Biology 2 - Final - VOCAB

Ecology

the study of the interconnections and interrelationships between organisms and their environment

Ecology can study relationships between the ___________ and ____________ species

same; different

Abiotic

non-living

Levels of organization

the different levels at which biology is studied

The levels of organization are…

atoms, cells, organisms, population, community, ecosystem, biosphere

Nested hierarchy

when the larger part of a system are made up of the smaller parts, levels of organization is an example of this

Sample/ population size (N)

the size of the sample or population being studied

Lambda (λ)

population growth rate, the ratio of population sizes in a closed population, (Nt+1/Nt)

Population dynamics

changed to a population over time, works in a cycle, growth decline stability and recovery

Carrying capacity (k)

the largest the population can stably be

Population size and dynamics are controlled by _________ factors, ________ _________ factors, and ____________

biotic; abiotic environmental; dispersal

BD model

the birth and death model, only for a closed population, the current population- those who died + those born

BIDE model

birth immigration death emigration, current population + birth +immigration - death - emigration

Birth rate (b)

the number of people born / population

Death rate (d)

the number of deaths / population

Population dynamics are determined by _______ _ ________

birth v. death

Community

a group of multiple species living together at the same place and time

Geographic range

an area made up of multiple communities

Intraspecific interactions

interactions between members of the same species

Interspecific interactions

interactions between members of different species

Predation

common negative direct interaction in a community, hunting

Competition

common negative direct interaction in a community, fighting for the same food

Indirect interactions

effecting another species through forces where they do not interact

Ecosystems

communities with physical, chemical , abiotic interactions, and physical factors

Physical features

land and geography, studied by geologists geographers and climatologists

Anthropogenic ecosystems

ecosystems where humans are major influences of physical and abiotic features

Anthropogenic ecosystems

ecosystems where humans are major influences on physical and abiotic features

Agroecosystems

ecosystems where human agriculture occurs

Succession

the series of changes in ecosystem conditions that occur after a major abiotic or biotic event or change, like a disturbance

Disturbances

major changes to an ecosystem that stress species, typically much of the biomass is changed or killed, typically kill much of a communities foundation species

Foundation species

species that play a major role in a community by providing habitat, food, etc. for many species

Human disturbance

a large change done by humans to a community

Clearcut

a human disturbance, all trees cut down and usually left to rot

Slash and burn

a human disturbance, a farming technique where an area is cut down and burned to release nutrients into the soil

Selective logging

a human disturbance, removal of just the valuable trees, leaves other trees intact

Primary succession

succession from a completely new substrate, starts with no biomass, ex. after a large volcano, fire, or glacier retreat

Nitrogen fixing plants

usually the first plants of a primary succession, use nitrogen to create their own fertilizer

Secondary succession

disturbances leaving residual biomass below or above ground

Pulse disturbance

a pulse of damage, death, or loss of biomass to a community

Press disturbance

a disturbance that does not allow succession to take place, ex. continuously grazing a field

Habitat mosaics

constant press disturbance that only allows some areas to undergo succession, creates a fragmented looks

habitat fragmentation

little pieces of habitat left behind by human press disturbances, leaves gaps between small fragments

Habitat edges

the outside line of fragmented habitats, causes edge effects

Soil aeration

the process of increasing air and water flow in the ground

Ecosystem engineer

things with pervasive qualities, alter the physical environment, ex. humans and elephants

Savanna

a grassland ecosystem with trees and shrubs

Herbivore outbreak

a biotic disturbance, many herbivores, eat and kill many trees and plants

Sequencing the human genome found the ___________ ___ _________ ________

sequence of human genes

“Omics”

fields related to the biggest biology and medicine topics, focus on a complete set of a biologicas molecule

Genomics

the field of biology that focuses on studying all of the DNA or the genome of an organism

Genomicists

people who study genomes

Genomics studies the number of _______, number of _______, and what they do

chromosomes; genes

the nuclear genome is __ % ____- _______ coding

97; non-protein

the mitochondrial genome is made up of ___ _________ chromosome, __ genes, which __ % are non-coding

one circular; 37; 3

Transcriptome

all of the RNA transcripts in a cell or which can be produced by a genome

Humans have _________ RNA transcripts

120,000

Regulatory RNA

binds to mRNA to change its function, changes transcription and ultimately protein production

Proteome

the complete set of proteins in a cell

Proteomics

the science and technology used to study proteomes

Metabolics

the study of small things created through metabolism

Microbiome

a community of microorganisms that live in a shared space

Metagenomics

the focus of genes that are very different between species, used to study microbiomes

Bioinformatics is also known as ____________ _________

computational biology

Bioinformatics

analyzes and stores DNA sequences

Annotations

additional notes and information about a DNA sequence

Spirochete

spring like shape

Sequencing begins with many ________ of a ________

copies; genome

The _______ step of DNA sequencing is _________ ________ each __________ into smaller pieces

first; randomly chopping; chromosome

Each DNA fragment in DNA sequencing is about around ____ base pairs

100

The _______ step in DNA sequencing is _______ DNA fragments into __________ _________ DNA

second; denaturing; single stranded

_________ is used to denature DNA in DNA sequencing

Heat

The ______ step in DNA sequencing is _______ an ________ ______ to the end of the DNA strands

third; ligating; adapter sequence

Adapter sequence

used in DNA sequencing, added to single stranded DNA, acts as a target sequence for a complementary primer

The ________ step in DNA replication is using a ______ like reaction to make _________ of the ______ ________

fourth; PCR; copies; DNA strands

The _________ step in DNA sequencing is ___________ or finding the ________ in each ________ _________

fifth; sequencing; bases; DNA fragment

The _______ step in DNA sequencing is _________ __________ or _________ the fragments into their ___________ sequence

sixth; genome assembly; organizing; orginal

Alignments

the original sequences made from DNA sequencing

Contiguous stretches (contigs)

a set of DNA fragments that overlap

De novo sequencing

the sequencing of a genome for the first time

Diploids are more complicated to sequence because of ___________ chromosomes, _________ genomes, and can be heterozygous or have __________ in their sequence

multiple; larger; differences

Reference genome

the first sequenced genome of an organism, acts as an example set of genes in a species, not fully representative, can have errors, regularly changed and updated

TATA box

similar to a -10 -35 sequence, helps the promoter bind to the DNA, upstream of the coding sequence, binds general transcription factors

General transcription factors

transcription factors involved in RNA pol binding to genes, on almost every gene, turn gene transcription on and off

Specific transcription factors

transcription factors involved in RNA pol binding to specific genes, turns gene transcription up or down

TFIID

a general transcription factor that binds to all promoters, binds directly to the TATA box, binds before RNA pol

Transcription initiation complex

TFIID binds to the TATA, additional factors bind, RNA pol binds, additional factors bind

The order of the initiation complex is:

regulatory protein binding site, general protein binding site, RNA pol binding site, and transcribed sequence

Enhancers and Silencers

short sequences where specific transcription factors bind on double-stranded DNA either enhancing or limiting DNA transcription, can be near or far from the promoter, can be located in an intron for another gene

TATAless genes

eukaryotic genes without a TATA box

DNA bending

DNA bends so the enhancer or silencer is across from the promoter

A mutation in an intron can affect a protein if it affects an _________ or _______

enhancer; silencer

Proteins bind to DNA or RNA through ___________ bonds in ___________ and __________ __________

hydrogen; major; minor grooves

Mononucleotides

A, T, C, G

Di-nucleotides

CC, GG, CG, GC

There are ____ to ____ thousand genes in the human genome

20; 22

The current human reference genome comes from __ people

11

____% of the human reference genome comes from one person, probably of _______ decent

70; African

Pseudogene

dead protein, a segment of DNA that structurally resembles a gene but is not capable coding for a protein, usually from a very mutated gene, can get missed when a genome is being annotated

_____________ genes vary the most between populations

Immune

Methylation

the addition of a methyl group - CH3, covalent but reversible