, respectively. The circulatory systems of multicellular organisms, such as mammals, transport glucose between tissues, which primarily use this metabolite for energy conversion processes (glycolytic path- way to generate ATP). Flowers contain nectar, a rich source of glucose (and fructose), which is used by honeybees as a nutrient source; when honeybees retrieve nectar, they cross-pollinate plants to help build a healthy ecosystem.
36
nucleotides (the building blocks of nucleic acids) are made up of 3 THINGS
• a nucleotide base (adenine, guanine, cytosine, thymine, or uracil); • a five-carbon ribose or deoxyribose sugar• one or more phosphate groups.
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Nucleotides are the building blocks of nucleic acids....... details about them
The common nucleotides in DNA and RNA contain a nucleotide base attached to the 1′-carbon of the ribose sugar and a phosphoryl group attached to the 5′-carbon. The 2′-carbon of ribonucleotides contains a hydroxyl group, whereas deoxyribonucleotideshave a hydrogen atom in this position.-G-C base pairs contain three hydrogen bonds.- A-T base pairs in DNA–DNA hybrids contain two hydrogen bonds. -A-U base pairs in DNA–RNA duplexes or RNA–RNA duplexes contain two hydrogen bonds. Hydrogen bonds are shown as dashed red lines between the base pairs.
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key differences DNA vs RNA
Deoxyribonucleotides are the monomeric units of DNA and lack a hydroxyl group on the carbon at the 2′ position (C-2′) of the ribose sugar, whereas ribonucleotides in RNA contain a hydroxyl group in this same position. As originally proposed by Watson and Crick and later confirmed by high-resolution X-ray crystallography, the DNA double helix contains two single polynucleotide strands that interact noncovalently to form a duplex. These strands are noncovalently associated through hydrogen bonds between the nucleotide bases, forming a duplex structure. The deoxyribonucleotide base pairs in DNA consist of guanine hydrogen-bonded to cytosine (G-C or C-G base pair) and adenine hydrogen-bonded to thymine (A-T or T-A base pair)RNA lacks the nucleotide base thymine and instead contains the nucleotide base uracil, which hydrogen bonds with adenine (A-U or U-A base pair)Because the chemical structures of nucleic acids are very similar, hybrid molecules of DNA and RNA can form, provided they contain complementary nucleotide bases to form G-C, A-T, or A-U base pairs
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hydrogen bond
Hydrogen bonds are a type of weak non-covalent interaction in which a hydrogen atom is shared between polar groups.
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polarity of DNA strands
The polarity of each DNA strand is determined by the bonds between the ribose and phosphate groups, which form the sugar–phosphate backbone.Two antiparallel DNA strands are held in register relative to each other by the hydrogen bonds between the nucleotide base pairs.
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How genome is copied....
1. DNA replication2. DNA transcription
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DNA replication
requires that DNA/genome be faithfully copied by a process called DNA replication and that segments of DNA, known as genes, be converted into RNA by DNA transcription. - so genome is copied during cell division by this process
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DNA transcription
- genes are converted into RNA by DNA transcription. Genes are functional units of DNA that are defined by the RNA products they produce. A variety of RNA products are generated by DNA transcription, one of which is mRNA, which is used to synthesize proteins by mRNA translation. The majority of RNA produced by DNA transcription is required for protein synthesis (rRNA and tRNA), RNA processing (snRNA), and regulation of gene expression or protein synthesis (miRNA). Under some conditions, RNA molecules can also be converted back into DNA by reverse transcription.
44
mRNA
A subset of the gene-encoded RNA molecules are called messenger RNA (mRNA) molecules. These are used as templates for protein synthesis in a process referred to as mRNA translation.DNA sequences are transcribed into mRNA by the enzyme RNA polymerase in the nucleus of eukaryotic cells. RNA polymerase synthesizes mRNA using ribonucleotides that form complementary base pairs with deoxyribonucleotides in the template strand of DNA. -The DNA sequence of the coding strand is the same as the RNA sequence in the mRNA, with the exception of uridine replacing thymidine. -The mRNA is then exported to the cytoplasm, where it is translated into protein.
45
mRNA translation
the TRANSLATION of mRNA requires a protein-synthesizing complex, which consists of ribosomes, tRNAs, and the mRNA. -Charged tRNAs bring amino acids into the ribosome complex, where they form complementary base pairs with the mRNA through codon–anticodon hydrogen bonds-Once the amino acid has been covalently linked to the growing polypeptide chain, the uncharged tRNA exits the ribosomal complex, making room for the next charged tRNA.
46
in addition to mRNA, cells also contain small nuclear RNA (snRNA) molecules
which are involved in RNA processing
47
micro RNA (miRNA) molecules
regulate gene expression and mRNA translation
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The most abundant RNA molecules in cells are......
ribosomal RNA (rRNA) molecules and transfer RNA (tRNA) mRNA translation molecules both of which are required for protein synthesis in addition to mRNA
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reverse trancription
converts RNA into DNA, still defined by the central dogma of molecular biology
50
In eukaryotic cells, the process of DNA transcription takes place
In eukaryotic cells, the process of DNA transcription takes place in the cell nucleus and leads to the production of mRNA transcripts. These transcripts are exported to the cytoplasm, where they are translated into polypeptide chains
51
In prokaryotic cells, DNA transcription and mRNA translation take place
in the cytosol, with mRNA molecules being translated as soon as they are synthesized.
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Dna transcription 2
the DNA sequence in the template strand forms complementary base pairs with the ribonucleotide sequence in the mRNA strand. (For example, the DNA sequence 3′-TAC-5′ corresponds to 5′-AUG-3′ in RNA.) In contrast, the DNA sequence in the non-template, or coding strand, is identical to the mRNA sequence, with the exception of uracil replacing thymine-After export to the cytoplasm, the mRNA is translated by ribosomes, which consist of proteins and rRNA. The ribosomes serve as binding sites for charged tRNA molecules, which deliver amino acids to the protein-synthesizing complex.
53
If the mutation is passed from the parents to their offspring...
then the mutation is contained within the DNA of a germ-line cell (egg and sperm cells in eukaryotes) and is referred to as an inherited genetic disease.
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if the DNA mutation occurs during the lifetime of the organism in a somatic cell
somatic cells= all cells that are not germ cells...then the consequences of this mutation—the disease phenotypes—are limited to the individual organism and are not inherited by its offspring. Tay–Sachs disease (a disorder of the nervous system) is an example of an inherited genetic disease, whereas most forms of cancer, such as the most common types of lung and colon cancer, are the result of DNA mutations that occur in damaged somatic cells.
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orthologous genes
Highly conserved gene sequences that encode proteins with the same function in different organisms they are thought to have risen from a common ancestral gene
56
Gene sequences evolve much more slowly......
than DNA sequences located between genes because natural selection provides a mechanism to preserve useful gene functions. Random nucleotide mutations that have no major effect on gene expression and function accumulate in flanking DNA at much higher rates than deleterious mutations accumulate within genes, the latter being eliminated by natural selection.
57
ex. The glucose- 6-phosphate dehydrogenase gene
is an orthologous gene in bacteria, yeast, worms, flies, and humans, with very high amino-acid-sequence conservation in regions of the protein required for enzymatic function. The consensus sequence identifies amino acid residueswithin the aligned sequencesthat are identical (\*), chemically conserved substitutions (:), or chemically related substitutions (.). p. 31
58
The protein glucose-6-phosphate dehydrogenase
is important in providing cells with a biomolecule called nicotinamide adenine dinucleotide phos- phate (NADPH; reduced form), which is required for oxidation–reduction reactions in cells. Glucose-6-phosphate dehydrogenase also has a critical role in the metabolism of ribose sugars, which are required for the backbone of nucleic acids. The fact that the amino acid sequence for this protein has gone unchanged for so long is evidence of its importance and of the long-term success of its efficient functioning.
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paralogous genes
Bioinformatic analyses suggest that in many cases, the second gene is, in fact, selectively retained and evolves to encode a protein with a related but distinct function. Related genes within a species are called paralogous genes and are considered members of a gene family. One ex is the nuclear receptor gene family, which encodes steroid receptor proteins that function as transcription factors (Figure 1.29b). Another example of paralogous genes is the globin gene family, which encodes proteins involved in oxygen transport.
60
photosynthetic autotrophs
use solar energy to oxidize H2O and produce O2 generating chemical energy in the form of glucose (C6H12O6). The plant uses this glucose at night for metabolic fuel to sustain aerobic respiration. solar energy is produced by thermonuclear fusion reactions (conversion of hydrogen to helium) in the Sun for the process of photosynthesis, which provides the necessary energy for life during the daylight hours and for carbon fixation.
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Heterotrophs
cannot convert solar energy into chemical energy directly and therefore depend on photosynthetic autotrophs to generate the O2 and glucose needed for aerobic respiration and to provide those essential nutrients required for life that heterotrophs cannot synthesize themselves.
62
photosynthesis
the process of oxidizing H2O to capture chemical energy and generate O2 is called photosynthesis
63
carbon fixation
is the conversion of Co2 to organic compounds
64
Both heterotrophs and photosynthetic autotrophs use
O2 and glucose (C6H12O6) for the process of aerobic respiration, which is a form of chemical energy conversion. Oxidation of H2O by photosynthetic organisms is the primary source of O2 in our atmosphere.
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The first law of thermodynamics states
that the total amount of energy in the universe remains the same, even though the form of energy may change. Put another way, energy can neither be created nor destroyed, only transformed (converted).
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The second law of thermodynamics states that
in the absence of an energy input, all spontaneous processes in the universe tend toward dispersal of energy (disorder), and moreover, that the measure of this disorder, called entropy, is always increasing in the universe. It is important to note that all biological energy conversion processes (as well as all mechanical energy conversion processes) are less than 100% efficient; some of the converted energy is lost as heat rather than used for work.
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EKhydrolysis
reaction where a macromolecule such as a protein is broken into two smaller molecules through the addition of water MACROMOLECULES BROKEN APART lysis--\> separation- they hydrolysis of ATP molecules provides the body's major source of energy, digestion is primarily the hydrolysis of macromolecules\*\*\* breaking a bond by adding the H and OH of water of either endhere is an example where water can act as a reactant or product compared to whne it acts in other scenarios as the solvent
68
dehydration
- two molecules are combined to form a larger molecule and water is formed as a byproduct\*\*\*COMBINATION OF TWO MOLECULES-reverse reaction of hydrolysis - this allows the formation of the bonds that make up biological molecules like PEPTIDE BONDS that make proteins and ESTER BONDS that are essential to triglycerides
69
ATP Hydrolysis
\* remember that here water serves as a nuc and attacks the electrophilic phosphoanhydride bond between the beta and Y phosphates of hte ATP molecule- the freed Y phosphate can then be used by a kinase enzyme to phosphorylate target proteins
70
water molecules hdyrogen bonding properties
- the ability of water molecules to form H bonds with each other elevates the boiling point - so water remains in a liquid state as a result\*\*\* in teh cellular enviornment
71
Hydrophobic
- Greek hydros= water, phobos=fear- H bonding also provides strong cohesive forces between water molecules "squeezing" hydrophobic molecules away from water and causing them to aggregate
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hydrophilic
hydros=watergreek philos= love- molecules or ionic compounds dissolve easily in water because their negatively charged ends are attracted to the partial positive charge of water's hydrogens while their posiitivelyt charged ends are attrcted to the partial negative charge of the oxygen- water moelcules surround (solvate) a hydrophilic molecule or ion
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EK Lipids
- low solubility in water and high solubility in non-polar organic solvents\*\*- lipids are non-polar and therefore hydrophobic- this property determines the behavior of lipids in the watery environment of the cellmajor lipids:- fatty acids-triacylglycerolsphospholipidsglycolipidssteroidsterpenes (vitamin A)waxes
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EK Role lipids play
- 1. energy storage2. cellular organization and structure, particularly in the membrane3. provision of precursor molecules for vitamins and hormones
75
Key function to remember for lipidsEK
\*\*\* long carbon chains allow energy storage\*\*\*\*\*\*that fats assemble into barriers separating aqueous environments because they are hydrophobic and that lipids are useful as precursors for signaling molecules because they can pass through cellular membranes\*\*\*
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EKfatty acids
- lipids-act as fuel for the body and are components of the cell membranes-are composed of long carbon chains truncated at one end by carboxylic acid-usually contain an even number of C, in humans hte max number of C in a fatty acid is 24-they can be saturated (no C-C double bonds) or unsaturated (one or more double C= C bonds)
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EKtriacylglycerols
simply fats and oils\*\*\*-constructed from a 3 C backbone called glycerol, which is attatched to three fatty acid chains-their function is to store energy in a cell- they can also provide thermal insulation adn padding to an organism
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EK adipocytes
latin adips=fatgreek kytos= cellfat cellsspecialized cells whose cytoplasm contains almost nothing but triglycerides
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EK phospholipids
- lipids with a phosphate group attachted, most important is phosphoglycerides which are built from a glycerol backbone like triglycerides but has a polar phospahte group replacing one fatty acidthe phosphate group lies on the opposite side of the glycerol from teh fatty acids , making phospholipid polar at the phosphate end an dnonpolar at the fatty endso this is amphipathic (Latin ambo= both)becuase polar and nonpolar ends, makes up membranes polar ends on the oustide, nonpolar C tails on the inside of membrane forms a barrier to polar molecuels that allows the regulation of their passage in and out of the cell
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EK glycolipids
similar to phosphoglycerides but with en or mroe carbohydrates attatchd to the three C glycerol backbone instead of a phosphate groupalso amphipathic
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EK sphingiolipids
same as phosphoglycerides with long chain fatty acid adn polar head group, but the backbone is an amino alcohol called sphingosine rather than glycerol - make up cell membrane like phospholipids, steroids, and glycolipids
82
EK steroids
4 ringed structures, like hormones, cholesterol and vitamin D cholesterol is v important to maintain membrane stability and fluidity and serves as the precursor for steroid hormones
83
EK waxes
formed by an ester linkage btw a long chain alcohol and a logn fatty acid chainwater repellent texture
84
Ek key functions of lipids
1. phospholipids serve as a structural component of membranes2. triacylglycerols store metabolic energy adn provide thermal insulation and padding3. steroids regulate metabolic activity4. some fatty acids (eicosanoids, like prostaglandins) even serve as local hormones
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EK carbs
-useful for storing energy and providing easily accessible energy to the body- liek with fats high concentration of C-H bonds in carbs allow for the storage of a large amount of energy up to 4 kcal/mol which is less than half the energy content of fatty acidscarbs do not store as much energy per gram as lipids simply because they do nto have as high a concentration of C-H bonds, alcohols are also present in teh carbon chainconsistent structure of carbs allows them to stack together in a cell which contributes to their usefulness for energy storagestructure of carbs allows them to join together through dehydration reaction forming long chains of polysacchrides for energy storage, reverse of this is hydrolysis reaction allows the release of single sugar molecules monosacchrides which the tissues use for energyglucose and fructose are most important exs
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EK Cn(H2O)n
carbs can be thought of as carbon and water in a fixed one to one ratio, for each carbon atom there exists one oxygen atom and 2 HFOR ANY CARB this is the formula
87
EK glycogen
- branched glucose polymer with alpha linkages found in all animal cells but large amounts are found in muscle and liver cells like most animals humans have enzymes to digest the alpha linkages of starch and glycogen but do not hav enzyme that can digest the beta linkages of cellulose (like grass) but cows do have bacteria in digestive system that release enzyme to digest the beta linkages in cellulose
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glucose/ATP
cell can oxidize glucose to transfer chemical energy to a more readily usable form ATP- if cell already has sufficient ATP glucose is polymerize dot the polysaccahride form glycogen or converted to fat
89
disulfide bonds
can stabilize proteins but are not DNA helix
90
Van der Waals
sum of the attractive and repulsive forces, not including covalent electrostatic interactions btw molecules
91
rule of thumb
hte more polar a molecule the greater hte dipole moment and consequently the stronger the intermolecular forcces-this is hwy at STP, water which can hydrogen bond is a liquid which carbon dioxide is a gas, which is nonpolar-the larger the molecule the more likely it is to have trong intermolecualr forces, indepdent of its polarity, take the alkanes as an example. the simplest alkane, methane CH4 is a gas at STP, moving up ins ize hexans C6H14 is a liquid, as the size of the chain inc even more like eicosane C20H42 is found as a solid at STP, in fact most waxes used for candles are long chain alkanes
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beta sheet, alpha helix
- secondary structure
- are reinforced by H bonds btw carbonyl oxygen of one amino acid and hte hydrogen on the amino group of another
- a single protein can contain both structures at various locations along its chain
- these areas contribute to conformational or overall shape
93
tertiary structure proteins
3d shape formed by curls and folds of peptide chain, 5 forces contribute to 3rd structure
1. covalent disulfide bonds btw two cystine amino acids on different parts of the chain, creating dimer cystine
2. electrostatic (ionic) interactions, mostly btw acidic and basic side chains like aspartic acid)
3. H bonds
4. van der waal forces
5. hydrophobic or nonpolar side chains pushed away from water toward center of the protein, hydrophobic bonding
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proline
turns that disrupt both alpha helix + beta pleated sheet formation are induced by proline because its physical structure, the R group binds to amine group, causing proline to be more rigid than a typical amino acid, causes kinks!
-binding prevents Pro from acting as H bond donor, causing formation of kinks that disrupt both alpha helices and beta-pleated sheets
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protein folding....
gathering of hydrophobic R groups away from the surrounding water is highly favorable because it allowed a decrease in the size of the highly ordered solvation layer, INC entropy of the system
96
denatured
when native conformation is disrupted protein is said to be denatured
-lost most of its 2, 3,4 structure
97
two types of proteins
structural made from long polymers like collagen, and globular proteins like enzymes, hormones, membrane pump and channels etc.
98
denaturing agent: urea
forces disrupted is Hydrogen bonds
99
denaturing agent: salt or change in pH
forces disrupted is electrostatic bonds
100
denaturing agent: beta- mercaptoethanol
forces disrupted is disulfide bonds
101
denaturing agent: organic solvents
forces disrupted is hydrophobic forces
102
denaturing agent: heat
all forces are disrupted
103
microtubules
make up Eu flagella (only thing with flagella is sperm) and cilia
- made from globular tubulin, which polymerizes under the right conditions to become structural protein
104
glycoproteins
proteins which carbohydrate groups attached
- AB antigens on red blood cells that determine an individual's blood type are examples of glycoproteins. These are a component of cellular plasma membranes and are generally more than 50% protein
- whenever see "glyco" think sugar, so proteins with sugars attached
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cytochrome
- kytos= cell, chroma= color or pigment ) are proteins which require a protesthetic, heme, haima= blood, group in order to function
- get their name from color that they add to the cell
- ex are hemoglobins and cytochromes of the ETC in inner membrane of mitochondria
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proteoglycans
mixture of proteins and carbohydrates, generally consist of more than 50% carbohydates
- major component of extracellular matrix
107
conjugated proteins
-proteins containing nonproteinaceous components are called conjugated proteins!
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Translation 1
Translation is the process in which an mRNA sequence is translated into a protein, with each codon corresponding to an amino acid. Transfer RNA, or tRNA, is a relatively small RNA molecule characterized by a hairpin structure that is responsible for “translating” between codons and amino acids. The other structure needed for translation is the ribosome, which is primarily made up of ribosomal RNA (rRNA). Ribosomes contain multiple rRNA strands with associated proteins, and have two major components: the large subunit (50S in prokaryotes and 60S in eukaryotes) and the small subunit (30S in prokaryotes, 40S in eukaryotes), with overall sizes of 70S for the prokaryotic ribosome and 80S for the eukaryotic ribosome. The large subunit catalyzes the formation of the polypeptide chain, while the small unit reads the RNA.
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translation 2
Translation has three main steps: initiation, elongation, and termination. Initiation occurs when the mRNA sequence binds to the small ribosomal subunit, either at a region in the 5' untranslated region known as the Shine-Dalgarno sequence (in prokaryotes) or to the 5' cap in eukaryotes. The first tRNA is known as the initiator tRNA, and it binds to the start codon (AUG). The initial amino acid is methionine in eukaryotes, but N-formylmethionine in prokaryotes. Once this happens, initiation factors facilitate the binding of the small ribosomal subunit to the large ribosomal subunit, forming the initiation complex.
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Translation 3
Elongation is the next step. During elongation, the ribosome reads the mRNA in the 5' to 3' direction and synthesizes a polypeptide from its N terminus to its C terminus, which is one of the reasons why amino acid sequences are traditionally written in the N-to-C order. Proteins known as elongation factors help move this process along. Three main binding sites are involved in elongation. The A site contains the next aminoacyl-tRNA complex, and at the P site a peptide bond is formed between the growing polypeptide chain and the incoming amino acid. The tRNA, which is now no longer “charged” with an attached amino acid, briefly pauses at the E site and detaches from the mRNA. After all of the charged tRNA sequences have been translated, translation is terminated.
