Biochemistry of the cell Flashcards
Is called the “Universal solvent”
Water
What are the unique properties of water?
Water is polar.
water is both cohesive and adhesive.
Water has high specific of heat.
Water has a high heat of vaporization.
Water has a high thermal conductivity
In each water molecule the two hydrogen atoms are linked the oxygen atom by?
Hydrogen bond
The two bond are highly polar because the oxygen is blank, while the hydrogen is blank
Strongly attractive for electrons, weakly attractive
When a positively charged region of one water molecule approaches a negatively charged region of a second water molecule , the electrical attraction between them can result in blank.
Hydrogen bond
Is described as the attraction between particles of the same substances.
Cohesion
is the attraction between two different substances.
Adhesion
A phenomenon where molecules will tow each other along when in a thin glass tube
Capillary action
Is the amount of heat needed to raise or lower 1g of a substance by 1C.
Specific heat
Is the energy needed to convert 1g of a substance from liquid to gas.
Heat of vaporization
What are the four major molecules that make up the cells?
Carbohydrates, Lipids, Proteins, Nucleic acid
Are made up of monomer called simple sugar, which are held by a covalent bond glycosidic bond to form polymer. Serve as source of energy to fuel cellular processes.
Carbohydrates
Is composed of only one sugar. Example of this.
Monosaccharides. Glucose, Fructose, Galactose
Made up of two simple sugars. Example of this.
Disaccharides. Sucrose, Maltose, Lactose
Made up of multiple monosaccharides. Example of this.
Polysaccharides. Glycogen, Starch, Cellulose, Chitin
Are mostly composed of fatty acids and glycerols, which are held by ester linkages
Lipids
Like oils and fats are composed of three fatty acids bonded to glycerol
Triglycerides
Those found in plant cuticles are composed of variable number of fatty acids bonded to long chain alcohol ].
Waxes
Are composed of polar phosphate and two fatty acids bonded via glycerol
Phospholipids
Are composed of four fused rings of carbon atom with functional group attached.
Steroids
Are made up of nucleotides that are held by phosphodiester. They are important for the storage, transmission, and usage of genetic information.
Nucleic Acids
Are made up of amino acids, which are covalently linked by peptide bond.
Proteins
The side chains of the 20 amino acids can be categorized in four groups.
Neutral-non polar, neutral-polar, acidic, basic
4 structures of protein.
Primary, secondary, tertiary, quaternary structures
Is the simplest level of a protein structure. It is simply the sequence of amino acids in a polypeptide chain.
Primary
Refers to the local folded structures that form within a polypeptide due to interactions between atoms of the proteins.
Secondary structures
Is the overall three-dimensional structure of the polypeptide.
Tertiary structure
Is formed when multiple polypeptide subunits are assembled.
Quaternary structures
are protein that are considered as biological catalyst.
Enzymes
Are substrate that sped up the rate of a chemical reaction.
Catalyst
Help biological processes become faster by lowering the activation energy that must be supplied to break the bond in the reactant.
Enzymes
The reactant to whom the enzyme acts
Substrate
the catalytic reaction then occurs in a specific part of the enzyme called the
Active site
Who discovered DNA?
Friedrich Miescher
was discovered as an annoying contaminant int he purification of proteins.
DNA
Discovered that DNA contains four bases
Albrecht Kossel
Are heterolytic rings with carbon and nitrogen atoms
Bases
Discovered in 1920s that there are 2 kinds of nucleic acids, which he called yeast acid
Phoebus Levene
A virus that carries only one DNA and four RNA
Cytomegalovirus
Discovered that DNA does not contain equal amounts of the four bases but the quantities differ depending on the surface of the DNA
Erwin Chargaff
The amount of adenine is always equal to the amount of thymine and the amount of guanine is equal to the amount of cytosine. This relationship is known as?
Chargaff’s rule
Condensed form of chromatin
Chromosomes
have no nucleus
Prokaryotes
Prokaryotes also frequently carry one or more smaller independent circular DNAs called?
Episomes and Plasmids
Do not integrate into the main chromosomes
Plasmids
Have real equivalent of the eukaryotic histones
euryarchaeota
Can reside in the cell as independent molecules or can integrate into the main chromosomes
Episomes
Are characterized by a nuclear membrane that surrounds their genetic patrimonium
Eukaryotes
Have no equivalent of the eukaryotic histones
Crenarchaeota
DNA replication and transcription take place in?
Nucleus
Protein synthesis occurs in?
Cytoplasm
Plays a vital role in in the transport of RNA and Proteins.
Nuclear membrane
Means colored body
Chromosomes
Were first discovered in the light microscope by using staining techniques
Chromosomes
The succession of nucleosomes forms a fibrous structure called?
Chromatin
The majority of the eukaryotic cells are?
Diploid
The two copies are called? one is derived from each parent
Homologous
Contains a single copy of each chromosomes
Haploid
Have more than two copies of each chromosome
Polyploid
This lacks of correlation between genome size and genetic complexity
C-value paradox
Number of genes/Mbp of DNA
Genome density
Intergenic regions consist of repetitive DNA
Microsatellites, Genome wild repeats, Pseudo genes
Confers a positive value or selective advantage to the host organic
Intergenic DNA
The separations require the action of a blank
Topoisomerase
The extremities of the linear eukaryotic chromosomes contain special sequences called? it plays an extremely important role in the replication of the linear eukaryotic DNA molecules
Telomeres
Plays an important role in the distribution of the sister chromatids to the daughter cells upon DNA replication and cell division.
Centromere
Is linked by two ester bonds with two sugar molecules
Single phosphoryl group
Impose the polarity of the DNA chain.
Phosphodiester linkage
The bases are attached to the sugar moieties by a blank formed between the C’1 atom of the sugar and the N1 atom of a pyrimidine residue or the N9 atom of a purine residue.
Glycosidic bond
How many hydrogen bonds for an A-T pair, G-C pair?
2, 3
Describe the purine and pyrimidine
Purine is a larger molecule, double ring structure while pyrimidine is smaller, one ring structure
What are the different forms of DNA?
B-form
A-form
Z-form
Where mostly the DNA exist in vivo?
B-form
Is a regular, right handle helix in which the turns run clockwise when locked at along the helical axis. The bases are lying approximately flat and perpendicular with respect to the helical axis.
B-form
Is a less hydrated form of DNA, it’s also shorter and larger than B-form DNA. Has more bps per turn. Bases are not lying flat as in B-form DNA, but they are slightly tilted with respect to the helical axis.
A-form
The only left-handed form of DNA. It has the least twisted structure and is underwound. Has only one groove, with a higher density of negative changes than the groove of B-form DNA.
Z-form
Is an important intermediated, generated by the action of the RecA protein in process of homologous DNA recombination.
Triple-Stranded DNA
Uses the complementary pairing of inverted repeat sequences in a single strand. It is also a structure that is widely found in nature and serves as a specific signal molecule in crucial cellular processes.
Cruciform structure
In nature, all DNA molecules are topologically blank
constrained
The crossing over of the helix over itself
Writhe
Plays an important role in vital processes such as DNA replication and transcription that generate tension in the DNA
Topoisomerase
Two major types of Topoisomerases
Type I and Type II
Is the simply the number of helical turns of one strand around the other.
Twist
Make transient single-stranded breaks and change the linking number in steps of one. Do not consume ATP and are monomeric enzymes.
Type I Topoisomerase
Make a covalent bond between the 5’ - phosphate end of the nick and the tyrosine residue and generate a free 3’ - OH end.
Type IA
A type of writhe which the long axis is twisted around itself.
Interwound or plectonomic
Is the total number of interwound or spiral writhes in cccDNA.
Writhing number (Wr)
Twist and writhe are convertible.
False (Interconvertible)
A type of writhe in which the long axis is wound in a cylindrical manner, as often occurs when DNA wraps around protein.
Spiral or toroid
It is the sum of two geometric components: the twist (Tw) and the writhe (Wr)
Lk
Make transient double stranded gaps and change the linking number in steps of two. Can generally act on both negatively and positively supercoiled DNA.
Type 11 Topoisomerase
Require the energy of ATP hydrolysis for their action
Type II Topoisomerase
Covalently link the tyrosine residue to the 3’ -P and generates free 5’ -OH bond
Type IB
