bio107 ch10,14,15

In the Frederick Griffith experiment, why did the mixture of heat-killed virulent and live nonvirulent bacteria kill the mouse?

DNA from the dead virulent bacteria transformed the live nonvirulent bacteria into virulent bacteria which killed the mouse

In the Hershey-Chase experiment, how was it concluded that DNA is the genetic material?

Radioactive DNA entered the bacterial cells while radioactive protein stayed outside. This showed that DNA carries genetic information.

DNA structure and its components

DNA nucleotide contains deoxyribose sugar, a phosphate group, and a nitrogenous base.

Thee 5’ carbon attaches to phosphate, the 1’ carbon attaches to the base, and the 3’ carbon has a free - OH group.

What is a phosphodiester bond?

A strong covalent bond connecting the sugar of one nucleotide to the rest

What are Chargaff’s rules? What are the base-pairing partners? What bonds hold them together?

A pairs with T and G pairs with C. Therefore A= T / G = C

Base pairs are held together by hydrogen bonds.

What is directionality of DNA ?

DNA strand has a 5’ and 3’ end.

Double stranded DNA is anti parallel:one strand runs 5’ to 3’ and the other runs 3’ to 5’

What is the difference between the major and minor groove?

The major groove is wider and exposes more information for protein binding; the minor groove is narrower

How did Meselson and stahl conclude dna replication is semi conservative?

Each new DNA molecule contains one parental strand and one newly made strand.

What is the purpose of DNA polymerase? Why does E. Coli have 3 DNA polymerases?

DNA polymerase builds new DNA. DNA polymerase removes RNA primers and replaces them with DNA.

Polymerase mainly helps with DNA repair and is the main DNA synthesizing enzyme

What is nuclease activity?

The ability of an enzyme to cut or remove nucleotides from DNA to RNA.

DNA is synthesized in which direction?

5’ to 3’ ONLY

What is the purpose of topoisomerase?

relieves twisting and supercoiling tension ahead of the replication fork

What is the replication fork?

The Y-shaped region where DNA is unwound and copied

Why is one DNA strand replicated continuously and the other discontinuously?

DNA polymerase only synthesizes 5’-3’. The leading strand is continuous; the lagging strand is discontinuous and made in Okazaki fragments

mismatch repair

Mismatch repair fixes incorrectly paired bases after replication

Photo repair

Uses light energy to repair IV damage such as thymine dimmers

Excision repair

Removes damaged DNA and replaces it with correct nucleotides

How do you transcribe DNA to RNA

Using complimentary pairings such as A = U , T = A , C to G, and G to C

IF RNA THERE CANNOT BE A ‘T’

What is the relationship between the coding, template, and RNA strand?

RNA polymerase reads the template strand.

RNA is complementary to the template strand.

The coding strand has the same sequence as RNA except DNA has T where RNA has U.

How is RNA read

In groups of 3 nucleotides called codons

What determines which nucleotide starts protein synthesis

The start codon AUG establishes where translation begins and sets the reading frame

What protein complex is responsible for protein synthesis?

The ribosome

Promoter

Where RNA polymerase binds

Start site

Where transcription begins

Terminator (exit site)

Sequence that signals transcription to stop

What allows RNA polymerase to recognize the promoter?

In bacteria, the sigma factor helps RNA polymerase recognize and bind the promoter

What allows the terminator to stop transcription?

A terminator sequence creates a signal that causes RNA polymerase to stop and release the RNA

What is the purpose of transcription factors?

Proteins that regulate transcription by activating or repressing gene expression

What is 5’ capping

Additional of a modified guanine cap to the 5’ end of eukaryotic mRNA

It protects mRNA and helps with translation

What is 3’ adenylation?

Addition of poly-A-tail to the 3’ end of eukaryotic mRNA, helping protect and stabilize it

What is removed during splicing

Introns

What are introns

Intervening sequences that do not code for proteins and are cut out during RNA processing before the mRNA makes proteins

What are exons

Code for proteins and stay in the final messenger RNA (mRNA)

What does the spliceosome consist of

SnRNPs (small nucleus ribonucleoproteins) which contain snRNA and proteins

What refers to genes being spliced together in different patterns

Alternative splicing

Why isn’t the number of proteins and pre-sliced mRNAs the same

Alternative splicing allows one pre-mRNA to produce multiple different proteins

What is alternative splicing

Different combinations of exons are joined so one gene can produce different proteins

What is the role of tRNA

Carries amino acids to the ribosome and uses its anticodon to pair with mRNA codons

What is the purpose of the ribosome?

Reads mRNA and links amino acids together to make a protein

What occurs in the A site of the ribosome

Incoming aminoacyl-tRNA arrive

What occurs in the P site of the ribosome

Holds the tRNA carrying the growing peptide

What occurs in the E site of the ribosomes

Empty tRNA exits

What sequence positions the small ribosomal subunit correctly in E. Coli/bacteria ?

Shine-Dalgarno sequence

During peptide formation, amino acids from the ___ site are moved and connected to the amino acids in the ___ site.

P site to A site

What are the 3 types of point mutations

Silent: amino acids stay the same

Missense: different amino acids

Nonsense: creates a premature stop codon

What is a frame shift mutation?

An insertion or deletion that shifts the reading frame, usually when the number added or removed is not a multiple of 3

How does binary fission work

Bacterial DNA replicates, the cell elongates, DNA copies separate, and the cell divides into two daughter cells

What happens during septation?

A septum forms between daughter cells

What is the role of ftsZ

FtsZ forms a ring at the cell midpoint that helps constrict and divide the cell

What is a haploid cell

A cell with one set of chromosomes (23)

What is a diploid cell

A cell with two sets of chromosomes, one set from each parent (46)

Humans have how many chromosomes?

46 chromosomes , 23 pairs

What comprises a nucleosome?

DNA wrapped around a core of 8 histone proteins

If there are only 4 different core histones, how is each nucleosome composed of 8 histones?

There are 2 copies of each of the 4 histones ( 2×4)

What are the four different core histones?

H2A , H2B, H3, H4

What are homologous chromosomes?

A pair of chromosomes, one from each parent, containing the same genes at the same locations but possibly different alleles.

What are sister chromatids?

Identical copies of one chromosome produced during DNA replication

What is the difference between homologous chromosomes and sister chromatids?

Homologous chromosomes are maternal and paternal versions with the same genes; sister chromatids are identical copies of the same chromosome.

What protein connects sister chromatids and where are they attached?

Cohesin holds sister chromatids together, especially at the centromere

What is kinetochore? What attaches to it ?

A protein structure on the centromere. Spindle microtubules attach to it during cell division.

What is each phase of the cell cycle?

G1; S ; G2 ; M ; CYTOKINESIS

G1

Cell grows and performs normal functions

S

DNA is replicated

G2

Cell grows and prepares for mitosis

M

Nucleus divides and chromosomes separate

Cytokinesis

Cytoplasm divides into two daughter cells

What are the phases of mitosis

Prophase, pro-metaphase, metaphase, anaphase, telophase

Prophase

Chromosomes condense and spindle begins forming

Pro-metaphase

Nuclear envelope breaks down and spindle attaches to kinetochores

Metaphase

Chromosomes line up in the middle

Anaphase

Sister chromatids separate to opposite poles

Telophase

New nuclear envelopes form and chromosomes decondense

What is a kinase

An enzyme that adds a phosphate group to a protein or other molecule (phosphorylation) often changing its activity

What is the difference between a CDK and other kinases?

A CDK (cyclin-dependent kinase) must bind to a cyclin to become active and helps regulate progression through the cell cycle.