Bio 1115 Exam 2

Central Dogma

theory stating that, in cells, information starts as DNA, is transcribed into RNA, and is translated into proteins

DNA

deoxyribonucleic acid; consists of two long polynucleotide chains

Nucleotides

building blocks of DNA

Adenine, Thymine, Cytosine, Guanine

nitrogen bases in DNA

Adenine, Uracil, Cytosine, Guanine

nitrogen bases in RNA

Codon

three-nucleotide sequence on messenger RNA that codes for a single amino acid

Phosphodiester bonds

bonds between nucleotides; hold DNA strands together

DNA backbone

made of deoxyribose sugar and Phosphate

2 hydrogen bonds

How many hydrogen bonds are between Adenine and Thymine?

3 hydrogen bonds

How many hydrogen bonds are between Cytosine and Guanine?

5' end of DNA

contains a phosphate group

3' end of DNA

contains a hydroxyl group (OH)

polarity

Two ends of a DNA strand have...

Hydrogen bonds

hold together two strands of DNA

True

T or F: The two strands of the DNA double helix run antiparallel to each other.

Gene

segment of DNA that codes for a protein

"Junk" DNA

excessive DNA that does not code for proteins (isn't useless, functions as a regulation system)

Chromosomes

threadlike structures made of DNA molecules, which contain the genes

Chromatid

one of two identical "sister" parts of a duplicated chromosome

Nucleus

Where are all chromosomes located?

46 (23 pairs); one pair is either XX or XY (with exceptions)

How many chromosomes do human cells have?

One

How many chromosomes in each pair come from each parent?

Centromere

site where microtubules attach during mitosis; the site where sister chromatids are combined before separation during mitosis

Replication origin

areas on chromosome where DNA replication begins

Replication forks

areas where the double helix separates

Telomere

non-coding DNA end of chromosomes; buffer region to protect chromosome from shortening

stay in one place; loosely organized so they don't tangle with each other

Eukaryotic chromosomes...

always highly condensed

DNA in chromosomes is...

Nucleosome

the basic unit of eukaryotic chromosome structure; beads on a string

Chromatin

clusters of DNA, RNA, and proteins in the nucleus of a cell

Chromatin remodeling

the process of tightening or loosening DNA strands around histones to activate or inactivate their functions

Heterochromatin vs Euchromatin

H: highly condense, no gene expression; genes shut down
E: less condensed, genes are actively expressed

X-inactivation

during development, females inactivate half of their X chromosomes in order to prevent producing double the amount of the protein

Semi-conservative replication

method of DNA replication in which parental strands separate, act as templates, and bond with a new DNA strand

what initiates DNA replication

when double helix is opened with the aid of inhibitor proteins.

At least how many replication origins per strand?

2

Semi-conservative replication steps

1. DNA helicase
2. Single shared binding proteins
3. DNA topoisomerase
4. DNA primase
5. DNA polymerase/sliding clamp
6. DNA ligase

DNA helicase

enzyme that unwinds DNA by breaking hydrogen bonds

SSB proteins

bind to open DNA to make sure two strands don't reconnect

DNA topoisomerase

enzyme that cuts individual strands to prevent overtwisting; brought back together by DNA ligase after

DNA Primase

enzyme that creates an RNA starting point for DNA polymerase to begin replication

DNA polymerase

enzyme that makes bonds between nucleotides, forming an identical strand of DNA during replication

Active sites of DNA Polymerase

Polymerizing: adds new strand of DNA
Editing: edits new strand of DNA

DNA ligase

enzyme that chemically links DNA fragments together

Nuclease

Enzyme that cuts out primers and damaged DNA

Which end of new DNA does DNA polymerase ALWAYS add nucleotides to?

3' end

Okazaki fragments

fragments of DNA produced on the lagging strand during DNA replication; joined later by DNA ligase

Pyrophosphate

remains after new nucleotide is bonded with a parent strand

Telomerase

(enzyme) builds telomeres; replicates the ends of eukaryotic chromosomes with nongenetic materials

They stop dividing and uncontrollable growth is no longer prevented

What happens when cells lose telomeres?

Continuously

How frequently does DNA damage occur?

Depurination

removing the nitrogen base with the addition of water

Deamination

a C base being replaced with a U base with the addition of water

What does UV radiation cause

Thymine dimers and photoproducts

Thymine dimers

covalent link of adjacent thymine bases that prevent replication

3 steps to fix DNA damage

1. Excision, 2. Resynthesis, 3. Ligation

Excision

when an exonuclease removes one specific nucleotide: getting rid of RNA primer

Resynthesis

when the original DNA sequence is restored by a repair DNA polymerase

Ligation

when the nicks in a backbone are resealed by DNA ligase

Mismatch repair

happens during DNA replication; cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides

Homologous recombination

happens during mitosis and DNA replication; process of repairing DNA breaks by one strand receiving the genetic information from a homologous DNA strand

nonhomologous end joining

process of repairing DNA double-helix breaks by ends being processed by nuclease and joined by DNA ligase

RNA polymerase

enzyme similar to DNA polymerase that synthesizes an RNA copy of DNA

Gene expression

accessing DNA information to build proteins

Steps to get from DNA to proteins

1. Transcription, 2. RNA Processing, 3. Translation

Transcription

DNA into mRNA; transcription factors (proteins) bind to "TATA" box on promoter region, RNA polymerase synthesizes RNA copy of DNA, and RNA polymerase reaches terminator and is released

"TATA" box

promoter DNA sequence crucial for transcription

Promoter

specific region of a gene where RNA polymerase can bind and begin transcription

Terminator

specific region of a gene where RNA polymerase is released

Precursor mRNA

result of transcription

RNA Processing

5' cap and Poly-A tail are added to precursor mRNA, 3' poly-A tail added, and intron sequences of it are removed

5' Cap

guanine nucleotide added to 5' end; serves as a site of ribosome attachment in translation

Intron

sequence of RNA that is not involved in coding for a protein

Poly-A tail

50 to 250 adenine nucleotides added to 3' end; acts as protection from RNA-degrading enzymes

Extron

sequence of RNA that codes for a protein

SnRNPs

recognize introns and snip them out

Lariat

"lasso" structure left behind after RNA splicing

mRNA

type of RNA that carries instructions from DNA in the nucleus to the ribosome

Area where translation takes place

On ribosomes in cytoplasm

Ribosome

site of protein synthesis

types of RNA

mRNA, rRNA, and tRNA

Translation

rRNA in ribosome allows mRNA and tRNA to form peptide bonds every 3 nucleotides (or 1 codon) and form an amino acid

rRNA

type of RNA that makes up part of the ribosome; synthesixed in nucleolus

AUG

start codon

tRNA

type of RNA that carries amino acids at the ribosome; adaptors between mRNA and amino acids during protein synthesis; has to match anticodon

Process of DNA to RNA

transcription

process of RNA to protein

translation

What is the problem with the central dogma?

Not a one-way street. You can add an arrow from RNA to DNA because not all DNA is in genes. Not all RNA is used to build proteins. Those proteins inhibit gene expression.

3 basic features of DNA structure

One 5-Carbon sugar (deoxyribose)
One 5’ phosphate group
One of four nitrogenous bases (A, T, G, C, U*)
U is used in RNA*

Base pairs in DNA are connected by what kind of bonds?

phosphodiester bonds

What is the difference between homologous chromosomes and sister chromatids?

Homologous Chr: both chromosomes in a pair; One from mother and one from father; Same genes (may have different alleles) in the same order in the DNA of the chromosome

Sister: identical copy of chromosomes made during replication; held together at centromere until mitosis separates them

Heterochromatin refers to _____ genes

shut down?

What happens when you change the DNA?

You change the DNA which changes the RNA which changes the protein

What end are nucleotides added to in DNA?

3'

genome

complete genetic information of an organism

How are chromosomes organized in nucleus?

Organized loosely

In mitosis, how are chromosomes organized in the nucleus

tightly condensed and compacted

Chromosomes have magnitudes of folding. Explain process.

DNA wrapped around histones → packing nucleosomes together (histone H1) → chromatin fiber folded into loops (non-histone proteins) → entire chromosome

Biggest example of X-inactivation

Calico cats

What is translation basically?

protein synthesis