Biochemistry Flashcards
Differentiate between hydrolysis and dehydration.
Hydrolysis = breaking macromolecules into their products USING WATER Dehydration = molecules into macromolecules RELEASING WATER
Describe the function of lipids.
- energy storage
- cellular organization and structure
- precursor molecules for vitamins and hormones
What class of lipid has most energy storage than any other macromolecule? Why?
Fatty acids because they have long carbon chains
How much energy is produced from fatty acids when oxidized?
9 Kcals
What are triglycerides functions?
- store energy (adipocytes)
- thermal insulation and padding
What are the simplest forms of phospholipids?
phosphatidic acids (phosphatids)
What are sphingolipids? Where are they found?
Instead of a glycerol backbone of a lipid, have an amino alcohol (sphingosine)
-found in membranes
What is cholesterols main functions?
membrane stability/fluidity and precursor to most steroid hormones
What are eicosanoids? Give example of one.
Released from cell membranes as local hormones for regulation of blood pressure, temperature and smooth muscle contraction
-ex = prostaglandins
In regards to lipoproteins, When will the lipoprotein be LESS DENSE? (i.e. a VLDL or LDL)
when there is MORE LIPID than there is PROTEIN
What is the generic molecular formula for carbohydrates?
Cn(H2O)n
Why are carbohydrates good for energy storage too?
They have carbon chains and are easily stackable
Glycogen is what type of carbohydrate?
Branched polymer with alpha-linkages
Which cells in the body absorb glucose AGAINST their concentration gradient?
epithelial cells in the digestive tract and the proxima tubule of the kidney
Differentiate between amylopectin and amylose (2 types of starch).
amylose = branched or not with alpha-linkages amylopectin = always branched
How is cellulose different than glycogen?
Cellulose is only found in plants, and is used as more of a structural material rather than storage, due to their BETA-linkages
Nucleotides are composed of…?
- a 5 carbon pentose sugar
- nitrogenous base
- phosphate group
What are the PURINES? Describe their structure.
Adenine and Guanine
-DOUBLE ringed structure
What are the PYRIMIDINES? Describe their structure.
Cytosine and Thymine
-SINGLE ringed structure
How many bonds are between Adenine and Thymine? Between Guanine and Cytosne?
2 between A and T
3 between G and C
In what direction does the DNA polymerase synthesize DNA?
5’ —> 3’
What is the phosphodiester bond?
bond between the phosphate group of one nucleotide and the 3rd Carbon of pentose sugar on next one.
How is RNA different from DNA?
- 2nd Carbon on pentose is NOT deoxygenated
- single stranded
- contains pyrimidine uracil instead of thymine
- moves through nuclear pores; not contained in nucleus
How does a peptide bond have double bond character?
The Nitrogen likes 4 bonds, and the Oxygen attracts electron density, which gives a partial negative and electrons then delocalize.
How is a peptide bond formed?
Via dehydration, creating an amide
Describe the secondary structure of proteins.
a single chain forms distinct shapes - alpha helix of beta sheets.
-responsible for overall conformation of protein
Describe the tertiary structure of proteins.
- 3D structure of protein
- Disulphide bonds, ionic interactions, H-bonds and hydrophobic bonding
Describe the quaternary structure of proteins.
2+ polypeptides come together and bind
-same forces acting on that as are in tertiary structure.
How does hydrophobic bonding occur?
salvation layer pushing the non polar molecules to the middle.
-occurs because it allows a decrease in size of highly ordered solvate later, which increases entropy.
What are the 5 denaturing agents and what forces they disrupt?
- Urea – H bonds
- Salt or pH change – ionic bonds
- Mercaptoethanol – disulphide bonds
- organic solvents – hydrophobic forces
- Heat – all of the above
How is the Vmax of enzyme kinetics PROPORTIONAL to the concentration of enzyme?
because as you increase the concentration of substrate, that increases the rate of reaction, but until the enzyme is saturated.
What is the Kcat of enzyme kinetics?
The number of substrate molecules one active site can convert to product in a given unit of time when an enzyme is saturated.
Vmax/[E]t
What is the Michaelis constant (Km)?
- the concentration of substrate at which the reaction rate is 1/2Vmax
- Km is INVERSLY proportional to enzyme-substrate affinity.
Differentiate between co-substrates and prosthetic groups (types of co enzymes)
Co-substrates: reversibly bind to enzyme and transfer chemical group to another substrate
Prosthetic groups: covalently bond to enzyme in reaction
What are the 4 types of enzyme regulation?
- Proteolytic cleavage (peptide bonds cleaved)
- Reversible covalent modification (phosphorylation and de-phos)
- Control proteins ( g-proteins or calmodulin)
- Allosteric interactions
How do competitive inhibitors affect Km or Vmax? Do they bind to active site or not?
Bind to active site
-INCREASE Km, Vmax unaffected
How do noncompetitive inhibitors affect Km or Vmax? Do they bind to active site or not?
Not active site, bind to the complex or just enzyme
-DECREASE Vmax, Km unaffected
How do uncompetitive inhibitors affect Km or Vmax? Do they bind to active site or not?
Not active site, bind to complex
-DECREASE Km and DECREASE Vmax
How do mixed inhibitors affect Km or Vmax? Do they bind to active site or not?
Not active site, bind to the complex or just enzyme
-INCREASE or DECREASE Km, DECREASE Vmax
Differentiate Lyases and Ligases -type enzymes.
- Lyases (aka synthase): catalyze reactions where functional groups are added - does NOT need ATP
- Ligases: catalyze condensation reactions coupled with hydrolysis of high energy molecules - DOES REQ. ATP.
How do histones cause DNA not to be transcribed?
Give proteins a positive charge that attracts the net negative charge of the DNA
What are the nucleosomes?
8 histones with DNA wrapped around them
What is chromatin made up of?
The nucleosomes (of histones and DNA)
Differentiate DNA methylation and histone acetylation.
Methylation = DNA cannot be transcribed Acetylation = DNA can be transcribed
Describe the 3 stages in transcription.
- Initiation: Promoter tells where to transcribe, RNA polymerase starts
- Elongation: creates an antisense (-) template strand and a (+) coding strand
- Termination: rho proteins dissociate
What are the 2 post-transcriptional modifications?
- 5’ cap: protect against degradation and serves as attachment site in protein synthesis
- Poly A tail: protect against degradation and aids in transport to cytoplasm
What are the differences between splicing and alternative splicing?
- Splicing: removes introns and keeps axons, uses small nuclear ribonucleoproteins (snRNP’s)
- Alternative splicing: incorporate sequences into mature RNA
The triplet code of the genome means…?
It is degenerative: more than one series of nucleotides may code for the same amino acid sequence
It is unambiguous: any single series of 3 nucleotides will code for one amino acid
What are the stop codons? The start codons?
STOP: UAA, UGA, UAG
START: AUG
What amino acid starts every protein for translation?
Methionine, (5’-CAU-3’)
What enzyme is important in stringing all the amino acids together?
peptides transferase
What are all the components in the replisome of DNA (origin of replication)?
- DNA helicase: unwinds DNA
- DNA polymerase: synthesizes new DNA strand
- Primase: creates primer to start replication
- DNA ligase: attaches fragments after replication
What are the defining features of all the stages in mitosis?
- Prophase: sister chromatids joined together. Nucleolus disappears
- Metaphase: chromosomes align in middle
- Anaphase: sister chromatids split.
- Telophase: nuclear membrane and nucleolus form. Cytokinesis continues
What is the difference between missense and nonsense mutation?
Missense: when a base substitution changes a codon. Can be neutral or have profound effects
Nonsense: Change in nucleotide sequence creates a stop codon.
What makes meiosis 1 and its steps different from the meiosis 2 and mitosis?
In prophase 1, homologous chromosomes line up at the middle and exchange nucleotides (called genetic recombination)
What is nondisjunction?
When in anaphase 1 or 2, the centromere of any chromosome does NOT split.
- in 1, 1 cell has 2 extra chromatids
- in 2, 1 cell has 1 extra chromatid
In gametogenesis, in which stages are the sperm haploid and diploid?
- Spermatagonium and primary spermatocytes are HAPLOID
- secondary spermatocytes and spermatids are DIPLOID
In gametogenesis in females, where is the process first halted?
The oogonium (haploid) goes through mitosis and produces primary oocytes (haploid). -It is halted in prophase 1 until menstruation starts
In gametogenesis in females, where is the process halted for the second time?
After primary oocytes go through rest of meiosis 1, creates secondary oocytes that are halted in metaphase 2. Completes meiosis 2 when sperm fertilizes
Glycolysis converts….? In the..?
Glucose into pyruvate. Glycolysis just happens in cytosol
What is produced form glycolysis?
- 2 3-Carbon pyruvate molecules
- 2 ATP (4 in total)
- 2 NADH
Does glycolysis happen anaerobically or aerobically?
both!
What is the main function of fermentation?
To regenerate NAD+ from NADH
What is the function of the Pentose-phosphate pathway?
- To generate NADPH, used for many metabolic or structural components.
- To generate 5-Carbon sugars for DNA and RNA
What is the function of chylomicrons?
Transport lipids from the intestines to the liver
Differentiate between VLDLs and HDL’s?
VLDL’s transport lipids and cholesterol to other parts of the body from the liver.
HDL’s pick up fatty acids and bring them back to the liver.
What does insulin promote in the body?
- Glycolysis in all tissues
- Glycogenesis in the liver and muscles
- Fatty acid synthesis in liver
- storage in the adipocytes
What does the glucagon promote in the body?
- Glycogenolysis in the liver and muscle
- Gluconeogenesis in liver
- Beta oxidation in all tissues
- Fatty acid release from adipocytes
What makes ATP an energy molecule?
The hydrolysis of the phosphoanhydride bond, as it is is spontaneous and exothermic
What are the products of the citric aid cycle?
1 ATP
3 NADH
1 FADH2
Describe the electron transport chain.
- Complex 1 (ubiquinone). 4 protons across the membrane from NADH
- Complex 2 (Q). No protons across membrane. FADH2 provides electrons
- Complex 3 (cytochrome c). 4 protons across membrane from QH2
- Complex 4. 2 protons across the membrane from cytochrome c, electrons then put onto O2
Out of the whole aerobic respiration cycle, how many ATP’s are produced?
36
1 NADH molecule produces how many ATP’s? How about FADH2?
1 NADH produces 2-3 ATP’s.
1 FADH2 produces 2 ATP.
What does the extraction technique utilize to separate compounds?
Solubility
In extraction, what is the main component to think about?
Weak acids/bases bind STRONG compounds, and Strong acids/bases will bind BOTH strong and weak compounds
Is crystallization efficient to fully seperate compounds?
No
The beads in column chromatography are…?
Polar! So non-polar molecules will elute first because they won’t stick around
How is paper chromatography different than the other forms?
The non-polar phase is MOBILE (paper is put into non-polar solvent, which travels up paper so the non-polar molecules come with)
What is the Rf value used in paper chromatography?
distance of compound / distance of solvent
How does size-exclusion chromatography seem backwards?
Because LARGE molecules elute first, b/c they dont penetrate into the stationary phase like small molecules can
In gel electrophoresis, what will the bands near the top represent, the bottom?
Near the top = larger masses of nucleic acids/ proteins
Near the bottom = smaller masses
How are proteins separated based on their isoelectric points?
In a stable pH gel, poteins in the pH region BELOW their pI are (+) and will move toward the more (-) cathode. At their pI, the protein will stop
A Northern blot visualizes…..?
A Souther blot visualizes…?
Northern = RNA Southern = DNA
What is a defining feature of a restriction/recognition site? (For restriction enzymes to notice)
They are usually palindromic
What is recombinant DNA?
When the SAME endonuclease cleaves 2 DNA fragments that can then by joined together
What is the innovative thing about DNA polymerase?
The polymerase enzyme used is heat resistant!
-so can denature DNA, add primers and enzyme, and polymerase will bind to desired DNA strand to trasncribe
(will double DNA each cycle)
