BIOL 3000 Gentics - Auburn Dr. S - Exam 3

6 billion

How many base pairs per cell (46 chromosomes)?

2 meters

How long is the DNA in a cell?

10 nm

How big is the nucleus?

Chromatin

complex of DNA with proteins

Histones

Protein in chromatin

Euchromatin and Heterochromatin

Types of chromatin

Euchromatin

lightly packed chromatin rich in gene concentration and is most often under active transcription.

Heterochromatin

tightly packed chromatin consisting mainly of genetically inactive sequences (can't read)

centromeres, telomeres, darker areas on a karyotype

Where is heterochromatin found?

Constitutive (all the time) heterochromatin

VERY gene poor; centromeres and telomeres; histones

Facultative heterochromatin (sometimes)

Gene Silencing; Barr bodies (method of gene control)

Folded fiber model

"yarn" would fold on its on and make type a and b fibers with one more dense than the other (didn't propose mechanism on how it would occur)

Nucleosome model

DNA wraps around proteins that are brought in

Nucleosome

simplest packaging structure of all eukaryotic chromatin; Localized areas of transcription; better fit for protein biosynthesis

Core Histones

H2A, H2B, H3 and H4

Linker Histone

H1

Core histones

Highly conserved during evolution; Consist of approximately 120 amino acids each; In combination form the core particle; 25% Lysine and Arganine

Dimers; 8

Core histones exists as ____ so actually _____ proteins in a core of a nucleosome

Linker Histone

Tissue specific expression and not highly conserved; Consist of approximately 200 amino acids; Loosely associated with core particle

False

Linker Histone is part of the core nucleosome.

10 nm fiber

when we go from DNA to just forming the nucleosome; primary packaging of the chromatin

Twice

How many times does DNA wrap around the histone?

Prevent DNA from moving

Why does histone has a little "tail" that clamps down on the DNA?

50

How many base pairs between nucleosomes?

Solenoid

30 nm fiber consisting of six nucleosomes

54

How many histones in a solenoid?

Supercoiling

reduces length of DNA by ~7 times

Binds two distinct regions of DNA

How does Histone H1 Work?

Linker DNA to portion of the 146 bp core

What does the Histone H1 bind?

Tighter

Histone H1 makes the chromatin (looser/tighter)?

Zig zag model

doesn't have the sharp bend of the solenoid model and allows for greater compaction (wrap around and go across)

300 nm fiber

Chromatin loops form when?

Topoisomerase II

What is the 300 nm fiber built around?

300 nm fiber

Can still move around; main compaction of chromatin

700 nm fiber

DNA diameter is ~700 nm; Metaphase Chromosome; Spiral scaffold composed of Topoisomerase II and about 15 non‐histone proteins;

700 nm fiber

Compaction level of Heterochromatin

Early prophase

chromosomes condense

Late prophase

nuclear envelope breaks down, mitotic spindle assembles

Metaphase

mitotic spindle arranges chromosomes at cell;s equator

Anaphase

sister chromatids separate

Telophase

cell plate forms

S

Interphase dna is replicated in the ______ phase

2-10 nm fiber

G1 Phase

30-300 nm fiber

G2 phase

Chromosome

metaphase

700 nm chromatin

Beginning of prophase

Pre-darwinian "great chain of being" thinking

humans at the top of the chart of genomic size (most complex organism)

Complexity

the state of having many parts and being difficult to understand or find an answer to

Biological complexity

intricate and multifaceted nature of living organisms, encompassing their hierarchical organization, diverse cell types, and complex interactions within and between systems

C-value

genome size (how much DNA in one cell)

Junk DNA

DNA that we don't what the function is

C value paradox

Excess DNA is present in the genome that does not seem to be essential for the development or evolutionary divergence of an organism (size of genome doesn't effect complexity)

The onion test

onions have 5 times more DNA than humans and show they are more "complex"

G-value

number of genes that coordinate with complexity

G‐value Paradox

The number of genes does not correlate with organismal complexity

10%

Highly Repetitive DNA Sequence makes up _____ of DNA.

Highly Repetitive DNA Sequence

Most is located in heterochromatic regions around the centromere / telomere. Occurs as variable length motifs (5‐100 bp), in long tracts of up to 100 Mb.

HR DNA Function

structural and organization role to nothing more than junk (non-coding DNA)

HR DNA example

alpha satellite DNA - from 2 to more than 30 repeats of 171 bp tandem repeat

30%

Moderately Repetitive DNA Sequence makes up ______ of DNA.

Moderately Repetitive DNA Sequence

Found mostly throughout the euchromatin (facultative heterochromatin). Present at between 10 ‐ 105 copies per genome. Average 300 bp in size.

MR DNA Function

'redundant' genes for histones, and ribosomal RNA and proteins

MR DNA example

microsatellite DNA (repeating sequences of 2‐30 bp of DNA); interspersed repetitive DNA (transposable elements)

Microsatellites

variable number of tandem repeats typically occurring in non‐coding regions of the genome and are useful genetic markers as they tend to by highly polymorphic

Slippage recognition

Microsatelites form by?

Microsatellite function

Used to sequence the human genome, Markers for certain disease conditions, Primary markers for DNA testing in forensic cases

Polymorphic

having various forms

Single Copy DNA Sequence (Unique)

ALWAYS Found throughout the euchromatin. Present at single or low copy number per genome. Coding DNA regions (genes. 20,000 protein coding genes)

1-5%

Single Copy DNA Sequence makes up _____ of DNA.

Highly Repetitive

Heterochromatin (tightly coiled)

Moderately Repetitive

Scattered throughout Euchromatin

Unique

Euchromatin; GENES

GENE

the basic physical and functional unit of heredity

Gene

Sequence of unique nucleotides (GENOTYPE) that carry the genetic information which is to be expressed (PHENOTYPE)

99.5; <1

_____ percent of genes are in all people and ____ are unique to a person.

True

We get one copy of our genes from our mother and one from our father.

Molecular Level "GENE"

DNA sequence that gives rise to an RNA molecule

Transcriptional unit

regulatory sequences, promoter, transcribed region, termination

Promoter

signals the beginning of transcription

Terminator

signals the end of transcription

Transcribed region

part of this region contains the information that specifies an amino acid sequence

Regulatory sequence

site for the binding of regulatory proteins is to influence the rate of transcription. Regulatory sequences can be found in a variety of locations

Transcribed Region

DNA to RNA (both introns and exons)

Exon

"coding sequences" = phenotype

Intron

"intervening sequences" = areas of genes that generally don't code for phenotype

5' Untranslated Region

mRNA that is directly upstream from the initiation codon. (differs in prok and euks; regulation of transcription)

3' Untranslated Region

section of messenger RNA (mRNA) that immediately follows the translation termination codon

Untranslated region

area of DNA before the RNA start codon

Promoter

promoter is a DNA sequence onto which the transcription machinery binds and initiates transcription

TATA Box

highly conserved sequence in DNA serving as the binding site for transcription factor binding (on/off) basal level of transcription

CAAT Box

5'‐GGCCAATCT‐3' consensus sequence that occurs upstream by 60‐ 100 bases to the initial transcription site. Typically required for inducible genes to be produced in sufficient amounts (DNA)

GC Box

region of DNA that can be bound with proteins (activators) to activate transcription of a gene or genes (DNA)

Enhancer or inhibitor regions

Regulatory regions and regulatory proteins

Terminator

section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription

Solitary Genes (Unique)

A single copy of a gene (haploid situation); two copies in diploid. Comprises the bulk of euchromatin (only need it at a certain point)

Duplicated Genes

Process by which a portion of a chromosome is duplicated resulting in an additional copy of a gene; Results in a copy of the original gene called a paralog gene; Either of the two genes may mutate and change the original; function of the gene; Usually occurs due to an error during Meiosis

Multigene Families

Set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions. Most often located in similar regions of the chromosome. Most often used or synthesized at different times

Pseudogenes

Dysfunctional relatives of genes that have lost their protein‐coding ability. Often the result of multiple mutations within a gene (probably used to be a gene; ancient gene)

Repeated Genes

Multiple copies of small genes clustered throughout the genome at specific sites. Present in high copy number (how many copies are there??). Many times present in a "head‐to‐tail" configuration (histones)

Central dogma

one gene (genotype), one mRNA intermediate, 1 "protein"