bios 220 exam 1

chapter 8-9

name the four important characteristics of dna

1. genetic materials must contain complex information

2. genetic material must replicate faithfully

3. genetic material must encode the phenotype

4. genetic material must have the capacity to vary.

nucleotide

sugar, phosphate, base

chargaff’s rule

The principle that in DNA, the amount of adenine equals thymine and the amount of guanine equals cytosine.

transforming principle

The substance that causes genetic transformation, originally identified in bacterial studies, indicating that DNA is the hereditary material.

ribose vs deoxyribose

Ribose is a five-carbon sugar found in RNA, while deoxyribose is a five-carbon sugar found in DNA, lacking one oxygen atom compared to ribose.

cytosine, uracil, thymine are

pyramidines

adenine and guanine are

purines

phosphate

is a chemical group consisting of a phosphorus atom bonded to four oxygen atoms, playing a crucial role in the structure of DNA and RNA. ALWAYS bonded to 5’ carbon

three levels dna is considered at

primary, secondary, tertiary

supercoiling

is the coiling of DNA that occurs when the helix twists in on itself to relieve strain from unwinding, affecting DNA's compactness and accessibility.

topoisomeres

are enzymes that regulate the degree of supercoiling in DNA by introducing or removing twists.

is most dna negative or positively supercoiled

Most DNA is negatively supercoiled, which helps in the unwinding of the helix during replication and transcription.

nucleiod

is the irregularly shaped region within a prokaryotic cell where the genetic material is located, typically containing a single, circular strand of DNA.

chromatin

A complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells, playing a crucial role in gene regulation and packaging.

heterochromatin vs euchromatin

Heterochromatin is tightly packed and generally transcriptionally inactive, while euchromatin is loosely packed and active in transcription, allowing for gene expression.

most abundant proteins in chromatin

histones

acetylation

is a biochemical process that involves the addition of an acetyl group to histones, resulting in a more open chromatin structure and increased gene expression.

methylation

is a biochemical process involving the addition of a methyl group to DNA or histones, typically leading to transcriptional repression and a more compact chromatin structure.

centromere is

the region of a chromosome where the two sister chromatids are joined and where the spindle fibers attach during cell division. it is very essential for chromosome movement in mitosis and meiosis.

what are telemeres

the protective caps at the ends of linear chromosomes that prevent DNA degradation and maintain chromosomal stability.

unique sequence dna

refers to specific DNA sequences that are distinct and vary between individuals, contributing to genetic diversity. These sequences can play a key role in identifying genetic traits.

moderately repetitive dna

DNA sequences that are repeated multiple times throughout the genome but are not present in sufficient quantity to be classified as highly repetitive. They often include genes for ribosomal RNA and histones. they exist in many copies

highly repetitive dna

DNA sequences that are repeated many times in tandem throughout the genome, often found in satellite DNA regions. These sequences tend to be non-coding and play roles in chromosome structure and function. rarely transcribed into rna

transforming agent/principle

refers to the substance responsible for transforming bacterial cells by introducing new genetic material, a concept demonstrated in experiments by Frederick Griffith and later confirmed by Avery, MacLeod, and McCarty.

what is dna composed of

DNA is composed of nucleotides, which include a phosphate group, a sugar (deoxyribose), and nitrogenous bases (adenine, thymine, cytosine, and guanine). These nucleotides link together in a double helix structure.

how are nucleotides connected?

Nucleotides are connected by phosphodiester bonds between the phosphate group of one nucleotide and the sugar of the next nucleotide, forming the backbone of the DNA strand. they are strong covalent bonds.

where does the addition to the polynucleotide strand occur

3’ - OH

RNA VS DNA

RNA is single-stranded, contains ribose sugar, and has uracil instead of thymine, whereas DNA is double-stranded, contains deoxyribose sugar, and has thymine.

name the stages of dna replication

The stages of DNA replication are initiation, unwinding, elongation, and termination.

initiation

-oriC

-an initiation protein

unwinding

-dna helicase binds to the lagging strand template and moves in the 5’ to 3’ direction

-single-strand binding proteins

-dna gyrase

elongation

-dna polymerase III adds nucleotides in the 5’ to 3’ direction

-DNA polymerase cannot initiate DNA synthesis on a bare template

dna polymerase I

removes the RNA nucleotides of a primer and replaces it with DNA nucleotides

DNA ligase

is an enzyme that joins Okazaki fragments on the lagging strand by creating phosphodiester bonds, thus facilitating the completion of DNA replication.

termination

where two replication forks meet

dna gyrase

Moves ahead of the replication fork, making and resealing breaks in the double-helical DNA to release the torque that builds up because of unwinding at the replication fork

eukaryotic genomes have

many origins of replication

eukaryotic chromosomes have

multiple linear DNA molecules that contain complex arrangements of genes and regulatory elements, enabling a diverse range of functions and regulation.

if telomerase is mutated and nonfunctional

chromosomes would shorten each generation

prokaryotes have no

histones or nucleus

fewer than 10 turns

positively coiled

more than 10

negatively super coiled

which are the most abundant proteins

histones

five major types of histones

include H1, H2A, H2B, H3, and H4, which help package DNA into nucleosomes, playing a critical role in gene regulation.

a nucleosome is composed of how many histones

eight histone proteins (2 of each)

why are centromeres important

Centromeres are essential for proper chromosome segregation during cell division, serving as the attachment point for spindle fibers and ensuring that sister chromatids are pulled apart accurately.

how does z dna differ from b dna

Z-DNA has a left-handed helix, while B-DNA has a right-handed helix. Z-DNA is more elongated and less stable than B-DNA.

griffith experiment

An experiment conducted by Frederick Griffith in 1928 that demonstrated the phenomenon of transformation, showing that non-virulent bacteria could acquire virulence from dead virulent bacteria.

hershey chase experiment

An experiment conducted by Alfred Hershey and Martha Chase in 1952 that demonstrated that DNA is the genetic material by using radioactive labeling to track DNA and protein in bacteriophages.

what are the groups at the 5 prime end

phosphate group

what are the groups at the 3 prime end

hydroxyl groups

how do prokaryotes and eukaryotes copy their dna

Prokaryotes copy their DNA through a process called binary fission (as they are dividing), while eukaryotes replicate their DNA during the S phase of the cell cycle using more complex mechanisms involving multiple origins of replication.

replication must be

accurate, and at a high speed

describe and diagram meselson and stahl’s experiment

A famous experiment that demonstrated the semi-conservative nature of DNA replication. It involved growing bacteria in heavy nitrogen, then switching them to light nitrogen, and observing the density of the resulting DNA after successive generations.

replicons

Regions of DNA that replicate from a single origin of replication.

theta replication

A mode of DNA replication observed in circular DNA, such as that of bacteria, where a double-stranded DNA molecule forms a structure resembling the Greek letter theta (θ) during replication.

rolling circle replication

A process of DNA replication that starts at a single origin and involves the cleavage of a circular DNA strand, allowing for the continuous synthesis of a new strand in a unidirectional manner, commonly seen in some viruses and plasmids.

linear replication

A type of DNA replication that occurs in eukaryotic chromosomes, where replication begins at multiple origins and proceeds bi-directionally along the linear DNA strand.

leading strand undergoes

continuous synthesis during DNA replication.

lagging strand undergoes

discontinuous synthesis in short fragments called Okazaki fragments, which are later joined together.

how are nucleotides added to dna

Nucleotides are added to the growing DNA strand by DNA polymerase, which binds to the template strand and catalyzes the formation of phosphodiester bonds between nucleotides.

why must one DNA strand be synthesized in the opposite direction of the other?

Because DNA strands are antiparallel, and elongation can only occur 5′ → 3′.

initiation stage of dna replication

is the process where DNA helicase unwinds the double helix, and primase synthesizes a short RNA primer to provide a starting point for DNA polymerase.

This stage prepares the template strands for replication, allowing DNA polymerase to begin synthesizing new DNA strands.

unwinding stage of dna replication

In the unwinding stage of DNA replication, the DNA double helix is separated into two single strands by the enzyme helicase, allowing access for the replication machinery to synthesize new DNA strands.

elongation stage of dna replication

is the stage where DNA polymerase adds nucleotides to the growing DNA strand in the 5' to 3' direction, using the template strand as a guide. This continues until the entire segment of DNA is replicated.

dna polymerase I

is an enzyme involved in DNA replication that primarily functions to remove RNA primers from the Okazaki fragments and replace them with DNA nucleotides, ensuring the integrity of the newly synthesized DNA.

dna ligase

an enzyme that joins together Okazaki fragments on the lagging strand during DNA replication and seals nicks in the DNA.

telomerase

is an enzyme that adds repetitive nucleotide sequences to the ends of chromosomes, called telomeres, to prevent them from shortening during DNA replication.

tandem repeats

are sequences of DNA that are repeated in direct succession, often used in genetic profiling and analysis.

in the central dogma genetic information flows from

DNA to RNA to protein.

which nucleotide pair is the strongest

is the guanine-cytosine (GC) pair, due to three hydrogen bonds formed between them compared to two hydrogen bonds in the adenine-thymine (AT) pair.