Cell Bio Credit Test Ppp3

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Genophore

Back 1

carrier of genetic information

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Nucleotide

Back 2

nitrogen-containing base + sugar pentose + phosphate

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nucleoside

Back 3

nitrogen-containing base + sugar pentose

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bases of DNA

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Adenine (A), Guanine (G) (purine)
Cytosine (C), Thymine (T) (pyrimidine)

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bonds of DNA

Back 5

phosphodiester bond between 3' OH and 5' phosphate
Hydrogen bonds between base pairs (AT=2, GC=3)

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Chromosomes Eucaryotic

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linear, 10^8 bp (human 5-25x10^7), in the nucleus containing histons (basic proteins) and acidic proteins (nonhistone proteins)

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Chromosomes prokaryotic

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circular, 10^6-10^7 bp. attached to plasma membrane by replication origin. contains proteins, nonhistons and histone like

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Histones

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H1 (linker histone), H2A, H2B, H3, H4 core is made of octamer of the last four histones, two of each, DNA is wound around the core

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Acidic proteins of chromosome

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Heterogenous group of proteins probably involved in 3D conformation

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Structural genes

Back 10

encode proteins

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Genes for RNA

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encode RNA which is NOT a template for translation (t and rRNA)

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DNA regulatory regions (of genes)

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Doesnt encode any proteins or RNA but carry information for binding specific molecules regulating gene expression

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Procaryotic gene

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conatins only uninterrupted DNA sequences coding for proteins, no introns/exons

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Eucaryotic gene

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contains Exons and Introns

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Mammalian cells expressed genes represent ___ % other regions/sequences

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7-10%
Regulatory regions; involved in regulation of gene expression
Repetetive sequences; DNA finger printing
Mobile elements (transposons): can copy&paste or cut&paste "jumping genes"
Pseudogenes: genes who has lost their function due to the accumulation of mutations

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Genome (definition)

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the complete set of DNA of the cell/organism

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Genome prokaryotic

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chromosome + possible plasmids

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genome eucaryote

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nuclear chromosome + mitochondrial chromosome (+ chloroplast chromosome + possible plasmids)
human genome (haploid) comprises approx. 30 000 genes

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Human genome (haploid set) # of genes

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ca 30 0000

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DNA replication
REPLICON

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a segment of DNA which represent a replication unit with its own replication origin

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DNA replication
REPLICATION ORIGIN

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a specific DNA sequence where replication starts after unwinding of the double helix, rich in T and A

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DNA replication
REPLICATION FORK

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two of them works in opposite directions from the replication origin.
Pro: 1000 bp/s
Eu: 100 bp/s

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DNA polymerase

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catalyzes the formation of phosphodiester bond between two nucleotides

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Nucleotide enters the DNA polymerase reaction as

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nucleoside triphosophate (ATP, GTP, CTP, TTP)

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2 important limitations of DNA polymerase

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Can synthesize only in 5'-3' direction
unable to start synthesis of a new strand

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Several types of DNA polymerase

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alfa: synthesis of lagging strand
delta: synthesis of leading strand
beta & epsilon: DNA repair
gamma: synthesis of mitochondrial DNA

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DNA polymerase uses ____ as a cofactor

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Magnesium ions

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Replication forks, made of, does

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made of helicase (motor protein, enzyme)
breaks hydrogen bonds between base pairs that keep double helix intact

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DNA polymerase, proofreading activity

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3'-5' direction, PREFERENTIALLY repairs mismatched base pairs of newly synthesized strand, before adding the next one

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Primase

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Enzyme that can start a new strand, makes a RNA primer to which the DNA polymerase then can continue to add nucleotides. Lacks proofreading skills.

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repair DNA polymerase

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replaces the RNA primer (synthesized by primase, removed by nuclease) with DNA

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DNA ligase

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joins the 5' end of one new DNA fragment with the 3' end of an other (okazaki)

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Single strand binding proteins

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proteins that bind to the opened DNA strand that is now exposed and would easily fold (by forming base pairs) thus making replication tricky!

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Sliding clamp

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protein fold that keeps DNA polymerase on DNA template. DNA polymerase can easily detach from template = good for recylcing of DNAp when synthesising Okazaki, bad for synthesis of longer strand (leading strand) Sliding clamp makes sure it stays in place

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DNA mismatch repair system

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recognizes distortion of the geometry of the DNA dbl helix caused by mismatched base pairs

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errors in DNA replication

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replication machine makes 1 per 10^7 bp, after mismatch repair system it goes down to 1 per 10^9 base pairs