Heterotrophs cannot obtain their energy directly from
The tendency for an atom to attract electrons to itself in a chemical bond is called
Because atoms can have the same number of protons but a different number of neutrons, elements have
The ability of atoms to combine with other atoms is determined by
the number and distribution of electrons
Each of the following can participate in H-bond formation except
The difference between an acid and a base is that an acid whereas a base .
releases H+ ions in solution; releases OH- ions
The optimum pH for growing strawberries is 6.5, whereas the optimum pH for growing blueberries is 4.5. Therefore, the number of hydrogen ions needed to grow strawberries is times the number needed for blueberries.
Which of the following best represents the backbone arrangements of two amino acids with a peptide bond?
The ration of a weak acid and its conjugate base at the point of maximum buffering capacity is
Which of the following pairs is not a correct monomer/polymer pairing?
With the exception of Glycine, all amino acids found in proteins are of
Amino acids can be classified by the
characteristics of their side chains-"R" groups
Which of the following is characteristics of proteins?
Some function as enzymes
The side chain of leucine is a hydrocarbon. In a folded protein, where would you expect to find leucine?
In the interior of a cytoplasmic enzyme and on the exterior of a protein embedded in a membrane
An a helix is an example of which level of protein structure?
Forces involved in folding of a protein into its native conformation include
hydrogen bonding, hydrophobic interactions, and electrostatic attraction
The difference between a and b-glucose is
in the orientation of OH and H atoms of the anomeric Carbon
DNA and RNA contain
Cellulose is the most abundant organic compound on Earth. Its main function is
to provide mechanical strength to plant cell walls.
Polymerization reactions in which polysaccharides are synthesized from monosaccharides
result in the formation of water
The tertiary structure of a protein is determined by its
interactions among side chain R groups
Which of the amino acids listed below would, when incorporated into a polypeptide chain (not at the N- or C-terminus), make the charge of the polypeptide more positive?
Which of the following protein structures is/are destroyed by denaturation
Secondary and Tertiary
insoluble in water, hydrophobic, and important for energy storage
Triglycerides are synthesized from
fatty acids and glycerol
A phospholipid differs from a triglyceride in that phospholipids
have both hydrophylic and hydrophobic parts
What is the result of decreasing the number of double bonds?
The oil is now a solid at room temperature
The "backbone" of nucleic acid molecules is made of
alternating sugars and phosphate groups
Which of the following is NOT a difference between DNA and RNA?
DNA is a polymer and RNA is a monomer
DNA carries genetic information in its
sequence of bases.
The amino acid substitution that is likely to cause the largest change in tertiary structure is
lysine to isoleucine
help polypeptide chains to fold correctly in the cell
Which of the following is an amino acid not found in protiens
Which of the following are principles on which to base column chromatography?
size, charge, and hydrophobicity of the protein.
Which set of amino acids would you expect to find on the surface of protein molecules found w/in the interior of biological membranes?
Ala, Phe, Leu, Met
Cell membranes typically display asymmentry. This means
The two leaves of a bilayer contain different collections of lipids and proteins
The plasma membranes of winter wheat are able to remain fluid when it is extremely cold by
replacing saturated fatty acids with unsaturated fatty acids
Which of the following cell membrane components serve as recognition signals for interactions between cells?
Glycolipids or glycoproteins
To which class of large biological molecules does the unknown liquid most likely belong?
What is the nucleotide sequence of the complementary strand of the the DNA molecule: AATGCGA
In addition to the bilayer lipids and proteins, membranes may contain in the form of and .
Carbs, glycoproteins, glycolipids
Characteristics of most living organisms include:
one or more cells, genetic information, and can regulate internal environment
Structure of a muscle
fiber, many nuclei, sarcolema, myofibril, thin filaments
contractile structure, with thick/thin filaments
defined by the length of the myosin, overlaps the actin
thick filaments attach to the mid line in A-band
defined by myosin, no actin, no overlap
defined by the actin, no myosin, no overlap
boundary of the sarcomere, where the filaments attach
functional unit of striated muscle with thick and thin filaments
(Z to Z)
Sliding Filament Model
- filaments do not change length - I bands contract - A bands stay the same - degree of overlap changes, sarcomere is shorter
myosin head groups = cross bridges
they are extensions of myosin filaments
- 6 polypeptide chain - tail and head (up to clusters of 300!) - head group attached to the actin
- globular protein monomer unit - G actin (globular) = 375 AAs can polymerize to long chain - F actin (filamentous)
myosin is a protein, head group is an ATP-ase
Steps of the "Sliding Filament Model"
- actin any myosin are bound - ATP bind to myosin, causing dissociation of actin-myosin - ATP hydrolyzed (by water) to ATP + P (P is still attached) - myosin re-attaches with ATP + P -phosphate is released, energy is released ----> protein conformation change - "rigor" state = no ATP, cross bridges do not dissociate
triggers the contraction
two associated proteins of actin
troponin has three polypeptides, one is troponin C
Steps of Calcium
- myosin binding site on actin is blocked by tropomyosin - calcium binds to troponin C - conformational change of troponin pushes tropomyosin away - allows myosin to bind
Stimulation proccess of Calcium release
- muscle receives signal from the brain - nerves release acetylcholine ( a neurotransmitter) - propagates a signal (does not bathe the muscle) - signal to cell membrane; stimulate a change in flow/voltage - voltage change over entire membrane
released by sarcoplasmic reticulum (specialized ER)
- reservoir of calcium - transverse tubule signals SR to release calcium = calcium release - attached to troponin C
- gives shapes to hollow organs - must stay contracted for long period of time - no striations... actin and myosin are criss-crossed - individual spindle-shaped cells with individual nuclei
- actin and myosin, but no myofibrils - has 2X the actin, 1/4 the myosin - myosin has no bare central region - has "dense bodies"; fibers attach obliquely - slower muscle contractions
- has actin and myosin - individual cells with own nucleus and membrane - intercalated discs - Ca+ binds to troponin C - highly oxidative - not activated by nerve impulses
a membrane partition with gap junctions
more mitochondria than fast twitch higher capacity for aerobic metabolism high oxidative capacity high myoglobin = contains iron
moderate amounts of mitochondria and myoglobin WHITE meat high glycolytic capacity = anaerobic exercise low oxidative capacity faster time to peak tension more developed sarcoplasm reticulum (faster release of calcium)
higher capillarization catabolism of FATS = prolonged exercise
- maximal rate of oxygen consumption - single best measurement of cardio-respiratory endurance and aerobic fitness
creatine phosphate (phosphocreatine)
energy storage molecule breaks down and drives a P onto ADP prevents ATP depletion will last about 3-15 seconds, then dependent on glycolysis
intensity of exercise where there is an abrupt increase in PCr hydrolysis and glycolysis, resulting in increased lactate
maximal amount of ATP able to be regenerated from PCr and glycolysis during intense exercise
"elements" that carried inherited information
"Origin of Species"
DNA discovered, called nuclein
were initially thought to be numerous and variable, were also thought to be genetic material
DNA was thought to consist of a monotonous repeat of bases DNA was thought to be identical in all organisms
Beadle and Tatum (1930s)
discovered that genes code for proteins
most were not convinced that DNA was genetic material discovered that % Guanine = % Cytosine, % Adenine = % Thymine.... .....and was species specific
mid 1940s-1950s genes were found ti be made from DNA
2 rings (5 carbon, 4 nitrogen)
one ring (4 carbons and 2 nitrogen)
Race for the structure of DNA
Watson and Crick, Linus Pauling, Rosalind Franklin and Maurice Wilkins
foud x-ray diffraction to show that DNA was a constant diameter (idea was stolen by Watson)
Steps in DNA replication
- mediated by DNA polymerase (endergonic)
1. each DNA strand serves as a template for a new strand 2. bases enter at attachment points as a triphosphate at 3' end 3. two phosphates are cleaved (pyrophosphate) 4. hydrogen bonds form with template base
DNA unwinds, forms a "replication bubble"
"replication fork" moves in opposite directions until replication is complete
synthesis is done by normal DNA polymerase
3' => 5' and DNA polymerase won't do this 1000 bases long requires a short primer of RNA, not of DNA
uses 3' end of RNA primer to begin synthesis occurs in fragments called "Okazaki fragments"
Mistakes in DNA
damage can be caused by chemicals, UV lights
common mistakes: depurination, deamination, thymine dimers (UV radiation)
these all result in mistakes in final proteins
requires a synthetic "polynucleotide" primer for each end
Step 1: - heat DNA so it unravels - decrease heat; primer attaches - elongation....nucleotides attach - rise in temperature halts step one - repeat
- only 3-5% of genome codes for protein - coding regions of genome are highly conserved; non coding regions are not conserved - large bits of repeating VNTRs - bits inherited from Mom and Dad are different lengths
RNA - 1960s
discovered to be an intermediate in protein synthesis
because: DNA in nucleus, RNA in cytoplasm protein made in cytoplasm ... RER ribosomes made from RNA
Crick's Central Dogma
DNA specifies RNA which specifies proteins
DNA vs RNA
Single (RNA) vs double (DNA) uracil (RNA) vs thymine (DNA) RNA can form base pairs within same molecule, or between different molecules
Kind of RNA
mRNA tRNA rRNA (2 sub units)
- DNA is blueprint for a protein; stays in the nucleus - DNA unwinds - DNA base sequence is copied to mRNA - DNA code, now sitting on mRNA, goes to ribosome (in cytosol) - DNA is translated on ribosome to a protein
4' = 4 possible AAs 4'' = 16 possible AAs 4''' = 64 possible AAs (triplet code)
- looking at protein synthesis in bacteria - artificially produced poly-Uracil - which produced poly-phenylaline - first demonstration that base sequence on RNA = order AAs
MIXED RNAs (with Adenine and Uracil) would make 8 possible AAs (2''' = 8) ^ demonstrates that mRNA is read sequentially in threes
mediated by RNA polymerase transcribes mRNA bases onto 3' end does not need a primer copies only one strand of DNA - the "template strand"
Steps to Transcription
1. Initiation 2. Elongation 3. Termination
Step One: Initiation
DNA unwinds RNA binds at promoter site "initiation site" is where first nucleotide is copied onto mRNA
first ribonucleotide attaches as a triphosphate
Step two: Elongation
- addition of more ucleotides "residues" - mRNA grows from 5' end to 3' end (RNA polymerase reads template DNA from 3' to 5' end) - growing mRNA molecule detaches from template - helix re-forms
Step three: Termination
RNA polymerase encounters "termination sites" RNA polymerase detaches from DNA template
Primary Transcripts and Mature mRNA
- only 3-5 % of genome codes for protein - when DNA is transcribed, non-coding regions are transcribes too - this results in a strand of "pre-mRNA"..... a "primary transcript"
- mRNA capped at 5' end with GTP - this stabilizes the transcript; protects from enzymes that degrade at 5' end - string of adenines (50 - 200) added to the 3' end - this also stabilizes the mRNA transcript
- non coding regions need to be removed for this to happen - Intron - non-coding DNA that is still transcribed - Exon - coding region that is expressed - mature mRNA are exported to cytosol and to the ribosome
Translation - the ribosome
site of protein synthesis 2 sub units note conserved structure!! each sub unit is made of RNA (structural) and protein
rRNA is coded for by rDNA (in nucleolus) about 280 copies of genes for rRNA exist
coded for by DNA made in nucleus about 75-80 bases long 40 different kinds: each tRNA carries with it a specific AA tRNA has a cloverleaf shape (internal base pairing) one end has the anitcodoon; other end carries an amino acid
"charged" tRNA: hooking the amino acid to tRNA requires enzymes and energy enzyme has binding sites for ATP, AA, tRNA
Steps to Translation:
1. Initiation 2. Elongation 3. Termination
free energy + small molecules --> complex molecules simple molecules to form more complex molecules. may make a single product, such as a protein (highly ordered) out of amino acids (less ordered) require or consume free energy ENDERGONIC
first law of thermodynamics
in any conversion of energy from one form to another, the total energy before and after the conversion is the same
second law of thermodynamics
disorder tends to increase; when energy is converted from one form to another, some of that energy becomes unavailiable to do work.
inhibitors covalently bond to certain side chains at active site of an enzyme, permanently inactivating the enzyme by destroying its capacity to interact with normal substrate
inhibitors similar enough to particular enzymes natural substrate to bind non covalently to active site but different enough to not catalyze a chemical reaction
the condition a eukaryotic cell is in for most of its life
a pair of homologous chromosomes may fail to separate in meiosis 1, or sister chromatids may fail to separate during meiosis II or mitosis
each centrosome consists of a pair, each one hollow tube lined with 9 microtubules
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